# Patent

## Title
Wheat stripe rust resistance genes and methods of use

## Abstract

Compositions and methods for enhancing the resistance of wheat and barley plants to wheat stripe rust caused by Puccinia striiformis f. sp. tritici are provided. The compositions comprise nucleic acid molecules encoding resistance (R) gene products and variants thereof and plants, seeds, and plant cells comprising such nucleic acid molecules. The methods for enhancing the resistance of wheat and barley plants to wheat stripe rust comprise introducing a nucleic acid molecule encoding an R gene product into a wheat or barley plant cell. Additionally provided are methods for using the wheat and barley plants in agriculture to limit wheat stripe rust.

## Background
CROSS-REFERENCE TO RELATED APPLICATIONS
This application is the U.S. National Stage of International Application PCT/US2016/060101, filed Nov. 2, 2016, which designates the U.S and was published by the International Bureau in English on May 11, 2017, and which claims the benefit of U.S. Provisional Patent Application No. 62/250,136, filed Nov. 3, 2015, all of which are hereby incorporated herein in their entirety by reference.


REFERENCE TO A SEQUENCE LISTING SUBMITTED AS A TEXT FILE
The official copy of the sequence listing is submitted electronically via EFS-Web as an ASCII formatted sequence listing with a file named 070294-0106SEQLST.TXT, created on Nov. 1, 2016, and having a size of 440 kilobytes, and is filed concurrently with the specification. The sequence listing contained in this ASCII formatted document is part of the specification and is herein incorporated by reference in its entirety.
FIELD OF THE INVENTION
The present invention relates to the fields of gene isolation and plant improvement, particularly to enhancing the resistance of plants to plant disease through the use of disease resistance genes.
BACKGROUND OF THE INVENTION
Plant diseases cause significant yield losses in world-wide wheat production. Among the most damaging diseases of wheat are the rusts. Wheat stripe rust (also known as wheat yellow rust) caused by Puccinia striiformis f. sp. tritici is currently the most damaging disease of wheat on the global scale (RustTracker.org, available on the worldwide web at rusttracker.cimmyt.org/?page_id=9; accessed Oct. 5, 2015). While wheat plants comprising resistance (R) genes against Puccinia striiformis f. sp. tritici have proven effective in limiting the agronomic losses caused by wheat stripe rust, new races of Puccinia striiformis f. sp. tritici have appeared recently for which the R genes are not effective. While pesticides can be used to control wheat stripe rust, pesticides are expensive and at odds with the sustainable intensification of agriculture, and in developing countries, pesticides are simply unaffordable for subsistence farmers.
The sustainable intensification of agriculture will require increased use of genetic solutions instead of chemical solutions (e.g. pesticides) to protect crops against pathogens and pests (Jones et al. (2014) Philos. T Roy. Soc. B 369:20130087). Wild relatives of domesticated crops, such as wheat, contain an immense diversity of useful R genes that are a valuable resource for sustainable disease control in wheat production. However, traditional methods for introducing R genes typically involve long breeding timelines to break linkage to deleterious alleles of other genes. R genes can be overcome within a few seasons when deployed one at a time (McDonald and Linde (2002) Annu. Rev. Phytopathol. 40:349-379). In addition to wild relatives of wheat, other grain species that are hosts for wheat pathogens have the potential to be sources of R genes for use in sustainable disease control in wheat production. Molecular cloning makes it possible to simultaneously introduce multiple R genes (Dangl et al. (2013) Science 341:746-751), which should delay resistance-breaking pathogen race evolution and thus, provide more durable resistance (McDonald and Linde (2002) Annu. Rev. Phytopathol. 40:349-379).
BRIEF SUMMARY OF THE INVENTION
The present invention provides nucleic acid molecules for resistance (R) genes that are capable of conferring upon a plant resistance to at least one race of a pathogen that causes plant disease, particularly resistance to at least one race of a pathogen in the genus Puccinia that causes a rust disease. In one embodiment, the present invention provides nucleic acid molecules comprising the R gene, Rps6, and variants thereof including, for example, orthologs and non-naturally occurring variants. In certain embodiments, the present invention provides nucleic acid molecules comprising Rps6 that are capable of conferring upon a plant, particularly a wheat or barley plant, resistance to Puccinia striiformis f. sp. tritici (Pst) that causes wheat stripe rust.
The present invention further provides plants, plant cells, and seeds comprising in their genomes one or more polynucleotide constructs of the invention. The polynucleotide constructs comprise a nucleotide sequence encoding a resistance (R) protein of the present invention. Such R proteins are encoded by the R genes of the present invention. In a preferred embodiment, the plants and seeds are transgenic grain plants and seeds, particularly wheat and barley plants and seeds, that have been transformed with one or more polynucleotide constructs of the invention. Preferably, such grain plants comprise enhanced resistance to Pst, when compared to the resistance of a control grain plant that does not comprise the polynucleotide construct.
The present invention provides methods for producing a plant with enhanced resistance to a plant disease, particularly a rust disease, more particularly wheat stripe rust. Such methods comprise introducing into at least one plant cell a polynucleotide construct comprising a nucleotide sequence of an R gene of the present invention. In some embodiments, the polynucleotide construct or part thereof is stably incorporated into the genome of the plant cell, and in other embodiments, the polynucleotide construct is not stably incorporated into the genome of the plant cell. The methods for producing a plant with enhanced resistance to a plant disease can optionally further comprise regenerating the plant cell into a plant that comprises in its genome the polynucleotide construct. Preferably, such a plant comprises enhanced resistance to the plant disease, relative to the resistance of a control plant to the plant disease. In certain embodiments, the plant is a wheat or barley that comprises enhanced resistance to wheat stripe rust caused by Pst, relative to the resistance of a control wheat or barley plant to Pst.
The present invention further provides methods for producing a barley plant with enhanced resistance to wheat stripe rust. Such methods comprise modifying in a barley plant or at least one cell thereof a non-functional allele of the resistance gene Rps6 so as to make a functional allele, whereby the resistance of the barley plant to wheat stripe rust is enhanced. In the methods of the present invention, modifying the non-functional allele comprises introducing at least one genetic modification into the non-functional allele. Such genetic modifications include, for example, one or more insertions, deletions, and/or substitutions of at least one base pair in the non-functional allele, whereby a functional allele is produced. The present invention additional provides non-transgenic and transgenic barley plants and seeds produced by such methods.
Methods of using the plants of the present invention in agricultural crop production to limit wheat stripe rust are also provided. The methods comprise planting a seed, particularly a wheat or barley seed, produced by a plant of the present invention, wherein the wheat or barley seed comprises at least one R gene nucleotide sequence of the present invention, particularly an Rps6 nucleotide sequence. The methods further comprise growing the plant under conditions favorable for the growth and development of the plant, and optionally harvesting at least one seed from the plant.
Additionally provided are non-transgenic and transgenic plants, plant parts, seeds, plant cells, other host cells, expression cassettes, and vectors comprising one or more of the nucleic acid molecules of the present invention.



BRIEF DESCRIPTION OF THE DRAWINGS
FIG. 1. Macroscopic and microscopic phenotypes of barley cultivars Abed Binder 12 and Russell inoculated with Pst.
FIG. 2. Histograms and two-way plot of chlorosis and colonization on the Abed Binder 12×Russell F2 population inoculated with Pst isolate 08/501. Histograms showing the segregation of chlorosis (A) and pCOL (B) in the F2 population. Parental and F1 phenotypes shown above plots (A: Abed Binder 12, R: Russell). (C) Two-way plot showing correlation of chlorosis and pCOL phenotypes. The phenotypes of Abed Binder 12 and Russell are shown as the triangle and square, respectively.
FIG. 3. Composite interval mapping of chlorosis and pCOL phenotypes in the Abed Binder 12×Russell F2 population inoculated with Pst. LOD curves were normalized (nLOD) for chlorosis (grey) and pCOL (black) based on individual experiment-wide thresholds (dashed line) based on 1,000 permutations. A step size of 2 cM was used, with the x-axis spanning the length of the AxR-Pst F2 population genetic map.
FIG. 4. Fine mapping of Rps6. (A) High-resolution genetic map based on a recombination screen including 2,894 gametes. Numbers shown on left are the number of recombination events between markers. Marker names are shown on the right, with letters after marker names indicating cosegregating KASP markers derived from a single WGS contig. (B) Physical map anchoring based on the high-resolution genetic map. BACs that are sequenced or have BES available are black, otherwise BACs are shown in grey. A truncated FPC 320 is shown based on the anchoring of markers.
FIG. 5. Identification and genetic mapping of five NLR candidate genes in the Rps6 region. (A) Abed Binder 12×Russell high-resolution F2 map used for fine mapping Rps6. (B) Doubled haploid derived F2 mapping population (DHMP). Numbers on left of linkage group show the number of recombination events between markers.
FIG. 6. Physical mapping of Rps6 and gene model of the candidate gene NLR-A. The BAC clone harbouring NLR A, NLR-D, and NLR-E derived from Abed Binder 12 (AB12) is shown on top. The locations of NLR candidates NLR-A, NLR-D, and NLR-E are indicated in the upper AB12 track, as well as additional genes in the locus including MLOC_8985 (G1), MLOC_41646 (G2), and MLOC_19985 (G3). The other grey boxes in the lower AB12 track represent repetitive sequence. The three additional tracks show alignments of whole genome shotgun contigs derived from Barke (Rps6), Bowman (Rps6), and Morex (rps6).
FIG. 7. A single nucleotide polymorphism differentiates three NLR-A haplotypes. (A) gDNA from Abed Binder 12 ‘A’ and Russell ‘R’ amplified with eight PCR primer pairs specific for NLR-A. (B) Top panel: gDNA from Rps6 and rps6 accessions amplified with primer pair A05/A11; Bottom panel: Digestion of PCR amplicons using TaqαI differentiates three NLR-A haplotypes (NLR-A1, NLR-A2, and nlr-a) in eight Rps6 differential accessions.
FIG. 8. NLR-A construct development for Agrobacterium tumefaciens-based transformation. T-DNA design flanked by the left (LB) and right (RB) border sequences includes a hygromycin resistance gene driven by a 35S promoter and nos terminator followed by 2.4 kb promoter, exons 1, 2, and 3, intron 3, exon 4, and 1.8 kb terminator of NLR-A. Other features include two replication origin sites (pSa-ORI and colEI-ori) and kanamycin resistance (npt1). An embodiment of the construct shown in FIG. 8 comprises the nucleotide sequence set forth in SEQ ID NO: 15.



SEQUENCE LISTING
The nucleotide and amino acid sequences listed in the accompanying sequence listing are shown using standard letter abbreviations for nucleotide bases, and three-letter code for amino acids. The nucleotide sequences follow the standard convention of beginning at the 5′ end of the sequence and proceeding forward (i.e., from left to right in each line) to the 3′ end. Only one strand of each nucleotide sequence is shown, but the complementary strand is understood to be included by any reference to the displayed strand. The amino acid sequences follow the standard convention of beginning at the amino terminus of the sequence and proceeding forward (i.e., from left to right in each line) to the carboxy terminus.
SEQ ID NO: 1 sets forth the nucleotide sequence of the R gene, Rps6, from Hordeum vulgare ‘Abed Binder 12’.
SEQ ID NO: 2 sets forth the nucleotide sequence of the coding region of the cDNA of Rps6 from H. vulgare ‘Abed Binder 12’. If desired, a stop codon (e.g. TAA, TAG, or TGA) can be operably linked to the 3′ end of nucleic acid molecule comprising SEQ ID NO: 2.
SEQ ID NO: 3 sets forth the amino acid sequence of the R protein encoded by Rps6 from H. vulgare ‘Abed Binder 12’.
SEQ ID NO: 4 set forth the nucleotide sequence of the bacterial artificial chromosome (BAC), BAC_4931-1-11E. This BAC is a nucleic acid molecule comprising nucleotide sequences that correspond to the region of the genome of H. vulgare ‘Abed Binder 12’ in which Rps6 is located.
SEQ ID NO: 5 sets forth the nucleotide sequence of the coding region of the cDNA of Rps6 from H. vulgare ‘Hindmarsh’. If desired, a stop codon (e.g. TAA, TAG, or TGA) can be operably linked to the 3′ end of nucleic acid molecule comprising SEQ ID NO: 2.
SEQ ID NO: 6 sets forth the amino acid sequence of the R protein encoded by Rps6 from H. vulgare ‘Hindmarsh’.
SEQ ID NO: 7 sets forth the nucleotide sequence of the coding region of the cDNA of Rps6 from H. vulgare ‘WBDC008’. If desired, a stop codon (e.g. TAA, TAG, or TGA) can be operably linked to the 3′ end of nucleic acid molecule comprising SEQ ID NO: 2.
SEQ ID NO: 8 sets forth the amino acid sequence of the R protein encoded by Rps6 from H. vulgare ‘WBDC008’.
SEQ ID NO: 9 sets forth the nucleotide sequence of the coding region of the cDNA of Rps6 from H. vulgare ‘WBDC085’. If desired, a stop codon (e.g. TAA, TAG, or TGA) can be operably linked to the 3′ end of nucleic acid molecule comprising SEQ ID NO: 2.
SEQ ID NO: 10 sets forth the amino acid sequence of the R protein encoded by Rps6 from H. vulgare ‘WBDC085’.
SEQ ID NO: 11 sets forth the nucleotide sequence of the coding region of the cDNA of Rps6 from H. vulgare ‘WBDC109’. If desired, a stop codon (e.g. TAA, TAG, or TGA) can be operably linked to the 3′ end of nucleic acid molecule comprising SEQ ID NO: 2.
SEQ ID NO: 12 sets forth the amino acid sequence of the R protein encoded by Rps6 from H. vulgare ‘WBDC109’.
SEQ ID NO: 13 sets forth the nucleotide sequence of the coding region of the cDNA of Rps6 from H. vulgare ‘WBDC110’. If desired, a stop codon (e.g. TAA, TAG, or TGA) can be operably linked to the 3′ end of nucleic acid molecule comprising SEQ ID NO: 2.
SEQ ID NO: 14 sets forth the amino acid sequence of the R protein encoded by Rps6 from H. vulgare ‘WBDC110’.
SEQ ID NO: 15 is the nucleotide sequence of the IHP_0205_NLR-A_construct described in Example 2 and illustrated in FIG. 8.
SEQ ID NO: 16 is the nucleotide sequence of the portion of the IHP_0205_NLR-A_T-DNA construct that is expected to be transferred to a plant during transformation with Agrobacterium tumefaciens comprising the IHP_0205_NLR-A_construct.
SEQ ID NO: 17 is the nucleotide sequence of the portion of the IHP_0205_NLR-A construct that comprises sequences of NLR-A.
SEQ ID NOS: 18-33 are the PCR primers that are referred to in Table 4.
SEQ ID NO: 34 is the nucleotide sequence of the IHP_0300_NLR-A_native construct described in Example 2.
SEQ ID NO: 35 is the nucleotide sequence of pBract202_TSL_pMla6_NLR-A_CDS_gDNA_tMla6 construct described in Example 2.
DETAILED DESCRIPTION OF THE INVENTION
The present inventions now will be described more fully hereinafter with reference to the accompanying drawings, in which some, but not all embodiments of the inventions are shown. Indeed, these inventions may be embodied in many different forms and should not be construed as limited to the embodiments set forth herein; rather, these embodiments are provided so that this disclosure will satisfy applicable legal requirements. Like numbers refer to like elements throughout.
Many modifications and other embodiments of the inventions set forth herein will come to mind to one skilled in the art to which these inventions pertain having the benefit of the teachings presented in the foregoing descriptions and the associated drawings. Therefore, it is to be understood that the inventions are not to be limited to the specific embodiments disclosed and that modifications and other embodiments are intended to be included within the scope of the appended claims. Although specific terms are employed herein, they are used in a generic and descriptive sense only and not for purposes of limitation.
The present invention relates to plant resistance (R) genes, particularly R genes that confer upon plant resistance to a plant disease caused by a plant pathogen. The present invention further relates to the mapping and isolation of an R gene that is capable of conferring upon a barley plant resistance to multiple races of wheat stripe rust caused by Puccinia striiformis f. sp. tritici (Pst). As disclosed hereinbelow, a Pst resistance gene from barley (Hordeum vulgare) designated as Rps6, was fine mapped to a 0.1 cM region of the barley genome. By anchoring the Rps6 locus to the barley physical map, this region was placed on a single fingerprinted contig spanning a physical region of 267 kb. After sequencing this region, several candidate genes encoding nucleotide-binding, leucine-rich repeat proteins (NLRB) were identified. From among these candidate NLR genes, NLR-A was determined to correspond to be Rps6.
The present invention provides nucleic acid molecules comprising the nucleotide sequences of R genes, particularly the nucleotide sequence of Rps6 and naturally occurring (e.g. orthologs and allelic variants) and synthetic or artificial (i.e. non-naturally occurring) variants thereof. Such nucleotide sequences of R genes, which are also referred to herein as R gene nucleotide sequences, encode R proteins. R gene nucleotide sequences of the invention include, but not limited to, wild-type R genes comprising a native promoter and the 3′ adjacent region comprising the coding region, cDNA sequences, and nucleotide sequences comprising only the coding region. Examples of such R gene nucleotide sequences include the nucleotide sequences set forth in SEQ ID NOS: 1, 2, 5, 7, 9, 11, and 13 and variants thereof. In embodiments in which the native R gene promoter is not used to drive the expression of the nucleotide sequence encoding the R protein, a heterologous promoter can be operably linked to a nucleotide sequence encoding an R protein of the invention to drive the expression of nucleotide sequence encoding an R protein in a plant.
Preferably, the R proteins of the invention are functional R proteins that are capable of conferring on a plant comprising the R protein enhanced resistance to a plant disease caused by a plant pathogen. More preferably, the R proteins of the invention are functional R proteins that are capable of conferring on a barley and/or wheat plant comprising the R protein enhanced resistance to wheat stripe rust caused by at least one race of Puccinia striiformis f. sp. tritici. In some embodiments, of the present invention, the R proteins of the present invention comprise broad-spectrum resistance to multiple (i.e. two or more) races of Puccinia striiformis f. sp. tritici. 
Functional R proteins of the present invention are encoded by functional alleles of the present invention. As used herein unless stated otherwise or apparent from the context of usage, a “non-functional allele of an R protein” of the present invention is an allele that is not capable of conferring resistance to at least one race of a particular plant pathogen to a plant that comprises the allele in a heterozygous or homozygous state.
Similarly, functional RPS6 proteins of the present invention are encoded by functional Rps6 alleles of the present invention. As used herein unless stated otherwise or apparent from the context of usage, a “non-functional allele of Rps6” of the present invention is an allele that is not capable of conferring resistance to a plant pathogen, particularly at least one race of Pst, to a barley plant that comprises the allele in a heterozygous or homozygous state. It is recognized that such a “non-functional allele” may encode a protein that comprises a biological activity or other function in a barley plant but nevertheless is non-functional with respect to resistance to Pst or other pathogen in the barley plant.
The present invention further provides transgenic plants comprising a polynucleotide construct which comprises an R gene nucleotide sequence of the invention, particularly an Rps6 nucleotide sequence. In some embodiments, the polynucleotide construct is stably incorporated into the genome of the plant, and in other embodiments, the plant is transformed by a transient transformation method and the polynucleotide construct is not stably incorporated into the genome of the plant. Methods for both the stable and transient transformation of plants are disclosed elsewhere herein or otherwise known in the art. In a preferred embodiment of the invention, the transgenic plants are grass plants, particularly grain plants, more particularly wheat or barley plants. Such transgenic comprise enhanced resistance to at least one plant disease, particularly a rust disease, more particularly wheat stripe rust caused by at least one, but preferably multiple, races of Puccinia striiformis f. sp. tritici. 
In certain embodiments, a transgenic plant of the invention comprises a polynucleotide construct comprising a nucleotide sequence encoding an R protein and a heterologous promoter that is operably linked for expression of the nucleotide sequence encoding an R protein. The choice of heterologous promoter can depend on a number of factors such as, for example, the desired timing, localization, and pattern of expression as well as responsiveness to particular biotic or abiotic stimulus. Promoters of interest include, but are not limited to, pathogen-inducible, constitutive, tissue-preferred, wound-inducible, and chemical-regulated promoters.
The present invention further provides methods for producing a plant with enhanced resistance to at least one plant disease. The methods comprise introducing a polynucleotide construct of the invention into at least one plant cell. In certain embodiments, the polynucleotide construct is stably incorporated into the genome of the plant cell. If desired, the methods can further comprise regenerating the plant cell into a transgenic or transformed plant comprising in its genome the polynucleotide construct. Preferably, such a regenerated plant is a wheat or barley plant comprising enhanced resistance to plant disease caused by a plant pathogen. In certain embodiments, the regenerated plant is a wheat or barley plant comprising enhanced resistance to more than one plant disease caused by more than one plant pathogen. In certain other embodiments, the regenerated plant is a wheat or barley plant comprising enhanced resistance to plant disease caused by one, two, three, four, five or more, or even all races, of a particular plant pathogen. In a preferred embodiment of the invention, the regenerated plant is a wheat or barley plant comprising enhanced resistance to wheat stripe rust caused by at least one race of Puccinia striiformis f. sp. tritici, relative to the resistance of a control wheat or barley plant to wheat stripe rust caused by the at least one race of Puccinia striiformis f. sp. tritici. In another preferred embodiment of the invention, the regenerated plant is a wheat or barley plant comprising enhanced resistance to wheat stripe rust caused by multiple races, or even all known races, of Puccinia striiformis f. sp. tritici, relative to the resistance of a control wheat or barley plant to wheat stripe rust caused by the same group of races of Puccinia striiformis f. sp. tritici. 
In yet another preferred embodiment of the invention, the regenerated plant is a wheat or barley plant comprising enhanced resistance to two, three, four, five or more different rust diseases caused by two, three, four, five or more different Puccinia spp., relative to the resistance of a control wheat or barley plant to the two, three, four, five or more different rust diseases caused by the two, three, four, five or more different Puccinia spp. The two or more Puccinia spp. can include, but is not required to include, Puccinia striiformis f. sp. tritici. The regenerated wheat or barley plant of this embodiment can comprise resistance against rust disease caused by one, two, three, four, five, or more races or even all known races, of each Puccinia spp.
The wheat and barley plants disclosed herein find use in methods for limiting wheat stripe rust in agricultural crop production, particularly in regions where wheat stripe rust is prevalent. The methods of the invention comprise planting a wheat seed or a barley seed produced by a wheat plant or a barley plant of the present invention, wherein the wheat seed or the barley seed comprises at least one R gene nucleotide sequence of the present invention, particularly an Rps6 nucleotide sequence. The methods further comprise growing the wheat or barley plant that originates from the seed under conditions favorable for the growth and development of the wheat or barley plant therefrom, and optionally harvesting at least one seed from the wheat or barley plant.
The present invention additionally provides methods for identifying a barley plant that displays newly conferred or enhanced resistance to wheat stripe rust. The methods find use in breeding barley plants for resistance to wheat stripe rust. Such resistant barley plants find use in the agricultural production of barley seeds. The methods comprise detecting in a barley plant the presence of at least one R gene, particularly Rps6 or functional variant thereof. In some embodiments of the invention, detecting the presence of the R gene comprises detecting the entire R gene in genomic DNA isolated from the barley plant. In preferred embodiments, however, detecting the presence of an R gene comprises detecting the presence of at least one marker within the R gene. In other embodiments of the invention, detecting the presence of an R gene comprises detecting the presence of the R protein encoded by the R gene using, for example, immunological detection methods involving antibodies specific to the R protein.
In the methods for identifying a barley plant that displays newly conferred or enhanced resistance to wheat stripe rust, detecting the presence of the R gene in barley can involve one or more to the following molecular biology techniques that are disclosed elsewhere herein or otherwise known in the art including, but not limited to, isolating genomic DNA and/or RNA from the barley plant, amplifying nucleic acid molecules comprising the R gene and/or marker therein by PCR amplification, sequencing nucleic acid molecules comprising the R gene and/or marker, identifying the R gene, the marker, or a transcript of the R gene by nucleic acid hybridization, and conducting an immunological assay for the detection of the R protein encoded by the R gene. It is recognized that oligonucleotide probes and PCR primers can be designed to identity the R genes of the present invention and that such probes and PCR primers can be utilized in methods disclosed elsewhere herein or otherwise known in the art to rapidly identify in a population of barley plants one or more barley plants comprising the presence of an R gene of the present invention.
Depending on the desired outcome, the polynucleotide constructs of the invention can be stably incorporated into the genome of the plant cell or not stably incorporated into genome of the plant cell. If, for example, the desired outcome is to produce a stably transformed plant with enhanced resistance to wheat stripe rust caused by at least one race of Puccinia striiformis f sp. tritici, then the polynucleotide construct can be, for example, fused into a plant transformation vector suitable for the stable incorporation of the polynucleotide construct into the genome of the plant cell. Typically, the stably transformed plant cell will be regenerated into a transformed plant that comprises in its genome the polynucleotide construct. Such a stably transformed plant is capable of transmitting the polynucleotide construct to progeny plants in subsequent generations via sexual and/or asexual reproduction. Plant transformation vectors, methods for stably transforming plants with an introduced polynucleotide construct and methods for plant regeneration from transformed plant cells and tissues are generally known in the art for both monocotyledonous and dicotyledonous plants or described elsewhere herein.
The present invention provides nucleic acid molecules comprising R genes. Preferably, such R genes are capable of conferring upon a host plant enhanced resistance to at least one race of at least one plant pathogen that causes a plant disease on the host plant. In certain preferred embodiments of the invention, such R genes are capable of conferring upon a wheat or barley plant enhanced resistance to at least one race of the pathogen that causes wheat stripe rust, Puccinia striiformis f. sp. tritici. Thus, such R genes find use in limiting wheat stripe rust caused by Puccinia striiformis f. sp. tritici in agricultural production. The R genes of the present invention include, but are not limited to, the R genes whose nucleotide sequences are disclosed herein but also include orthologs and other variants that are capable of conferring to a wheat or barley plant resistance to wheat stripe rust caused by at least one race, but preferably multiple races, of Puccinia striiformis f. sp. tritici. Methods are known in the art or otherwise disclosed herein for determining the resistance of a plant to a plant disease caused by a plant pathogen such as, for example, stripe rust caused by Puccinia striiformis f. sp. tritici. 
The methods of the present invention find use in producing plants with enhanced resistance to a plant disease caused by a plant pathogen. Typically, the methods of the present invention will enhance or increase the resistance of the subject plant to one race of a plant pathogen or to each of two or more races of the plant pathogen by at least 25%, 50%, 75%, 100%, 150%, 200%, 250%, 500% or more when compared to the resistance of a control to same race or races of the plant pathogen. Unless stated otherwise or apparent from the context of a use, a control plant for the present invention is a plant that does not comprise the polynucleotide construct of the present invention. Preferably, the control plant is essentially identical (e.g. same species, subspecies, and variety) to the plant comprising the polynucleotide construction of the present invention accept the control does not comprise the polynucleotide construct. In some embodiments, the control will comprise a polynucleotide construct but not comprise the one or more R gene sequences that are in a polynucleotide construction of the present invention.
Additionally, the present invention provides transformed plants, seeds, and plant cells produced by the methods of present invention and/or comprising a polynucleotide construct of the present invention. Also provided are progeny plants and seeds thereof comprising a polynucleotide construct of the present invention. The present invention also provides seeds, vegetative parts, and other plant parts produced by the transformed plants and/or progeny plants of the invention as well as food products and other agricultural products produced from such plant parts that are intended to be consumed or used by humans and other animals including, but not limited to pets (e.g., dogs and cats) and livestock (e.g., pigs, cows, chickens, turkeys, and ducks).
The methods of the invention can be used to enhance the resistance of a plant to a rust disease, particularly a rust disease caused by a Puccinia spp., particularly to stripe rust caused by Puccinia striiformis f. sp. tritici. Preferred plants for use in the methods of the present invention are grass plants, particularly grain plants, more particularly barley and wheat plants.
The present invention encompasses isolated or substantially purified polynucleotide (also referred to herein as “nucleic acid molecule”, “nucleic acid” and the like) or protein (also referred to herein as “polypeptide”) compositions including, for example, polynucleotides and proteins comprising the sequences set forth in the accompanying Sequence Listing as well as variants and fragments of such polynucleotides and proteins. An “isolated” or “purified” polynucleotide or protein, or biologically active portion thereof, is substantially or essentially free from components that normally accompany or interact with the polynucleotide or protein as found in its naturally occurring environment. Thus, an isolated or purified polynucleotide or protein is substantially free of other cellular material or culture medium when produced by recombinant techniques, or substantially free of chemical precursors or other chemicals when chemically synthesized. Optimally, an “isolated” polynucleotide is free of sequences (optimally protein encoding sequences) that naturally flank the polynucleotide (i.e., sequences located at the 5′ and 3′ ends of the polynucleotide) in the genomic DNA of the organism from which the polynucleotide is derived. For example, in various embodiments, the isolated polynucleotide can contain less than about 5 kb, 4 kb, 3 kb, 2 kb, 1 kb, 0.5 kb, or 0.1 kb of nucleotide sequence that naturally flank the polynucleotide in genomic DNA of the cell from which the polynucleotide is derived. A protein that is substantially free of cellular material includes preparations of protein having less than about 30%, 20%, 10%, 5%, or 1% (by dry weight) of contaminating protein. When the protein of the invention or biologically active portion thereof is recombinantly produced, optimally culture medium represents less than about 30%, 20%, 10%, 5%, or 1% (by dry weight) of chemical precursors or non-protein-of-interest chemicals.
Fragments and variants of the disclosed polynucleotides and proteins encoded thereby are also encompassed by the present invention. By “fragment” is intended a portion of the polynucleotide or a portion of the amino acid sequence and hence protein encoded thereby. Fragments of polynucleotides comprising coding sequences may encode protein fragments that retain biological activity of the full-length or native protein. Alternatively, fragments of a polynucleotide that are useful as hybridization probes generally do not encode proteins that retain biological activity or do not retain promoter activity. Thus, fragments of a nucleotide sequence may range from at least about 20 nucleotides, about 50 nucleotides, about 100 nucleotides, and up to the full-length polynucleotide of the invention.
Polynucleotides that are fragments of a native R polynucleotide comprise at least 16, 20, 50, 75, 100, 125, 150, 175, 200, 300, 400, 500, 1000, 2000, 5000, 7500, 10000, 12500 contiguous nucleotides, or up to the number of nucleotides present in a full-length R polynucleotide disclosed herein (for example, 12800 nucleotides for SEQ ID NO: 1 and 3126 nucleotides for SEQ ID NOS: 2, 5, 7, 9, 11, and 13).
“Variants” is intended to mean substantially similar sequences. For polynucleotides, a variant comprises a polynucleotide having deletions (i.e., truncations) at the 5′ and/or 3′ end; deletion and/or addition of one or more nucleotides at one or more internal sites in the native polynucleotide; and/or substitution of one or more nucleotides at one or more sites in the native polynucleotide. As used herein, a “native” polynucleotide or polypeptide comprises a naturally occurring nucleotide sequence or amino acid sequence, respectively. For polynucleotides, conservative variants include those sequences that, because of the degeneracy of the genetic code, encode the amino acid sequence of one of the R proteins of the invention. Naturally occurring allelic variants such as these can be identified with the use of well-known molecular biology techniques, as, for example, with polymerase chain reaction (PCR) and hybridization techniques as outlined below. Variant polynucleotides also include synthetically derived polynucleotides, such as those generated, for example, by using site-directed mutagenesis but which still encode an R protein of the invention. Generally, variants of a particular polynucleotide of the invention will have at least about 80%, 85%, 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, 99% or more sequence identity to that particular polynucleotide as determined by sequence alignment programs and parameters as described elsewhere herein. In certain embodiments of the invention, variants of a particular polynucleotide of the invention will have at least about 80%, 85%, 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, 99% or more sequence identity to at least one nucleotide sequence selected from the group consisting of SEQ ID NOS: 1, 2, 5, 7, 9, 11, and 13, and optionally comprises a non-naturally occurring nucleotide sequence that differs from at least one nucleotide sequence selected from the group consisting of the nucleotide sequence set forth in SEQ ID NO: 1, 2, 5, 7, 9, 11, and 13 by at least one nucleotide modification selected from the group consisting of the substitution of at least one nucleotide, the addition of at least one nucleotide, and the deletion of at least one nucleotide.
Variants of a particular polynucleotide of the invention (i.e., the reference polynucleotide) can also be evaluated by comparison of the percent sequence identity between the polypeptide encoded by a variant polynucleotide and the polypeptide encoded by the reference polynucleotide. Thus, for example, a polynucleotide that encodes a polypeptide with a given percent sequence identity to the polypeptide of SEQ ID NO: 3, 6, 8, 10, 12, or 14 is disclosed. Percent sequence identity between any two polypeptides can be calculated using sequence alignment programs and parameters described elsewhere herein. Where any given pair of polynucleotides of the invention is evaluated by comparison of the percent sequence identity shared by the two polypeptides they encode, the percent sequence identity between the two encoded polypeptides is at least about 60%, 65%, 70%, 75%, 80%, 85%, 86%, 87%, 88%, 89%, 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, 99% or more sequence identity. In certain embodiments of the invention, variants of a particular polypeptide of the invention will have at least about 80%, 85%, 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, 99% or more sequence identity to at least one of the full-length amino acid sequences set forth in SEQ ID NO: 3, 6, 8, 10, 12, and 14, and optionally comprises a non-naturally occurring amino acid sequence that differs from at least one of the full-length amino acid sequences set forth in SEQ ID NO: 3, 6, 8, 10, 12, and 14 by at least one nucleotide modification selected from the group consisting of the substitution of at least one amino acid, the addition of at least one amino acid, and the deletion of at least one amino acid.
“Variant” protein is intended to mean a protein derived from the native protein by deletion (so-called truncation) of one or more amino acids at the N-terminal and/or C-terminal end of the native protein; deletion and/or addition of one or more amino acids at one or more internal sites in the native protein; or substitution of one or more amino acids at one or more sites in the native protein. Such variants may result from, for example, genetic polymorphism or from human manipulation. Biologically active variants of an R protein will have at least about 80%, 85%, 86%, 87%, 88%, 89%, 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, 99% or more sequence identity to the amino acid sequence for the native protein (e.g. the amino acid sequence set forth in SEQ ID NO: 3, 6, 8, 10, 12, or 14) as determined by sequence alignment programs and parameters described elsewhere herein. A biologically active variant of a protein of the invention may differ from that protein by as few as 1-15 amino acid residues, as few as 1-10, such as 6-10, as few as 5, as few as 4, 3, 2, or even 1 amino acid residue.
The proteins of the invention may be altered in various ways including amino acid substitutions, deletions, truncations, and insertions. Methods for such manipulations are generally known in the art. Methods for mutagenesis and polynucleotide alterations are well known in the art. See, for example, Kunkel (1985) Proc. Natl. Acad. Sci. USA 82:488-492; Kunkel et al. (1987) Methods in Enzymol. 154:367-382; U.S. Pat. No. 4,873,192; Walker and Gaastra, eds. (1983) Techniques in Molecular Biology (MacMillan Publishing Company, New York) and the references cited therein. Guidance as to appropriate amino acid substitutions that do not affect biological activity of the protein of interest may be found in the model of Dayhoff et al. (1978) Atlas of Protein Sequence and Structure (Natl. Biomed. Res. Found., Washington, D.C.), herein incorporated by reference. Conservative substitutions, such as exchanging one amino acid with another having similar properties, may be optimal.
Thus, the genes and polynucleotides of the invention include both the naturally occurring sequences as well as mutant and other variant forms. Likewise, the proteins of the invention encompass both naturally occurring proteins and artificial or non-naturally occurring proteins as well as variants and modified forms thereof. More preferably, such variants confer to a plant or part thereof comprising the variant enhanced resistance wheat stripe rust caused by at least one race of Puccinia striiformis f. sp. tritici. In some embodiments, the mutations that will be made in the DNA encoding the variant will not place the sequence out of reading frame. Optimally, the mutations will not create complementary regions that could produce secondary mRNA structure. See, EP Patent Application Publication No. 75,444.
The deletions, insertions, and substitutions of the protein sequences encompassed herein are not expected to produce radical changes in the characteristics of the protein. However, when it is difficult to predict the exact effect of the substitution, deletion, or insertion in advance of doing so, one skilled in the art will appreciate that the effect will be evaluated by routine screening assays. That is, the activity can be evaluated by assays that are disclosed herein below.
For example, a wheat or barley plant that is susceptible to wheat stripe rust caused by a particular race or races of Puccinia striiformis f. sp. tritici can be transformed with an Rps6 polynucleotide, regenerated into a transformed or transgenic plant comprising the polynucleotide, and tested for resistance to wheat stripe rust caused by the particular race or races of Puccinia striiformis f. sp. tritici using standard resistance assays known in the art or described elsewhere herein. Preferred variant polynucleotides and polypeptides of the present invention confer or are capable of conferring upon a wheat or barley plant enhanced resistance to at least one race, but preferably two or more races, of Puccinia striiformis f. sp. tritici that is known to cause wheat stripe rust in a susceptible wheat or barley plant.
Variant polynucleotides and proteins also encompass sequences and proteins derived from a mutagenic and recombinogenic procedure such as DNA shuffling. Strategies for such DNA shuffling are known in the art. See, for example, Stemmer (1994) Proc. Natl. Acad. Sci. USA 91:10747-10751; Stemmer (1994) Nature 370:389-391; Crameri et al. (1997) Nature Biotech. 15:436-438; Moore et al. (1997) J. Mol. Biol. 272:336-347; Zhang et al. (1997) Proc. Natl. Acad. Sci. USA 94:4504-4509; Crameri et al. (1998) Nature 391:288-291; and U.S. Pat. Nos. 5,605,793 and 5,837,458.
The polynucleotides of the invention can be used to isolate corresponding sequences from other organisms, particularly other plants. In this manner, methods such as PCR, hybridization, and the like can be used to identify such sequences based on their sequence homology to the sequences set forth herein. Sequences isolated based on their sequence identity to the entire sequences set forth herein or to variants and fragments thereof are encompassed by the present invention. Such sequences include sequences that are orthologs of the disclosed sequences. “Orthologs” is intended to mean genes derived from a common ancestral gene and which are found in different species as a result of speciation. Genes found in different species are considered orthologs when their nucleotide sequences and/or their encoded protein sequences share at least 60%, 70%, 75%, 80%, 85%, 86%, 87%, 88%, 89%, 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, 99%, or greater sequence identity. Functions of orthologs are often highly conserved among species. Thus, isolated polynucleotides that encode R proteins and which hybridize under stringent conditions to at least one of the R proteins disclosed herein or otherwise known in the art, or to variants or fragments thereof, are encompassed by the present invention.
In one embodiment, the orthologs of the present invention have coding sequences comprising at least 80%, 85%, 86%, 87%, 88%, 89%, 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, 99%, or greater nucleotide sequence identity to the nucleotide sequence set forth in at least one of SEQ ID NOS: 2, 5, 7, 9, 11 or 13 and/or encode proteins comprising least 80%, 85%, 86%, 87%, 88%, 89%, 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, 99%, or greater amino acid sequence identity to at least one of the amino acid sequence set forth in SEQ ID NOS: 3, 6, 8, 10, 12, and 14.
As an NLR protein, RPS6, the R protein encoded by Rps6, comprises certain conserved domains. The conserved domains in the amino acid sequence of RPS6 (SEQ ID NO: 3) include, for example, a coiled-coil domain (amino acids 39 to 189), a nucleotide-binding domain (amino acids 190 to 384) and a leucine-rich repeat domain (amino acids 586 to 988). Preferably, variant RPS6 proteins of the present invention comprise a coiled-coil domain, a nucleotide-binding domain, and a leucine-rich repeat domain corresponding to the domains disclosed above.
In some embodiments, variant RPS6 proteins of the present invention comprise a higher percentage of amino acid sequence identity to one, two, or three of such conserved domains than to the full-length amino acid sequence of the RPS6 (SEQ ID NO: 3) protein disclosed herein. Preferably, such variants comprise a corresponding domain or domains having at least 95%, 96%, 97%, 98%, 99%, or 100% sequence identity to one, two, or three of the conserved domains of NLR proteins and further comprise an amino acid sequence having at least 80%, 85%, 86%, 87%, 88%, 89%, 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, or 99% identity to the amino acid set forth in SEQ ID NO: 3.
It is recognized that domains in variant RPS6 proteins corresponding to those conserved domains, as well as any particular conserved amino acids therein, can be identified by methods known to those of skill in the art or disclosed elsewhere herein such as, for example, multiple sequence alignment. It is further recognized that the positions of such conserved domains and conserved amino acids within a particular variant RPS6 can vary from the positions in the amino acid sequences set forth in SEQ ID NO: 3 and that through methods such as, for example, multiple sequence alignment, the corresponding positions of such conserved domains and conserved amino acids can be determined for any variant RPS6 protein of the present invention.
Preferably, the variant RPS6 proteins of the present invention and the polynucleotides encoding them confer, or are capable of conferring upon a barley or wheat plant comprising such a protein or polynucleotide, enhanced resistance to at least one race of Puccinia striiformis f. sp. tritici that is known to cause wheat stripe rust in a susceptible wheat or barley plant.
In a PCR approach, oligonucleotide primers can be designed for use in PCR reactions to amplify corresponding DNA sequences from cDNA or genomic DNA extracted from any plant of interest. Methods for designing PCR primers and PCR cloning are generally known in the art and are disclosed in Sambrook et al. (1989) Molecular Cloning: A Laboratory Manual (2d ed., Cold Spring Harbor Laboratory Press, Plainview, N.Y.). See also Innis et al., eds. (1990) PCR Protocols: A Guide to Methods and Applications (Academic Press, New York); Innis and Gelfand, eds. (1995) PCR Strategies (Academic Press, New York); and Innis and Gelfand, eds. (1999) PCR Methods Manual (Academic Press, New York). Known methods of PCR include, but are not limited to, methods using paired primers, nested primers, single specific primers, degenerate primers, gene-specific primers, vector-specific primers, partially-mismatched primers, and the like.
In hybridization techniques, all or part of a known polynucleotide is used as a probe that selectively hybridizes to other corresponding polynucleotides present in a population of cloned genomic DNA fragments or cDNA fragments (i.e., genomic or cDNA libraries) from a chosen organism. The hybridization probes may be genomic DNA fragments, cDNA fragments, RNA fragments, or other oligonucleotides, and may be labeled with a detectable group such as 32P, or any other detectable marker. Thus, for example, probes for hybridization can be made by labeling synthetic oligonucleotides based on the polynucleotides of the invention. Methods for preparation of probes for hybridization and for construction of cDNA and genomic libraries are generally known in the art and are disclosed in Sambrook et al. (1989) Molecular Cloning: A Laboratory Manual (2d ed., Cold Spring Harbor Laboratory Press, Plainview, N.Y.).
For example, an entire polynucleotide disclosed herein, or one or more portions thereof, may be used as a probe capable of specifically hybridizing to corresponding polynucleotide and messenger RNAs. To achieve specific hybridization under a variety of conditions, such probes include sequences that are unique among the sequence of the gene or cDNA of interest sequences and are optimally at least about 10 nucleotides in length, and most optimally at least about 20 nucleotides in length. Such probes may be used to amplify corresponding polynucleotides for the particular gene of interest from a chosen plant by PCR. This technique may be used to isolate additional coding sequences from a desired plant or as a diagnostic assay to determine the presence of coding sequences in a plant. Hybridization techniques include hybridization screening of plated DNA libraries (either plaques or colonies; see, for example, Sambrook et al. (1989) Molecular Cloning: A Laboratory Manual (2d ed., Cold Spring Harbor Laboratory Press, Plainview, N.Y.).
Hybridization of such sequences may be carried out under stringent conditions. By “stringent conditions” or “stringent hybridization conditions” is intended conditions under which a probe will hybridize to its target sequence to a detectably greater degree than to other sequences (e.g., at least 2-fold over background). Stringent conditions are sequence-dependent and will be different in different circumstances. By controlling the stringency of the hybridization and/or washing conditions, target sequences that are 100% complementary to the probe can be identified (homologous probing). Alternatively, stringency conditions can be adjusted to allow some mismatching in sequences so that lower degrees of similarity are detected (heterologous probing). Generally, a probe is less than about 1000 nucleotides in length, optimally less than 500 nucleotides in length.
Typically, stringent conditions will be those in which the salt concentration is less than about 1.5 M Na ion, typically about 0.01 to 1.0 M Na ion concentration (or other salts) at pH 7.0 to 8.3 and the temperature is at least about 30° C. for short probes (e.g., 10 to 50 nucleotides) and at least about 60° C. for long probes (e.g., greater than 50 nucleotides). Stringent conditions may also be achieved with the addition of destabilizing agents such as formamide. Exemplary low stringency conditions include hybridization with a buffer solution of 30 to 35% formamide, 1 M NaCl, 1% SDS (sodium dodecyl sulphate) at 37° C., and a wash in 1× to 2×SSC (20×SSC=3.0 M NaCl/0.3 M trisodium citrate) at 50 to 55° C. Exemplary moderate stringency conditions include hybridization in 40 to 45% formamide, 1.0 M NaCl, 1% SDS at 37° C., and a wash in 0.5× to 1×SSC at 55 to 60° C. Exemplary high stringency conditions include hybridization in 50% formamide, 1 M NaCl, 1% SDS at 37° C., and a wash in 0.1×SSC at 60 to 65° C. Optionally, wash buffers may comprise about 0.1% to about 1% SDS. Duration of hybridization is generally less than about 24 hours, usually about 4 to about 12 hours. The duration of the wash time will be at least a length of time sufficient to reach equilibrium.
Specificity is typically the function of post-hybridization washes, the critical factors being the ionic strength and temperature of the final wash solution. For DNA-DNA hybrids, the Tm can be approximated from the equation of Meinkoth and Wahl (1984) Anal. Biochem. 138:267-284: Tm=81.5° C.+16.6 (log M)+0.41 (% GC)−0.61 (% form)−500/L; where M is the molarity of monovalent cations, % GC is the percentage of guanosine and cytosine nucleotides in the DNA, % form is the percentage of formamide in the hybridization solution, and L is the length of the hybrid in base pairs. The Tm is the temperature (under defined ionic strength and pH) at which 50% of a complementary target sequence hybridizes to a perfectly matched probe. Tm is reduced by about 1° C. for each 1% of mismatching; thus, Tm, hybridization, and/or wash conditions can be adjusted to hybridize to sequences of the desired identity. For example, if sequences with ≥90% identity are sought, the Tm can be decreased 10° C. Generally, stringent conditions are selected to be about 5° C. lower than the thermal melting point (Tm) for the specific sequence and its complement at a defined ionic strength and pH. However, severely stringent conditions can utilize a hybridization and/or wash at 1, 2, 3, or 4° C. lower than the thermal melting point (Tm); moderately stringent conditions can utilize a hybridization and/or wash at 6, 7, 8, 9, or 10° C. lower than the thermal melting point (Tm); low stringency conditions can utilize a hybridization and/or wash at 11, 12, 13, 14, 15, or 20° C. lower than the thermal melting point (Tm). Using the equation, hybridization and wash compositions, and desired Tm, those of ordinary skill will understand that variations in the stringency of hybridization and/or wash solutions are inherently described. If the desired degree of mismatching results in a Tm of less than 45° C. (aqueous solution) or 32° C. (formamide solution), it is optimal to increase the SSC concentration so that a higher temperature can be used. An extensive guide to the hybridization of nucleic acids is found in Tijssen (1993) Laboratory Techniques in Biochemistry and Molecular Biology—Hybridization with Nucleic Acid Probes, Part I, Chapter 2 (Elsevier, New York); and Ausubel et al., eds. (1995) Current Protocols in Molecular Biology, Chapter 2 (Greene Publishing and Wiley-Interscience, New York). See Sambrook et al. (1989) Molecular Cloning: A Laboratory Manual (2d ed., Cold Spring Harbor Laboratory Press, Plainview, N.Y.).
It is recognized that the R protein coding sequences of the present invention encompass polynucleotide molecules comprising a nucleotide sequence that is sufficiently identical to the nucleotide sequence of SEQ ID NO: 1, 2, 5, 7, 9, 11 and/or 13. The term “sufficiently identical” is used herein to refer to a first amino acid or nucleotide sequence that contains a sufficient or minimum number of identical or equivalent (e.g., with a similar side chain) amino acid residues or nucleotides to a second amino acid or nucleotide sequence such that the first and second amino acid or nucleotide sequences have a common structural domain and/or common functional activity. For example, amino acid or nucleotide sequences that contain a common structural domain having at least about 45%, 55%, or 65% identity, preferably 75% identity, more preferably 85%, 86%, 87%, 88%, 89%, 90%, 95%, 96%, 97%, 98% or 99% identity are defined herein as sufficiently identical.
To determine the percent identity of two amino acid sequences or of two nucleic acids, the sequences are aligned for optimal comparison purposes. The percent identity between the two sequences is a function of the number of identical positions shared by the sequences (i.e., percent identity=number of identical positions/total number of positions (e.g., overlapping positions)×100). In one embodiment, the two sequences are the same length. The percent identity between two sequences can be determined using techniques similar to those described below, with or without allowing gaps. In calculating percent identity, typically exact matches are counted.
The determination of percent identity between two sequences can be accomplished using a mathematical algorithm. A preferred, nonlimiting example of a mathematical algorithm utilized for the comparison of two sequences is the algorithm of Karlin and Altschul (1990) Proc. Natl. Acad. Sci. USA 87:2264, modified as in Karlin and Altschul (1993) Proc. Natl. Acad. Sci. USA 90:5873-5877. Such an algorithm is incorporated into the NBLAST and XBLAST programs of Altschul et al. (1990) J. Mol. Biol. 215:403. BLAST nucleotide searches can be performed with the NBLAST program, score=100, wordlength=12, to obtain nucleotide sequences homologous to the polynucleotide molecules of the invention. BLAST protein searches can be performed with the XBLAST program, score=50, wordlength=3, to obtain amino acid sequences homologous to protein molecules of the invention. To obtain gapped alignments for comparison purposes, Gapped BLAST can be utilized as described in Altschul et al. (1997) Nucleic Acids Res. 25:3389. Alternatively, PSI-Blast can be used to perform an iterated search that detects distant relationships between molecules. See Altschul et al. (1997) supra. When utilizing BLAST, Gapped BLAST, and PSI-Blast programs, the default parameters of the respective programs (e.g., XBLAST and NBLAST; available on the world-wide web at ncbi.nlm.nih.gov). Another preferred, non-limiting example of a mathematical algorithm utilized for the comparison of sequences is the algorithm of Myers and Miller (1988) CABIOS 4:11-17. Such an algorithm is incorporated into the ALIGN program (version 2.0), which is part of the GCG sequence alignment software package. When utilizing the ALIGN program for comparing amino acid sequences, a PAM120 weight residue table, a gap length penalty of 12, and a gap penalty of 4 can be used. Alignment may also be performed manually by inspection.
Unless otherwise stated, sequence identity/similarity values provided herein refer to the value obtained using the full-length sequences of the invention and using multiple alignment by mean of the algorithm Clustal W (Nucleic Acid Research, 22(22):4673-4680, 1994) using the program AlignX included in the software package Vector NTI Suite Version 7 (InforMax, Inc., Bethesda, Md., USA) using the default parameters; or any equivalent program thereof. By “equivalent program” is intended any sequence comparison program that, for any two sequences in question, generates an alignment having identical nucleotide or amino acid residue matches and an identical percent sequence identity when compared to the corresponding alignment generated by CLUSTALW (Version 1.83) using default parameters (available at the European Bioinformatics Institute website on the world-wide web at: ebi.ac.uk/Tools/clustalw/index.html).
The use of the term “polynucleotide” is not intended to limit the present invention to polynucleotides comprising DNA. Those of ordinary skill in the art will recognize that polynucleotides, can comprise ribonucleotides and combinations of ribonucleotides and deoxyribonucleotides. Such deoxyribonucleotides and ribonucleotides include both naturally occurring molecules and synthetic analogues. The polynucleotides of the invention also encompass all forms of sequences including, but not limited to, single-stranded forms, double-stranded forms, hairpins, stem-and-loop structures, and the like.
The polynucleotide constructs comprising R protein coding regions can be provided in expression cassettes for expression in the plant or other organism or in a host cell of interest. The cassette will include 5′ and 3′ regulatory sequences operably linked to the R protein coding region. “Operably linked” is intended to mean a functional linkage between two or more elements. For example, an operable linkage between a polynucleotide or gene of interest and a regulatory sequence (i.e., a promoter) is functional link that allows for expression of the polynucleotide of interest. Operably linked elements may be contiguous or non-contiguous. When used to refer to the joining of two protein coding regions, by operably linked is intended that the coding regions are in the same reading frame. The cassette may additionally contain at least one additional gene to be cotransformed into the organism. Alternatively, the additional gene(s) can be provided on multiple expression cassettes. Such an expression cassette is provided with a plurality of restriction sites and/or recombination sites for insertion of the R protein coding region to be under the transcriptional regulation of the regulatory regions. The expression cassette may additionally contain selectable marker genes.
The expression cassette will include in the 5′-3′ direction of transcription, a transcriptional and translational initiation region (i.e., a promoter), a R protein coding region of the invention, and a transcriptional and translational termination region (i.e., termination region) functional in plants or other organism or non-human host cell. The regulatory regions (i.e., promoters, transcriptional regulatory regions, and translational termination regions) and/or the R protein coding region or of the invention may be native/analogous to the host cell or to each other. Alternatively, the regulatory regions and/or the R protein coding region of the invention may be heterologous to the host cell or to each other.
As used herein, “heterologous” in reference to a nucleic acid molecule or nucleotide sequence is a nucleic acid molecule or nucleotide sequence that originates from a foreign species, or, if from the same species, is modified from its native form in composition and/or genomic locus by deliberate human intervention. For example, a promoter operably linked to a heterologous polynucleotide is from a species different from the species from which the polynucleotide was derived, or, if from the same/analogous species, one or both are substantially modified from their original form and/or genomic locus, or the promoter is not the native promoter for the operably linked polynucleotide. As used herein, a chimeric gene comprises a coding sequence operably linked to a transcription initiation region that is heterologous to the coding sequence.
The present invention provides host cells comprising at least of the nucleic acid molecules, expression cassettes, and vectors of the present invention. In preferred embodiments of the invention, a host cell is a plant cell. In other embodiments, a host cell is selected from the group consisting of a bacterium, a fungal cell, and an animal cell. In certain embodiments, a host cell is non-human animal cell. However, in some other embodiments, the host cell is an in-vitro cultured human cell.
While it may be optimal to express the R protein using heterologous promoters, the native promoter of the corresponding R gene may be used.
The termination region may be native with the transcriptional initiation region, may be native with the operably linked R protein coding region of interest, may be native with the plant host, or may be derived from another source (i.e., foreign or heterologous to the promoter, the R protein of interest, and/or the plant host), or any combination thereof. Convenient termination regions are available from the Ti-plasmid of A. tumefaciens, such as the octopine synthase and nopaline synthase termination regions. See also Guerineau et al. (1991) Mol. Gen. Genet. 262:141-144; Proudfoot (1991) Cell 64:671-674; Sanfacon et al. (1991) Genes Dev. 5:141-149; Mogen et al. (1990) Plant Cell 2:1261-1272; Munroe et al. (1990) Gene 91:151-158; Ballas et al. (1989) Nucleic Acids Res. 17:7891-7903; and Joshi et al. (1987) Nucleic Acids Res. 15:9627-9639.
Where appropriate, the polynucleotides may be optimized for increased expression in the transformed plant. That is, the polynucleotides can be synthesized using plant-preferred codons for improved expression. See, for example, Campbell and Gowri (1990) Plant Physiol. 92:1-11 for a discussion of host-preferred codon usage. Methods are available in the art for synthesizing plant-preferred genes. See, for example, U.S. Pat. Nos. 5,380,831, and 5,436,391, and Murray et al. (1989) Nucleic Acids Res. 17:477-498, herein incorporated by reference.
Additional sequence modifications are known to enhance gene expression in a cellular host. These include elimination of sequences encoding spurious polyadenylation signals, exon-intron splice site signals, transposon-like repeats, and other such well-characterized sequences that may be deleterious to gene expression. The G-C content of the sequence may be adjusted to levels average for a given cellular host, as calculated by reference to known genes expressed in the host cell. When possible, the sequence is modified to avoid predicted hairpin secondary mRNA structures.
The expression cassettes may additionally contain 5′ leader sequences. Such leader sequences can act to enhance translation. Translation leaders are known in the art and include: picornavirus leaders, for example, EMCV leader (Encephalomyocarditis 5′ noncoding region) (Elroy-Stein et al. (1989) Proc. Natl. Acad. Sci. USA 86:6126-6130); potyvirus leaders, for example, TEV leader (Tobacco Etch Virus) (Gallie et al. (1995) Gene 165(2):233-238), MDMV leader (Maize Dwarf Mosaic Virus) (Virology 154:9-20), and human immunoglobulin heavy-chain binding protein (BiP) (Macejak et al. (1991) Nature 353:90-94); untranslated leader from the coat protein mRNA of alfalfa mosaic virus (AMV RNA 4) (Jobling et al. (1987) Nature 325:622-625); tobacco mosaic virus leader (TMV) (Gallie et al. (1989) in Molecular Biology of RNA, ed. Cech (Liss, N.Y.), pp. 237-256); and maize chlorotic mottle virus leader (MCMV) (Lommel et al. (1991) Virology 81:382-385). See also, Della-Cioppa et al. (1987) Plant Physiol. 84:965-968.
In preparing the expression cassette, the various DNA fragments may be manipulated, so as to provide for the DNA sequences in the proper orientation and, as appropriate, in the proper reading frame. Toward this end, adapters or linkers may be employed to join the DNA fragments or other manipulations may be involved to provide for convenient restriction sites, removal of superfluous DNA, removal of restriction sites, or the like. For this purpose, in vitro mutagenesis, primer repair, restriction, annealing, resubstitutions, e.g., transitions and transversions, may be involved.
A number of promoters can be used in the practice of the invention. The promoters can be selected based on the desired outcome. The nucleic acids can be combined with constitutive, tissue-preferred, or other promoters for expression in plants. Such constitutive promoters include, for example, the core CaMV 35S promoter (Odell et al. (1985) Nature 313:810-812); rice actin (McElroy et al. (1990) Plant Cell 2:163-171); ubiquitin (Christensen et al. (1989) Plant Mol. Biol. 12:619-632 and Christensen et al. (1992) Plant Mol. Biol. 18:675-689); pEMU (Last et al. (1991) Theor. Appl. Genet. 81:581-588); MAS (Velten et al. (1984) EMBO J. 3:2723-2730); ALS promoter (U.S. Pat. No. 5,659,026), and the like. Other constitutive promoters include, for example, U.S. Pat. Nos. 5,608,149; 5,608,144; 5,604,121; 5,569,597; 5,466,785; 5,399,680; 5,268,463; 5,608,142; and 6,177,611.
Tissue-preferred promoters can be utilized to target enhanced expression of the R protein coding sequences within a particular plant tissue. Such tissue-preferred promoters include, but are not limited to, leaf-preferred promoters, root-preferred promoters, seed-preferred promoters, and stem-preferred promoters. Tissue-preferred promoters include Yamamoto et al. (1997) Plant J. 12(2):255-265; Kawamata et al. (1997) Plant Cell Physiol. 38(7):792-803; Hansen et al. (1997) Mol. Gen Genet. 254(3):337-343; Russell et al. (1997) Transgenic Res. 6(2):157-168; Rinehart et al. (1996) Plant Physiol. 112(3):1331-1341; Van Camp et al. (1996) Plant Physiol. 112(2):525-535; Canevascini et al. (1996) Plant Physiol. 112(2):513-524; Yamamoto et al. (1994) Plant Cell Physiol. 35(5):773-778; Lam (1994) Results Probl. Cell Differ. 20:181-196; Orozco et al. (1993) Plant Mol Biol. 23(6):1129-1138; Matsuoka et al. (1993) Proc Natl. Acad. Sci. USA 90(20):9586-9590; and Guevara-Garcia et al. (1993) Plant J. 4(3):495-505. Such promoters can be modified, if necessary, for weak expression.
Generally, it will be beneficial to express the gene from an inducible promoter, particularly from a pathogen-inducible promoter. Such promoters include those from pathogenesis-related proteins (PR proteins), which are induced following infection by a pathogen; e.g., PR proteins, SAR proteins, beta-1,3-glucanase, chitinase, etc. See, for example, Redolfi et al. (1983) Neth. J. Plant Pathol. 89:245-254; Uknes et al. (1992) Plant Cell 4:645-656; and Van Loon (1985) Plant Mol. Virol. 4:111-116. See also WO 99/43819, herein incorporated by reference.
Of interest are promoters that are expressed locally at or near the site of pathogen infection. See, for example, Marineau et al. (1987) Plant Mol. Biol. 9:335-342; Matton et al. (1989) Molecular Plant-Microbe Interactions 2:325-331; Somsisch et al. (1986) Proc. Natl. Acad. Sci. USA 83:2427-2430; Somsisch et al. (1988) Mol. Gen. Genet. 2:93-98; and Yang (1996) Proc. Natl. Acad. Sci. USA 93:14972-14977. See also, Chen et al. (1996) Plant J. 10:955-966; Zhang et al. (1994) Proc. Natl. Acad. Sci. USA 91:2507-2511; Warner et al. (1993) Plant J. 3:191-201; Siebertz et al. (1989) Plant Cell 1:961-968; U.S. Pat. No. 5,750,386 (nematode-inducible); and the references cited therein. Of particular interest is the inducible promoter for the maize PRms gene, whose expression is induced by the pathogen Fusarium moniliforme (see, for example, Cordero et al. (1992) Physiol. Mol. Plant Path. 41:189-200).
Also of interest are the native promoters from other resistance genes from the target species. These promoters are often pathogen-inducible, and are likely to express the resistance gene at appropriate levels and in appropriate tissues. Examples of such promoters are the Sr57/Lr34, Sr33, and Sr35 promoters of wheat (Risk et al. (2012) Plant Biotechnol J 10: 447-487; Periyannan et al. (2013) Science 341: 786-788; Saintenac et al. (2013) Science 341: 783-786).
Additionally, as pathogens find entry into plants through wounds or insect damage, a wound-inducible promoter may be used in the constructions of the invention. Such wound-inducible promoters include potato proteinase inhibitor (pin II) gene (Ryan (1990) Ann. Rev. Phytopath. 28:425-449; Duan et al. (1996) Nature Biotechnology 14:494-498); wun1 and wun2, U.S. Pat. No. 5,428,148; win1 and win2 (Stanford et al. (1989) Mol. Gen. Genet. 215:200-208); systemin (McGurl et al. (1992) Science 225:1570-1573); WIP1 (Rohmeier et al. (1993) Plant Mol. Biol. 22:783-792; Eckelkamp et al. (1993) FEBS Letters 323:73-76); MPI gene (Corderok et al. (1994) Plant J. 6(2):141-150); and the like, herein incorporated by reference.
Chemical-regulated promoters can be used to modulate the expression of a gene in a plant through the application of an exogenous chemical regulator. Depending upon the objective, the promoter may be a chemical-inducible promoter, where application of the chemical induces gene expression, or a chemical-repressible promoter, where application of the chemical represses gene expression. Chemical-inducible promoters are known in the art and include, but are not limited to, the maize In2-2 promoter, which is activated by benzenesulfonamide herbicide safeners, the maize GST promoter, which is activated by hydrophobic electrophilic compounds that are used as pre-emergent herbicides, and the tobacco PR-1a promoter, which is activated by salicylic acid. Other chemical-regulated promoters of interest include steroid-responsive promoters (see, for example, the glucocorticoid-inducible promoter in Schena et al. (1991) Proc. Natl. Acad. Sci. USA 88:10421-10425 and McNellis et al. (1998) Plant J. 14(2):247-257) and tetracycline-inducible and tetracycline-repressible promoters (see, for example, Gatz et al. (1991) Mol. Gen. Genet. 227:229-237, and U.S. Pat. Nos. 5,814,618 and 5,789,156), herein incorporated by reference.
The expression cassette can also comprise a selectable marker gene for the selection of transformed cells. Selectable marker genes are utilized for the selection of transformed cells or tissues. Marker genes include genes encoding antibiotic resistance, such as those encoding neomycin phosphotransferase II (NEO) and hygromycin phosphotransferase (HPT), as well as genes conferring resistance to herbicidal compounds, such as glufosinate ammonium, bromoxynil, imidazolinones, and 2,4-dichlorophenoxyacetate (2,4-D). Additional selectable markers include phenotypic markers such as β-galactosidase and fluorescent proteins such as green fluorescent protein (GFP) (Su et al. (2004) Biotechnol Bioeng 85:610-9 and Fetter et al. (2004) Plant Cell 16:215-28), cyan florescent protein (CYP) (Bolte et al. (2004) J. Cell Science 117:943-54 and Kato et al. (2002) Plant Physiol 129:913-42), and yellow florescent protein (PhiYFPTM from Evrogen, see, Bolte et al. (2004) J. Cell Science 117:943-54). For additional selectable markers, see generally, Yarranton (1992) Curr. Opin. Biotech. 3:506-511; Christopherson et al. (1992) Proc. Natl. Acad. Sci. USA 89:6314-6318; Yao et al. (1992) Cell 71:63-72; Reznikoff (1992) Mol. Microbiol. 6:2419-2422; Barkley et al. (1980) in The Operon, pp. 177-220; Hu et al. (1987) Cell 48:555-566; Brown et al. (1987) Cell 49:603-612; Figge et al. (1988) Cell 52:713-722; Deuschle et al. (1989) Proc. Natl. Acad. Aci. USA 86:5400-5404; Fuerst et al. (1989) Proc. Natl. Acad. Sci. USA 86:2549-2553; Deuschle et al. (1990) Science 248:480-483; Gossen (1993) Ph.D. Thesis, University of Heidelberg; Reines et al. (1993) Proc. Natl. Acad. Sci. USA 90:1917-1921; Labow et al. (1990) Mol. Cell. Biol. 10:3343-3356; Zambretti et al. (1992) Proc. Natl. Acad. Sci. USA 89:3952-3956; Baim et al. (1991) Proc. Natl. Acad. Sci. USA 88:5072-5076; Wyborski et al. (1991) Nucleic Acids Res. 19:4647-4653; Hillenand-Wissman (1989) Topics Mol. Struc. Biol. 10:143-162; Degenkolb et al. (1991) Antimicrob. Agents Chemother. 35:1591-1595; Kleinschnidt et al. (1988) Biochemistry 27:1094-1104; Bonin (1993) Ph.D. Thesis, University of Heidelberg; Gossen et al. (1992) Proc. Natl. Acad. Sci. USA 89:5547-5551; Oliva et al. (1992) Antimicrob. Agents Chemother. 36:913-919; Hlavka et al. (1985) Handbook of Experimental Pharmacology, Vol. 78 (Springer-Verlag, Berlin); Gill et al. (1988) Nature 334:721-724. Such disclosures are herein incorporated by reference.
The above list of selectable marker genes is not intended to be limiting. Any selectable marker gene can be used in the present invention.
Numerous plant transformation vectors and methods for transforming plants are available. See, for example, An, G. et al. (1986) Plant Pysiol., 81:301-305; Fry, J., et al. (1987) Plant Cell Rep. 6:321-325; Block, M. (1988) Theor. Appl Genet. 76:767-774; Hinchee, et al. (1990) Stadler. Genet. Symp. 203212.203-212; Cousins, et al. (1991) Aust. J. Plant Physiol. 18:481-494; Chee, P. P. and Slightom, J. L. (1992) Gene. 118:255-260; Christou, et al. (1992) Trends. Biotechnol. 10:239-246; D'Halluin, et al. (1992) Bio/Technol. 10:309-314; Dhir, et al. (1992) Plant Physiol. 99:81-88; Casas et al. (1993) Proc. Nat. Acad Sci. USA 90:11212-11216; Christou, P. (1993) In Vitro Cell. Dev. Biol.-Plant; 29P:119-124; Davies, et al. (1993) Plant Cell Rep. 12:180-183; Dong, J. A. and Mchughen, A. (1993) Plant Sci. 91:139-148; Franklin, C. I. and Trieu, T. N. (1993) Plant. Physiol. 102:167; Golovkin, et al. (1993) Plant Sci. 90:41-52; Guo Chin Sci. Bull. 38:2072-2078; Asano, et al. (1994) Plant Cell Rep. 13; Ayeres N. M. and Park, W. D. (1994) Crit. Rev. Plant. Sci. 13:219-239; Barcelo, et al. (1994) Plant. J. 5:583-592; Becker, et al. (1994) Plant. J. 5:299-307; Borkowska et al. (1994) Acta. Physiol Plant. 16:225-230; Christou, P. (1994) Agro. Food. Ind. Hi Tech. 5: 17-27; Eapen et al. (1994) Plant Cell Rep. 13:582-586; Hartman, et al. (1994) Bio-Technology 12: 919923; Ritala, et al. (1994) Plant. Mol. Biol. 24:317-325; and Wan, Y. C. and Lemaux, P. G. (1994) Plant Physiol. 104:3748.
Plant transformation vectors that find use in the present invention include, for example, T-DNA vectors or plasmids, which are suitable for use in Agrobacterium-mediated transformation methods that are disclosed elsewhere herein or otherwise known in the art. Examples of such T-DNA vectors or plasmids are the IHP_0205_NLR-A_construct (SEQ ID NO: 15), the IHP_0300_NLR-A_native construct (SEQ ID NO: 34), and the pBract202_TSL_pMla6_NLR-A_CDS_gDNA_tMla6 construct (SEQ ID NO: 35). The IHP_0205_NLR-A_construct (SEQ ID NO: 15) comprises a hygromycin resistance gene driven by a 35S promoter and nos terminator followed by 2.4 kb promoter, exons 1, 2, and 3, intron 3, exon 4, and 1.8 kb terminator of NLR-A, flanked by the left (LB) and right (RB) T-DNA border sequences, and further comprises two replication origin sites (pSa-ORI and colEI-ori) and kanamycin resistance (npt1). The IHP_0300_NLR-A_native construct (SEQ ID NO: 34) comprises a hygromycin resistance gene driven by a 35S promoter and nos terminator followed by the native sequence of NLR-A containing all four exons and three introns that is approximately 17 kb in length, flanked by the left (LB) and right (RB) T-DNA border sequences, and further comprises two replication origin sites (pSa-ORI and colEI-ori) and kanamycin resistance (npt1). The pBract202_TSL_pMla6_NLR-A_CDS_gDNA_tMla6 construct (SEQ ID NO: 35) comprises a hygromycin resistance gene driven by a 35S promoter and nos terminator followed by 1.2 kb of promoter sequence, a 464 bp 5′UTR of Mla6 (GenBank Acession No. AJ302293), the native coding sequence of NLR-A containing exons 1, 2, and 3 and introns 1 and 2 that is approximately 12 kb, 47 bp 3′-UTR of Mla6, and a 1.6 kb terminator from Mla6, flanked by the left (LB) and right (RB) T-DNA border sequences, and further comprises two replication origin sites (pSa-ORI and colEI-ori) and kanamycin resistance (npt1).
The methods of the invention involve introducing a polynucleotide construct into a plant. By “introducing” is intended presenting to the plant the polynucleotide construct in such a manner that the construct gains access to the interior of a cell of the plant. The methods of the invention do not depend on a particular method for introducing a polynucleotide construct to a plant, only that the polynucleotide construct gains access to the interior of at least one cell of the plant. Methods for introducing polynucleotide constructs into plants are known in the art including, but not limited to, stable transformation methods, transient transformation methods, and virus-mediated methods.
By “stable transformation” is intended that the polynucleotide construct introduced into a plant integrates into the genome of the plant and is capable of being inherited by progeny thereof. By “transient transformation” is intended that a polynucleotide construct introduced into a plant does not integrate into the genome of the plant.
For the transformation of plants and plant cells, the nucleotide sequences of the invention are inserted using standard techniques into any vector known in the art that is suitable for expression of the nucleotide sequences in a plant or plant cell. The selection of the vector depends on the preferred transformation technique and the target plant species to be transformed.
Methodologies for constructing plant expression cassettes and introducing foreign nucleic acids into plants are generally known in the art and have been previously described. For example, foreign DNA can be introduced into plants, using tumor-inducing (Ti) plasmid vectors. Other methods utilized for foreign DNA delivery involve the use of PEG mediated protoplast transformation, electroporation, microinjection whiskers, and biolistics or microprojectile bombardment for direct DNA uptake. Such methods are known in the art. (U.S. Pat. No. 5,405,765 to Vasil et al.; Bilang et al. (1991) Gene 100: 247-250; Scheid et al., (1991) Mol. Gen. Genet., 228: 104-112; Guerche et al., (1987) Plant Science 52: 111-116; Neuhause et al., (1987) Theor. Appl Genet. 75: 30-36; Klein et al., (1987) Nature 327: 70-73; Howell et al., (1980) Science 208:1265; Horsch et al., (1985) Science 227: 1229-1231; DeBlock et al., (1989) Plant Physiology 91: 694-701; Methods for Plant Molecular Biology (Weissbach and Weissbach, eds.) Academic Press, Inc. (1988) and Methods in Plant Molecular Biology (Schuler and Zielinski, eds.) Academic Press, Inc. (1989). The method of transformation depends upon the plant cell to be transformed, stability of vectors used, expression level of gene products and other parameters.
Other suitable methods of introducing nucleotide sequences into plant cells and subsequent insertion into the plant genome include microinjection as Crossway et al. (1986) Biotechniques 4:320-334, electroporation as described by Riggs et al. (1986) Proc. Natl. Acad. Sci. USA 83:5602-5606, Agrobacterium-mediated transformation as described by Townsend et al., U.S. Pat. No. 5,563,055, Zhao et al., U.S. Pat. No. 5,981,840, direct gene transfer as described by Paszkowski et al. (1984) EMBO J. 3:2717-2722, and ballistic particle acceleration as described in, for example, Sanford et al., U.S. Pat. No. 4,945,050; Tomes et al., U.S. Pat. No. 5,879,918; Tomes et al., U.S. Pat. No. 5,886,244; Bidney et al., U.S. Pat. No. 5,932,782; Tomes et al. (1995) “Direct DNA Transfer into Intact Plant Cells via Microprojectile Bombardment,” in Plant Cell, Tissue, and Organ Culture: Fundamental Methods, ed. Gamborg and Phillips (Springer-Verlag, Berlin); McCabe et al. (1988) Biotechnology 6:923-926); and Lec1 transformation (WO 00/28058). Also see, Weissinger et al. (1988) Ann. Rev. Genet. 22:421-477; Sanford et al. (1987) Particulate Science and Technology 5:27-37 (onion); Christou et al. (1988) Plant Physiol. 87:671-674 (soybean); McCabe et al. (1988) Bio/Technology 6:923-926 (soybean); Finer and McMullen (1991) In Vitro Cell Dev. Biol. 27P:175-182 (soybean); Singh et al. (1998) Theor. Appl. Genet. 96:319-324 (soybean); Datta et al. (1990) Biotechnology 8:736-740 (rice); Klein et al. (1988) Proc. Natl. Acad. Sci. USA 85:4305-4309 (maize); Klein et al. (1988) Biotechnology 6:559-563 (maize); Tomes, U.S. Pat. No. 5,240,855; Buising et al., U.S. Pat. Nos. 5,322,783 and 5,324,646; Tomes et al. (1995) “Direct DNA Transfer into Intact Plant Cells via Microprojectile Bombardment,” in Plant Cell, Tissue, and Organ Culture: Fundamental Methods, ed. Gamborg (Springer-Verlag, Berlin) (maize); Klein et al. (1988) Plant Physiol. 91:440-444 (maize); Fromm et al. (1990) Biotechnology 8:833-839 (maize); Hooykaas-Van Slogteren et al. (1984) Nature (London) 311:763-764; Bowen et al., U.S. Pat. No. 5,736,369 (cereals); Bytebier et al. (1987) Proc. Natl. Acad. Sci. USA 84:5345-5349 (Liliaceae); De Wet et al. (1985) in The Experimental Manipulation of Ovule Tissues, ed. Chapman et al. (Longman, N.Y.), pp. 197-209 (pollen); Kaeppler et al. (1990) Plant Cell Reports 9:415-418 and Kaeppler et al. (1992) Theor. Appl. Genet. 84:560-566 (whisker-mediated transformation); D'Halluin et al. (1992) Plant Cell 4:1495-1505 (electroporation); Li et al. (1993) Plant Cell Reports 12:250-255 and Christou and Ford (1995) Annals of Botany 75:407-413 (rice); Osjoda et al. (1996) Nature Biotechnology 14:745-750 (maize via Agrobacterium tumefaciens); all of which are herein incorporated by reference.
The polynucleotides of the invention may be introduced into plants by contacting plants with a virus or viral nucleic acids. Generally, such methods involve incorporating a polynucleotide construct of the invention within a viral DNA or RNA molecule. Further, it is recognized that promoters of the invention also encompass promoters utilized for transcription by viral RNA polymerases. Methods for introducing polynucleotide constructs into plants and expressing a protein encoded therein, involving viral DNA or RNA molecules, are known in the art. See, for example, U.S. Pat. Nos. 5,889,191, 5,889,190, 5,866,785, 5,589,367 and 5,316,931; herein incorporated by reference.
If desired, the modified viruses or modified viral nucleic acids can be prepared in formulations. Such formulations are prepared in a known manner (see e.g. for review U.S. Pat. No. 3,060,084, EP-A 707 445 (for liquid concentrates), Browning, “Agglomeration”, Chemical Engineering, Dec. 4, 1967, 147-48, Perry's Chemical Engineer's Handbook, 4th Ed., McGraw-Hill, New York, 1963, pages 8-57 and et seq. WO 91/13546, U.S. Pat. Nos. 4,172,714, 4,144,050, 3,920,442, 5,180,587, 5,232,701, 5,208,030, GB 2,095,558, U.S. Pat. No. 3,299,566, Klingman, Weed Control as a Science, John Wiley and Sons, Inc., New York, 1961, Hance et al. Weed Control Handbook, 8th Ed., Blackwell Scientific Publications, Oxford, 1989 and Mollet, H., Grubemann, A., Formulation technology, Wiley VCH Verlag GmbH, Weinheim (Germany), 2001, 2. D. A. Knowles, Chemistry and Technology of Agrochemical Formulations, Kluwer Academic Publishers, Dordrecht, 1998 (ISBN 0-7514-0443-8), for example by extending the active compound with auxiliaries suitable for the formulation of agrochemicals, such as solvents and/or carriers, if desired emulsifiers, surfactants and dispersants, preservatives, antifoaming agents, anti-freezing agents, for seed treatment formulation also optionally colorants and/or binders and/or gelling agents.
In specific embodiments, the polynucleotide constructs and expression cassettes of the invention can be provided to a plant using a variety of transient transformation methods known in the art. Such methods include, for example, microinjection or particle bombardment. See, for example, Crossway et al. (1986) Mol Gen. Genet. 202:179-185; Nomura et al. (1986) Plant Sci. 44:53-58; Hepler et al. (1994) PNAS Sci. 91: 2176-2180 and Hush et al. (1994) J. Cell Science 107:775-784, all of which are herein incorporated by reference. Alternatively, the polynucleotide can be transiently transformed into the plant using techniques known in the art. Such techniques include viral vector system and Agrobacterium tumefaciens-mediated transient expression as described elsewhere herein.
The cells that have been transformed may be grown into plants in accordance with conventional ways. See, for example, McCormick et al. (1986) Plant Cell Reports 5:81-84. These plants may then be grown, and either pollinated with the same transformed strain or different strains, and the resulting hybrid having constitutive expression of the desired phenotypic characteristic identified. Two or more generations may be grown to ensure that expression of the desired phenotypic characteristic is stably maintained and inherited and then seeds harvested to ensure expression of the desired phenotypic characteristic has been achieved. In this manner, the present invention provides transformed seed (also referred to as “transgenic seed”) having a polynucleotide construct of the invention, for example, an expression cassette of the invention, stably incorporated into their genome.
In certain embodiments of the invention, the nucleotide sequence of a non-functional allele at an R gene locus of the present invention can be modified in planta to a functional allele that provides resistance to at least one race of a plant pathogen. In one embodiment of the invention, a non-functional allele that is present at the Rps6 locus in a barley plant can be modified to a functional allele that provides resistance to, for example, at least one, two, three, or four races of Puccinia striiformis f. sp. tritici. In another embodiment of the invention, a non-functional allele that is present at the Rps6 locus in a barley plant can be modified to a functional allele that provides resistance to at least one, two, three, or four races of at least two Puccinia spp. that cause rust disease on a barley plant. For example, a non-functional allele at the Rps6 locus can be modified to form whereby the modified allele comprises the nucleotide sequence of Rps6 set forth in SEQ ID NO: 1. In another example, a non-functional allele at the Rps6 locus can be modified to form whereby the modified allele comprises a coding sequence comprising the nucleotide sequence set forth in SEQ ID NO: 3, 6, 8, 10, 12, or 14, or variant thereof and/or encodes an amino acid sequence comprising the amino acid sequence set forth in SEQ ID NO: 3, 6, 8, 10, 12, or 14, or variant thereof.
Any methods known in the art for modifying DNA in the genome of a plant can be used to modify the nucleotide sequences of an R gene in planta, e.g. to modify the nucleotide sequence of a non-functional allele to that of a functional allele that provides resistance to a plant pathogen. Such modifications to the DNA in the genome of a plant include, for example, insertions, deletions, substitutions, and combinations thereof. The insertions, deletions, and substitutions can be made using any method known in the art such as, for example, by genome editing techniques as described elsewhere herein or otherwise known in the art.
The insertions comprise an insertion of at least one nucleotide or base pair (bp) in an allele of an R gene of the present invention. The insertion can comprise insertion of any size DNA fragment into the genome. The inserted DNA can be 1 bp in length, 1-5 bp in length, 5-10 bp in length, 10-15 bp in length, 15-20 bp in length, 20-30 bp in length, 30-50 bp in length, 50-100 bp in length, 100-200 bp in length, 200-300 bp in length, 300-400 bp in length, 400-500 bp in length, 500-600 bp in length, 600-700 bp in length, 700-800 bp in length, 800-900 bp in length, 900-1000 bp in length, 1000-1500 bp.
The deletions comprise the deletion of at least one bp from an allele of an R gene of the present invention. As used herein, a “deletion” is meant the removal of one or more nucleotides or base pairs from the DNA. Provided herein, a deletion in an allele of an R gene can be the removal of at least 1, at least 20, at least 50, at least 100, at least 500, at least 1000, at least 5000 or more bp.
The substitutions comprise the replacement of at least one bp from an allele of an R gene of the present invention with another bp. As used herein, a “substitution” is meant the replacement of one or more nucleotides or base pairs from the DNA with non-identical nucleotides or base pairs. When the substitution comprises two or more nucleotides, the two or more nucleotides can be contiguous or non-contiguous within the DNA sequence of the allele. Provided herein, a substitution in an allele of an R gene can be the replacement of at least 1, at least 20, at least 50, at least 100, at least 500, at least 1000, at least 5000 or more base pairs. In some embodiments, the substitution can be the nucleotide sequence of the entire allele or any portion or portions thereof such as, for example, the transcribed region, the 5′ untranslated region, the 3′ untranslated region, an exon, or an intron.
In certain embodiments of the invention, the modification of a non-functional allele at an R gene locus is a homozygous modification. By “homozygous modification” is meant that the modification is in both alleles of the R gene locus in a particular genome of a plant. In other cases, the modification of the R gene locus gene is heterozygous, that is, the modification is only in one allele of the of the R gene locus in the genome of a plant. It is recognized the plants of the invention include, for example, crop plants with genomes that are diploid or polyploid (e.g. tetraploid or hexaploid), including autopolyploids and allopolyploids. An autopolyploid is an organism having more than two sets of chromosomes, all of which were derived from the same species. An allopolyploid is an organism having two or more complete sets of chromosomes that are derived from different species. Depending on the particular the crop plant, 1, 2, 3, 4, 5, 6 or more alleles at an R gene locus of the plant can be modified using the methods disclosed.
Such methods known in the art for modifying DNA in the genome of a plant include, for example, genome editing techniques, such as, for example, methods involving targeted mutagenesis, homologous recombination, and mutation breeding. Targeted mutagenesis or similar techniques are disclosed in U.S. Pat. Nos. 5,565,350; 5,731,181; 5,756,325; 5,760,012; 5,795,972, 5,871,984, and 8,106,259; all of which are herein incorporated in their entirety by reference. Methods for gene modification or gene replacement comprising homologous recombination can involve inducing double breaks in DNA using zinc-finger nucleases (ZFN), TAL (transcription activator-like) effector nucleases (TALEN), Clustered Regularly Interspaced Short Palindromic Repeats/CRISPR-associated nuclease (CRISPR/Cas nuclease), or homing endonucleases that have been engineered endonucleases to make double-strand breaks at specific recognition sequences in the genome of a plant, other organism, or host cell. See, for example, Durai et al., (2005) Nucleic Acids Res 33:5978-90; Mani et al. (2005) Biochem Biophys Res Comm 335:447-57; U.S. Pat. Nos. 7,163,824, 7,001,768, and 6,453,242; Arnould et al. (2006) J Mol Biol 355:443-58; Ashworth et al., (2006) Nature 441:656-9; Doyon et al. (2006) J Am Chem Soc 128:2477-84; Rosen et al., (2006) Nucleic Acids Res 34:4791-800; and Smith et al., (2006) Nucleic Acids Res 34:e149; U.S. Pat. App. Pub. No. 2009/0133152; and U.S. Pat. App. Pub. No. 2007/0117128; all of which are herein incorporated in their entirety by reference.
TAL effector nucleases (TALENs) can be used to make double-strand breaks at specific recognition sequences in the genome of a plant for gene modification or gene replacement through homologous recombination. TAL effector nucleases are a class of sequence-specific nucleases that can be used to make double-strand breaks at specific target sequences in the genome of a plant or other organism. TAL effector nucleases are created by fusing a native or engineered transcription activator-like (TAL) effector, or functional part thereof, to the catalytic domain of an endonuclease, such as, for example, FokI. The unique, modular TAL effector DNA binding domain allows for the design of proteins with potentially any given DNA recognition specificity. Thus, the DNA binding domains of the TAL effector nucleases can be engineered to recognize specific DNA target sites and thus, used to make double-strand breaks at desired target sequences. See, WO 2010/079430; Morbitzer et al. (2010) PNAS 10.1073/pnas.1013133107; Scholze and Boch (2010) Virulence 1:428-432; Christian et al. Genetics (2010) 186:757-761; Li et al. (2010) Nuc. Acids Res. (2010) doi:10.1093/nar/gkq704; and Miller et al. (2011) Nature Biotechnology 29:143-148; all of which are herein incorporated by reference.
The CRISPR/Cas nuclease system can also be used to make double-strand breaks at specific recognition sequences in the genome of a plant for gene modification or gene replacement through homologous recombination. The CRISPR/Cas nuclease is an RNA-guided (simple guide RNA, sgRNA in short) DNA endonuclease system performing sequence-specific double-stranded breaks in a DNA segment homologous to the designed RNA. It is possible to design the specificity of the sequence (Cho S. W. et al., Nat. Biotechnol. 31:230-232, 2013; Cong L. et al., Science 339:819-823, 2013; Mali P. et al., Science 339:823-826, 2013; Feng Z. et al., Cell Research: 1-4, 2013).
In addition, a ZFN can be used to make double-strand breaks at specific recognition sequences in the genome of a plant for gene modification or gene replacement through homologous recombination. The Zinc Finger Nuclease (ZFN) is a fusion protein comprising the part of the FokI restriction endonuclease protein responsible for DNA cleavage and a zinc finger protein which recognizes specific, designed genomic sequences and cleaves the double-stranded DNA at those sequences, thereby producing free DNA ends (Urnov F. D. et al., Nat Rev Genet. 11:636-46, 2010; Carroll D., Genetics. 188:773-82, 2011).
Breaking DNA using site specific nucleases, such as, for example, those described herein above, can increase the rate of homologous recombination in the region of the breakage. Thus, coupling of such effectors as described above with nucleases enables the generation of targeted changes in genomes which include additions, deletions and other modifications.
Mutation breeding can also be used in the methods and compositions provided herein. Mutation breeding methods can involve, for example, exposing the plants or seeds to a mutagen, particularly a chemical mutagen such as, for example, ethyl methanesulfonate (EMS) and selecting for plants that possess a desired modification in the Rps6 gene. However, other mutagens can be used in the methods disclosed herein including, but not limited to, radiation, such as X-rays, Gamma rays (e.g., cobalt 60 or cesium 137), neutrons, (e.g., product of nuclear fission by uranium 235 in an atomic reactor), Beta radiation (e.g., emitted from radioisotopes such as phosphorus 32 or carbon 14), and ultraviolet radiation (preferably from 2500 to 2900 nm), and chemical mutagens such as base analogues (e.g., 5-bromo-uracil), related compounds (e.g., 8-ethoxy caffeine), antibiotics (e.g., streptonigrin), alkylating agents (e.g., sulfur mustards, nitrogen mustards, epoxides, ethylenamines, sulfates, sulfonates, sulfones, lactones), azide, hydroxylamine, nitrous acid, or acridines. Further details of mutation breeding can be found in “Principals of Cultivar Development” Fehr, 1993 Macmillan Publishing Company the disclosure of which is incorporated herein by reference.
The nucleic acid molecules, expression cassettes, vectors, and polynucleotide constructs of the present invention may be used for transformation of any plant species, including, but not limited to, monocots and dicots. Preferred plants of the present invention are grass plants including domesticated and non-domesticated species in the Poaceae family such as, for example, turfgrasses, sugarcane, grain plants, and bamboos. More preferred plants are grain plants including, but not limited to, wheat, barley, oats, maize, rice, sorghum, rye, millet, spelt, and triticale.
As used herein, the term “barley plant” generally refers to a plant that is a member of the species Hordeum vulgare L. including, but not limited to, two-rowed barley with shattering spikes (wild barley; previously classified as H. spontaneum K. Koch), two-rowed barley with non-shattering spikes (previously classified as H. distichum L.), six-row barley with non-shattering spikes (previously classified as H. hexastichum L.), and six-row with shattering spikes (previously classified as H. agriocrithon Aber).
As used herein, the term “wheat plant” generally refers to a plant that is a member of the Triticum genus or a member of another genus within the Triticeae tribe, particularly a member of another genus that is capable of producing interspecific hybrids with at least one Triticum sp. Examples of such another genus within the Triticeae tribe are Aegilops and Secale. 
The wheat plants of the present invention include, for example, domesticated and non-domesticated plants. The wheat plants of the present invention include, but are not limited to, the following Triticum, Aegilops and Secale species: T. aestivum, T. monococcum, T. turgidum, T. boeoticum, T. timopheevii, and T. urartu, A. tauschii, S. cereale, and hybrids thereof. Examples of T. aestivum subspecies included within the present invention are aestivum (common wheat), compactum (club wheat), macha (macha wheat), vavilovi (vavilovi wheat), spelt (T. spelta), and sphaecrococcum (shot wheat). Examples of T. turgidum subspecies included within the present invention are turgidum, carthlicum, dicoccom, durum, paleocoichicum, polonicum, turanicum, and dicoccoides. Examples of T. monococcum subspecies included within the present invention are monococcum (einkorn) and aegilopoides. In one embodiment of the present invention, the wheat plant is a member of the Triticum turgidum species; and in particular, a member of the Durum subspecies, for example, a Ciccio, Colosseo, or Utopia cultivar. It is recognized that a wheat plant of the present invention can be a domesticated or a non-domesticated wheat plant.
The present invention also encompasses triticale plants, triticale plant parts, and triticale plant cells comprising an R gene of the invention. As used herein, a “triticale plant” refers to a plant that is created by crossing a rye plant (Secale cereale) with either a tetraploid wheat plant (e.g. Triticum turgidum) or a hexaploid wheat plant (e.g. Triticum aestivum). The present invention also includes seeds produced by the triticale plants described herein and methods for controlling weeds in the vicinity of the triticale plants described herein. As used herein, the term “wheat plant” encompasses triticale plants unless stated otherwise or apparent from the context of use.
Examples of plant species of interest include, but are not limited to, peppers (Capsicum spp; e.g., Capsicum annuum, C. baccatum, C. chinense, C. frutescens, C. pubescens, and the like), tomatoes (Lycopersicon esculentum), tobacco (Nicotiana tabacum), eggplant (Solanum melongena), petunia (Petunia spp., e.g., Petunia×hybrida or Petunia hybrida), pea (Pisum sativum), bean (Phaseolus vulgaris), corn or maize (Zea mays), Brassica sp. (e.g., B. napus, B. rapa, B. juncea), particularly those Brassica species useful as sources of seed oil, alfalfa (Medicago saliva), rice (Oryza sativa), rye (Secale cereale), sorghum (Sorghum bicolor, Sorghum vulgare), millet (e.g., pearl millet (Pennisetum glaucum), proso millet (Panicum miliaceum), foxtail millet (Setaria italica), finger millet (Eleusine coracana)), sunflower (Helianthus annuus), safflower (Carthamus tinctorius), soybean (Glycine max), tobacco (Nicotiana tabacum), potato (Solanum tuberosum), peanuts (Arachis hypogaea), cotton (Gossypium barbadense, Gossypium hirsutum), strawberry (e.g. Fragaria×ananassa, Fragaria vesca, Fragaria moschata, Fragaria virginiana, Fragaria chiloensis), sweet potato (Ipomoea batatus), cassava (Manihot esculenta), coffee (Coffea spp.), coconut (Cocos nucifera), oil palm (e.g. Elaeis guineensis, Elaeis oleifera), pineapple (Ananas comosus), citrus trees (Citrus spp.), cocoa (Theobroma cacao), tea (Camellia sinensis), banana (Musa spp.), avocado (Persea americana), fig (Ficus casica), guava (Psidium guajava), mango (Mangifera indica), olive (Olea europaea), papaya (Carica papaya), cashew (Anacardium occidentale), macadamia (Macadamia integrifolia), almond (Prunus amygdalus), sugar beets (Beta vulgaris), sugarcane (Saccharum spp.), oats (Avena sativa), barley (Hordeum vulgare), Brachypodium distachyon and other Brachypodium spp., switchgrass (Panicum virgatum) turfgrasses (e.g. Poa pratensis, Festuca arundinacea, Festuca spp., Cynodon dactylon, Cynodon spp., Lolium perenne, Lolium multiflorum, Agrostis palustris, Zoysia japonica, Zoysia spp., Stenotaphrum secundatum, Eremochloa ophiuroides), vegetables, ornamentals, and conifers. In specific embodiments, plants of the present invention are crop plants (e.g. maize, sorghum, wheat, millet, rice, barley, oats, sugarcane, alfalfa, soybean, peanut, sunflower, cotton, safflower, Brassica spp., lettuce, strawberry, apple, and citrus etc.).
Vegetables include, but are not limited to, tomatoes (Lycopersicon esculentum), lettuce (e.g., Lactuca sativa), green beans (Phaseolus vulgaris), lima beans (Phaseolus limensis), peas (Lathyrus spp.), and members of the genus Cucumis such as cucumber (C. sativus), cantaloupe (C. cantalupensis), and musk melon (C. melo). Ornamentals include, for example, azalea (Rhododendron spp.), hydrangea (Macrophylla hydrangea), hibiscus (Hibiscus rosasanensis), roses (Rosa spp.), tulips (Tulipa spp.), daffodils (Narcissus spp.), petunias (Petunia hybrida), carnation (Dianthus caryophyllus), poinsettia (Euphorbia pulcherrima), and chrysanthemum.
As used herein, the term “plant” is intended to encompass plants at any stage of maturity or development, any plant part or parts taken or derived from any such plant unless otherwise clearly indicated by context. As used herein, the term “plant” includes, for example, plant cells, plant protoplasts, plant cell tissue cultures from which plants can be regenerated, plant calli, plant clumps, and plant cells that are intact in plants or parts of plants such as embryos, pollen, ovules, seeds, tubers, propagules, leaves, flowers, branches, fruits, roots, root tips, anthers, and the like. Plant parts include, but are not limited to, plant organs, stems, roots, flowers, ovules, stamens, leaves, embryos, meristematic regions, plant tissues, callus tissue, anther cultures, gametophytes, sporophytes, pollen, microspores, plant cells, protoplasts, and the like. The term “plant” is also intended to encompass a seed. Progeny, variants, and mutants of the regenerated plants are also included within the scope of the invention, provided that these parts comprise the introduced polynucleotides. As used herein, “progeny” and “progeny plant” comprise any subsequent generation of a plant whether resulting from sexual reproduction and/or asexual propagation, unless it is expressly stated otherwise or is apparent from the context of usage.
In some embodiments of the present invention, a plant cell is transformed with a polynucleotide construct encoding an R protein of the present invention. The term “expression” as used herein refers to the biosynthesis of a gene product, including the transcription and/or translation of said gene product. The “expression” or “production” of a protein or polypeptide from a DNA molecule refers to the transcription and translation of the coding sequence to produce the protein or polypeptide, while the “expression” or “production” of a protein or polypeptide from an RNA molecule refers to the translation of the RNA coding sequence to produce the protein or polypeptide. Examples of polynucleotide constructs and nucleic acid molecules that encode R proteins are described elsewhere herein.
The use of the terms “DNA” or “RNA” herein is not intended to limit the present invention to polynucleotide molecules comprising DNA or RNA. Those of ordinary skill in the art will recognize that the methods and compositions of the invention encompass polynucleotide molecules comprised of deoxyribonucleotides (i.e., DNA), ribonucleotides (i.e., RNA) or combinations of ribonucleotides and deoxyribonucleotides. Such deoxyribonucleotides and ribonucleotides include both naturally occurring molecules and synthetic analogues including, but not limited to, nucleotide analogs or modified backbone residues or linkages, which are synthetic, naturally occurring, and non-naturally occurring, which have similar binding properties as the reference nucleic acid, and which are metabolized in a manner similar to the reference nucleotides. Examples of such analogs include, without limitation, phosphorothioates, phosphoramidates, methyl phosphonates, chiral-methyl phosphonates, 2-O-methyl ribonucleotides, peptide-nucleic acids (PNAs). The polynucleotide molecules of the invention also encompass all forms of polynucleotide molecules including, but not limited to, single-stranded forms, double-stranded forms, hairpins, stem-and-loop structures, and the like. Furthermore, it is understood by those of ordinary skill in the art that the nucleotide sequences disclosed herein also encompasses the complement of that exemplified nucleotide sequence.
The invention is drawn to compositions and methods for producing a plant with enhanced resistance to a plant disease caused by a plant pathogen, particularly to compositions and methods for producing a plant with enhanced resistance to wheat stripe rust caused by Pst, more particularly to compositions and methods for producing a wheat or barley plant with enhanced resistance to wheat stripe rust caused by Pst. By “resistance to a plant disease” or “disease resistance” is intended that the plants avoid the disease symptoms that are the outcome of plant-pathogen interactions. That is, one or more pathogens are prevented from causing a plant disease or plant diseases and the associated disease symptoms, or alternatively, the disease symptoms caused by the one or more pathogens is minimized or lessened.
The present invention encompasses the polynucleotide constructs disclosed herein or in the accompanying sequence listing and/or drawings including, but not limited to, a polynucleotide construct comprising a nucleotide sequence selected from the group consisting of SEQ ID NOS: 17-19. The present invention further encompasses plants, plant cells, host cells, and vectors comprising at least one of such polynucleotide constructs, as well as food products produced from such plants. Additionally encompassed by the present invention are uses of plants comprising at least one of such polynucleotide constructs in the methods disclosed elsewhere herein such as, for example, methods of limiting wheat stripe rust in agricultural crop production.
Plant pathogens include, for example, bacteria, insects, nematodes, fungi, oomycetes, and the like. The preferred pathogens of the present invention are fungal pathogens, particularly fungal pathogens that cause rust diseases, including, but not limited to, Puccinia brachypodii (purple false brome rust), Puccinia coronata (crown rust), Puccinia graminis (stem rust), Puccinia striiformis (stripe rust), Puccinia pseudostriiformis (stripe rust), Puccinia pseudo-hordei (barley grass stripe rust), Puccinia gansensis (stripe rust), Puccinia striiformoides (stripe rust), Puccinia hordei (barley leaf rust), Puccinia recondita (wheat leaf rust), Puccinia sorghi (maize leaf rust), Puccinia poae-nemoralis, Puccinia poarum, Puccinia emaculata, and Uromyces dactylidis. It is believed that the Rps6 nucleotide sequences of the present invention are capable of conferring resistance against rust diseases caused by one or more of these fungal pathogens. See Castro et al. (2003) Theor. Appl. Genet. 107:922-930, Derevnina et al. (2015) Theor. Appl. Genet. 128: 187-197, and Niks et al. (2013) Eur. J. Plant Pathol. 136:393-405; herein incorporated by reference. Other plant pathogens of interest for the present invention are Blumeria graminis (powdery mildew) and Magnaporthe grisea (also known as M. oryzae; blast disease). It has been reported that resistance to powdery mildew and blast disease in barley both map in vicinity of Rps6 suggesting that Rps6 may be capable of conferring resistance to powdery mildew and/or blast disease in addition to being capable of conferring resistance to stripe rust. See Schonfeld et al. (1996) Theor. Appl. Genet. 93:48-56, herein incorporated by reference.
In some preferred embodiments, the present invention provides plants and methods of producing plants comprising enhanced resistance to at least one race of Puccinia striiformis f. sp. tritici. In other preferred embodiments, the present invention provides plants and methods of producing plants comprising enhanced resistance to multiple races of Puccinia striiformis f. sp. tritici. As used herein, “multiple races” is intended to mean at least two races of a particular plant pathogen, but preferably three, four, five or more races of the plant pathogen.
Other fungal pathogens of interest are those that cause diseases in grain crop plants including, for example, Ustilago nuda (barley loose smut), Ustilago triticiv (wheat loose smut), Ustilago nigra (barley false loose smut), Ustilago avenae (oat loose smut), Ustilago kolleri (oat covered smut), and Ustilago maydis (maize smut).
Other pathogens for the major crops include: Soybeans: Phytophthora megasperma fsp. glycinea, Macrophomina phaseolina, Rhizoctonia solani, Sclerotinia sclerotiorum, Fusarium oxysporum, Diaporthe phaseolorum var. sojae (Phomopsis sojae), Diaporthe phaseolorum var. caulivora, Sclerotium rolfsii, Cercospora kikuchii, Cercospora sojina, Peronospora manshurica, Colletotrichum dematium (Colletotichum truncatum), Corynespora cassiicola, Septoria glycines, Phyllosticta sojicola, Alternaria alternata, Pseudomonas syringae p.v. glycinea, Xanthomonas campestris p.v. phaseoli, Microsphaera diffusa, Fusarium semitectum, Phialophora gregata, Soybean mosaic virus, Glomerella glycines, Tobacco Ring spot virus, Tobacco Streak virus, Phakopsora pachyrhizi, Pythium aphanidermatum, Pythium ultimum, Pythium debaryanum, Tomato spotted wilt virus, Heterodera glycines Fusarium solani; Canola: Albugo candida, Alternaria brassicae, Leptosphaeria maculans, Rhizoctonia solani, Sclerotinia sclerotiorum, Mycosphaerella brassicicola, Pythium ultimum, Peronospora parasitica, Fusarium roseum, Alternaria alternata; Alfalfa: Clavibacter michiganese subsp. insidiosum, Pythium ultimum, Pythium irregulare, Pythium splendens, Pythium debaryanum, Pythium aphanidermatum, Phytophthora megasperma, Peronospora trifoliorum, Phoma medicaginis var. medicaginis, Cercospora medicaginis, Pseudopeziza medicaginis, Leptotrochila medicaginis, Fusarium oxysporum, Verticillium albo-atrum, Xanthomonas campestris p.v. alfalfae, Aphanomyces euteiches, Stemphylium herbarum, Stemphylium alfalfae, Colletotrichum trifolii, Leptosphaerulina briosiana, Uromyces striatus, Sclerotinia trifoliorum, Stagonospora meliloti, Stemphylium botryosum, Leptotrichila medicaginis; Wheat: Pseudomonas syringae p.v. atrofaciens, Urocystis agropyri, Xanthomonas campestris p.v. translucens, Pseudomonas syringae p.v. syringae, Alternaria alternata, Cladosporium herbarum, Fusarium graminearum, Fusarium avenaceum, Fusarium culmorum, Ustilago tritici, Ascochyta tritici, Cephalosporium gramineum, Collotetrichum graminicola, Erysiphe graminis f. sp. tritici, Puccinia graminis f. sp. tritici, Puccinia recondita f. sp. tritici, Puccinia striiformis, Pyrenophora tritici-repentis, Septoria nodorum, Septoria tritici, Septoria avenae, Pseudocercosporella herpotrichoides, Rhizoctonia solani, Rhizoctonia cerealis, Gaeumannomyces graminis var. tritici, Pythium aphanidermatum, Pythium arrhenomanes, Pythium ultimum, Bipolaris sorokiniana, Barley Yellow Dwarf Virus, Brome Mosaic Virus, Soil Borne Wheat Mosaic Virus, Wheat Streak Mosaic Virus, Wheat Spindle Streak Virus, American Wheat Striate Virus, Claviceps purpurea, Tilletia tritici, Tilletia laevis, Ustilago tritici, Tilletia indica, Rhizoctonia solani, Pythium arrhenomannes, Pythium gramicola, Pythium aphanidermatum, High Plains Virus, European wheat striate virus; Sunflower: Plasmopora halstedii, Sclerotinia sclerotiorum, Aster Yellows, Septoria helianthi, Phomopsis helianthi, Alternaria helianthi, Alternaria zinniae, Botrytis cinerea, Phoma macdonaldii, Macrophomina phaseolina, Erysiphe cichoracearum, Rhizopus oryzae, Rhizopus arrhizus, Rhizopus stolonifer, Puccinia helianthi, Verticillium dahliae, Envinia carotovorum pv. carotovora, Cephalosporium acremonium, Phytophthora cryptogea, Albugo tragopogonis; Corn: Colletotrichum graminicola, Fusarium moniliforme var. subglutinans, Envinia stewartii, F. verticillioides, Gibberella zeae (Fusarium graminearum), Stenocarpella maydi (Diplodia maydis), Pythium irregulare, Pythium debaryanum, Pythium graminicola, Pythium splendens, Pythium ultimum, Pythium aphanidermatum, Aspergillus flavus, Bipolaris maydis O, T (Cochliobolus heterostrophus), Helminthosporium carbonum I, II & III (Cochliobolus carbonum), Exserohilum turcicum I, II & III, Helminthosporium pedicellatum, Physoderma maydis, Phyllosticta maydis, Kabatiella maydis, Cercospora sorghi, Ustilago maydis, Puccinia sorghi, Puccinia polysora, Macrophomina phaseolina, Penicillium oxalicum, Nigrospora oryzae, Cladosporium herbarum, Curvularia lunata, Curvularia inaequalis, Curvularia pallescens, Clavibacter michiganense subsp. nebraskense, Trichoderma viride, Maize Dwarf Mosaic Virus A & B, Wheat Streak Mosaic Virus, Maize Chlorotic Dwarf Virus, Claviceps sorghi, Pseudonomas avenae, Envinia chrysanthemi pv. zea, Envinia carotovora, Corn stunt spiroplasma, Diplodia macrospora, Sclerophthona macrospora, Peronosclerospora sorghi, Peronosclerospora philippinensis, Peronosclerospora maydis, Peronosclerospora sacchari, Sphacelotheca reiliana, Physopella zeae, Cephalosporium maydis, Cephalosporium acremonium, Maize Chlorotic Mottle Virus, High Plains Virus, Maize Mosaic Virus, Maize Rayado Fino Virus, Maize Streak Virus, Maize Stripe Virus, Maize Rough Dwarf Virus; Sorghum: Exserohilum turcicum, C. sublineolum, Cercospora sorghi, Gloeocercospora sorghi, Ascochyta sorghina, Pseudomonas syringae p.v. syringae, Xanthomonas campestris p.v. holcicola, Pseudomonas andropogonis, Puccinia purpurea, Macrophomina phaseolina, Perconia circinata, Fusarium moniliforme, Alternaria alternata, Mpolaris sorghicola, Helminthosporium sorghicola, Curvularia lunata, Phoma insidiosa, Pseudomonas avenae (Pseudomonas alboprecipitans), Ramulispora sorghi, Ramulispora sorghicola, Phyllachara sacchari, Sporisorium reilianum (Sphacelotheca reiliana), Sphacelotheca cruenta, Sporisorium sorghi, Sugarcane mosaic H, Maize Dwarf Mosaic Virus A & B, Claviceps sorghi, Rhizoctonia solani, Acremonium strictum, Sclerophthona macrospora, Peronosclerospora sorghi, Peronosclerospora philippinensis, Sclerospora graminicola, Fusarium graminearum, Fusarium oxysporum, Pythium arrhenomanes, Pythium graminicola, etc.; Tomato: Corynebacterium michiganense pv. michiganense, Pseudomonas syringae pv. tomato, Ralstonia solanacearum, Xanthomonas vesicatoria, Xanthomonas perforans, Alternaria solani, Alternaria porri, Collectotrichum spp., Fulvia fulva Syn. Cladosporium fulvum, Fusarium oxysporum f. lycopersici, Leveillula taurica/Oidiopsis taurica, Phytophthora infestans, other Phytophthora spp., Pseudocercospora fuligena Syn. Cercospora fuligena, Sclerotium rolfsii, Septoria lycopersici, Meloidogyne spp.; Potato: Ralstonia solanacearum, Pseudomonas solanacearum, Envinia carotovora subsp. Atroseptica Envinia carotovora subsp. Carotovora, Pectobacterium carotovorum subsp. Atrosepticum, Pseudomonas fluorescens, Clavibacter michiganensis subsp. Sepedonicus, Corynebacterium sepedonicum, Streptomyces scabiei, Colletotrichum coccodes, Alternaria alternate, Mycovellosiella concors, Cercospora solani, Macrophomina phaseolina, Sclerotium bataticola, Choanephora cucurbitarum, Puccinia pittieriana, Aecidium cantensis, Alternaria solani, Fusarium spp., Phoma solanicola f. foveata, Botrytis cinerea, Botryotinia fuckeliana, Phytophthora infestans, Pythium spp., Phoma andigena var. andina, Pleospora herbarum, Stemphylium herbarum, Erysiphe cichoracearum, Spongospora subterranean Rhizoctonia solani, Thanatephorus cucumeris, Rosellinia sp. Dematophora sp., Septoria lycopersici, Helminthosporium solani, Polyscytalum pustulans, Sclerotium rolfsii, Athelia rolfsii, Angiosorus solani, Ulocladium atrum, Verticillium albo-atrum, V. dahlia, Synchytrium endobioticum, Sclerotinia sclerotiorum, Candidatus Liberibacter solanacearum; Banana: Colletotrichum musae, Armillaria mellea, Armillaria tabescens, Pseudomonas solanacearum, Phyllachora musicola, Mycosphaerella fijiensis, Rosellinia bunodes, Pseudomas spp., Pestalotiopsis leprogena, Cercospora hayi, Pseudomonas solanacearum, Ceratocystis paradoxa, Verticillium theobromae, Trachysphaera fructigena, Cladosporium musae, Junghuhnia vincta, Cordana johnstonii, Cordana musae, Fusarium pallidoroseum, Colletotrichum musae, Verticillium theobromae, Fusarium spp., Acremonium spp., Cylindrocladium spp., Deightoniella torulosa, Nattrassia mangiferae, Dreschslera gigantean, Guignardia musae, Botryosphaeria ribis, Fusarium solani, Nectria haematococca, Fusarium oxysporum, Rhizoctonia spp., Colletotrichum musae, Uredo musae, Uromyces musae, Acrodontium simplex, Curvularia eragrostidis, Drechslera musae-sapientum, Leptosphaeria musarum, Pestalotiopsis disseminate, Ceratocystis paradoxa, Haplobasidion musae, Marasmiellus inoderma, Pseudomonas solanacearum, Radopholus similis, Lasiodiplodia theobromae, Fusarium pallidoroseum, Verticillium theobromae, Pestalotiopsis palmarum, Phaeoseptoria musae, Pyricularia grisea, Fusarium moniliforme, Gibberella fujikuroi, Envinia carotovora, Envinia chrysanthemi, Cylindrocarpon musae, Meloidogyne arenaria, Meloidogyne incognita, Meloidogyne javanica, Pratylenchus coffeae, Pratylenchus goodeyi, Pratylenchus brachyurus, Pratylenchus reniformia, Sclerotinia sclerotiorum, Nectria foliicola, Mycosphaerella musicola, Pseudocercospora musae, Limacinula tenuis, Mycosphaerella musae, Helicotylenchus multicinctus, Helicotylenchus dihystera, Nigrospora sphaerica, Trachysphaera frutigena, Ramichloridium musae, and Verticillium theobromae. 
Non-limiting examples of the compositions and methods of the present invention are as follows:

    1. A nucleic acid molecule comprising a member selected from the group consisting of:


(a) a barley Rps6 gene;
(b) the nucleotide sequence set forth in SEQ ID NO: 1, 2, 5, 7, 9, 11, 13, 15, 34, or 35;
(c) a nucleotide sequence encoding the amino acid sequence set forth in SEQ ID NO: 3, 6, 8, 10, 12, or 14;
(d) a nucleotide sequence having at least 85% nucleotide sequence identity to at least one of the full-length nucleotide sequences set forth in SEQ ID NOS: 1, 2, 5, 7, 9, 11, and 13, wherein the nucleic acid molecule is capable of conferring resistance to wheat stripe rust to a plant comprising the nucleic acid molecule; and
(e) a nucleotide sequence encoding a polypeptide having at least 85% amino acid sequence identity to at least one of the full-length amino acid sequence set forth in SEQ ID NOS: 3, 6, 8, 10, 12, and 14, wherein the nucleic acid molecule is capable of conferring resistance to wheat stripe rust to a plant comprising the nucleic acid molecule.

    2. The nucleic acid molecule of embodiment 1, wherein the nucleic acid molecule is an isolated nucleic acid molecule.
    3. The nucleic acid molecule of embodiment 1 or 2, wherein the nucleic acid molecule is not naturally occurring.
    4. The nucleic acid molecule of embodiment 1 or 2, wherein the barley Rps6 gene is the barley Rps6 gene that is located in the region of the genome of a barley plant corresponding to SEQ ID NO: 4.
    5. The nucleic acid molecule of any one of embodiments 1-4, wherein the nucleic acid molecule of (d) or (e) encodes a protein comprising a coiled-coil domain, a nucleotide-binding domain, and a leucine-rich repeat domain.
    6. The nucleic acid molecule of embodiment 5, wherein at least one of the coiled-coil domain, the nucleotide-binding domain, and the leucine-rich repeat domain comprises an amino acid sequence having at least 95%, 96%, 97%, 98%, 99%, or 100% to the corresponding domain in SEQ ID NO: 3.
    7. An expression cassette comprising the nucleic acid molecule of any one of embodiments 1-6 and an operably linked heterologous promoter.
    8. A vector comprising the nucleic acid molecule of any one of embodiments 1-6 or the expression cassette of embodiment 7.
    9. A host cell transformed with the nucleic acid molecule of any one of embodiments 1-6, the expression cassette of embodiment 7, or the vector of embodiment 8.
    10. The host cell of embodiment 9, wherein the host cell is a plant cell, a bacterium, a fungal cell, or an animal cell.
    11. The host cell of embodiment 9 or 10, wherein the plant cell is a barley plant cell, a wheat plant cell, or a Brachypodium distachyon plant cell.
    12. A plant or seed transformed with the nucleic acid molecule of any one of embodiments 1-6, the expression cassette of embodiment 7, or the vector of embodiment 8.
    13. The plant or seed of embodiment 12, wherein the plant is a wheat plant or a barley plant and the seed is wheat seed or barley seed.
    14. A transgenic plant or seed comprising stably incorporated in its genome a polynucleotide construct comprising a member selected from the group consisting of:


(a) a barley Rps6 gene;
(b) the nucleotide sequence set forth in SEQ ID NO: 1, 2, 5, 7, 9, 11, or 13;
(c) a nucleotide sequence encoding the amino acid sequence set forth in SEQ ID NO: 3, 6, 8, 10, 12, or 14;
(d) a nucleotide sequence having at least 85% nucleotide sequence identity to at least one of the full-length nucleotide sequences set forth in SEQ ID NOS: 1, 2, 5, 7, 9, 11, and 13, wherein the nucleic acid molecule is capable of conferring resistance to wheat stripe rust to a plant comprising the nucleic acid molecule; and
(e) a nucleotide sequence encoding a polypeptide having at least 85% amino acid sequence identity to at least one of the full-length amino acid sequence set forth in SEQ ID NOS: 3, 6, 8, 10, 12, and 14, wherein the nucleic acid molecule is capable of conferring resistance to wheat stripe rust to a plant comprising the nucleic acid molecule.

    15. The transgenic plant or seed of embodiment 14, wherein the nucleic acid molecule of (d) or (e) encodes a protein comprising a coiled-coil domain, a nucleotide-binding domain, and a leucine-rich repeat domain.
    16. The transgenic plant or seed of embodiment 15, wherein at least one of the coiled-coil domain, the nucleotide-binding domain, and the leucine-rich repeat domain comprises an amino acid sequence having at least 95%, 96%, 97%, 98%, 99%, or 100% to the corresponding domain in SEQ ID NO: 3.
    17. The transgenic plant or seed of any one of embodiments 14-16, wherein the polynucleotide construct comprises the nucleotide sequence of any one of (b)-(e) and further comprises a promoter operably linked for the expression of the nucleotide sequence in a plant.
    18. The transgenic plant or seed of embodiment 17, wherein the promoter is selected from the group consisting of pathogen-inducible, constitutive, tissue-preferred, wound-inducible, and chemical-regulated promoters.
    19. The transgenic plant or seed of any one of embodiments 14-18, wherein the transgenic plant or seed comprises enhanced resistance to wheat stripe rust caused by multiple races of Puccinia striiformis f. sp. tritici, relative to the resistance of a control plant.
    20. The transgenic plant or seed of any one of embodiments 14-19, wherein the transgenic plant is a transgenic wheat plant and the transgenic seed is a transgenic wheat seed.
    21. The transgenic plant or seed of any one of embodiments 14-19, wherein the transgenic plant is a transgenic barley plant and the transgenic seed is a transgenic barley seed.
    22. The transgenic plant or seed of any one of embodiments 14-19, wherein the transgenic plant is a transgenic Brachypodium distachyon plant and the transgenic seed is a transgenic Brachypodium distachyon seed.
    23. The transgenic plant or seed of any one of embodiments 14-22, wherein the polynucleotide construct is a heterologous nucleic acid molecule.
    24. A method for producing a plant with enhanced resistance to a plant disease, the method comprising introducing a polynucleotide construct into at least one plant cell, the polynucleotide construct comprising a member selected from the group consisting of:


(a) a barley Rps6 gene;
(b) the nucleotide sequence set forth in SEQ ID NO: 1, 2, 5, 7, 9, 11, or 13;
(c) a nucleotide sequence encoding the amino acid sequence set forth in SEQ ID NO: 3, 6, 8, 10, 12, or 14;
(d) a nucleotide sequence having at least 85% nucleotide sequence identity to at least one of the full-length nucleotide sequences set forth in SEQ ID NOS: 1, 2, 5, 7, 9, 11, and 13, wherein the nucleic acid molecule is capable of conferring resistance to the plant disease to a plant comprising the nucleic acid molecule; and
(e) a nucleotide sequence encoding a polypeptide having at least 85% amino acid sequence identity to at least one of the full-length amino acid sequence set forth in SEQ ID NOS: 3, 6, 8, 10, 12, and 14, wherein the nucleic acid molecule is capable of conferring resistance to the plant disease to a plant comprising the nucleic acid molecule.

    25. The method of embodiment 24, wherein the nucleic acid molecule of (d) or (e) encodes a protein comprising a coiled-coil domain, a nucleotide-binding domain, and a leucine-rich repeat domain.
    26. The method of embodiment 25, wherein at least one of the coiled-coil domain, the nucleotide-binding domain, and the leucine-rich repeat domain comprises an amino acid sequence having at least 95%, 96%, 97%, 98%, 99%, or 100% to the corresponding domain in SEQ ID NO: 3.
    27. The method of any one of embodiments 24-26, wherein the plant disease is a rust disease.
    28. The method of any one of embodiments 24-27, wherein the pathogen is in the genus Puccinia. 
    29. The method of any one of embodiments 24-28, wherein the plant is a grass plant.
    30. The method of any one of embodiments 24-29, wherein the plant is a grain plant.
    31. The method of any one of embodiments 24-30, wherein the plant is barley, wheat, or Brachypodium distachyon. 
    32. The method of any one of embodiments 24-31, wherein the polynucleotide construct is stably incorporated into the genome of the plant cell.
    33. The method of any one of embodiments 24-32, wherein the barley, wheat, or Brachypodium distachyon plant cell is regenerated into a barley, wheat, or Brachypodium distachyon plant comprising in its genome the polynucleotide construct.
    34. The method of any one of embodiments 24-33, wherein the polynucleotide construct comprises the nucleotide sequence of any one of (b)-(e) and further comprises a promoter operably linked for the expression of the nucleotide sequence in a plant.
    35. The method of embodiment 34, wherein the promoter is selected from the group consisting of pathogen-inducible, constitutive, tissue-preferred, wound-inducible, and chemical-regulated promoters.
    36. The method of any one of embodiments 31-35, wherein the barley, wheat, or Brachypodium distachyon plant comprising the polynucleotide construct comprises enhanced resistance to wheat stripe rust caused by at least one race of Puccinia striiformis f. sp. tritici, relative to the resistance of a control barley plant, wheat, or Brachypodium distachyon. 
    37. The method of any one of embodiments 31-35, wherein the barley, wheat, or Brachypodium distachyon plant comprising the polynucleotide construct comprises enhanced resistance to wheat stripe rust caused by multiple races of Puccinia striiformis f. sp. tritici, relative to the resistance of a control barley, wheat, or Brachypodium distachyon plant.
    38. A plant produced by the method of any one of embodiments 24-37.
    39. A seed of the plant of embodiment 38, wherein the seed comprises the polynucleotide construct.
    40. A method for producing a barley plant with enhanced resistance to wheat stripe rust, the method comprising modifying in a barley plant or at least one cell thereof, a non-functional allele of the resistance gene Rps6 so as to make a functional allele, whereby the resistance of the barley plant to wheat stripe rust is enhanced.
    41. The method of embodiment 40, wherein said modifying a non-functional allele comprises introducing at least one genetic modification selected from the group consisting of an insertion, a deletion, and a substitution of at least one base pair in the non-functional allele.
    42. The method of embodiment 40 or 41, wherein said modifying a non-functional allele comprises at least one member selected from the group consisting of targeted mutagenesis, homologous recombination, and mutation breeding.
    43. The method of any one of embodiments 40-42, wherein the functional allele comprises a nucleotide sequence selected from the group consisting of:


(a) the nucleotide sequence set forth in SEQ ID NO: 1;
(b) a nucleotide sequence comprising the coding sequence for the amino acid sequence set forth in SEQ ID NO: 3, 6, 8, 10, 12, or 14; and
(c) a nucleotide sequence encoding a polypeptide having at least 85% amino acid sequence identity to at least one of the full-length amino acid sequence set forth in SEQ ID NOS: 3, 6, 8, 10, 12, and 14, wherein the nucleic acid molecule is capable of conferring resistance to wheat stripe rust to a plant comprising the nucleic acid molecule.

    44. The method of embodiment 43, wherein the polypeptide of (c) comprises a coiled-coil domain, a nucleotide-binding domain, and a leucine-rich repeat domain.
    45. The method of embodiment 44, wherein at least one of the coiled-coil domain, the nucleotide-binding domain, and the leucine-rich repeat domain comprises an amino acid sequence having at least 95%, 96%, 97%, 98%, 99%, or 100% to the corresponding domain in SEQ ID NO: 3.
    46. The method of any one of embodiments 40-45, wherein the barley plant comprises enhanced resistance to wheat stripe rust caused by multiple races of Puccinia striiformis f. sp. tritici, relative to the resistance of a control barley plant.
    47. A barley plant produced by the method of any one of embodiments 40-46.
    48. A seed of the barley plant of embodiment 47, wherein the seed comprises the polynucleotide construct.
    49. A method of limiting wheat stripe rust in agricultural crop production, the method comprising planting a seed according to any one of embodiments 12-23, 39, and 48 and growing a plant under conditions favorable for the growth and development of the plant.
    50. The method of embodiment 49, further comprising harvesting an at least one seed from the plant.
    51. The method of embodiment 49 or 50, wherein the seed is a wheat seed or a barley seed.
    52. Use of the plant or seed of any one of embodiments 12-23, 38, 39, 47, and 48 in agriculture.
    53. A human or animal food product produced using the plant or seed of any one of embodiments 12-23, 38, 39, 47, and 48.
    54. A polypeptide comprising an amino acid sequence selected from the group consisting of:


(a) the amino acid sequence encoded by the nucleotide sequence set forth in SEQ ID NO: 1;
(b) the amino acid sequence encoded by the nucleotide sequence set forth in SEQ ID NO: 2, 5, 7, 9, 11, or 13;
(c) the amino acid sequence set forth in SEQ ID NO: 3, 6, 8, 10, 12, or 14; and
(d) an amino acid sequence having at least 85% sequence identity to at least one of the full-length amino acid sequence set forth in SEQ ID NOS: 3, 6, 8, 10, 12, and 14, wherein a polypeptide comprising the amino acid sequence is capable of conferring resistance to stripe rust to a wheat or barley plant comprising the polypeptide, and optionally, wherein the polypeptide is not naturally occurring.

    55. The polypeptide of embodiment 54, wherein the polypeptide of (d) comprises a coiled-coil domain, a nucleotide-binding domain, and a leucine-rich repeat domain.
    56. The polypeptide of embodiment 55, wherein at least one of the coiled-coil domain, the nucleotide-binding domain, and the leucine-rich repeat domain comprises an amino acid sequence having at least 95%, 96%, 97%, 98%, 99%, or 100% to the corresponding domain in SEQ ID NO: 3.
    57. The polypeptide of any one of embodiments 54-56, wherein the polypeptide is an isolated polypeptide.
    58. The polypeptide of any one of embodiments 54-57, wherein the polypeptide is not naturally occurring.


Additional embodiments of the methods and compositions of the present invention are described elsewhere herein.
The following examples are offered by way of illustration and not by way of limitation.
EXAMPLES
Example 1: Isolation and Fine Mapping of Rps6
Mapping of Rps6: Differential phenotypes were observed between Abed Binder 12 and Russell inoculated with Pst isolates 08/501 and 08/21. Russell rarely showed pustules but had a clear microscopic phenotype of colonization (FIG. 1). We inoculated the Abed Binder 12×Russell F2 populations with Pst isolate 08/501 (AxR-P st). The parents, F1 and 92 F2 plants were phenotyped using macroscopic and microscopic evaluation of Pst colonization (pCOL). Pustule formation was not observed for the AxR-Pst F2 population, although segregation was observed for chlorosis and pCOL (FIG. 2A-2B). A strong correlation between chlorosis and pCOL was observed (r2=0.88) (FIG. 2C). The F1 displayed a similar resistant phenotype to Abed Binder 12. To map resistance to Pst, we genotyped the AxR-Pst F2 population with the barley oligonucleotide assay (BOPA1; 1,536 SNP-based markers; Close et al. 2009). A total of 535 polymorphic OPA markers were identified between Abed Binder 12 and Russell and they were used to generate a genetic map with eight linkage groups. In addition, 26 CAPS markers and 28 Sequenom MassARRAY markers were used to generate a final map consisting of 589 markers over seven linkage groups, representing 362 non-redundant marker haplotypes and a total genetic distance of 1,131 cM. Quantitative trait locus (QTL) analysis using composite interval mapping with chlorosis and pCOL phenotypes on the AxR-Pst population identified a major effect locus on the long arm of chromosome 7H that was contributed by Abed Binder 12 (FIG. 3). The QTL accounted for 57.7% and 69.4% of the phenotypic variation for chlorosis and pCOL, respectively. In both instances, marker U32_7356_p1, positioned at 169.7 cM, was the most strongly linked marker (Table 1)







TABLE 1







Significant QTLs from composite interval mapping of chlorosis and pCOL


phenotypes in the Abed Binder 12 x Russell F2 population inoculated with Pst isolate 08/501
















Trait
Chra
cM
Peak Marker
EWTb
LOD
AEEc
DEEd
D/Ae
PVEf



















Chlorosis
3H
155.7
1_0893
4.38
6.52
−0.47
−0.07
0.15
0.13


Chlorosis
7H
169.7
U32_7356_p1
4.38
21.57
0.99
−0.51
−0.52
0.58


pCOL
3H
158.3
1_0694
4.20
4.60
−0.12
0.03
−0.21
0.08


pCOL
7H
169.7
U32_7356_p1
4.20
26.59
0.40
−0.15
−0.39
0.69





aChromosome.


bExperimental-wide threshold.


cAdditive effect estimate, positive values indicate the contribution of resistance from Abed Binder 12.


dDominance effect estimate.


eEstimate of dominance to additivity ratio.


fPercent of the phenotypic variation explained.






Fine mapping Rps6: We carried out a recombination screen and saturated the locus with markers based on the genomic resources available in barley. The recombination screen was carried out using seed bulked from F3 plants that were heterozygous for Rps6 in a F2:3 family that segregated only for Rps6. The KASP markers K_2547604b and K_1579285b were generated from Sequenom markers S_43900 and S_3446, respectively, and used as flanking markers that span a 6.0 cM region encompassing Rps6. In total, 2,894 gametes were characterized, identifying 135 recombination events between the flanking markers. Progeny tests were performed using individuals with recombinant chromosomes and scored homozygous or segregating for resistance, or homozygous susceptible. Marker saturation of the Rps6 interval was performed by (1) comparing genomic contigs derived from cultivars Barke, Bowman, and Morex to identify SNPs or (2) by aligning reads from RNAseq on Abed Binder 12 and Russell to whole genome shotgun (WGS) contigs anchored to the Rps6 region (IBGSC (2012) Nature 491:711-716; Mascher et al. (2013) Plant J. 76:718-727). These analyses were performed twice; initially using the anchored contigs from the IBGSC reference anchoring that included 78 contigs between 127.12 cM and 129.21 cM (IBGSC (2012) Nature 491:711-716). Later, a larger interval was investigated including 1,345 contigs between 126.20 cM and 131.44 cM based on an updated anchoring (Mascher et al. (2013) Plant J. 76:718-727). RNAseq data was aligned to WGS contigs and manually curated to identify SNPs polymorphic between Abed Binder 12 and Russell. A total of 102 SNPs were successfully converted into Kompetitive Allele Specific PCR (KASP) markers and surveyed on recombinant individuals in the Rps6 region. In total, 49 KASP markers representing 30 WGS contigs mapped between the Rps6 flanking markers. At a fine scale, contigs mapped in a different order relative to their current anchoring in the barley POPSEQ anchored contigs, although at the rough scale the general order was preserved. The markers collapsed into 18 marker bins and positioned Rps6 in a 0.1 cM region, flanked by K_361382 (proximal) and K_37596 (distal) (FIG. 4). Rps6 is located 0.07 cM from the proximal marker with only two recombination events to be resolved between them. Contrastingly, only a single recombination event differentiates the distal marker with Rps6.
Anchoring of Rps6 to the physical map of barley: The Rps6 locus was anchored to the barley physical map using the available BES and shotgun sequenced BACs in the Rps6 region (IBGSC (2012) Nature 491:711-716). In the proximal region, several KASP markers map to the physical map on FPC 8887 based on BES and sequenced BACs. Using currently available information it is unclear if FPC 8887 is correctly orientated based on our marker order. Marker K_58199 defines a boundary on FPC 320, indicating that K_361382 is located on the physical sequence between K_58199 and K_57421 (FIG. 4). Rps6 cosegregates with markers K_57421 and K_49978, which both map to proximal region of FPC 320. The entire distal region from K_58199 to K_1579285 is well anchored to FPC 320. Annotated genes in the region include MLOC_18254 on contig 1579877 and two NLRs present on contigs 49978 and 37596. The high confidence gene model MLOC_65262 is present on contig 49978 and cosegregates with Rps6 based on the resolution of our recombination screen, whereas the NLR on contig 37596 is separated by a critical recombination event. MLOC_65262 is preferentially expressed in roots, with little or no expression in leaves in Morex (IBGSC (2012) Nature 491:711-716).
Candidate gene analysis in the Rps6 region: To identify candidate NLR genes at the Rps6 locus we utilised existing barley genomics resources in combination with transcriptome assemblies from six barley accessions. We selected a region harbouring Rps6 based on linkage mapping of the region (FIG. 5). Using marker colinearity, we identified 665 WGS contigs anchored to the Rps6 region derived from the cultivars Morex, Barke, and Bowman (IBGSC (2012) Nature 491:711-716) (Table 2). The contigs were anchored in 16 genetic bins and each bin contained a variable number of contigs ranging from 1 to 442. To check for the presence of candidate genes in the anchored sequence information, we searched for motifs associated with NLRs using the motif alignment and search tool (MAST) according to the parameters and motifs reported by Jupe et al. ((2012) BMC Genomics 13:75). Eleven WGS contigs contained NLR motifs (Table 3). These contigs were compared to identify whether similar contigs had been identified in each parent. Indeed, we observed redundancy between accessions and the contigs collapsed into 5 homologous groups. We provisionally designated the putative NLRs harboured in the contigs as NLR-A, NLR-B, NLR-C, NLR-D, and NLR-E. The only Morex contig identified via MAST analysis grouped with the NLR-D homologous group and was the high confidence gene MLOC_65262 cosegregating with Rps6 in the high-resolution genetic map (Table 3). The second annotated NLR identified from Morex contig 37596 in the barley physical map was not identified using MAST analysis, as only contigs contained in the original anchoring of IBGSC (IBGSC (2012) Nature 491:711-716) were interrogated. However, BLAST analysis indicated that the annotated NLR on contig 37596 grouped with the NLR-E homologous group. NLR-E was separated from Rps6 by a critical recombination event in the high-resolution genetic map.







TABLE 2







Anchored WGS contigs in the Rps6 region.












Accession
Contigs
Mean length (bp)
Total Length (kb)
















Barke
213
3,239
690



Bowman
215
4,008
860



Morex
237
3,782
900

















TABLE 3







Identification of five candidate NLR genes in the Rps6 region.














RNAseq expression analysis1,2













MAST analysis on POPseq
Rps6
rps6

















Gene
WGS contigs
E-value
A
G
B
S
R
M
MLOC ID





NLR-A
barke_contig_2780081 
1.50E−43
H
H
H
ND
ND
ND
NA



bowman_contig_200425 
6.80E−43









NLR-B
barke_contig_268211
2
ND
ND
ND
ND
ND
ND
NA



bowman_contig_856833
0.11









NLR-C
barke_contig_1788934 
5.40E−36
L
L
H
L
ND
ND
NA



bowman_contig_874416 
9.30E−37









NLR-D
barke_contig_417389
5.70E−47
ND
ND
ND
ND
ND
ND
MLOC_65262



bowman_contig_852986 
3.60E−47










morex_contig_49978
1.40E−40









NLR-E
barke_contig_480243
2.20E−49
L
L
L
H
H
H
NA



bowman_contig_859170 
3.10E−47










morex_contig_375961









Expression analysis of candidate genes at the Rps6 locus: To investigate the five NLR candidate genes in more detail we established expression profiles for each gene using transcript assemblies for six key accessions harbouring Rps6 or rps6 (accessions Abed Binder 12, Golden Promise, Barke, SusPtrit, Russell, and Manchuria) (Table 3). The WGS contigs harbouring NLR motifs were used to search the assemblies for transcripts corresponding to the NLR candidates. Strikingly, transcripts corresponding to NLR-A were only detected in accessions harbouring Rps6, showing a clear expression polymorphism between resistant and susceptible genotypes (Table 3). No allelic diversity was evident in the NLR-A transcripts found in the Rps6 accessions. Conversely, NLR-E exhibited an inverse expression polymorphism between Rps6 and rps6 accessions. A comparison of the NLR-E transcripts derived from Russell and Manchuria (rps6), and the Barke/Bowman (Rps6) WGS contigs, revealed a single synonymous substitution. This, coupled with the critical recombination event separating NLR-E (K_37596ab) from Rps6 in the high-resolution genetic map, excluded NLR-E as a candidate gene. We did not detect any expression of NLRB or NLR-D. This was consistent with the annotation of NLR-D (MLOC 65262) as a root-expressed gene in the barley high confidence gene assembly (IBGSC (2012) Nature 491:711-716). In the case of NLR-C, we did not observe any expression polymorphisms differentiating Rps6 from rps6 accessions.
Gene model of NLR-A: We constructed a gene model for NLR-A by aligning the Abed Binder 12 NLR-A transcript to Barke contig 2780081, originally identified as harbouring NLR-A using MAST analysis (Table 3). We observed a perfect alignment with the exception of approximately 600 bp of sequence at the 5′ of the Abed Binder 12 transcript. Therefore, we searched the anchored Barke WGS contigs using the unaligned 5′ sequence and identified an additional Barke contig (contig 54347) to which the 5′ sequence aligned (FIG. 6). We assembled a full gene model for NLR-A by concatenating the Barke contigs and re-aligning the Abed Binder 12 NLR-A transcript (FIG. 6). This model proposed that NLR-A consisted of four exons and three introns. Interestingly, the second intron was approximately 8.8 kbp in length. However, according to POPSEQ anchoring of the Barke contigs, contig 54347 was anchored 4.4 cM distal to contig 2780081.
Mapping of candidate genes at the Rps6 locus: Genetic mapping had excluded NLR-E as a candidate gene and showed that NLR-D cosegregated with Rps6. We also wanted to map NLR-A, NLRB, and NLR-C into the high-resolution genetic map to see where they were positioned relative to the Rps6 locus. We initiated a PCR based strategy for identifying SNP markers for NLR-A. To do this, we designed PCR primers along the length of the concatenated Barke contigs 54347 and 2780081. PCR amplification using these primers on Abed Binder 12 and Russell genomic DNA, showed a clear presence/absence polymorphism between Abed Binder 12 and Russell (FIG. 7). This result was concurrent with the absence of an NLR-A transcript in the Russell transcriptome. However, failure to amplify NLR-A from Russell gDNA meant it would not be possible to precisely map NLR-A in the Abed Binder 12×Russell mapping population as it is a dominant marker. Therefore, we hypothesised that it may be possible to amplify NLR-A in different accessions known to harbour Rps6 or rps6.
Using the SusPtrit×Golden Promise doubled-haploid (DH) genetic map we identified two DH lines that harboured Rps6 or rps6 in the absence of other genes. Using these lines, and the key accessions used for RNAseq analysis, we PCR amplified gDNA using eight primer pairs that amplified the 5′ and 3′ ends of NLR-A. We observed three NLR-A haplotypes, in the eight different accessions, which we named NLR-A1, NLR-A2, and nlr-a (Table 4). The Rps6 containing accessions Abed Binder 12, Barke, Golden Promise, and SusPtrit×Golden Promise DH line 64 (DH-064) represented the NLR-A1 haplotype exhibiting 100% amplification of all primers tested. Russell and Manchuria, both susceptible to P. striiformis f. sp. tritici, showed no amplification of any of the primers (nlr-a haplotype). However, SusPtrit and SusPtrit×Golden Promise DH line 21 (DH-021) showed successful amplification of 50% of the primers tested and represented the NLR-A2 haplotype. Sanger sequencing of the PCR amplicons revealed a SNP in the putative NBS domain of NLR-A between the SusPtrit and Golden Promise alleles. Using this SNP, we developed a CAPS marker that showed clear differentiation of the different haplotypes (FIG. 7). The absence of any amplicons in nlr-a accessions suggested that NLR-A was deleted in these lines. In order to map NLR-A, we crossed DH-021 with DH-064 to create a DH derived F2 mapping population (DHMP). A linkage map was constructed using 43 KASP markers including markers for NLR-A and NLR-E. NLR-A and NLR-E co-segregated with K_366867. This positioned NLR-A and NLR-E at the Rps6 locus based on marker colinearity with the Abed Binder 12×Russell high-resolution mapping population (FIG. 5). NLR-D markers were not polymorphic on the DHMP population and we were unable to determine the position of NLR-D in the DHMP population.







TABLE 4







Eight primer pairs differentiate three NLR-A haplotypes.












PCR primer combination


















Accession
Allele
A02/A08
B02/B08
C02/C08
D02/D08
A05/A11
B05/B11
C05/C11
D05/D11
Haplotype





Abed
Rps6
+
+
+
+
+
+
+
+
NLR-A1


Binder 12












Barke
Rps6
+
+
+
+
+
+
+
+
NLR-A1


Golden
Rps6
+
+
+
+
+
+
+
+
NLR-A1


Promise












SxGP DH- 
Rps6
+
+
+
+
+
+
+
+
NLR-A1


064












SusPtrit
rps6
−
−
−
−
+
+
+
+
NLR-A2


SxGP DH-
rps6
−
−
−
−
+
+
+
+
NLR-A2


021












Russell
rps6
−
−
−
−
−
−
−
−
nlr-a


Manchuria
rps6
−
−
−
−
−
−
−
−
nlr-a









In order to map NLRB and NLR-C, we designed markers based on SNPs identified between Barke and Morex WGS contigs harbouring the genes. NLRB mapped distal to Rps6 and excluded the gene as a candidate gene for Rps6 (FIG. 5). NLR-C markers were not polymorphic in the high-resolution genetic map but we were able to map NLR-C distal to Rps6 in the DHMP population (FIG. 5). Taken together, these results excluded NLRB, NLR-C, and NLR-E as candidate genes for Rps6. The presence of a putative deletion region harbouring NLR-A and a clear expression polymorphism between Rps6 and rps6 harbouring accessions supports NLR-A as a candidate gene for Rps6.
Physical map of the Rps6 locus: We initiated physical mapping of the Rps6 region using an Abed Binder 12 BAC library. A PCR screen, using two sets of primers, identified a single BAC clone harbouring NLR-A (primer pairs A02/A08 and A05/A11; FIG. 6). We sequenced the BAC clone with Pacific Biosciences long read sequencing using a SMRT cell with C4-P6 chemistry and were able to construct and annotate a single contiguous BAC sequence (FIG. 6). The clone mostly consisted of repetitive and low complexity sequence (Table 5). However, the clone harboured three CNL genes: NLR-A, NLR-D, and NLR-E (FIG. 6 and Table 5). Signatures of three additional genes annotated in the barley low confidence gene set were identified on the BAC: MLOC_8985.1, MLOC_41646.1, and MLOC_19985.1. All three were annotated as unknown proteins although InterPro scan revealed MLOC_19985.1 contains an F-box domain. Comparison of NLR-A, NLR-D, and NLR-E showed high homology between the genes at the amino acid level (approx. 60%) and in the DNA coding sequence (approx. 70%) (Tables 6 and 7). Despite the similarity, alignment of the Abed Binder 12 RNAseq reads to the BAC contig differentiated NLR-A, NLR-D, and NLR-E and demonstrated that NLR-A was highly expressed compared to NLR-E and NLR-D (FIG. 6). This result confirmed the earlier expression analysis performed using de novo assembly of the RNAseq data. The physical linkage of NLR-A, NLR-D, and NLR-E was consistent with the genetic linkage of these genes in the high-resolution and DHMP mapping populations. We anchored the BAC clone to the Abed Binder 12×Russell genetic map using markers K_49978 (NLR-D) and K_37596 (NLR-E). A single recombination event separates these markers and defines the distal physical region of the Rps6 locus. The Rps6 proximal marker, K_361382, does not reside within the BAC clone and the boundary of the proximal physical region has yet to be defined. Alignment of whole genome shotgun sequence contigs derived from Barke, Bowman, and Morex found the presence of NLR-A in Barke and Bowman, whereas the region is absent in Morex (FIG. 6).







TABLE 5







Annotation of Abed Binder 12 BAC clone 4931-1-11E 


harbouring NLR-A.











Length



Name
(bp)














LTR/Copia BARE1_HV
3,826



DNA/CMC-EnSpm
4,601



DNA/CMC-EnSpm
536



DNA/CMC-EnSpm
1,229



DNA/CMC-EnSpm
5,270



DNA/CMC-EnSpm
1,098



Low complexity A-rich
94



DNA/CMC-EnSpm
2,396



DNA/CMC-EnSpm
1,111



Unknown REP1_SB
52



LTR/Copia IKEROS_HV
5,817



Satellite TREP106
253



LINE/L1 LINE1-56_SBi
669



LINE/L1 LINE1-55_SBi
213



DNA/TcMar-Stowaway
88



ICARUS_TM




NLR-A
3,723



DNA-8-1_TA
138



Low complexity
89



Low_complexity
34



LTR/Gypsy SUKKULA1_HV-LTR
753



LTR/Copia WIS2_TM-int
1,230



LTR/Copia BARE-2_HV_LTR
1,356



LINE/L1 LINE1-61_SBi
98



LTR/Copia BARE1_HV
8,113



LTR/Copia BARE1_HV
8,945



LINE/L1 LINE1-20_SBi
87



LINE/L1 LINE1-47_SBi
86



DNA/CMC-EnSpm
49



DNA/TcMar-Stowaway
145



DNA/PIF-Harbinger HARB-5_SBi
911



Satellite TREP106
531



Satellite TREP106
535



Satellite TREP106
107



NLR-D
2,700



LTR/Copia Copia-8_PD-I
52



Low_complexity GA-rich
49



LINE/L1 L1_TD
325



LINE/L1 L1_TD
976



LTR/Copia BARE-2_HV_LTR
1,811



LTR/Copia BARE-2_HV
8,586



LTR/Copia BARE-2_HV_LTR
1,811



LTR/Gypsy Gypsy-12_TA-LTR solo
795



DNA IR12_TM
17



MLOC.19985.1
1,212



LTR/Copia WIS2_TM-LTR
1,753



LTR/Copia Angela
8,804



LTR/Copia WIS2_TM-LTR
1,762



LTR/Copia Copia1_HV-int
3,877



LTR/Copia Copial_HV-LTR solo
325



DNA/PIF-Harbinger
250



MLOC_41646.1
296



DNA/CMC-EnSpm EnSpm-N3_TA
489



DNA/CMC-EnSpm EnSpm-21_SBi
133



LTR/Copia Copia19-ZM_I-int
212



MLOC_8985.1
462



DNA/CMC-EnSpm
263



DEIMOS
275



DNA/TcMar-Stowaway
258



NLR-E
3,936

















TABLE 6







Amino acid and DNA similarity between full length 


NLR-A, NLR-D, and NLR-E.









Whole length (aa) % similarity













NLR-A
NLR-B
NLR-C
NLR-D
NLR-E
















Whole
NLR-A

—
35
58
63


length
NLR-B
—

—
—
—


(gDNA)
NLR-C
49
—

33
37


%
NLR-D
67
—
49

67


similarity
NLR-E
70
—
50
73
















TABLE 7







Amino acid similarity for NBS and LRR domains of 


NLR-A, NLR-D, and NLR-E.











NBS domain (aa) % similarity















NLR-A
NLR-B
NLR-C
NLR-D
NLR-E





LRR
NLR-A

—
49
75
80


domain
NLR-B
—

—
—
—


(aa) %
NLR-C
38
—

44
48


similarity
NLR-D
59
—
41

86



NLR-E
57
—
49
63









Identification of Rps6 from diverse accessions: To investigate the frequency of Rps6 in barley we assembled a panel of 134 accessions that included wild, landrace, elite 2-row, and elite 6-row barleys (Table 8). The panel was inoculated with P. striiformis f. sp. trilici isolate 08/21 and phenotyped using the macroscopic observations of chlorosis and infection and using microscopic assays pCOL and pPUST. We initiated a crossing block to generate populations segregating for resistance to Puccinia striiformis f. sp. trilici. Resistant accessions used as parental lines in crosses were selected using the phylogenetic relationships and phenotypic information collected for the barley diversity panel to achieve a representative sample of the diversity. A total of 13 F2 populations and 2 BC1 populations were created and in each case the susceptible parent was Manchuria, a 6-row cultivar (Table 9). Polymorphic markers linked to Rps6 and two additional known loci (Rpst1 and Rpst3) were identified for each population using OPA genotyping data derived from parental accessions. OPA markers were converted to KASP markers and assayed on a minimum of 93 individuals for each F2 population. Each population was phenotyped using pCOL and pPUST and single marker regression was used to ascertain the percent variation explained by Rps6 in each population. In addition, we also analysed three existing populations, including a RIL and two DH populations. In total, we analysed 18 populations that represented diversity from each phylogenetic clade (Table 9). Rps6 was detected in several accessions, contributing to resistance in 40% (6 out of 15) of the populations (Tables 10 and 11).







TABLE 8







Accessions of barley used for inoculation with P. striiformis f. sp. tritici.













Accession 
PI/CI 







name
Number
Row
Status
Isolate
CHL
INF
















Commander

2
cultivar
Pst 08/21
0
0


Hindmarsh

2
cultivar
Pst 08/21
0
0


Maritime

2
cultivar
Pst 08/21
1.21
0


Clipper
PI 349366
2
cultivar
Pst 08/21
1
0


Finniss

2
cultivar
Pst 08/21
1.38
0


Q21861
PI 584766
2
breeding
Pst 08/21
2
0


Bancroft
PI 605474
2
cultivar
Pst 08/21
0.5
0


Betzes

2
cultivar
Pst 08/21
0
0


SM89010

2
cultivar
Pst 08/21
0.5
0


Bowman
PI 483237
2
cultivar
Pst 08/21
0
0


BCD47
PI 659444
2
genetic
Pst 08/21
0.5
0


Sebastian

2
cultivar
Pst 08/21
0
0


Rainbow

2
cultivar
Pst 08/21
0
0


Fractal

2
cultivar
Pst 08/21
0
0


Optic

2
cultivar
Pst 08/21
0
0


Feltwell

2
cultivar
Pst 08/21
0
0


Saloon

2
cultivar
Pst 08/21
0
0


Power

2
cultivar
Pst 08/21
0
0


Henley

2
cultivar
Pst 08/21
0
0


Tipple

2
cultivar
Pst 08/21
0
0


Heron

2
cultivar
Pst 08/21
0
0


Atem

2
cultivar
Pst 08/21
0
0


Onyx

2
cultivar
Pst 08/21
0
0


Barke

2
cultivar
Pst 08/21
0
0


Ria

2
cultivar
Pst 08/21
0
0


Prisma

2
cultivar
Pst 08/21
0
0


Triumph

2
cultivar
Pst 08/21
0
0


Trumpf
PI 548762
2
cultivar
Pst 08/501
0
0


Diamant
CIho 15226
2
cultivar
Pst 11/08
1
0


Derkado

2
cultivar
Pst 08/21
0
0


Heather

2
cultivar
Pst 08/21
0
0


Tardus

2
cultivar
Pst 08/21
0
0


Zephyr
PI 339815
2
cultivar
Pst 08/21
0.5
0


Carlsberg II
CIho 15218
2
cultivar
Pst 11/08
0
0


Maythorpe

2
cultivar
Pst 08/21
0
0


Golden Promise
PI 343079
2
cultivar
Pst 08/21
0
0


Pallas
CIho 11313
2
cultivar
Pst 11/08
0
0


Siri

2
cultivar
Pst 08/21
0
0


Sultan 5

2
cultivar
Pst 11/08
0
0


Cambrinus
PI 321779
2
cultivar
Pst 08/21
1
0


Ingrid

2
cultivar
Pst 08/501
0
0


M1460

—
genetic
Pst 08/21
0
0


Haisa
CIho 9855
2
cultivar
Pst 08/501
0
0


Varunda
PI 410865
2
cultivar
Pst 08/501
0
0


Emir
CIho 13541
2
cultivar
Pst 11/08
0
0


Mazurka
PI 399501
2
cultivar
Pst 08/21
1
0


Minerva

2
cultivar
Pst 08/21
0
0


Vada

2
cultivar
Pst 08/501
0
0


Baronesse
PI 568246
2
cultivar
Pst 08/21
0
0


Jive

2
cultivar
Pst 08/21
0
0


Apex

2
cultivar
Pst 08/501
0
0


Armelle
PI 410855
2
cultivar
Pst 08/21
0
0


Chevalier
CIho 156
2
cultivar
Pst 08/21
0
0


Stauffers 
PI 467580
2
cultivar
Pst 08/501
0
0


Obersulzer








Malteria Heda
CIho 15224
2
cultivar
Pst 11/08
0.5
0


Probstdorfer 
CIho 15222
2
cultivar
Pst 08/501
0
0


Vollkorn








Heils Franken
PI 327917
2
cultivar
Pst 11/08
0
0


Haruna Nijo

2
cultivar
Pst 08/21
0
0


CIho 4196
CIho 4196
2
landrace
Pst 08/21
0
0


L94

2
landrace
Pst 08/501
1
0


Grannenlose
PI 548740
2
landrace
Pst 08/21
1.5
0


Zweizeilige








Hiproly
PI 60693
2
landrace
Pst 08/501
1
0


Abyssinian 14
CIho 7202
2
landrace
Pst 08/501
3
1


Benton
PI 539105
6
cultivar
Pst 08/21
0
0


HOR 2926
PI 548734
—
—
Pst 11/08
0
0


HOR 1428
PI 548708
2
landrace
Pst 11/08
0
0


SusPtrit

6
genetic
Pst 08/21
3
4


OWB Recessive
GSHO 3451
6
genetic
Pst 08/21
2
0


Trebi
PI 537442
6
cultivar
Pst 08/21
0
0


Steptoe
CIho 15229
6
cultivar
Pst 08/21
3.5
0


Algerian
PI 539104
6
cultivar
Pst 08/21
1
0


Abed Binder 12
PI 327961
6
cultivar
Pst 08/21
0
0


Duplex
CIho 12420
6
landrace
Pst 08/21
0
0


Cebada Capa

6
cultivar
NA
NA
NA


Psaknon
CIho 6305
6
breeding
Pst 08/21
0
0


WBDC 350

2
wild
Pst 08/21
0
0


WBDC 045

2
wild
Pst 08/21
0
0


Spontaneum I
PI 293413
2
wild
Pst 08/501
0
0


WBDC 259

2
wild
Pst 08/21
1
0.5


WBDC 241

2
wild
Pst 08/21
3
1


22
PI 466309
2
wild
Pst 08/501
2.5
1


WBDC 085

2
wild
Pst 08/21
0
0


WBDC 148

2
wild
Pst 08/21
3
1


WBDC 013

2
wild
Pst 08/21
0
0


WBDC 334

2
wild
Pst 08/21
2
3


WBDC 247

2
wild
Pst 08/21
3
2


32
PI 466444
2
wild
Pst 08/501
1
0


WBDC 072

2
wild
Pst 08/21
3
0.5


20007
PI 284752
2
wild
Pst 08/501
0.5
0


WBDC 038

2
wild
Pst 08/21
3
3


WBDC 199

2
wild
Pst 08/21
0
0


55
PI 466279
2
wild
Pst 08/501
3.5
0


WBDC 253

2
wild
Pst 08/21
0
0


WBDC 008

2
wild
Pst 08/21
0
0


WBDC 110

2
wild
Pst 08/21
0.5
0


WBDC 068

2
wild
Pst 08/21
0.5
0


WBDC 109

2
wild
Pst 08/21
2
0


WBDC 112

2
wild
Pst 08/21
0.5
0


OWB Dominant
GSHO 3450
2
genetic
Pst 08/21
4
0


OUH602

2
wild
Pst 08/21
4
3


WBDC 343

2
wild
Pst 08/21
1.5
0


G-88
PI 466211
2
wild
Pst 08/501
1
0


Spiti
CIho 14349
6
landrace
Pst 08/21
1.5
0


Black Hull-less
PI 24849
6
landrace
Pst 08/21
3
3


West China
CIho 7556
6
breeding
Pst 08/21
0
0


Nigrate
CIho 2444
6
landrace
Pst 08/21
0.5
0


Durani
PI 125311
6
landrace
Pst 08/21
0.5
1


WBDC 172

2
wild
Pst 08/21
0



Multan
PI 57956
6
landrace
Pst 08/21
0
0


Kwan
PI 39367
6
landrace
Pst 08/21
0
0


Rupee
CIho 4355
6
landrace
Pst 08/21
0
0


15
CIho 11619
6
—
Pst 08/21
0.5
0


Long Glumes
CIho 6168
2
genetic
Pst 08/21
0
0


HOR 3401
PI 327764
6
landrace
Pst 08/21
0
0


Hanna
CIho 906
2
breeding
Pst 08/21
0
0


Dopla

6
cultivar
Pst 08/21
0.5
0


Regina

6
cultivar
NA
NA
NA


Igri
PI 428488
2
cultivar
Pst 08/21
0
0


DH46

—
genetic
Pst 08/21
2
1


Parasol

—
cultivar
NA
NA
NA


Manas

—
cultivar
Pst 08/21
0.5
0


Franger
PI 180669
6
cultivar
Pst 08/21
0.5
1


Astrix
PI 339826
6
cultivar
Pst 08/21
0.5
0


Fong Tien

6
—
Pst 11/08
3.5
2.5


Manchuria
CIho 2330
6
cultivar
Pst 08/21
3
0.5


Bigo
CIho 13611
6
cultivar
Pst 08/21
0
0


Foster

6
cultivar
Pst 08/21
1.5



Morex
CIho 15773
6
cultivar
Pst 08/21
1.5
0


Russell
PI 483127
6
cultivar
Pst 08/21
1
0
















TABLE 9







Eighteen structured populations inoculated 


with P. striiformis f. sp. tritici.










Resistant Accession
Cross
Type
N













Abed Binder 12
Manchuria x Abed Binder 12
F2
96



Manchuria x (Manchuria x 
BC1
90



Abed Binder 12 F1)




Betzes
Manchuria x Betzes
F2
94


CIho 4196
Foster x CIho 4196
RIL
89


Duplex
Duplex x Manchuria
F2
94


Emir
Manchuria x Emir
F2
94


Golden Promise
SusPtrit x Golden Promise
DH
122


Grannenlose 
Grannenlose Zweizeilige x 
F2
92


Zweizeilige
Manchuria




Haruna Nijo
Haruna Nijo x OUH602
DH
94


Heils Franken
Manchuria x Heils Franken
F2
93



Manchuria x (Manchuria x 
BC1
93



Heils Franken F1)




HOR 1428
Manchuria x HOR 1428
F2
94


HOR 2926
Manchuria x HOR 2926
F2
92


I 5
I 5 x Manchuria
F2
94


Sultan 5
Manchuria x Sultan 5
F2
190


WBDC 008
WBDC 008 x Manchuria
F2
92


WBDC 085
WBDC 085 x Manchuria
F2
94
















TABLE 10







Composite interval mapping of resistance to P. striiformis f. sp. tritici in several


mapping populations.

















Resistant







EW
AE
PV


Accession
Cross
Type
Trait
Chr
cM
Peak Marker
LOD
T
E
E




















CIho 4196
Foster x CIho 4196
RIL
CHL
1H
8.93
owbGBS32429_p1
20.24
3.19
0.32
0.53





CHL
6H
20.62
1_0136
3.82
3.19
0.12
0.07





pCOL
1H
9.50
0711N16_R1_p1
14.99
3.17
0.10
0.38





pCOL
1H
71.06
1_0357
4.69
3.17
0.05
0.09





pCOL
7H
145.28
1_0888
4.37
3.17
0.05
0.09


Golden Promise
SusPtrit x Golden
DH
CHL
1H
12.55
BOPA2_12_30817
19.64
3.26
0.76
0.28



Promise

CHL
4H
89.12
BOPA1_4361-1867
6.73
3.26
0.39
0.07





CHL
7H
161.20
SCRI_RS_155652
18.30
3.26
0.72
0.25





INF
1H
14.21
BOPA2_12_30950
4.91
3.03
0.39
0.11





INF
4H
89.95
SCRI_RS_121084
4.07
3.03
0.36
0.09





INF
7H
164.52
SCRI_RS_206322
5.52
3.03
0.43
0.12





pCOL
1H
12.55
BOPA2_12_30817
18.13
3.25
0.18
0.23





pCOL
4H
89.12
BOPA1_4361-1867
12.54
3.25
0.14
0.14





pCOL
7H
161.20
SCRI_RS_155652
20.20
3.25
0.19
0.26





pPUST
1H
14.21
BOPA2_12_30950
4.51
3.10
0.08
0.10





pPUST
4H
89.12
BOPA1_4361-1867
3.71
3.10
0.08
0.09





pPUST
7H
164.52
SCRI_RS_206322
4.69
3.10
0.09
0.11


Hama Nijo
Haruna NO x 
DH
CHL
1H
13.34
1_0419
32.80
3.02
−1.23
0.69



OUH602

CHL
4H
91.75
2_1243
4.42
3.02
−0.37
0.06





CHL
5H
109.89
1_1200
3.62
3.02
−0.33
0.05





INF
1H
15.34
1_0419
7.52
2.92
−0.57
0.28





INF
4H
91.49
1_0785
4.54
2.92
−0.39
0.13





pCOL
1H
13.34
1_0419
32.88
3.12
−0.35
0.71





pCOL
5H
97.21
2_1168
3.59
3.12
−0.09
0.05





pCOL
7H
164.10
1_0454
4.05
3.12
−0.09
0.05





pPUST
1H
15.34
1_0419
6.96
2.81
−0.14
0.27





pPUST
2H
74.78
2_0528
2.81
2.81
0.07
0.08





pPUST
4H
87.49
1_0785
3.66
2.81
−0.09
0.11


Barke
Morex x Barke
DH
CHL
1H
11.69
2_1174
16.42
3.09
0.53
0.38





CHL
5H
167.68
3_0666
7.79
3.09
0.34
0.14





CHL
6H
45.35
1_0061
3.28
3.09
−0.20
0.05





CHL
7H
139.49
1_0687
6.41
3.09
0.32
0.11





pCOL
1H
11.84
2_0665
20.53
3.16
0.20
0.51





pCOL
5H
165.52
2_0876
7.24
3.16
0.10
0.12





pCOL
7H
149.17
2_0483
5.78
3.16
0.09
0.09





Chr: Chromosome.


Cross: Direction of cross is determined by Mother x Father, designation of alleles are A and B for Mother and Father, respectively.


AEE: Allelic effect estimate, negative and positive values indicate resistance is contributed by the A and B alleles, respectively.


PVE: Percent of the phenotypic variation explained.













TABLE 11







Marker-trait association at the Rpst1 , Rps6, and Rpst3 loci in diverse barley F2


populations inoculated with P. striiformis f sp. tritici.


















Resistant









DEE/



Accession
Cross
Type
Trait
Chr
Marker
LOD
MTT
AEE
DEE
AEE
PVE





















Abed Binder
Manchuria x 
F2
CHL
7H
U32_3345_P1
8.35
1.36
0.61
−0.77
−1.27
0.33


12
Abed

INF
7H
U32_3345_P1
2.29
1.13
0.24
−0.24
−1.00
0.10



Binder 12

pCOL
7H
U32_3345_P1
20.09
1.35
0.26
−0.20
−0.78
0.61





pPUST
4H
3_0718_60_R
2.12
1.35
−0.06
−0.04
0.55
0.09





pPUST
7H
U32_3345_P1
3.21
1.17
0.07
−0.05
−0.82
0.13



Manchuria x 
BC1
CHL
4H
3_0718_60_R
2.28
0.98
NA
0.58
NA
0.03



(Manchuria

CHL
7H
U32_3345_P1
26.32
0.85
NA
2.72
NA
0.67



x Abed 

INF
7H
U32_3345_P1
6.46
0.90
NA
1.47
NA
0.27



Binder 12)

pCOL
4H
3_0718_60_R
1.60
0.81
NA
0.12
NA
0.02





pCOL
7H
U32_3345_P1
26.48
0.84
NA
0.69
NA
0.69





pPUST
4H
3_0718_60_R
0.92
0.81
NA
0.10
NA
0.03





pPUST
7H
U32_3345_P1
5.78
0.84
NA
0.27
NA
0.24


Betzes
Manchuria x 
F2
CHL
1H
HV5_963924_P1
14.19
1.35
0.95
−0.52
−0.54
0.41



Betzes

CHL
4H
1_0751_120_F
7.39
1.35
0.69
−0.35
−0.51
0.18





pCOL
1H
HV5_963924_P1
17.74
1.43
0.29
−0.13
−0.44
0.45





pCOL
4H
1_0751_120_F
9.71
1.39
0.20
−0.14
−0.69
0.20





INF
1H
HV5_963924_P1
2.63
1.26
0.20
−0.29
−1.46
0.11





INF
4H
1_0751_120_F
2.36
1.24
0.26
−0.18
−0.68
0.10


Emir
Manchuria x 
F2
CHL
1H
HV5_963924_P1
3.19
1.32
0.28
−0.05
−0.16
0.08



Emir

CHL
4H
GBS0288
1.81
1.41
0.22
−0.03
−0.13
0.04





CHL
7H
U32_2966_P1
10.25
1.34
0.53
−0.50
−0.95
0.31





pCOL
1H
HV5_963924_P1
2.88
1.54
0.07
0.02
0.34
0.07





pCOL
4H
GBS0288
1.66
1.44
0.06
−0.02
−0.34
0.04





pCOL
7H
U32_2966_P1
12.68
1.37
0.18
−0.16
−0.88
0.39


Grannenlose
Grannenlose 
F2
CHL
4H
2_0384_120_F
1.85
1.30
−0.44
0.26
−0.60
0.09


Zweizeilige
Zweizeilige

pCOL
4H
2_0384_120_F
2.88
1.40
−0.13
0.12
−0.96
0.13



x Manchuria

INF
1H
206D11_T7_p1_281_F
2.30
1.16
0.19
−0.13
−0.66
0.11





pPUST
1H
206D11_T7_p1_281_F
1.22
1.18
0.02
−0.01
−0.45
0.06


Heils 
Manchuria x 
F2
CHL
1H
206D11_T7_p1_281_F
61.27
1.45
1.49
−1.47
−0.99
0.95


Franken
Heils

pCOL
1H
206D11_T7_p1_281_F
59.08
1.34
0.44
−0.41
−0.92
0.95



Franken

INF
1H
206D11_T7_p1_281_F
2.82
1.35
0.30
−0.24
−0.81
0.13





pPUST
1H
206D11_T7_p1_281_F
2.82
1.21
0.06
−0.05
−0.93
0.13



Manchuria x 
BC1
CHL
1H
206D11_T7_p1_281_F
6.73
0.78
NA
−1.50
NA
0.29



(Manchuria

pCOL
1H
206D11_T7_p1_281_F
7.89
0.86
NA
−0.29
NA
0.32



x Heils Franken)

INF
1H
206D11_T7_p1_281_F
3.67
0.83
NA
−0.85
NA
0.17





pPUST
1H
206D11_T7_p1_281_F
3.03
0.75
NA
−0.16
NA
0.14


HOR 1428
Manchuria x 
F2
CHL
1H
HV5_963924_P1
2.64
1.26
0.50
−0.30
−0.59
0.12



HOR 1428

pCOL
1H
HV5_963924_P1
2.24
1.35
0.14
−0.05
−0.35
0.10


HOR 2926
Manchuria x 
F2
CHL
1H
HV5_963924_P1
12.25
1.28
0.78
−0.55
−0.71
0.42



HOR 2926

pCOL
1H
HV5_963924_P1
7.69
1.39
0.19
−0.13
−0.65
0.32



I 5 x Manchuria
F2
CHL
1H
206D11_T7_p1_281_F
11.71
1.27
−1.02
−0.54
0.53
0.44





pCOL
1H
206D11_T7_p1_281 F
14.45
1.35
−0.30
−0.15
0.50
0.49





pCOL
4H
1_0510_120_F
1.96
1.37
−0.09
−0.01
0.10
0.05


Sultan 5
Manchuria x 
F2
CHL
4H
contig_134516_375_F
6.32
X
0.27
−0.08
−0.30
0.06



Sultan 5

CHL
7H
BOPA1_4671-856_192_F
43.54
X
0.85
−0.73
−0.85
0.62


WBDC 008
WBDC 008 x 
F2
CHL
7H
SCRI_RS_185445_60_F
13.49
1.32
−1.61
0.21
−0.13
0.49



Manchuria

pCOL
7H
SCRI_RS_185445_60_F
12.41
1.29
−0.32
0.05
−0.14
0.46





INF
4H
1_1398_77_F
2.05
1.27
−0.27
−0.16
0.61
0.08





INF
7H
SCRI_RS_185445_60_F
3.92
1.28
−0.37
−0.36
0.95
0.16





pPUST
4H
1_1398_77_F
1.50
1.13
−0.06
−0.03
0.46
0.06





pPUST
7H
SCRI_RS_185445_60_F
4.34
1.46
−0.10
−0.09
0.90
0.18


WBDC 085
WBDC 085 x 
F2
CHL
4H
1_1398_77_F
1.60
1.38
−0.35
0.54
−1.53
0.06



Manchuria

CHL
7H
OZ_43640_p1_174_F
3.85
1.35
−0.81
0.30
−0.37
0.16





pCOL
4H
1_1398_77_F
1.83
1.44
−0.10
0.07
−0.66
0.07





pCOL
7H
OZ_43640_p1_174_F
4.92
1.43
−0.19
0.08
−0.43
0.20





Chr: Chromosome.


Cross: Direction of cross is determined by Mother x Father, designation of alleles are A and B for Mother and Father, respectively.


AEE: Allelic effect estimate, negative and positive values indicate resistance is contributed by the A and B alleles, respectively.


DEE: Dominance effect estimate.


PVE: Percent of the phenotypic variation explained.






Association of NLR-A and Rps6: A total of 38 accessions were selected for transcriptome sequencing (Table 12). RNAseq was performed using either HiSeq 2000 or HiSeq 2500 systems, with paired end reads of length 100 or 150 bp. Transcriptomes were assembled using Trinity and BLAST was used to identify the presence or absence of NLR-A. We identified a strong association with expression of NLR-A and expression of resistance at the Rps6 locus (Table 12). In total, seven accessions were found to express NLR-A and Rps6; and 15 accessions were found to lack expression of NLR-A and Rps6. Tophat alignments were performed on the genomic sequence of NLR-A using the RNAseq derived from 38 barley accessions. The majority of accessions contained the same coding sequence including Abed Binder 12, Aramir, Barke, BCD12, BCD47, Commander, Emir, Finniss, Golden Promise, Pallas, Sultan 5, and WBDC013, whereas accessions Hindmarsh, WBDC008, WBDC085, WBDC109, and WBDC110 contained polymorphisms relative to the Abed Binder 12 allele. In addition, Bowman was found to be identical to Abed Binder 12 based on WGS contigs aligned to NLR-A (FIG. 6). WBDC008 has the most polymorphisms, with 16 synonymous and 5 non-synonymous mutations relative to Abed Binder 12. Non-synonymous mutations include Q95E (WBDC008, WBDC109, WBDC110), N148K (WBDC008, WBDC085, WBDC109, WBDC110), S535P (Hindmarsh), L539S, W665L, and K680E (WBDC008), and A920V (WBDC109 and WBDC110).







TABLE 12







Association of NLR-A and Rps6 in diverse barley accessions 


based on expression and mapping, respectively.











USDA-
Presence 
Presence 


Accession
GRIN
of NLR-A
of Rps6





Abed Binder 12
PI 327961
Expressed
Rps6


Aramir

Expressed
Not tested


Barke

Expressed
Rps6


BCD12
PI 659443
Expressed
Not tested


BCD47
PI 659444
Expressed
Not tested


Betzes

Not expressed
rps6


Bowman
PI 483237
Present in genome
Not tested


CI 16139
CI 16139
Not expressed
rps6


CI 16147
CI 16147
Not expressed
rps6


CI 16153
CI 16153
Not expressed
rps6


CIho 4196
CIho 4196
Not expressed
rps6


Commander
CIho 6011
Expressed
Not tested


Duplex
CIho 12420
Not expressed
rps6


Emir
CIho 13541
Expressed
Rps6


Finniss

Expressed
Not tested


Fong Tien

Not expressed
rps6


Golden Promise
PI 343079
Expressed
Rps6


Grannenlose 
PI 548740
Not expressed
rps6


Zweizeilige





Haruna Nijo

Not expressed
rps6


Heils Franken
PI 327917
Not expressed
rps6


Hindmarsh

Expressed
Not tested


HOR 1428
PI 328669
Not expressed
rps6


I 5
CIho 11619
Not expressed
rps6


Igri
PI 428488
Not expressed
Not tested


Manchuria
CIho 2330
Not expressed
rps6


Maritime

Not expressed
Not tested


Pallas
CIho 11313
Expressed
Not tested


Q21861
PI 584766
Not expressed
Not tested


Russell
PI 483127
Not expressed
rps6


Sultan 5

Expressed
Rps6


SusPtrit

Not expressed
rps6


WBDC 008

Expressed
Rps6


WBDC 013

Expressed?
Not tested


WBDC 085

Expressed
Rps6


WBDC 109

Expressed
Not tested


WBDC 110

Expressed
Not tested


WBDC 172

Not expressed
Not tested


WBDC 259

Not expressed
Not tested









Molecular cloning of NLR-A: The genomic region encompassing the NLR-A transcript is 12.8 kb in length. This substantial size is primarily due to intron 2, which is 8.8 kb in length. Difficulty has been faced previously with using large T-DNA constructs using Agrobacterium-based transformation; therefore we adopted a cloning strategy that would allow for retention of native genomic sequence for the promoter and terminator of NLR-A, but removing either intron 2 or introns 1 and 2. PCR primers were developed to amplify NLR-A into two parts: fragment 1 contained 2.4 kb promoter, exons 1 and 2, and intron 1, and approximately half of intron 2, and fragment 2 that contained a portion of exon 3, intron 3, exon 4, and a 1.8 kb terminator region. Both regions were amplified from the BAC derived from Abed Binder 12 genomic DNA containing NLR-A, cloned into the pCR-XL-TOPO vector, transformed into E. coli, and sequenced. In parallel, cDNA generated from Abed Binder 12 RNA was used to amplify the entire coding sequence of NLR-A (fragment 3), cloned into the pSC-B vector, transformed into E. coli, and sequenced. The design of the T-DNA construct included a hygromycin resistance gene driven by a 35S promoter and nos terminator followed by 2.4 kb promoter, exons 1, 2, and 3, intron 3, exon 4, and 1.8 kb terminator of NLR-A. Primers were developed that amplified from cloned fragments 1, 2, and 3, ensuring that 40 base pair overlaps existed between all three fragments and the backbone vector pBract202. Fragments were assembled using Gibson assembly and were used for transformation with Agrobacterium tumefaciens (FIG. 8).
Materials and Methods
Genetic material: Abed Binder 12 (PI 327961), Russell (PI 483127), and Manchuria (CIho 2330) were obtained from the United States Department of Agriculture, Agricultural Research Service (USDA-ARS) Grain Resources Information Network (GRIN). Accessions SusPtrit and Golden Promise were obtained from Rients Niks (Wageningen UR). Accession Barke was obtained from Nils Stein (Leibniz-Institut für Pflanzengenetik and Kulturpflanzenforschung).
Pathogen material: Pathogen assays were carried out using either P. striiformis f. sp. tritici isolates 08/501 or 08/21. P. striiformis f. sp. tritici isolates were collected by The National Institute for Agricultural Botany in 2008. P. striiformis f. sp. tritici isolates 08/21 and 08/501 urediniospores were bulked, and maintained, on the susceptible wheat cvs. Solstice and Victo, respectively.
Inoculation assays: For plant inoculations, seeds were sown a peat-based compost. Plants were grown in a controlled environment chamber at 18° C. day and 11° C. night using a 16 h light and 8 h dark cycle with lighting provided by metal halide bulbs (Philips MASTER HPI-T Plus 400W/645 E40). Inoculations were performed on 14-day-old seedlings when the first leaf was fully emerged and prior to the emergence of the second leaf. Inoculum was prepared by mixing fresh spores with talcum powder at a weight ratio of 1:16. A compressed air pump was used to disseminate inoculum onto seedlings positioned on a spinning platform. After inoculation, seedling pots were sealed in plastic bags and stored in the dark at 6° C. in order to achieve the high humidity required for successful germination. Seedlings were returned to the controlled environment growth chamber after 48 to 72 hours post inoculation. Disease symptoms were scored 14 days post inoculation.
Phenotyping: Plants inoculated with P. striiformis f. sp. tritici were scored using a phenotyping scale that measured the macroscopic phenotypes of chlorosis (leaf yellowing) and infection (pustule formation). Plants were individually scored on a continuous nine-point scale ranging from 0 to 4, with increments of 0.5. Scores reflected the percentage of the inoculated leaf surface expressing the disease symptom. A score of 0 indicated no expression of the phenotype (0% coverage), whereas a score of 4 indicated extensive expression of the phenotype (100% coverage). For microscopic phenotyping, first leaves of inoculated seedlings were harvested with scissors and placed in 15 mL centrifuge tubes filled with 1.0 M KOH and a droplet of surfactant (Silwet L-77, Loveland Industries Ltd.). Tubes were incubated at 37° C. for 12 to 16 hours. The KOH solution was decanted and leaves were washed three times using 15 mL of 50 mM Tris HCL-pH7.5. Leaf samples were then incubated overnight at 4° C. in a 2.0% w/v staining solution containing wheat germ agglutinin conjugated to fluorescein isothiocyanate (WGA-FITC; Sigma Aldrich; L4895-10MG) dissolved in 50 mM Tris HCL. Leaves were washed with sterile water and mounted on microscope slides. Mounts were visualized under blue light excitation using a fluorescence microscope with GFP filter under a 5× objective. Each field of view (FOV) was 2.72 mm×2.04 mm. Data was collected by estimating the amount of colonization and pustule formation in non-overlapping FOVs covering the length and breadth of the leaf. Disease symptoms were estimated to be less than 15%, between 15 and 50%, or greater than 50% by assigning the values 0, 0.5 and 1 to each FOV. Percent colonization (pCOL) and pustule formation (pPUST) scores, ranging from 0 to 100%, were calculated by averaging the values relative to the number of FOVs in each leaf.
DNA extraction: DNA from all populations was extracted from leaf tissue following a CTAB-based protocol adapted for 96-well based format modified from (Stewart and Via (1993) BioTechniques 14:748-750) that provides PCR-grade genomic DNA.
Abed Binder 12×Russell F2 genetic map construction: The concentration of gDNA was estimated using the PicoGreen dsDNA quantification assay (Life Technologies; P11496) and was normalized to 60 ng/μL. Oligonucleotide assay (OPA) genotyping using the barley BOPA1 design that includes 1,536 SNP-based markers was performed at the University of California, Los Angeles Southern California Genotyping Consortium (Los Angeles, Calif., USA) (Close et al. 2009). Additional markers were developed as either cleaved amplified polymorphic sequence (CAPS) or Sequenom MassARRAY markers to bridge gaps between unlinked chromosome arms and increase marker density. For CAPS marker development, we identified type II restriction enzymes that digest at polymorphic positions using CAPS Designer (available on the world-wide web at: solgenomics.net/tools/caps_designer/caps_input.pl). CAPS marker PCR reactions were prepared by mixing 2 μL buffer (10×), 0.4 μL dNTPs, 0.4 μL forward primer, 0.4 μL reverse primer, 0.2 μL Taq polymerase, 2 μL gDNA at 10 ng/μL, and 14.6 μL H2O. The PCR cycling started with an initial denaturation step at 94° C. for five minutes and then proceeded through a cycle of 94° C. for 20 seconds, annealing at 56° C. for 30 seconds and primer extension at 72° C. for one minute for a total of 35 cycles. The procedure ended with a final extension at 72° C. for five minutes before being held at 16° C. Digestions were performed according to the manufacturer's instructions for individual enzymes. Electrophoresis was used to resolve restriction fragments using 2.0% TBE agarose gels stained with ethidium bromide. Gel images were taken using a Bio-Rad ChemDoc XRS+ imaging system and markers were scored manually. GBS CAPS markers are described in (Kota et al. (2008) Funct. Integr. Genomics 8:223-233). All primers and restriction enzymes for CAPS markers are detailed in ESM 1. For Sequenom marker development, SNP sequences were extracted in IUPAC format with 40 to 60 bp flanking sequence. This sequence was used as a template for primer design using MassARRAY software v3.1 for the multiplexing up to 32 SNP assays. Sequenom genotyping was carried out at the Iowa State University Genomic Technologies Facility (Ames, Iowa, USA). All SNPs and WGS contig source information for Sequenom markers are detailed in ESM 2.
Genetic map construction: A genetic map was constructed using 589 markers including 535 barley OPA (Close et al. (2009) BMC Genomics 10:582), 26 CAPS markers, and 28 Sequenom markers. JoinMap v4 (Kyazma B. V., Wageningen, Netherlands) was used using default parameters and an independence LOD threshold of 4.0. Genetic distances were estimated using the Kosambi mapping function. Integrity of the genetic map was evaluated through comparison with the current OPA consensus genetic map of barley (Muñoz-Amatriain et al. (2011) Plant Genome 4:238-249) and with two-point linkage tests using R/qtl (v1.33-7).
QTL and ANOVA analyses: Composite interval mapping was performed with QTL Cartographer (v1.17j) using model 6, the selection of five background markers, a step size of 2 cM, and a window size of 10 cM (Basten et al. (1994) “Zmap—a QTL cartographer,” in: Smith et al. (eds) Proceedings of the 5th World Congress on Genetics Applied to Livestock Production: Computing Strategies and Software, Guelph, Ontario, Canada). Significant QTLs were extracted using the Eqtl module under the H0:H3 model using experiment-wide thresholds (EWT) that were calculated using 1,000 permutations with the reselection of background markers using a threshold of α<0.05 (Doerge and Churchill (1996) Genetics 142:285-294; Lauter et al. (2008) Plant Genome 1:99-110). ANOVA analyses for testing the linkage of individual markers were performed with R/qtl.
Transcriptome sequencing and assembly: Leaf tissue was harvested from first and second leaves 18 days after sowing for accessions described in Table 12. Samples were flash frozen in liquid nitrogen, and stored at −80° C. Samples were homogenised in liquid nitrogen-chilled pestle and mortars. RNA was extracted from samples using TRI-reagent (Sigma-Aldrich; T9424) according to the manufacturers protocol. DNA was removed by treating samples with RQ1 RNase free DNase (Promega; M6101). Samples were purified using RNeasy mini spin columns following the RNA Cleanup protocol (Qiagen; product No. 74104). The quality and integrity of the RNA samples were assessed using RNA Nano Chips (Agilent Technologies; product no. 5067-1511) on an Agilent 2100 Bioanalyzer. Abed Binder 12 and Russell RNA libraries were constructed using Illumina TruSeq RNA library preparation (Illumina; RS-122-2001). Final library insert sizes were predicted to be 411 and 339 bp for Abed Binder 12 and Russell, respectively. Barcoded libraries were sequenced using 100 bp paired-end reads on one lane of a Hiseq 2000/2500. This generated 32.0 and 59.3 million paired end reads for Abed Binder 12 and Russell, respectively. All library preparation and sequencing was performed at The Genome Analysis Centre (Norwich, UK). RNAseq data quality was assessed with FastQC and reads were removed using Trimmomatic (v0.32) with parameters set at ILLUMINACLIP:TruSeq3-PE.fa:2:30:10, LEADING:3, TRAILING:3, SLIDINGWINDOW:4:15, and MINLEN:100. These parameters will remove all reads with adapter sequence, ambiguous bases, or a substantial reduction in read quality. Transcriptome assembly was performed using Trinity (v2013-11-10) using default parameters.
Marker development for saturation at the Rps6 locus: Initial marker development was guided by two approaches to identify sequences anchored to the Rps6 region. This included the identification of anchored unigenes based on marker colinearity with existing genetic maps (Moscou et al. (2011) PLoS Genet 7:e1002208; Muñoz-Amatriain et al. (2011) Plant Genome 4:238-249; Potokina et al. (2008) Plant 53:90-101) and orthologous rice genes based on the barley genome zipper (Mayer et al. (2011) Plant Cell 23:1249-1263). A region on rice chromosome 6 was selected including 38 genes (Os06g43140 to Os06g43900). Best BLASTn hits returned from the cv. Morex WGS assembly (IBGSC (2012) Nature 491:711-716) were used as template for PCR primer design using Primer3 (libprimer3 release 2.3.6). All BLASTn queries were performed using blastall (v2.2.23). Abed Binder 12 and Russell gDNA was used as template for PCR amplification and Sanger sequencing. SNPs were identified by aligning sequence files using Seqman software (DNAstar Lasergene v11). SNPs were then used to develop markers using Cleaved Amplified Polymorphic Sequences or Sequenom MassARRAY iPLEX platform as described above.
Subsequent marker development involved either (1) the comparison of genomic contigs derived from cvs. Barke, Bowman, and Morex or (2) the comparison of Abed Binder 12 and Russell RNAseq aligned reads to WGS contigs anchored to the Rps6 region (IBGSC (2012) Nature 491:711-716; Mascher et al. (2013) Plant J. 76:718-727). Geneious (v8.1.6) was used for read alignment using Geneious mapping function with default parameters and data visualization (Kearse et al. (2012) Bioinformatics 28:1647-1649). SNPs were converted into Kompetitive Allele Specific PCR (KASP) markers using a similar approach as described in (Ramirez-Gonzalez et al. (2015) Bioinformatics 31:2038-2039). All WGS contig source information, SNPs, KASP marker template, and primers are detailed in ESM 3. KASP assays were performed at the John Innes Centre Genotyping Facility (Norwich, UK).
Recombination screen and phenotyping: A recombination screen was carried out using seed bulked from F3 plants selected from a single F2:3 family that were heterozygous for Rps6. Sequenom markers were converted into KASP markers and used as flanking markers to identify recombinant chromosomes. Two independent progeny tests were performed using individuals with recombinant chromosomes. A total of 16 individuals per family per replicate were scored for macroscopic observation of chlorosis and infection.
Example 2: Transformation of Barley with Rps6 and Testing for Wheat Stripe Rust Resistance
Yeo et al. ((2014) Theor. Appl. Genet. 127:325-337) previously established the doubled haploid population SusPtrit×Golden Promise (SxGP DH) to identify a transformable barley accession that was also susceptible to several heterologous rusts of barley. We found that the accession SxGP DH-47 was susceptible to wheat stripe rust and had previously been shown to be competent for Agrobacterium-based transformation (Yeo et al. (2014) Theor. Appl. Genet. 127:325-337). Transformation of SxGP DH-47 barley is performed as described by Bartlett et al. ((2008) Plant Methods 4:22) with a modification on the use of immature embryo-derived callus for infection with Agrobacterium tumefaciens rather than immature embryos. Briefly, immature embryos are harvested from barley plants grown in a greenhouse, with embryos approximately 1.5 to 2 mm in diameter. In contrast to Bartlett et al. ((2008) Plant Methods 4:22), immature embryos with embryonic axis removed are placed on callus induction media for approximately four weeks. Immature embryo-derived calli are inoculated with A. tumefaciens strain AGL1 containing: (1) the T-DNA plasmid IHP_0205_NLR-A construct (SEQ ID NO: 15), the T-DNA plasmid IHP_0300 NLR-A native construct (SEQ ID NO: 34), or the T-DNA plasmid pBract202_TSLpMla6 NLR-A_CDS_gDNA_tMla6 construct (SEQ ID NO: 35); and (2) the pSoup plasmid. Calli are co-cultivated with A. tumefaciens for two days. All other steps in the transformation procedure are equivalent to Bartlett et al. ((2008) Plant Methods 4:22).
Seed (T1) derived from the hemizygous T0 plants containing a T-DNA insert are grown for two weeks, inoculated with P. striiformis f. sp. tritici isolate 08/21, and then scored for resistance or susceptibility as described above in Example 1 (see “Inoculation assays” in the Materials and Methods section). Several independent T-DNA insertion events are tested. In each experiment, individual T1 plants are scored for resistant and susceptible phenotypes, and confirmation of Rps6 function is established by associating the presence/absence of the T-DNA insert with resistance/susceptibility.
Example 3: Transformation of Wheat with Rps6 and Testing for Wheat Stripe Rust Resistance
Transformation of wheat (Triticum aestivum ‘Fielder’) is carried out as described by Periyannan et al. ((2013) Science 341: 786-788). T-DNA inserts include the original promoter and coding sequences for NLR-A (SEQ ID NO: 17) from barley contained in one of the T-DNA plasmids (SEQ ID NO: 15, 34, or 35) described in Example 2, as well as the genomic segment of the open reading frame of NLR-A (SEQ ID NO: 2) fused to a promoter and terminator from a highly expressed NLR gene from wheat. Phenotypic screens for resistance or susceptibility of transformed wheat plants to wheat stripe rust will be carried out as described above in Example 2 for barley.
Example 4: Transformation of Brachypodium distachyon with Rps6 and Testing for Wheat Stripe Rust Resistance
Transformation of the model grass species Brachypodium distachyon is carried out essentially as described by Vain et al. ((2008) Plant Biotechnol. J. 6: 236-245; doi:10.1111/j.1467-7652.2007.00308.x). T-DNA inserts include the original promoter and coding sequences for NLR-A (SEQ ID NO: 17) from barley contained in one of the T-DNA plasmids (SEQ ID NO: 15, 34, or 35) described in Example 2, as well as the genomic segment of the open reading frame of NLR-A (SEQ ID NO: 2) fused to a promoter and terminator from a highly expressed NLR gene from wheat. Phenotypic screens for resistance or susceptibility to wheat stripe rust will be carried out as described above in Dawson et al. ((2015) Front. Plant Sci. 6: 876; doi: 10.3389/fpls.2015.00876).
The article “a” and “an” are used herein to refer to one or more than one (i.e., to at least one) of the grammatical object of the article. By way of example, “an element” means one or more element.
Throughout the specification the word “comprising,” or variations such as “comprises” or “comprising,” will be understood to imply the inclusion of a stated element, integer or step, or group of elements, integers or steps, but not the exclusion of any other element, integer or step, or group of elements, integers or steps.
All publications and patent applications mentioned in the specification are indicative of the level of those skilled in the art to which this invention pertains. All publications and patent applications are herein incorporated by reference to the same extent as if each individual publication or patent application was specifically and individually indicated to be incorporated by reference.
Although the foregoing invention has been described in some detail by way of illustration and example for purposes of clarity of understanding, it will be obvious that certain changes and modifications may be practiced within the scope of the appended claims.

## Claims

1. A transgenic plant, plant cell, or seed comprising stably, incorporated in its genome a heterologous polynucleotide construct comprising a member selected from the group consisting of:
(a) the nucleotide sequence set forth in SEQ ID NO: 1 or 2; and
(b) a nucleotide sequence encoding the amino acid sequence set forth in SEQ ID NO: 3.

2. A method for producing a plant with enhanced resistance to a plant disease, the method comprising introducing a heterologous polynucleotide construct into at least one plant cell, the heterologous polynucleotide construct comprising a member selected from the group consisting of:
(a) the nucleotide sequence set forth in SEQ ID NO: 1 or 2; and
(b) a nucleotide sequence encoding the amino acid sequence set forth in SEQ ID NO: 3;
and regenerating said plant from said pant cell, wherein the regenerated plant comprises said heterologous polynucleotide construct.

3. The method of claim 2, wherein the plant is barley, wheat, or Brachypodium distachyon.

4. The method of claim 2, wherein the heterologous polynucleotide construct is stably incorporated into the genome of the plant cell.

5. A method of limiting wheat stripe rust in agricultural crop production, the method comprising planting a transgenic seed and growing from said seed a plant under conditions favorable for the growth and development of the plant, wherein the transgenic seed comprises stably incorporated in its genome a heterologous polynucleotide construct comprising a member selected from the group consisting of:
(a) the nucleotide sequence set forth in SEQ ID NO: 1 or 2; and
(b) a nucleotide sequence encoding the amino acid senquence set forth in SEQ ID NO: 3.

6. The transgenic plant, plant cell, or seed of claim 1, wherein the transgenic plant is a wheat or barley plant, the transgenic plant cell is a wheat or a barley plant cell, and the transgenic seed is wheat or barley seed.