bluuebunny/crossref_metadata_2025 huggingface dataset:
A consensus map of barley integrating SSR, RFLP, and AFLP markers
Authors: Karakousis A. , Gustafson J. P. , Chalmers K. J. , Barr A. R. , Langridge P.
Published: December 2003

A consensus map of barley combining simple sequence repeat (SSR), restriction fragment length polymorphism (RFLP), and amplified fragment length polymorphism (AFLP) markers has been developed by combining 5 Australian barley linkage maps, Galleon × Haruna Nijo, Chebec × Harrington, Clipper × Sahara, Alexis × Sloop, and Amaji Nijo × WI2585, using the software package JOINMAP 2.0. The new consensus map consists of 700 markers, with 136 being SSRs, and has a total genetic distance of 933 cM. The consensus map order appears to be in good agreement with the Australian barley linkage maps, with the exception of a small inversion located close to the centromere of chromosome 5H. Similarly, the SSR map orders are in good agreement with SSR markers integrated into the doubled haploid linkage map of Lina × Hordeum spontaneum, Canada Park. The new consensus map provides a framework to cross examine and align partial and complete barley linkage maps using markers common to many barley maps. This map will allow researchers to rapidly and accurately select SSR markers for chromosome regions of interest for barley genetic and plant breeding studies.
Potential of SSR markers for plant breeding and variety identification in Australian barley germplasm
Authors: Karakousis A. , Barr A. R. , Chalmers K. J. , Ablett G. A. , Holton T. A. , Henry R. J. , Lim P. , Langridge P.
Published: December 2003

SSR markers closely linked to 18 loci that control 16 important barley traits were assessed for their applicability in Australian barley breeding programs. A panel of 40 genotypes routinely used by the South Australian Barley Improvement Program (SABIP) was used to examine the usefulness of these SSR markers for marker assisted selection (MAS). The success of monitoring a trait locus from donor to recipient lines ranged from 10 to 98%, depending on the marker. SSRs with a high polymorphic information content (PIC) value were found to be the most useful for application in MAS. The assessment also indicated that SSRs derived from genomic sequences were more successful for MAS than those designed from expressed sequence tags. A total of 130 SSR markers were screened among 2 panels of Australian barley genotypes to determine which markers would be the most useful for discriminating Australian germplasm. PIC values generated by this screening were also compared with those generated using a panel of European barley genotypes. Using ordinary correlations (parametric), rank correlations (non-parametric), and partial correlations (multi-variate), a strong association was found between the 2 Australian panels, but no or weak correlation was observed between the 2 Australian panels and the European dataset. It can therefore be concluded that PIC values generated by SSR markers screened with European genotypes cannot be used to predict the usefulness of an SSR marker for discriminating Australian genotypes. From PIC values generated in this study, 36 SSR markers have been selected for the discrimination of Australian genotypes. These markers all show high and/or consistent PIC values among Australian and European barley genotypes.
Mapping and QTL analysis of the barley population Galleon × Haruna Nijo
Authors: Karakousis A. , Barr A. R. , Kretschmer J. M. , Manning S. , Logue S. J. , Roumeliotis S. , Collins H. M. , Chalmers K. J. , Li C. D. , Lance R. C. M. , Langridge P.
Published: December 2003

A genetic linkage map consisting of 435 molecular markers has been constructed using a doubled-haploid mapping population derived from a cross between the Australian barley feed variety Galleon and Haruna Nijo, a Japanese barley cultivar of high malting quality. This map was used to locate the genes conferring CCN and SFNB resistance from Galleon and to locate malting and brewing quality genes from Haruna Nijo. Closely linked markers to the trait loci have been identified and are now being widely implemented in Australian breeding programs.
Mapping and QTL analysis of the barley population Clipper × Sahara
Authors: Karakousis A. , Barr A. R. , Kretschmer J. M. , Manning S. , Jefferies S. P. , Chalmers K. J. , Islam A. K. M. , Langridge P.
Published: December 2003

A genetic linkage map consisting of 211 molecular markers has been generated using a doubled-haploid population derived from a cross between the Australian barley variety Clipper and the Algerian landrace Sahara 3771. The map was used in subsequent trait mapping studies to locate the genes conferring boron tolerance and cereal cyst nematode resistance from Sahara 3371 and to map several plant type and developmental genes. Closely linked markers to the trait loci have been identified and are now being widely implemented in Australian breeding programs.
Typing Mlo alleles for powdery mildew resistance in barley by single nucleotide polymorphism analysis using MALDI-ToF mass spectrometry
Authors: Paris M. , Potter R. H. , Lance R. C. M. , Li C. D. , Jones M. G. K.
Published: December 2003

Single nucleotide polymorphisms (SNPs) have been identified in a range of plant genomes. Development of rapid, low-cost methods to enable their validation and implementation as molecular markers is now required for practical applications. We report the development of single and multi-nucleotide primer extension assays to genotype co-dominant SNPs from small quantities of barley leaf tissue. In the single nucleotide primer extension assay, a genotyping primer with its 3′ end directly flanking a SNP was annealed to a target sequence and extended by a single dideoxynucleotide triphosphate complementary to the polymorphic base. In the multi-nucleotide primer extension assay, designed to facilitate allele calling, the genotyping primer with its 3′ end flanking the SNP was extended by either 1 or 2 nucleotides, depending on the allele encountered. Extension products were analysed using MALDI-ToF mass spectrometry and, making use of the molecular weight difference between DNA bases, the incorporated nucleotides were identified by the increase in mass of the extended primers. Based on a SNP identified in the barley Mlo gene, primer extension assays were designed and used for co-dominant marker-assisted selection of barley seedlings segregating for mlo-mediated resistance to powdery mildew. This allowed accurate selection of progeny lines carrying alleles for resistance to powdery mildew, including heterozygotes. Doubled haploid barley progenies were screened for Mlo alleles and a complete correlation between mlo/mlo genotype and resistant phenotype was found The method has been used by barley breeders for routine selection of barley genotypes resistant to powdery mildew.
Mapping and QTL analysis of the barley population Alexis × Sloop
Authors: Barr A. R. , Jefferies S. P. , Broughton S. , Chalmers K. J. , Kretschmer J. M. , Boyd W. J. R. , Collins H. M. , Roumeliotis S. , Logue S. J. , Coventry S. J. , Moody D. B. , Read B. J. , Poulsen D. , Lance R. C. M. , Platz G. J. , Park R. F. , Panozzo J. F. , Karakousis A. , Lim P. , Verbyla A. P. , Eckermann P. J.
Published: December 2003

Two populations between the German malting variety Alexis and the Australian malting variety Sloop were constructed, mapped, phenotyped, and subjected to quantitative trait loci analysis. One population consisted of 153 F4-derived recombinant inbred lines and the other of 111 doubled haploid lines. This paper describes 18 field and laboratory experiments conducted with the populations and summarises the traits mapped and analysed. The genetic basis of 5 traits (malt extract, resistance to leaf rust, resistance to powdery mildew, early flowering, plant stature) important to Australian efforts to improve malting barley varieties was elucidated. Detailed maps for these populations are shown in this paper, while a consensus map incorporating these maps and further experiments on the populations are described elsewhere in this issue.
Use of putative QTLs and structural genes in marker assisted selection for diastatic power in malting barley (Hordeum vulgare L.)
Authors: Coventry S. J. , Collins H. M. , Barr A. R. , Jefferies S. P. , Chalmers K. J. , Logue S. J. , Langridge P.
Published: December 2003

The usefulness of marker assisted selection (MAS) to improve diastatic power was demonstrated by selecting quantitative trait loci (QTLs) and structural gene alleles involved in enhanced diastatic power and activity of its component hydrolytic enzymes from Alexis, Amagi Nijo, Harrington, Haruna Nijo, and Sloop. Six unmapped breeders' populations involving these donor sources of malting quality were used for MAS. For each population, individual lines were pooled into classes separated on the basis of either the presence or absence of malting quality parent marker alleles at each of 9 identified loci (QTLs or structural genes). Diastatic power, β-amylase, and α-amylase activities were determined for each line, and used to compare alternative marker allele class means. Lines carrying malting parent marker alleles at a chromosome 5H locus abg463 were associated with 21–44% higher α-amylase activity levels, depending on the cross. The malting parent alleles at the chromosome 4H Bmy1 locus were associated with increased diastatic power and β-amylase activity. A simple PCR marker detecting the Bmy1 locus was found to be effective in screening for improved diastatic power, β-amylase activity, and thermostability. Lines carrying malting parent alleles at the chromosome 2H Bmy2 locus produced differences in diastatic power and β-amylase activity that, after adjusting for the correlated effect of malt protein, became non-significant. The Alexis allele of the chromosome 1H EBmac501 locus was associated with significant differences in all traits for a population carrying this source. The implication of these results to the improvement of diastatic power through MAS is discussed.
The determinants and genome locations influencing grain weight and size in barley (Hordeum vulgare L.)
Authors: Coventry S. J. , Barr A. R. , Eglinton J. K. , McDonald G. K.
Published: December 2003

Grain weight and size are traits important to malting and feed barley. Understanding the determinants of grain weight and size, especially under stressful growing environments, will aid breeding efforts to improve these traits. The determinants of grain weight and size are discussed in relation to the pre- and post-anthesis periods of barley development. Genetic mapping of the loci influencing grain weight and size has provided a fundamental understanding of these traits, and a summary of mapped quantitative trait loci (QTLs) from Australian and international mapping populations is presented. The influence of developmental loci on grain weight and size QTLs, approaches to discovering non-developmentally related loci, and prospects for a marker assisted selection approach to improving grain weight and size are discussed.
Barley malting quality: are we selecting the best?
Authors: Cullis B. R. , Smith A. B. , Panozzo J. F. , Lim P.
Published: December 2003

This paper presents an analysis of several key barley malting traits from 2 mapping populations grown as a series of multi-environment field trials. The analysis is based on a mixed model that includes terms for all sources of variation in the trait data, namely varieties, variety by trial interaction, variation between plots in the field, and variation between samples in the laboratory processes required to measure the traits. The base-line model is extended to accommodate variance heterogeneity and correlated effects for many of the terms in the model. The results show that accounting for these phenomena may cause substantial changes in variety rankings. The methods of design and analysis proposed in this paper for barley quality trait data do not have common usage so if adopted in future there is an opportunity for substantial improvements in response to selection.
Mapping and validation of chromosome regions associated with high malt extract in barley (Hordeum vulgare L.)
Authors: Collins H. M. , Panozzo J. F. , Logue S. J. , Jefferies S. P. , Barr A. R.
Published: December 2003

Malt extract represents the soluble material extracted from malt during the mashing process of barley. The measurement of malt extract is used by maltsters and brewers to assess the quality of the barley they are purchasing and is therefore one of the most important parameters used by breeders to assess the quality of new barley varieties before release. This paper identifies and investigates several regions (quantitative trait loci, QTLs) found to be associated with malt extract and discusses the uses of these regions for marker assisted selection (MAS).Eight regions of the barley genome were found to be associated with malt extract in 3 mapping populations. Five regions were found in the Sloop/Alexis and Sloop-sib/Alexis mapping populations on chromosomes 1H, 2H, 3H, 4H, and 5H. Two regions were found in the Chebec/Harrington population on chromosomes 1H and 5H and a single region was found on chromosome 2H in the Galleon/Haruna Nijo mapping population. Markers from 6 of these regions were investigated using several breeding populations with a high malt extract variety as a parent. The 'allele' from the high malt extract parent was found to be associated with a significant increase in malt extract in 4 regions, 2 regions on chromosome 2H and 2 regions on chromosome 5H.
Mapping and QTL analysis of the barley population Mundah × Keel
Authors: Long N. R. , Jefferies S. P. , Warner P. , Karakousis A. , Kretschmer J. M. , Hunt C. , Lim P. , Eckermann P. J. , Barr A. R.
Published: December 2003

The barley mapping population Mundah × Keel was devised to characterise and map chromosome regions associated with improved growth and grain yield on sandy soils of low fertility. A low level of polymorphism between the parents proved problematic for the construction of a detailed linkage map of this population. Despite this, significant quantitative trait loci (QTLs) for specific traits were detected, providing an insight into the probable chromosome regions associated with sand adaptation. In addition, this population is being employed to identify loci associated with the expression of traits for moisture stress and frost tolerance, and resistance to spot form of net blotch and leaf scald.
A major QTL controlling seed dormancy and pre-harvest sprouting/grain α-amylase in two-rowed barley (Hordeum vulgare L.)
Authors: Li C. D. , Tarr A. , Lance R. C. M. , Harasymow S. , Uhlmann J. , Westcot S. , Young K. J. , Grime C. R. , Cakir M. , Broughton S. , Appels R.
Published: December 2003

Barley seed dormancy is controlled by multiple genes that have a strong interaction with the environment. Lack of adequate dormancy results in pre-harvest sprouting in the field under wet weather conditions. On the other hand, too much dormancy has a detrimental effect in the malting house. There is only a very 'narrow window' of dormancy for malting barley. Harrington barley, which has been a dominant malting variety in the international market and widely used in Australia barley breeding programs, is highly susceptible to pre-harvest sprouting. A doubled haploid (DH) population derived from a cross of Chebec/Harrington was used to search for molecular markers linked with seed dormancy and pre-harvest sprouting. One major quantitative trait locus (QTL) was identified to control pre-harvest sprouting measured by α-amylase activity in barley grains, and could explain >70% of the phenotypic variation. This QTL was located on chromosome 5HL and flanked by restriction fragment length polymorphism (RFLP) marker CDO506 and simple sequence repeat (SSR) marker GMS1. The SSR marker (GMS1) linked with this QTL was further validated in a Stirling/Harrington DH population. A minor QTL on chromosome 2H accounted for 8% of phenotypic variation. Two QTLs for seed dormancy were located on chromosomes 2H and 5HL. The major QTL for dormancy coincided with the QTL for pre-harvest sprouting at chromosome 5HL and explained 61% of phenotypic variation. Since the presence of the Harrington allele at this locus favoured not only pre-harvest sprouting, but also increased malting extract, diastatic power, α-amylase, and free amino acid nitrogen, development of high malting quality varieties with pre-harvest sprouting tolerance would appear to be difficult.
Mapping and QTL analysis of the barley population Chebec × Harrington
Authors: Barr A. R. , Karakousis A. , Lance R. C. M. , Logue S. J. , Manning S. , Chalmers K. J. , Kretschmer J. M. , Boyd W. J. R. , Collins H. M. , Roumeliotis S. , Coventry S. J. , Moody D. B. , Read B. J. , Poulsen D. , Li C. D. , Platz G. J. , Inkerman P. A. , Panozzo J. F. , Cullis B. R. , Smith A. B. , Lim P. , Langridge P.
Published: December 2003

A doubled haploid population of 120 individuals was produced from the parents Chebec, an Australian 2-row barley of feed quality with resistance to the cereal cyst nematode, and Harrington, a 2-rowed, Canadian variety of premium malting quality. This paper describes 18 field and laboratory experiments conducted with the population and summarises the traits mapped and analysed. The genomic location of 25 traits and genes is described and marker–trait associations for 5 traits (malt extract, diastatic power, resistance to cereal cyst nematode, early flowering, resistance to pre-harvest sprouting) important to Australian efforts to improve malting barley varieties have been used in practical breeding programs. Detailed maps for these populations are shown in this paper, while a consensus map incorporating these maps and further experiments on the populations are described elsewhere in this issue.
Mapping and QTL analysis of the barley population Amagi Nijo × WI2585
Authors: Pallotta M. A. , Asayama S. , Reinheimer J. M. , Davies P. A. , Barr A. R. , Jefferies S. P. , Chalmers K. J. , Lewis J. , Collins H. M. , Roumeliotis S. , Logue S. J. , Coventry S. J. , Lance R. C. M. , Karakousis A. , Lim P. , Verbyla A. P. , Eckermann P. J.
Published: December 2003

A map for the barley doubled haploid population Amagi Nijo × WI2585 was constructed to examine manganese efficiency derived from Amagi Nijo. Manganese efficiency conferred by the previously identified locus Mel1 was validated. No other loci contributing to manganese efficiency were identified, possibly because of poor maker coverage in some regions. The map was additionally used to look for loci contributing to some aspects of malting quality. A locus on 2HL was found to be associated with malt extract, and 2 loci on 4HL and 5H, respectively, were found to be associated with diastatic power.
The molecular genetics of disease resistance in barley
Authors: Williams K. J.
Published: December 2003

The molecular genetics of disease resistance of barley and its wild relatives is reviewed, and the implications of recent findings for resistance breeding and the potential for disease control using gene technologies are discussed. As a resource for barley researchers and breeders, a chromosome map and list of mapped resistance genes, their source, and associated molecular markers are presented, updated to ultimo 2002. Genetic mapping of major genes and quantitative trait loci for many major diseases is revealing a heterogeneous distribution of resistance loci on chromosomes, with more than half of mapped loci occurring in clusters. Relatively few resistance loci have been identified in the cultivated barley germplasm. Studies have shown that wild Hordeum species contain resistance genes for the major diseases, although their allelic relationship to previously mapped genes is unknown. The structure of genes involved in race-specific and race-non-specific barley powdery mildew resistance has been determined. Isolation of resistance genes for other major diseases is essential and may be accelerated via genomics techniques such as EST sequencing, subtractive hybridisation, or expression profiling. Current strategies for molecular manipulation of barley disease resistance are based on the over-expression of defence-related or disease-signalling genes from other species.
Application of SSR markers in the construction of Australian barley genetic maps
Authors: Ablett G. A. , Karakousis A. , Banbury L. , Cakir M. , Holton T. A. , Langridge P. , Henry R. J.
Published: December 2003

Simple sequence repeat (SSR) or microsatellite markers were examined for polymorphisms among the parents of 12 barley mapping populations. Of 259 SSRs screened, 149 were mapped on 1 or more of the 12 doubled haploid populations studied. The relative genetic positions of the 149 mapped SSR markers on Australian varieties are presented in the form of a consensus map. A database was created based on the results of screenings of barley varieties with a series of SSR markers. Details of the markers are at: http://www.scu.edu.au/research/ cpcg/Barley/index.php. A procedure is suggested for mapping new populations with microsatellites using this information and information available on other databases. These 12 populations have been mapped with SSR markers that act as 'anchors' for other types of genetic markers and for traits of interest. Some challenges in mapping SSRs were detailed. Multi-locus markers can cause confusion since one marker can map at different locations. Polymorphisms should be confirmed in new mapping varieties since some variation of allele size is seen in different sources of varieties of the same name, possibly due to differences in sources of germplasm. Lack of standardisation between laboratories or between analytical systems may also lead to differences in called allele sizes. SSRs proved to be adaptable to several technologies and economical, providing a preferred marker system for mapping new barley populations and to 'anchor' other types of markers.
Development and allele diversity of microsatellite markers linked to the aluminium tolerance gene Alp in barley
Authors: Raman H. , Karakousis A. , Moroni J. S. , Raman R. , Read B. J. , Garvin D. F. , Kochian L. V. , Sorrells M. E.
Published: December 2003

Aluminium (Al) toxicity is one of the main factors restricting barley production in acidic soils. The utilisation of barley cultivars tolerant to Al is one of the most economic strategies for expanding barley production in these soils. Among barley genotypes, the cultivar Dayton has been reported to exhibit the highest level of Al tolerance. The gene conferring Al tolerance in Dayton, Alp, has been mapped to the long arm of chromosome 4H using RFLP markers. However, such markers are not useful for routine marker-assisted selection in breeding programs due to the cost and labour associated with their use. To increase the ease by which marker-assisted selection can be conducted for Alp, we sought to identify microsatellite markers linked to this gene. Several such markers that flank Alp were identified in a mapping population from a cross between Dayton and Harlan Hybrid. The most tightly linked microsatellite markers, HVM68 and Bmag353, flank Alp and are 5.3 cM and 3.1 cM from this locus, respectively. The linkage between Bmag353 and Alp was validated in a separate F3 population derived from the cross between Dayton and F6ant28B48-16, where this microsatellite marker was found to predict the Al tolerance phenotype with over 95% accuracy. Allele diversity for the 3 most tightly linked microsatellite markers was evaluated among 40 barley genotypes currently used in Australian barley breeding programs. The high levels of polymorphism detected among the genotypes with the markers indicated that the microsatellite markers, especially Bmag353 and Bmac310, will be broadly useful for marker-assisted selection of Alp in breeding programs seeking to improve Al tolerance.
Mapping and validation of the genes for resistance to Pyrenophora teres f. teres in barley (Hordeum vulgare L.)
Authors: Cakir M. , Gupta S. , Platz G. J. , Ablett G. A. , Loughman R. , Emebiri L. C. , Poulsen D. , Li C. D. , Lance R. C. M. , Galwey N. W. , Jones M. G. K. , Appels R.
Published: December 2003

Identification and deployment of disease resistance genes are key objectives of Australian barley breeding programs. Two doubled haploid (DH) populations derived from Tallon × Kaputar (TK) and VB9524 × ND11231 (VN) crosses were used to identify markers for net type net blotch (NTNB) (Pyrenophora teres f. teres). The maps included 263 and 250 markers for TK and VN populations, respectively. The TK population was screened with 5 pathotypes and the VN population with 1 pathotype of NTNB as seedlings in the glasshouse. In addition, the TK population was subjected to natural infection in the field at Hermitage Research Station, Qld. Analyses of the markers were performed using the software packages MapManager and Qgene. One region on chromosome 6H was strongly associated with resistance to NTNB in both populations (R2 = 83% for TK and 66% for VN). In the TK population, 2 more quantitative trait loci (QTLs) were identified on chromosomes 2H and 3H, with R2 values of 30% and 31%, respectively. These associations were consistent over all pathotypes studied during the seedling stage. The same QTL on chromosome 6H was also found to be highly significantly associated (R2 = 65%) with the adult plant (field) response in the TK population. There are several very closely linked markers showing strong associations in these regions. Association of the 4 markers on chromosome 6H QTL with resistance to the NTNB has been validated in 2 other DH populations derived from barley crosses Pompadour × Stirling and WPG8412 × Stirling. These markers present an opportunity for marker assisted selection of lines resistant to NTNB in barley breeding programs.
Leaf scald resistance genes in Hordeum vulgare and Hordeum vulgare ssp. spontaneum: parallels between cultivated and wild barley
Authors: Genger R. K. , Williams K. J. , Raman H. , Read B. J. , Wallwork H. , Burdon J. J. , Brown A. H. D.
Published: December 2003

The prerequisite for breeding barley varieties with durable scald resistance is a diversity of genes each with molecular markers for their manipulation in crosses. Here we compare the outcomes of genetic analysis of scald resistance in 5 doubled haploid mapping populations of cultivated barley with 9 third-backcross families that derive from a set of diverse wild barley populations. In all cases, resistance was assessed as seedling infection type responses, but the Sloop/Halcyon population was also tested for adult plant resistance in field trials at two sites. In the latter case, the major quantitative trait locus for field resistance was coincident with that for seedling response on chromosome 3H. Most of the other cultivated barley sources of resistance in this study (1 cultivar and 3 breeders populations synthesised for resistance) also resolved to markers in the region of this 3H locus. In contrast, the genetic basis of resistance in wild barley populations resolved to at least 5 chromosome locations (1HS, 3H, 6HS, 7HL, and 7HS). Useful markers were of several kinds including proteins, isozymes, PCR based on RFLPs, AFLP, and SSR loci. Thus, wild barley increases the range of options for pyramid breeding and provides linked molecular markers that will be useful in manipulating those genes, or in the analysis of resistance in new sources.
Molecular mapping as a tool for pre-emptive breeding for resistance to the exotic barley pathogen, Puccinia striiformis f. sp. hordei
Authors: Cakir M. , Spackman M. , Wellings C. R. , Galwey N. W. , Moody D. B. , Poulsen D. , Ogbonnaya F. C. , Vivar H.
Published: December 2003

Barley stripe rust (BSR), caused by Puccinia striiformis f. sp. hordei, has been a major disease problem to the barley industry worldwide that has not, to date, been detected in Australia. This paper describes the mapping of stripe rust resistance genes in Tallon/Kaputar (TK) and Arapiles/Franklin (AF) populations. The paper also reports on the usefulness of markers associated with alternative sources of resistance previously identified in the varieties Orca and Shyri in the USA. Stripe rust screening was conducted at the adult plant stage in Toluca, Mexico, for 2 years. Two major quantitative trait loci (QTLs) were found on chromosomes 2H and 5H in both populations. One region on chromosome 5H was highly significantly associated with resistance to stripe rust (R2 = 68% and 34% in TK and AF, respectively). The QTL on chromosome 2H accounted for 36% of the variation in TK and 10% of the variation in the AF population. These associations were consistent over both years. Further work will involve screening for additional markers in the target regions to identify polymorphism that can be used to select for multiple resistances in the absence of the pathogen.
Molecular basis of barley quality
Authors: Fox G. P. , Panozzo J. F. , Li C. D. , Lance R. C. M. , Inkerman P. A. , Henry R. J.
Published: December 2003

The quality of barley for the range of end uses from animal feed to brewing is determined by many genes, making the breeding of new barley varieties difficult. Understanding of the molecular basis of barley quality has been advanced by biochemical studies. More recently, molecular genetic tools are allowing the analysis of the biochemical factors contributing to grain quality. Many genetic loci influencing key quality attributes have been identified by gene mapping. Limited success has been reported in using this information to select for quantitative trait loci for these quality traits in plant breeding. Genomic techniques allowing more detailed analysis of variations in the barley genome in relation to quality promise to extend significantly the value of molecular genetic approaches to barley quality improvement. Definition of the genetic basis of malting quality requires the identification of the genes involved in germination and endosperm modification. Feed quality remains difficult to define. Recent advances are likely to accelerate the rate of discovery, providing new options for analysis of barley quality.
Mapping and QTL analysis of the barley population Tallon × Kaputar
Authors: Cakir M. , Poulsen D. , Galwey N. W. , Ablett G. A. , Chalmers K. J. , Platz G. J. , Park R. F. , Lance R. C. M. , Panozzo J. F. , Read B. J. , Moody D. B. , Barr A. R. , Johnston P. , Li C. D. , Boyd W. J. R. , Grime C. R. , Appels R. , Jones M. G. K. , Langridge P.
Published: December 2003

A genetic map of barley with 224 AFLP and 39 simple sequence repeat (SSR) markers was constructed using a doubled haploid (DH) mapping population from a cross between the varieties Tallon and Kaputar. Linkage groups were assigned to individual barley chromosomes using the published map locations of the SSR markers as reference points. This genetic map was used to identify markers with linkage to agronomic, disease, and quality traits in barley. The population, which comprised 65 lines, was tested in a range of environments across Australia. Quantitative trait loci (QTLs) analyses were performed using software packages MapMaker, MapManager, and Qgene. Significant associations with markers were found for several traits. Grain yield showed significant association with regions on chromosomes 2H, 3H, and 5H over a range of sites throughout Australia. Regions on chromosomes 2H and 3H explained 30% and 26% of variation in lodging, respectively. Among quality traits, diastatic power was associated with regions on chromosomes 1H, 2H, and 5H (R2 = 37%). Hot water extract was associated with a region on chromosome 6H and a marker not assigned to a chromosome (R2 = 45%). There were also environment-specific QTLs for the traits analysed. The markers identified here present an opportunity for marker assisted selection of lines for these traits in barley breeding programs.Mapping and QTL analysis of Tallon × Kaputar
The analysis of quantitative trait loci in multi-environment trials using a multiplicative mixed model
Authors: Verbyla A. P. , Eckermann P. J. , Thompson R. , Cullis B. R.
Published: December 2003

A new approach for multi-environment quantitative trait locus (QTL) analysis based on an appropriate genetic model is presented. To accommodate a multi-environment analysis, the size of a QTL effect is assumed to be a random effect. The approach results in a multiplicative mixed model for QTL × environment interaction of the factor analytic type. The full genetic model may also include a factor analytic model for the residual genotype × environment interaction, whereas the environmental model for the non-genetic variation involves local, global, and extraneous variation. The approach is used to determine QTLs for yield in the Arapiles × Franklin doubled haploid population of the National Barley Molecular Marker Program. Analysis leads to the determination of 8 QTLs. Many of these QTLs are associated with other traits.
Mapping genes for resistance to Puccinia hordei in barley
Authors: Park R. F. , Poulsen D. , Barr A. R. , Cakir M. , Moody D. B. , Raman H. , Read B. J.
Published: December 2003

Six doubled haploid barley populations (Alexis × Sloop, Chebec × Harrington, Arapiles × Franklin, Patty × Tallon, Tallon × Kaputar, and Sloop × Halcyon) and a recombinant inbred population (WI2875-1 × Alexis) were assessed for response to selected pathotypes of the barley leaf rust pathogen, Puccinia hordei, at the seedling growth stage. Resistance genes were postulated for the parents of each population based on their reaction to selected pathotypes. In most cases, the resistance genes postulated in the cultivars were validated by QTL mapping analyses of the progeny populations. The resistance genes detected and mapped were Rph2, Rph3, Rph4, Rph12, and Rph19. The chromosomal locations of these 5 genes were consistent with previous reports, with Rph2 mapping near to the centromere on the short arm of chromosome 5H, Rph4 mapping to chromosome 1H, Rph12 mapping to the long arm of chromosome 5H, and Rph3 and Rph19 mapping ~30 cM apart on the long arm of chromosome 7H.
Quantitative trait loci controlling kernel discoloration in barley (Hordeum vulgare L.)
Authors: Li C. D. , Lance R. C. M. , Collins H. M. , Tarr A. , Roumeliotis S. , Harasymow S. , Cakir M. , Fox G. P. , Grime C. R. , Broughton S. , Young K. J. , Raman H. , Barr A. R. , Moody D. B. , Read B. J.
Published: December 2003

Barley kernel discoloration (KD) leads to substantial annual loss in value through downgrading and discounting of malting barley. KD is a difficult trait to introgress into elite varieties as it is controlled by multiple genes and strongly influenced by environment and maturity. As the first step towards marker assisted selection for KD tolerance, we mapped quantitative trait loci (QTLs) controlling KD measured by grain brightness [Minolta L; (Min L)], redness (Min a), and yellowness (Min b) in 7 barley populations. One to 3 QTLs were detected for grain brightness in various populations, and one QTL could account for 5–31% of the phenotypic variation. The QTL located around the centromere region of chromosome 2H was consistently detected in 6 of the 7 populations, explaining up to 28% of the phenotypic variation. In addition, QTLs for grain brightness were most frequently identified on chromosomes 3H and 7H in various populations. Australian varieties Galleon, Chebec, and Sloop contribute an allele to increase grain brightness on chromosome 7H in 3 different populations. A major gene effect was detected for grain redness. One QTL on chromosome 4H explained 54% of the phenotypic variation in the Sloop/Halcyon population, and was associated with the blue aleurone trait. A second QTL was detected on the long arm of chromosome 2H in 3 populations, accounting for 23–47% of the phenotypic variation. The major QTLs for grain yellowness were mapped on chromosomes 2H and 5H. There were strong associations between the QTLs for heading date, grain brightness, and yellowness. The molecular markers linked with the major QTLs should be useful for marker assisted selection for KD.
Identification of QTLs associated with variations in grain protein concentration in two-row barley
Authors: Emebiri L. C. , Moody D. B. , Panozzo J. F. , Chalmers K. J. , Kretschmer J. M. , Ablett G. A.
Published: December 2003

Grain protein concentration (GPC) is arguably the most important factor when marketing malting barleys. Excessively high and excessively low GPC are both undesirable for malting and brewing. GPC variation is influenced to a high degree by the environment and exhibits relatively large genotype × environment interaction. Identification of molecular markers linked to genes influencing GPC would allow barley breeders to select for GPC independent of environmental effects. A genetic linkage map with 270 markers was constructed to identify the genetic basis for variation in GPC, using 180 doubled haploid lines from a cross of VB9524 and ND11231*12. The parental genotypes were chosen on the basis of their known low GPC phenotype and their lack of common ancestry. A combination of composite interval and multiple-trait quantitative trait locus (QTL) mapping approach allowed the identification of QTLs with specific impact on GPC, and those likely to depend on or be influenced by variations in grain yield and heading date. The study identified a major QTL with a 'stable' and specific effect on GPC and located near the centromeric region of chromosome 5H. The QTL accounted for ~21% of the phenotypic variation in this trait. The allele for reduced GPC at this region was inherited from the ND11231*12 parent, with additive effect of ~1% in GPC. Additional QTLs with minor effects (5–10% explained variation) were also detected on chromosome 2H, 4H, and 7H. The parent VB9524 was the source of the low GPC alleles at these regions.
Conventional and molecular genetic analysis of factors contributing to variation in the timing of heading among spring barley (Hordeum vulgare L.) genotypes grown over a mild winter growing season
Authors: Boyd W. J. R. , Li C. D. , Grime C. R. , Cakir M. , Potipibool S. , Kaveeta L. , Men S. , Kamali M. R. Jalal , Barr A. R. , Moody D. B. , Lance R. C. M. , Logue S. J. , Raman H. , Read B. J.
Published: December 2003

Factors contributing to variation in heading date in spring barley were examined in several studies commencing with a survey of developmental variation in a large collection of genotypes and concluding with the molecular genetic analysis of 7 doubled haploid populations. Genotypes varied considerably in their specific responses to photoperiod and vernalisation, and in the duration of a pre-inductive (or juvenile) phase defined in this paper as a 'basic vegetative period'. The latter includes differential genotype responses to ambient temperature and their interaction with photoperiod. Combinations of these largely independent environmental variables account for variation in heading date associated with differences in growing season conditions, particularly geographic region, sowing dates, and cultivar adaptation. Under extended and natural (short) photoperiods, in both summer and winter field plantings, conventional genetic analysis was characterised by simple Mendelian segregation combined with considerable transgressive segregation within distinct early and late flowering subpopulations. Equivalent transgressive segregation characterised molecular genetic analysis that identified 16 quantitative trait loci (QTLs) with contributions ranging from >50% of the variation recorded to <10%. These were dominated by 2 QTLs located on chromosome 2, one of which on 2HS was associated with response to extended photoperiod and the other, located near the centromere, with variation in the duration of the basic vegetative period. As only one population segregated for response to vernalisation, all analyses were restricted to parents and progeny homozygous for no response. Three other QTLs on 1HL, 3HL, and 5HL were primarily associated with vernalised parents and progeny characterised by prostrate seedling growth habits, which questions any assumption of a pleiotrophic association between genes for vernalisation and growth habit.The potential for exploiting markers for selection is considered to be limited by the considerable transgressive segregation observed in lines homozygous for parental alleles, and the limited understanding of the causes of variation in the phenotypic expression of the QTLs identified. Such markers would be useful in the selection of backcrossed progeny and in developing materials for investigating fundamental mechanisms contributing to developmental variation.
Resistance in cultivated barleys to Pyrenophora teres f. teres and prospects of its utilisation in marker identification and breeding
Authors: Gupta S. , Loughman R. , Platz G. J. , Lance R. C. M.
Published: December 2003

Net type net blotch (NTNB) is a prevalent disease in Australia, causing significant losses in barley yield and quality. Its impact can be reduced with the identification and utilisation of effective sources of resistance. Sixty-nine cultivated barley lines were screened as seedlings against 9 isolates of Pyrenophora teres f. teres from Australia, and in the field in Western Australia. Resistance expressed in seedlings was frequently expressed in adult plants in the field, indicating that these sources are potentially useful for resistance breeding. Of these lines, 24 with the best overall resistance were identified, which could be used against virulence diversity present in P. teres f. teres in Australia.As a prelude to the evaluation of established mapping populations in the Australian Barley Molecular Marker Program, 42 parental lines were screened against a range of Australian isolates of P. teres f. teres. Variation in net blotch responses was observed among parents of the mapping populations. Ten principal mapping populations appear to provide opportunities to map resistances and identify molecular markers linked to NTNB resistance genes effective against Australian pathotypes.
Mapping of genomic regions associated with net form of netblotch resistance in barley
Authors: Raman H. , Platz G. J. , Chalmers K. J. , Raman R. , Read B. J. , Barr A. R. , Moody D. B.
Published: December 2003

Quantitative trait loci (QTLs) associated with resistance to net blotch and their chromosomal locations were determined from analyses of doubled haploid progeny of Alexis/Sloop, Arapiles/Franklin, Sloop/Halcyon, and recombinant inbred lines of Sloop-sib/Alexis. Five QTLs on chromosomes 2H, 3H, and 4H were found to be associated with seedling resistance to the net form of net blotch. In Arapiles/Franklin and Alexis/Sloop populations, 4 significant QTLs explaining 9–17% of the variation in net blotch resistance were detected on 2H and 3H. A major locus, QRpts4L accounting for 64% of the variation in infection type, was detected on 4H in the Sloop/Halcyon population. In Sloop/Halcyon, 2 microsatellite markers, EBmac0906 and GMS089, and AFLP marker P13/M50-108, co-segregated and detected maximum variability for net blotch resistance as revealed by bootstrap analysis. EBmac0906 and Bmac0181 were validated in F2 progeny of an Ant29/Halcyon population and reliably predicted phenotypes of 93% of lines resistant and susceptible to net blotch. These markers may be used within breeding programs to select alleles favourable for net blotch resistance derived from Halcyon.
A comparison of the genetics of seedling and adult plant resistance to the spot form of net blotch (Pyrenophora teres f. maculata)
Authors: Williams K. J. , Platz G. J. , Barr A. R. , Cheong J. , Willsmore K. , Cakir M. , Wallwork H.
Published: December 2003

Spot form of net blotch (SFNB) (Pyrenophora teres f. maculata) is an economically damaging foliar disease of barley in many of the world's cereal-growing areas. The gene Rpt4 that confers seedling resistance to SFNB has been mapped on the long arm of chromosome 7H, but no genes for adult plant resistance (APR) have been identified. A lack of field resistance to SFNB in breeders' lines selected for Rpt4 led us to investigate the genetics of APR to this disease. Five doubled-haploid populations were phenotyped for seedling and adult plant reaction. Markers linked to Rpt4 explained a large part of the seedling variation, but little of the APR. In 2 mapped populations, major quantitative trait loci (QTLs) for APR distal to Rpt4 on chromosome 7H were identified. QTLs contributing to APR on chromosomes 4H or 5H were also identified in each population. Association of the 5H QTL with a gene for cereal cyst nematode resistance and the probable effect of this linkage on the historical development of cultivars with adult plant resistance to SFNB is discussed.
Mapping and QTL analysis of the barley population Sloop × Halcyon
Authors: Read B. J. , Raman H. , McMichael G. , Chalmers K. J. , Ablett G. A. , Platz G. J. , Raman R. , Genger R. K. , Boyd W. J. R. , Li C. D. , Grime C. R. , Park R. F. , Wallwork H. , Prangnell R. , Lance R. C. M.
Published: December 2003

A genetic linkage map of Hordeum vulgare L. 1280 cM in length, composed of 257 AFLP, RFLP, SNP, and microsatellite markers, has been constructed. The map was based on a doubled haploid population made from the cross Sloop (spring type) × Halcyon (winter type). The genetic map was used to identify qualitative major genes and quantitative trait loci (QTLs) affecting traits related to growth and flowering, grain colour, and disease resistance. Nine QTLs associated with grain colour (brightness, redness, yellowness, blue aleurone colour), plant height, 'intrinsic lateness', awn emergence, response to photoperiod, and spring or winter habit were located on 1H, 2H, 3H, 4H, and 5H. Eight QTLs associated with resistance to scald, net form of net blotch, leaf rust and powdery mildew were identified on chromosomes 1H, 2H, 3H, 4H, 5H, and 7H. The estimated magnitude of the QTL effects ranged from 9 to 85% of the total phenotypic variance. Resistances to leaf scald, net blotch, and leaf rust, and photoperiod and grain colour, were each controlled by at least one major gene.
Cutaneous Immunization Rapidly Activates Liver Invariant Vα14 NKT Cells Stimulating B-1 B Cells to Initiate T Cell Recruitment for Elicitation of Contact Sensitivity
Authors: Campos Regis A. , Szczepanik Marian , Itakura Atsuko , Akahira-Azuma Moe , Sidobre Stephane , Kronenberg Mitchell , Askenase Philip W.
Published: December 2003

T cell recruitment to elicit contact sensitivity (CS) requires a CS-initiating process mediated by B-1 cells that produce IgM, which activates complement to promote T cell passage into the tissues. We now show that Vα14i NKT cells induce B-1 cell activation likely by releasing IL-4 early postimmunization. The CS initiation process is absent in Jα18−/− and CD1d−/− NKT cell–deficient mice and is reconstituted by populations enriched for Vα14i NKT cells. Transfers are not effective if cells are derived from IL-4−/− mice. Staining with specific tetramers directly showed that hepatic Vα14i NKT cells increase by 30 min and nearly double by 2 h postimmunization. Transfer of immune B-1 cells also reconstitutes CS responses in NKT cell–deficient mice. The B-1 cells act downstream of the Vα14i NKT cells to restore CS initiation. In addition, IL-4 given systemically to Jα18−/− or CD1d−/− NKT cell–deficient mice reconstitutes elicitation of CS. Further, splenocytes from immune Jα18−/− mice produce less antigen (Ag)-specific IgM antibodies compared with sensitized WT mice. Together these findings indicate that very early after skin immunization Vα14i NKT cells are stimulated to produce IL-4, which activates B-1 cells to produce Ag-specific IgM, subsequently needed to recruit effector T cells for elicitation of CS responses.