DETECTION OF WHEAT FUNGAL PATHOGENS USING THE POLYMERASE CHAIN REACTION

Abstract: Internal Transcribed Spacer (ITS) DNA sequences from the ribosomal RNA gene region are described for different species and strains of wheat fungal pathogens, including Fusarium spp. and Microdochium nivale. Specific primers from within these sequences are identified as being useful for the identification of the fungal isolates using PCR-based techniques.

Description: DETECTION OF WHEAT FUNGAL PATHOGENS USING THE POLYMERASE CHAIN REACTION The present invention relates to the use of species-specific primers in polymerase chain reaction assays for the detection of fungal pathogens of wheat. The use of these primers enables the detection of specific isolates of fungal pathogens and the monitoring of disease development in plant populations. There is a real need for the development of technology that will allow the identification of specific races of pathogen fungi early in the infection process. By identifying the specific race of a pathogen before disease symptoms become evident in the crop stand, the agriculturist can assess the likely effects of further development of the pathogen in the crop variety in which it has been identified and can choose an appropriate fungicide if such application is deemed necessary. The present invention is drawn to methods of identification of different pathotypes of plant pathogenic fungi. The invention provides Internal Transcribed Spacer (ITS) DNA sequences that show variability between different fungal pathotypes. Such DNA sequences are useful in the method of the invention as they can be used to derive primers for use in polymerase chain reaction (PCR)-based diagnostic assays. These primers generate unique fragments in PCR reactions in which the DNA template is provided by specific fungal pathotypes and can thus be used to identify the presence or absence of specific pathotypes in host plant material before the onset of disease symptoms. In a preferred embodiment, the invention provides ITS1 and ITS2 DNA sequences for the pathogens Fusarium poae, Fusarium avenaceum, and Microdochium nivale. In another preferred embodiment, the invention provides ITS-derived diagnostic primers for the detection of Fusarium spp. and Microdochium nivale. This invention provides the possibility of assessing potential damage in a specific crop variety-pathogen strain relationship and of utilizing judiciously the diverse armory of fungicides that is available. Furthermore, the invention can be used to provide detailed information on the development and spread of specific pathogen races over extended geographical areas. The invention provides a method of detection that is especially suitable for diseases with a long latent phase. Kits useful in the practice of the invention are also provided. The kits find particular use in the identification of the fungal pathogens Fusarium spp. and Microdochium nivale. The present invention provides unique DNA sequences that are useful in identifying different pathotypes of plant pathogenic fungi. Particularly, the DNA sequences can be used as primers in PCR-based analysis for the identification of fungal pathotypes. The DNA sequences of the invention include the Internal Transcribed Spacer (ITS) sequences of the ribosomal RNA gene regions of particular fungal pathogens as well as primers derived from these regions that are capable of identifying the particular pathogen. These ITS DNA sequences from different pathotypes within a pathogen species or genus, which vary between the different members of the species or genus, can be used to identify those specific members. Biomedical researchers have used PCR-based techniques for some time and with moderate success to detect pathogens in infected animal tissues. Only recently, however, has this technique been applied to detect plant pathogens. The presence of Gaumannomyces graminis in infected wheat has been detected using PCR of sequences specific to the pathogen mitochondrial genome (Schlesser et al., 1991 ; Applied and Environ. Microbiol. 57: 553-556), and random amplified polymorphic DNA (i.e. RAPD) markers were able to distinguish numerous races of Gremmeniella abietina, the causal agent of scleroderris canker in conifers. U.S. Patent No. 5,585,238 (herein incorporated by reference in its entirety) describes primers derived from the ITS sequences of the ribosomal RNA gene region of strains of Septoria, Pseudocercosporella, and Mycosphaerella and their use in the identification of these fungal isolates using PCR-based techniques. In addition, WO 95/29260 (herein incorporated by reference in its entirety) describes primers derived from the ITS sequences of the ribosomal RNA gene region of strains of Fusarium and their use in the identification of these fungal isolates using PCR-based techniques. Furthermore, European Patent Application No. 97810779.5 (herein incorporated by reference in its entirety) describes primers derived from the ITS sequences of the ribosomal RNA gene region of strains of Cercospora, Helminthosporium, Kabatiella, and Puccinia and their use in the identification of these fungal isolates using PCR-based techniques. Ribosomal genes are suitable for use as molecular probe targets because of their high copy number. Despite the high conservation between mature rRNA sequences, the non-transcribed and transcribed spacer sequences are usually poorly conserved and are thus suitable as target sequences for the detection of recent evolutionary divergence. Fungal rRNA genes are organized in units, each of which encodes three mature subunits of 18S (small subunit), 5.8S, and 28S (large subunit). These subunits are separated by two Internal Transcribed Spacers, ITS1 and ITS2, of around 300 bp (White et al., 1990; In: PCR Protocols; Eds.: Innes et al.; pages 315-322). In addition, the transcriptional units are separated by non-transcribed spacer sequences (NTSs). The ITS and NTS sequences are particularly suitable for the detection of specific pathotypes of different fungal pathogens. The DNA sequences of the invention are from the Internal Transcribed Spacer sequences of the ribosomal RNA gene region of different plant pathogens. The ITS DNA sequences from different pathotypes within a pathogen species or genus vary among the different members of the species or genus. Once having determined the ITS sequences of a pathogen, these sequences can be aligned with other ITS sequences. In this manner, primers can be derived from the ITS sequences. That is, primers can be designed based on regions within the ITS sequences that contain the greatest differences in sequence among the fungal pathotypes. These sequences and primers based on these sequences can be used to identify specific pathogens. Particular DNA sequences of interest include ITS DNA sequences from Fusarium poae, Microdochium nivale, and Fusarium avenaceum. Such ITS DNA sequences are disclosed in SEQ ID NOs: 22-24, respectively. Sequences of representative oligonucleotide primers derived from these ITS sequences are disclosed in SEQ ID NOs: 7-18. The sequences find use in the PCR-based identification of the pathotypes of interest. Encompassed by the present invention are isolated DNA molecules comprising an Internal Transcribed Spacer sequence selected from ITS1 of Fusarium poae, ITS2 of Fusarium poae, ITS1 of Microdochium nivale, ITS2 of Microdochium nivale, ITS1 of Fusarium avenaceum, and ITS2 of Fusarium avenaceum. More preferred are isolated DNA molecules wherein ITS1 of Fusarium poae comprises nucleotides 31-180 of SEQ ID NO:22, wherein ITS2 of Fusarium poae comprises nucleotides 338-489 of SEQ ID NO:22, wherein ITS1 of Microdochium nivale comprises nucleotides 31-175 of SEQ ID NO:23, wherein ITS2 of Microdochium nivale comprises nucleotides 333-499 of SEQ ID NO:23, wherein ITS1 of Fusarium avenaceum comprises nucleotides 31-181 of SEQ ID NO:24, and wherein ITS2 of Fusarium avenaceum comprises nucleotides 339-504 of SEQ ID NO:24. Methods for the use of the primer sequences of the invention in PCR analysis are well known in the art. For example, see U.S. Patent Nos. 4,683,195 and 4,683,202, as well as Schlesser et al. (1991 ) Applied and Environ. Microbiol. 57:553-556. See also, Nazar et al. (1991 ; Physiol. and Molec. Plant Pathol. 39: 1-11), which used PCR amplification to exploit differences in the ITS regions of Verticillium albo-atrum and Verticillium dahliae and therefore distinguish between the two species; and Johanson and Jeger (1993; Mycol. Res. 97: 670-674), who used similar techniques to distinguish the banana pathogens Mycosphaerella fijiensis and Mycospharella musicola. The ITS DNA sequences of the invention can be cloned from fungal pathogens by methods known in the art. In general, the methods for the isolation of DNA from fungal isolates are known. See, Raeder & Broda (1985) Letters in Applied Microbiology 2:17 '-20; Lee etal. (1990) Fungal Genetics Newsletter 35:23-24; and Lee and Taylor (1990) In: PCR Protocols: A Guide to Methods and Applications, Innes etal. (Eds.); pages 282-287. Alternatively, the ITS sequences of interest can be determined by PCR amplification. In an exemplified embodiment, primers to amplify the entire ITS region were designed according to White etal. (1990; In: PCR Protocols; Eds.: Innes et al. pages 315-322), and the amplified ITS sequence was subcloned into the pCRII cloning vector. The subcloned sequence included the left hand ITS (ITS1), the right hand ITS (ITS2), as well as the centrally located 5.8S rRNA gene. This was undertaken for several species of Fusarium, including Fusarium poae and Fusarium avenaceum, as well as Microdochium nivale. The determined ITS sequences were compared within each pathogen group to locate divergences that might be useful to test in PCR to distinguish the different species and/or strains. The ITS DNA sequences that were determined are shown in SEQ ID NOs: 19-24 and the comparative alignment is shown in FIGURE 1. From the identification of divergences, numerous primers were synthesized and tested in PCR-amplification. Templates used for PCR-amplification testing were firstly purified pathogen DNA, and subsequently DNA isolated from infected host plant tissue. Thus, it was possible to identify pairs of primers that were diagnostic, i.e. that identified one particular pathogen species or strain but not another species or strain of the same pathogen. Primers were also designed to regions highly conserved among the species to develop genus-specific primers as well as primers that will identify any of several fungal pathogens that cause a particular disease. For example, primers were developed to detect Fusarium caused by various fungal pathogens, including Fusarium spp. and Microdochium nivale. Preferred primer combinations are able to distinguish between the different species or strains in infected host tissue, i.e. host tissue that has previously been infected with a specific pathogen species or strain. This invention provides numerous primer combinations that fulfill this criterion for different Fusarium spp. and Microdochium nivale. The primers of the invention are designed based on sequence differences among the fungal ITS regions. A minimum of one base pair difference between sequences can permit design of a discriminatory primer. Primers designed to a specific fungal DNA's ITS region can be used in combination with a primer made to a conserved sequence region within the ribosomal DNA's coding region to amplify species-specific PCR fragments. In general, primers should have a theoretical melting temperature between about 60 to about 70 degree °C to achieve good sensitivity and should be void of significant secondary structure and 3' overlaps between primer combinations. Primers generally have sequence identity with at least about 5-10 contiguous nucleotide bases of ITS1 or ITS2, preferably with at least 10 contiguous nucleotide bases of ITS1 or ITS2. In preferred embodiments, primers are anywhere from approximately 5-30 nucleotide bases long. Preferred is within the scope of the invention is an oligonucleotide primer for use in identification of a fungal pathogen, wherein said oligonucleotide primer is selected from the group consisting of SEQ ID NO's:7-15. A further embodiment of the present invention is a pair of oligonucleotide primers for use in the amplification-based detection of a fungal Internal Transcribed Spacer DNA sequence, wherein at least one of said primers is the oligonucleotide primer according to the invention. Preferred is a pair of oligonucleotide primers, wherein said pair is selected from the oligonucleotide primers according to claim 8 to 12. The present invention relates to method for the detection of a fungal pathogen, comprising the steps of: (a) isolating DNA from a plant leaf infected with a pathogen; (b) subjecting said DNA to polymerase chain reaction amplification using at least one primer according to claim 4; and (c) detecting said fungal pathogen by visualizing the product or products of said polymerase chain reaction amplification. Preferred is said method for the detection of a fungal pathogen, wherein said fungal pathogen is selected from Fusarium poae and Microdochium nivale. Further encompassed by the present invention is a method for the detection of a fungal pathogen, comprising the steps of: (a) isolating DNA from a plant leaf infected with a pathogen; (b) amplifying a part of the Internal Transcribed Spacer sequence of said pathogen using said DNA as a template in a polymerase chain reaction with a pair of primers according to claim 5; and (c) detecting said fungal pathogen by visualizing the amplified part of the Internal Transcribed Spacer sequence. Preferred is said method for the detection of a fungal pathogen, wherein said fungal pathogen is selected from Fusarium poae and Microdochium nivale. The present invention lends itself readily to the preparation of "kits" containing the elements necessary to carry out the process. Such a kit may comprise a carrier being compartmentalized to receive in close confinement therein one or more container, such as tubes or vials. One of the containers may contain unlabeled or detectably labeled DNA primers. The labeled DNA primers may be present in lyophilized form or in an appropriate buffer as necessary. One or more containers may contain one or more enzymes or reagents to be utilized in PCR reactions. These enzymes may be present by themselves or in admixtures, in lyophilized form or in appropriate buffers. Finally, the kit may contain all of the additional elements necessary to carry out the technique of the invention, such as buffers, extraction reagents, enzymes, pipettes, plates, nucleic acids, nucleoside triphosphates, filter paper, gel materials, transfer materials, autoradiography supplies, and the like. Preferred within the scops of the present invention is a diagnostic kit used in detecting a fungal pathogen, comprising the pair of primers for use in the amplification-based detection of a fungal Internal Transcribed Spacer DNA sequence, wherein at least one of said primers is the oligonucleotide primer accoding to the invention. The examples below show typical experimental protocols that can be used in the isolation of ITS sequences, the selection of suitable primer sequences, the testing of primers for selective and diagnostic efficacy, and the use of such primers for disease and fungal isolate detection. Such examples are provided by way of illustration and not by way of limitation. DESCRIPTION OF THE FIGURE FIGURE 1/3,2/3,3/3 Sequence Alignment of the ITS regions from Fusarium culmorum, Fusarium graminearum, Fusarium poae, Microdochium nivale, and Fusarium moniliforme. BRIEF DESCRIPTION OF THE SEQUENCES IN THE SEQUENCE LISTING SEQ ID NO:1 Oligonucleotide Primer ITS1. SEQ ID NO:2 Oligonucleotide Primer ITS2. SEQ ID NO:3 Oligonucleotide Primer ITS3. SEQ ID NO:4 Oligonucleotide Primer ITS4. SEQ ID NO:5 M13 Universal-20 Primer. SEQ ID NO:6 Reverse Primer used in Example 2. SEQ ID NO:7 Oligonucleotide Primer JB605. SEQ ID NO:8 Oligonucleotide Primer JB606. SEQ ID NO:9 Oligonucleotide Primer JB607. SEQ ID NO:10 Oligonucleotide Primer JB609. SEQ ID NO:11 Oligonucleotide Primer JB610. SEQ ID NO: 12 Oligonucleotide Primer JB611. SEQ ID NO:13 Oligonucleotide Primer JB612. SEQ ID NO:14 Oligonucleotide Primer JB613. SEQ ID NO:15 Oligonucleotide Primer JB614. SEQ ID NO:16 Oligonucleotide Primer JB578. SEQ ID NO:17 Oligonucleotide Primer JB571. SEQ ID NO: 18 Oligonucleotide Primer JB572. SEQ ID NO:19 Consensus DNA sequence of the ITS region PCR-amplified from Fusarium culmorum isolates R-5106, R-5126 and R-5146, comprising in the 5' to 3' direction: 3' end of the small subunit rRNA gene, Internal Transcribed Spacer 1 , 5.8S rRNA gene, Internal Transcribed Spacer 2, and 5' end of the large subunit rRNA gene. SEQ ID NO:20 Consensus DNA sequence of the ITS region PCR-amplified from Fusarium graminearum isolates R-8417, R-8422 and R-8546, comprising in the 5' to 3' direction: 3' end of the small subunit rRNA gene, Internal Transcribed Spacer 1 , 5.8S rRNA gene, Internal Transcribed Spacer 2, and 5' end of the large subunit rRNA gene. SEQ ID NO:21 DNA sequence of the ITS region PCR-amplified from Fusarium moniliforme isolate 4551 , comprising in the 5' to 3' direction: 3' end of the small subunit rRNA gene, Internal Transcribed Spacer 1 , 5.8S rRNA gene, Internal Transcribed Spacer 2, and 5' end of the large subunit rRNA gene. SEQ ID NO:22 Consensus DNA sequence of the ITS region PCR-amplified from Fusarium poae isolates T-427, T-534, and T-756, comprising in the 5' to 3' direction: 3' end of the small subunit rRNA gene, Internal Transcribed Spacer 1 , 5.8S rRNA gene, Internal Transcribed Spacer 2, and 5' end of the large subunit rRNA gene. SEQ ID NO:23 Consensus DNA sequence of the ITS region PCR-amplified from Microdochium nivale isolates 72, 520, and 18222, comprising in the 5' to 3' direction: 3' end of the small subunit rRNA gene, Internal Transcribed Spacer 1 , 5.8S rRNA gene, Internal Transcribed Spacer 2, and 5' end of the large subunit rRNA gene. SEQ ID NO:24 Consensus DNA sequence of the ITS region PCR-amplified from Fusarium avenaceum isolates 64452 and R-4045, comprising in the 5' to 3' direction: 3' end of the small subunit rRNA gene, Internal Transcribed Spacer 1 , 5.8S rRNA gene, Internal Transcribed Spacer 2, and 5' end of the large subunit rRNA gene. EXAMPLES Standard recombinant DNA and molecular cloning techniques used here are well known in the art and are described by J. Sambrook, E. F. Fritsch and T. Maniatis, Molecular Cloning: A Laboratory manual. Cold Spring Harbor laboratory, Cold Spring Harbor, NY (1989) and by T.J. Silhavy, M.L. Berman, and L.W. Enquist. Experiments with Gene Fusions, Cold Spring Harbor Laboratory, Cold Spring Harbor, NY (1984) and by Ausubel, F.M. et al., Current Protocols in Molecular Biology, pub. by Greene Publishing Assoc. and Wiley-lnterscience (1987). Example 1 : Fungal Isolates and Genomic Fungal DNA Extraction See Table 1 for a listing of the fungal isolates used and their source. Fungi are grown in 150 ml potato dextrose broth inoculated with mycelial fragments from PDA (Potato Dextrose Agar) cultures. Cultures are incubated on an orbital shaker at 28°C for 7-11 days. Mycelia are pelleted by centrifugation and then ground in liquid nitrogen, and total genomic DNA is extracted using the protocol of Lee and Taylor (1990; In: PCR Protocols: A Guide to Methods and Applications; Eds.: Innes et al.; pages 282-287). Table 1 : Source of Test Isolates ' Novartis Crop Protection Limited, Basel, Switzerland 2 American Type Culture Collection, Rockville, Maryland, USA Dr. Paul Nelson, Penn State University, USA 4 Dr. Loral Castor, Novatis Seeds Research, Bloomington, Illinois, USA 5 Dr. Peter Ueng, USDA, Beltsville, Maryland, USA novartis Crop Protection Inc., Research Triangle Park, NC, USA Example 2: Isolation of the Internal Transcribed Spacer (ITS) Regions Approximately 550-bp long internal transcribed spacer region fragments are PCR amplified from 10 ng of genomic DNA isolated from F. graminearum isolates R-8417, R- 8422 and R-8546, F. culmorum isolates R-5106, R-5126 and R-5146, F. moniliforme isolate #4551 , F. poae isolates T-0427, T-0534 and T-0756, M. nivale isolates 520, 72 and 18222, and F avenaceum isolates 64452 and R-4045 using 50 pmol of primers ITS1 (5' TCCGTAGGTGAACCTGCGG-3'; SEQ ID NO:1) and ITS4 (5'- TCCTCCGCTTATTGATATGC-3 ' ; SEQ ID NO:4). PCRs are performed as described in Example 4. PCR products are purified using Promega's Wizard DNA Clean-up kit (Madison, Wl). The DNA sequences of the ITS regions are determined by the dideoxy method using the Applied Biosystems (Foster City, CA) automated sequencer with the primers ITS1 (SEQ ID NO:1), ITS2 (5'-GCTGCGTTCTTCATCGATGC-3'; SEQ ID NO:2), ITS4 (SEQ ID NO:4) and the M13 universal -20 (5'-GTAAAACGACGGCCAGT-3'; SEQ ID NO:5) and Reverse (5'-AACAGCTATGACCATG-3'; SEQ ID NO:6) primers. The ITS primers ITS1 , ITS2, ITS3, and ITS4 are detailed in White etal. (1990; In: PCR Protocols; Eds.: Innes etal. pages 315-322). PCR products from amplifications with F. moniliforme isolate #4551 , F poae isolates T-0427, T-0534 and T-0756 and M. nivale isolates 520, 72 and 18222 are cloned using the Invitrogen Corporation's (San Diego, CA) TA Cloning Kit (part no. K2000-01) using the PCR2.1 cloning vector. Example 3: DNA Extraction from Wheat DNA is extracted from wheat using a bulk maceration method. The bulk maceration method is used to isolate DNA from several naturally infected wheat heads or stems from the field to optimize the field sampling method for high throughput analysis. Bulk Maceration Method: (1 ) Place the appropriate number of wheat heads or stems in a Bioreba (Reinach, Switzerland) heavy duty plastic bag (cat#490100). Weigh the plant tissue, plastic bag with leaves minus the tare (weight of the plastic bag). (2) Add an equal volume (ml) of Muller Extraction Buffer (0.1 % w/v Tween-80; 0.04 M Tris-CI, pH 7.7; 0.15 M NaCI; 0.1% w/v BSA-Pentex fraction V; 0.01% w/v sodium azide; 200 mM EDTA) per weight (g) of wheat tissue. Macerate the tissue using a Bioreba Homex 6 homogenizer set at 70. Grind the leaves until the tissue is fibrous. (3) Pool the extracts from multiple bags, if used, and vortex well. Aliquote the extraction juice into eppendorf tubes on ice. (a) Boil 100 μl of the concentrated extract for 5 minutes. (b) Place the boiled extract on ice. (c) Make a 1 :10 dilution by adding 10 μl from the boiled, concentrated extract to 90 μl of sterile dH 2 0. (d) Store the diluted extracts on ice until ready to use. Example 4: Polymerase Chain Reaction Amplification Polymerase chain reactions are performed with the GeneAmp Kit from Perkin- Elmer/Cetus (Norwalk, CT; part no. N808-0009) using 50 mM KCI, 2.5 mM MgCl2, 10 mM Tris-HCI, pH8.3, containing 200 μM of each dTTP, dATP, dCTP, and dGTP, 50 pmol each primer, 2.5 units of Taq polymerase and 10 ng of genomic DNA or 1 μl of 1 :10 diluted plant extract in a final volume of 50 μl. Reactions are run for 30 - 40 cycles of 15 s at 94°C, 15 s at 50°C - 70°C, and 45 s at 72°C in a Perkin-Elmer/Cetus Model 9600 thermal cycler. The products are analyzed by loading 10 μl of each PCR sample on a 1.0% agarose gel and electrophoresing. Example 5: Synthesis and Purification of Oligonucleotides Oligonucleotides (primers) are synthesized by, for example, either Integrated DNA Technologies (Coralville, IA) or Midland Certified Reagent Company (Midland, Texas). Example 6: Selection of Species-Specific Primers FIGURE 1 shows an alignment of the sequences of the ITS regions of F. culmorum, F. graminearum, F. poae, M. nivale, and F. moniliforme. Oligonucleotide primers such as those shown below in Table 2 are synthesized according to Example 5 based on analysis of the aligned sequences. Primers are designed to the regions that contain the greatest differences in sequence among the fungal species. Primers are also designed to regions highly conserved among the species in attempt to develop genus-specific primers. In addition, the published ribosomal gene-specific primers ITS1 , ITS2, ITS3 and ITS4 (White et al., 1990; In: PCR Protocols; Eds.: Innes et al. pages 315-322) are synthesized for testing in combination with the primers specific for the ITS regions. Primers targeted to Fusarium spp. from WO 95/29260 are also used in combination with the newly designed primers to test for novel specificities. Table 2: Primers Designed for Fungal Detection Primer Template Primer Primer Sequence Fusarium spp. ' JB605 5-CCAAACCATGTGAACTTACC3' (SEQ ID NO: 7) M. nivale JB606 5OGACTACCTAAACTCTGTT3' (SEQ ID NO: 8) M. nivale JB607 5ΑGGGATCATTACCGAGTTT3' (SEQ ID NO: 9) M. nivale JB609 5TCCGGCTTGCAGAAGCGAG3' (SEQ ID NO: 10) M. nivale JB610 5OAAGGGTGCGGTTTATGGCT3' (SEQ ID NO: 11) M. nivale JB611 5OCCACCGCCGGTGGAC3' (SEQ ID NO: 12) M. nivale JB612 5OGTGCTGTCTCTCGGGAC3' (SEQ ID NO: 13) M. nivale JB613 5ΑGTCAATCTGAATCAAACTAAG3' (SEQ ID NO: 14) M. nivale JB614 5-CTAAACTCTGTTAATTTTTGTCAA3' (SEQ ID NO: 15) Fusarium spp. 2 JB578 5 * CCGCGACGATTACCAG3'(SEQ ID NO: 16) F. gram. + F. culm. 3 JB571 5TAACGATATGTAAATTACTACGCT3' (SEQ ID NO: 17) F. gram. + F. culm. 3 JB572 5'AAGTTGGGGTTTAACGGC3' (SEQ ID NO: 18) 18S ΓDNA rrsi 5TCCGTAGGTGAACCTGCGG3' (SEQ ID NO: 1) 5.8S rDNA ITS2 5OCTGCGTTCTTCATCGATGC3' (SEQ ID NO: 2) 5.8S rDNA ITS3 5OCATCGATGAAGAACGCAGC3' (SEQ ID NO: 3) 25S rDNA ITS4 5TCCTCCGCTTATTGATATGC3- (SEQ ID NO: 4) 1 Fusarium spp. includes F. graminearum, F. culmorum, F. avenaceum, F. poae and F. moniliforme. 2 Fusarium spp. includes F. graminearum, F. culmorum, F. poae, F. moniliforme and F. roseum. 3 Primer combination only tested against F. graminearum, F. culmorum and M. nivale. Example 7: Determination of Primer Specificity to Purified Fungal Genomic DNA PCRs are performed according to Example 4 using different primer combinations (Table 3) in an attempt to amplify a single specific fragment. Specific PCR amplification products are produced from primers designed from the ITS regions between the 18S and 25S ribosomal DNA subunits of each fungal strain of interest. Table 3: ITS-Derived Diagnostic PCR Primers Primer Approximate size Specificity 5 ' Primer 3 'Primer of amplified fragment M. nivale JB612 (SEQ ID NO:13) ITS4 (SEQ ID NO:4) 472 bp M. nivale JB613 (SEQ ID NO:14) JB610 (SEQ ID NO:l 1) 337 bp M. nivale JB614 (SEQ ID NO:15) JB610 (SEQ ID NO:11) 355 bp M. nivale JB613 (SEQ ID NO:14) rTS4 (SEQ ID NO:4) 413 bp M. nivale JB614 (SEQ ID NO:15) ITS4 (SEQ ID NO:4) 431 bp M. nivale JB611 (SEQ ID NO:12) JB609 (SEQ ID NO: 10) 346 bp M. nivale JB611 (SEQ ID NO:12) rTS4 (SEQ ID NO:4) 450 bp M. nivale ITSl (SEQ ID NO:l) JB609 (SEQ ID NO:10) 452 bp M. nivale ΓΓS I(SEQ ID NO:1) JB610 (SEQ ID NO:l 1) 480 bp M. nivale JB605 (SEQ ID NO:7) JB610 (SEQ ID NO:l 1) 433 bp M. nivale JB606 (SEQ ID NO:8) JB610 (SEQ ID NO:11) 362 bp M. nivale JB607 (SEQ ID NO:9) JB610 (SEQ ID NO:11) 460 bp Fusarium spp. ' + M. niv JB605 (SEQ ID NO:7) rTS4 (SEQ ID NO:4) 509 bp Fusarium spp. 2 JB605 (SEQ ID NO:7) JB578 (SEQ ID NO:16) 417 bp F. gram . + F. culm ? JB605 (SEQ ID NO:7) JB572 (SEQ ID NO: 18) 440 bp F. gram . + F. culm . 3 JB605 (SEQ ID NO:7) JB571 (SEQ ID NO: 17) 400 bp 1 Fusarium spp. includes F. graminearum, F. culmorum, F. avenaceum, F. poae and F. moniliforme. 2 Fusarium spp. includes F. graminearum, F. culmorum, F. poae, F. moniliforme and F. roseum. 3 Primer combination only tested against F. graminearum, F. culmorum and M. nivale. Example 8: Determination of Primer Specificity to Plant Tissue Infected with Fungi and Cross-Reactivity with Other Cereal Fungal Pathogens Total genomic DNA is isolated as described in Example 3 from healthy wheat heads and from wheat heads inoculated with M. nivale, F. graminearum, F. culmorum, or F avenaceum. PCRs are performed as described in Example 4 testing primer combinations such as those listed in Table 3 against DNA from the wheat tissue. Purified fungal genomic DNAs are obtained as described in Example 1 and PCR assayed as described in Example 4 using the diagnostic primers. Other fungal DNA species and isolates are tested for the ability of the diagnostic primers to cross-react therewith. The results of representative experiments are as follows: M. n/Va/e-specific primer combination JB612 (SEQ ID NO: 13) and ITS4 (SEQ ID NO: 4) amplified a 472 bp fragment from DNA from all of the M. nivale isolates listed in Table 1 and from M. n/Va/e-infected wheat tissue. This primer combination did not amplify a diagnostic fragment from healthy wheat tissue nor from purified genomic DNA from F. graminearum, F. culmorum, F. avenaceum, F. poae or F. moniliforme. This primer combination also did not amplify a diagnostic fragment from purified genomic DNA isolated from the following common cereal pathogens: P. herpotrichoides R- and W-pathotypes, C. cereale, D. sorokiniana, C. herbarum, S. glycines, S. tritici, C. arachidicola, S. nodorum, R. solani and S. avenae f .sp. triticea. Similar diagnostic results were obtained with M. nivale- specific primer combination JB613 (SEQ ID NO:14) and JB610 (SEQ ID NO:11). Primer combination JB613 (SEQ ID NO:14) and ITS4 (SEQ ID NO:4) amplified a 413 bp fragment, and primer combination JB614 (SEQ ID NO:15) and ITS4 (SEQ ID NO:4) amplified a 431 bp fragment from DNA from M. nivale isolate #520 and from wheat infected with M. nivale. These primer combinations did not amplify any fragments from healthy wheat tissue, nor from DNA from F. graminearum isolate #R-8422 and F. culmorum isolate #R-5391. The remaining M. n/Va/e-specific primer combinations listed in Table 3 amplified a PCR fragment from DNA from M. nivale isolate #520 but not from DNA from F. graminearum isolate #R-8422 nor F. culmorum isolate #R-5391. Primer combination JB605 (SEQ ID NO:7) and ITS4 (SEQ ID NO:4) amplified a 509 bp fragment from DNA from ail of the M. nivale isolates listed in Table 1. This primer combination also amplified a 509 bp fragment from DNA from all of the F. graminearum, F. culmorum, F. avenaceum, F. poae and F. moniliforme isolates listed in Table 1. This primer combination did not amplify a diagnostic fragment from purified genomic DNA isolated from the following cereal pathogens: P. herpotrichoides R- and W-pathotypes, C. cereale, D. sorokiniana, C. herbarum, S. glycines, S. tritici, C. arachidicola, S. nodorum, R. solani and S. ai enae f.sp. triticea. Primer combination JB605 (SEQ ID NO:7) and ITS4 (SEQ ID NO:4) also amplified a diagnostic fragment from wheat infected with Fusarium spp. but not from healthy wheat. Primer combinations JB605 (SEQ ID NO:7) and JB571 (SEQ ID NO:17), JB605 (SEQ ID NO:7) and JB572 (SEQ ID NO:18), and JB605 (SEQ ID NO:7) and JB578 (SEQ ID NO:16) amplified 400 bp, 440 bp and 417 bp fragments, respectively, from DNA from F graminearum isolate #R-8422 and F. culmorum isolate #R-5391 , but not from M. nivale isolate #520. In addition, primer combination JB605 (SEQ ID NO:7) and JB578 (SEQ ID NO:16) amplified a diagnostic fragment from all of the F. graminearum, F. moniliforme, F. roseum, F. poae and F. culmorum isolates listed in Table 1 ; however, this primer combination did not amplify from any of the F. avenaceum isolates nor M. nivale isolates listed in Table 1. Primer combinations JB605 (SEQ ID NO:7) and JB571 (SEQ ID NO:17), JB605 (SEQ ID NO:7) and JB572 (SEQ ID NO:18), and JB605 (SEQ ID NO:7) and JB578 (SEQ ID NO:16) did not amplify a diagnostic fragment from healthy wheat or from purified genomic DNA isolated from the cereal pathogens P. heφotrichoides R- and W-pathotypes, C. cereale, D. sorokiniana, C. herbarum, S. glycines, S. tritici, C. arachidicola, S. nodorum, R. solani and S. a venae f.sp. triticea. While the present invention has been described with reference to specific embodiments thereof, it will be appreciated that numerous variations, modifications, and further embodiments are possible, and accordingly, all such variations, modifications and embodiments are to be regarded as being within the scope of the present invention.

Claims: What Is Claimed Is: 1. An isolated DNA molecule comprising an Internal Transcribed Spacer sequence selected from ITS1 of Fusarium poae, ITS2 of Fusarium poae, ITS1 of Microdochium nivale, ITS2 of Microdochium nivale, ITS1 of Fusarium avenaceum, and ITS2 of Fusarium avenaceum. 2. An isolated DNA molecule according to claim 1 , wherein ITS1 of Fusarium poae comprises nucleotides 31-180 of SEQ ID NO:22, wherein ITS2 of Fusarium poae comprises nucleotides 338-489 of SEQ ID NO:22, wherein ITS1 of Microdochium nivale comprises nucleotides 31-175 of SEQ ID NO:23, wherein ITS2 of Microdochium nivale comprises nucleotides 333-499 of SEQ ID NO:23, wherein ITS1 of Fusarium avenaceum comprises nucleotides 31-181 of SEQ ID NO:24, and wherein ITS2 of Fusarium avenaceum comprises nucleotides 339-504 of SEQ ID NO:24. 3. An oligonucleotide primer for use in amplification-based detection of a fungal Internal Transcribed Spacer sequence, wherein said primer has sequence identity with at least about 5-10 contiguous nucleotides of the Internal Transcribed Spacer sequence of claim 2. 4. An oligonucleotide primer for use in amplification-based detection of a fungal Internal Transcribed Spacer DNA sequence, wherein said primer has sequence identity with at least 10 contiguous nucleotides of the Internal Transcribed Spacer sequence of claim 2. 5. A pair of oligonucleotide primers for use in the amplification-based detection of a fungal Internal Transcribed Spacer DNA sequence, wherein at least one of said primers is the oligonucleotide primer of claim 4. 6. An oligonucleotide primer for use in identification of a fungal pathogen, wherein said oligonucleotide primer is selected from the group consisting of SEQ ID NO's:7-15. 7. A pair of oligonucleotide primers for use in the amplification-based detection of a fungal Internal Transcribed Spacer DNA sequence, wherein at least one of said primers is the oligonucleotide primer of claim 6. 8. A pair of oligonucleotide primers according to claim 7, wherein said pair is selected from the following primer pairs: SEQ ID NO:13 and SEQ ID NO:4; SEQ ID NO:14 and SEQ ID NO:11 ; SEQ ID NO:15 and SEQ ID NO:11 ; SEQ ID NO:14 and SEQ ID NO:4; SEQ ID NO:15 and SEQ ID NO:4; SEQ ID NO:12 and SEQ ID NO:10; SEQ ID NO:12 and SEQ ID NO:4; SEQ ID NO:1 and SEQ ID NO:10; SEQ ID NO:1 and SEQ ID NO:11 ; SEQ ID NO:7 and SEQ ID NO:11 ; SEQ ID NO:8 and SEQ ID NO:11 ; SEQ ID NO:9 and SEQ ID NO:11; SEQ ID NO:7 and SEQ ID NO:4; SEQ ID NO:7 and SEQ ID NO:16; SEQ ID NO:7 and SEQ ID NO:18; and SEQ ID NO:7 and SEQ ID NO:17. A pair of oligonucleotide primers according to claim 8, wherein said pair of primers are used to detect Microdochium nivale, and wherein said pair is selected from the following primer pairs: SEQ ID NO:13 and SEQ ID NO:4; SEQ ID NO:14 and SEQ ID NO:11 ; SEQ ID NO:15 and SEQ ID NO:11 ; SEQ ID NO:14 and SEQ ID NO:4; SEQ ID NO:15 and SEQ ID NO:4; SEQ ID NO:12 and SEQ ID NO:10; SEQ ID NO:12 and SEQ ID NO:4; SEQ ID NO:1 and SEQ ID NO:10 SEQ ID NO:1 and SEQ ID NO:11 SEQ ID NO:7 and SEQ ID NO:11 SEQ ID NO:8 and SEQ ID NO:11 ; and SEQ ID NO:9 and SEQ ID NO:11. 10. A pair of oligonucleotide primers according to claim 8, wherein said pair of primers are used to detect Microdochium nivale, F. graminearum, F. culmorum, F. avenaceum, F. poae, and F. moniliforme, and wherein said pair comprises SEQ ID NO:7 and SEQ ID NO:4. 11. A pair of oligonucleotide primers according to claim 8, wherein said pair of primers are used to detect F. graminearum, F. moniliforme, F. roseum, F. poae, and F. culmorum and wherein said pair comprises SEQ ID NO:7 and SEQ ID NO:16. 12. A pair of oligonucleotide primers according to claim 8, wherein said pair of primers are used to detect F. graminearum and F. culmorum, and wherein said pair is selected from the following primer pairs: SEQ ID NO:7 and SEQ ID NO:18; and SEQ ID NO:7 and SEQ ID NO:17. 13. A method for the detection of a fungal pathogen, comprising the steps of: (a) isolating DNA from a plant leaf infected with a pathogen; (b) subjecting said DNA to polymerase chain reaction amplification using at least one primer according to claim 4; and (c) detecting said fungal pathogen by visualizing the product or products of said polymerase chain reaction amplification. 14. The method of claim 13, wherein said fungal pathogen is selected from Fusarium poae and Microdochium nivale. 15. A method for the detection of a fungal pathogen, comprising the steps of: (a) isolating DNA from a plant leaf infected with a pathogen; (b) amplifying a part of the Internal Transcribed Spacer sequence of said pathogen using said DNA as a template in a polymerase chain reaction with a pair of primers according to claim 5; and (c) detecting said fungal pathogen by visualizing the amplified part of the Internal Transcribed Spacer sequence. 16. The method of claim 15, wherein said fungal pathogen is selected from Fusarium poae and Microdochium nivale. 17. A diagnostic kit used in detecting a fungal pathogen, comprising the primer of claim 4. 18. A diagnostic kit used in detecting a fungal pathogen, comprising the pair of primers of claim 5. 19. An isolated DNA molecule according to claim 1 , wherein said Internal Transcribed Spacer sequence is selected from ITS1 and ITS2 of Fusarium poae. 20. An isolated DNA molecule according to claim 19, wherein ITS1 of Fusarium poae comprises nucleotides 31 -180 of SEQ ID NO:22 and wherein ITS2 of Fusarium poae comprises nucleotides 338-489 of SEQ ID NO:22. 21. An oligonucleotide primer for use in amplification-based detection of a fungal Internal Transcribed Spacer DNA sequence, wherein said primer has sequence identity with at least 10 contiguous nucleotides of the Internal Transcribed Spacer sequence of claim 20. 22. An isolated DNA molecule according to claim 1 , wherein said Internal Transcribed Spacer sequence is selected from ITS1 and ITS2 of Microdochium nivale. 23. An isolated DNA molecule according to claim 22, wherein ITS1 of Microdochium nivale comprises nucleotides 31-175 of SEQ ID NO:23 and wherein ITS2 of Microdochium nivale comprises nucleotides 333-499 of SEQ ID NO:23. 24. An oligonucleotide primer for use in amplification-based detection of a fungal Internal Transcribed Spacer DNA sequence, wherein said primer has sequence identity with at least 10 contiguous nucleotides of the Internal Transcribed Spacer sequence of claim 23. 25. An isolated DNA molecule according to claim 1 , wherein said Internal Transcribed Spacer sequence is selected from ITS1 and ITS2 of Fusarium avenaceum. 26. An isolated DNA molecule according to claim 25, wherein ITS1 of Fusarium avenaceum comprises nucleotides 31-181 of SEQ ID NO:24 and wherein ITS2 of Fusarium avenaceum comprises nucleotides 339-504 of SEQ ID NO:24. 27. An oligonucleotide primer for use in amplification-based detection of a fungal Internal Transcribed Spacer DNA sequence, wherein said primer has sequence identity with at least 10 contiguous nucleotides of the Internal Transcribed Spacer sequence of claim 26.

Inventors: BECK JAMES JOSEPH, BECK, JAMES, JOSEPH
Applicants: NOVARTIS AG, NOVARTIS ERFIND VERWALT GMBH, NOVARTIS-ERFINDUNGEN VERWALTUNGSGESELLSCHAFT M.B.H.
Application year: 1998
Main classification: C12Q1
IPC codes: C07K14, C12N15, C12Q1, C12R1