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Chittaragi A, Pramesh D, Naik GR, Naik MK, Yadav MK, Ngangkham U, Siddepalli ME, Nayak A, Prasannakumar MK, Eranna C. Multilocus sequence analysis and identification of mating-type idiomorphs distribution in Magnaporthe oryzae population of Karnataka state of India. J Appl Microbiol 2022; 132:4413-4429. [PMID: 35332630 DOI: 10.1111/jam.15546] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2021] [Revised: 02/17/2022] [Accepted: 03/22/2022] [Indexed: 11/27/2022]
Abstract
AIMS To investigate the genetic diversity, population structure, and mating-type distribution among the eco-distinct isolates of Magnaporthe oryzae from Karnataka, India. METHODS AND RESULTS A set of 38 isolates of M. oryzae associated with leaf blast disease of rice were collected from different rice ecosystems of Karnataka, India, and analyzed for their diversity at actin, β-tubulin, calmodulin, translation elongation factor 1-α (TEF-1-α), and internal transcribed spacer (ITS) genes/region. The isolates were grouped into two clusters based on the multilocus sequence diversity, the majority being in cluster-IA (n=37), and only one isolate formed cluster-IB. Population structure was analyzed using 123 SNP data to understand the genetic relationship. Based on K=2 and ancestry threshold of >70%, blast strains were classified into two subgroups (SG1 and SG2) whereas, based on K=4 and ancestry threshold of >70%, blast strains were classified into four subgroups (SG1, SG2, SG3, and SG4). We have identified 13 haplotype groups where haplotype-group-2 was predominant (n=20) in the population. The Tajima's and Fu's Fs neutrality tests exhibited many rare alleles. Further, the mating-type analysis was also performed using MAT1 gene-specific primers to find the potentiality of sexual reproduction in different ecosystems. The majority of the isolates (54.5%) had MAT1-2 idiomorph, whereas 45.5 per cent of the isolates possessed MAT1-1 idiomorph. CONCLUSIONS The present study found the genetically homogenous population of M. oryzae by multilocus sequence analysis. Both mating types, MAT1-1 and MAT1-2, were found within the M. oryzae population of Karnataka. SIGNIFICANCE AND IMPACT OF STUDY The study on the population structure and sexual mating behavior of M. oryzae is important in developing region-specific blast-resistant rice cultivars. This is the first report of MAT1 idiomorphs distribution in the M. oryzae population in any Southern state of India.
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Affiliation(s)
- Amoghavarsha Chittaragi
- Department of Plant Pathology, University of Agricultural and Horticultural Sciences, Shivamogga, Karnataka, India.,Rice Pathology Laboratory, All India Coordinated Rice Improvement Programme, University of Agricultural Sciences, Karnataka, India
| | - Devanna Pramesh
- Rice Pathology Laboratory, All India Coordinated Rice Improvement Programme, University of Agricultural Sciences, Karnataka, India
| | - Ganesha R Naik
- Department of Plant Pathology, University of Agricultural and Horticultural Sciences, Shivamogga, Karnataka, India
| | - Manjunath K Naik
- Department of Plant Pathology, University of Agricultural and Horticultural Sciences, Shivamogga, Karnataka, India
| | - Manoj K Yadav
- ICAR-National Rice Research Institute, Cuttack, India
| | - Umakanta Ngangkham
- ICAR-Research Complex for North-Eastern Hill Region, Manipur Centre, Imphal, Manipur, India
| | - Manjunatha E Siddepalli
- Rice Pathology Laboratory, All India Coordinated Rice Improvement Programme, University of Agricultural Sciences, Karnataka, India
| | - Anusha Nayak
- Rice Pathology Laboratory, All India Coordinated Rice Improvement Programme, University of Agricultural Sciences, Karnataka, India
| | - M K Prasannakumar
- Department of Plant Pathology, University of Agricultural Sciences, Bengaluru, India
| | - Chidanandappa Eranna
- Rice Pathology Laboratory, All India Coordinated Rice Improvement Programme, University of Agricultural Sciences, Karnataka, India
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Sheoran N, Ganesan P, Mughal NM, Yadav IS, Kumar A. Genome assisted molecular typing and pathotyping of rice blast pathogen, Magnaporthe oryzae, reveals a genetically homogenous population with high virulence diversity. Fungal Biol 2021; 125:733-747. [PMID: 34420700 DOI: 10.1016/j.funbio.2021.04.007] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/26/2020] [Revised: 04/19/2021] [Accepted: 04/26/2021] [Indexed: 01/25/2023]
Abstract
Genome sequence-driven molecular typing tools have the potential to uncover the population biology and genetic diversity of rapidly evolving plant pathogens like Magnaporthe oryzae. Here, we report a new molecular typing technique -a digitally portable tool for population genetic analysis of M. oryzae to decipher the genetic diversity. Our genotyping tool exploiting allelic variations in housekeeping and virulence genes coupled with pathotyping revealed a prevalence of genetically homogenous populations within a single-field and plant niches such as leaf and panicle. The M. oryzae inciting leaf-blast and panicle-blast were confirmed to be genetically identical with no or minor nucleotide polymorphism in 17 genomic loci analyzed. Genetic loci such as Mlc1, Mpg1, Mps1, Slp1, Cal, Ef-Tu, Pfk, and Pgk were highly polymorphic as indicated by the haplotype-diversity, the number of polymorphic sites, and the number of mutations. The genetically homogenous single field population showed high virulence variability or diversity on monogenic rice differentials. The study indicated that the genetic similarity displayed by the isolates collected from a particular geographical location had no consequence on their virulence pattern on rice differentials carrying single/multiple resistance genes. The data on virulence diversity showed by the identical Sequence Types (STs) is indicative of no congruence between polymorphic virulence genes-based pathotyping and conserved housekeeping genes-based genotyping.
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Affiliation(s)
- Neelam Sheoran
- Division of Plant Pathology, ICAR-Indian Agricultural Research Institute, New Delhi, India.
| | - Prakash Ganesan
- Division of Plant Pathology, ICAR-Indian Agricultural Research Institute, New Delhi, India.
| | - Najeeb M Mughal
- Mountain Research Centre for Field Crops, Sher-e-Kashmir University of Agricultural Sciences & Technology of Kashmir, India.
| | - Inderjit Singh Yadav
- School of Agricultural Biotechnology, Punjab Agricultural University, Ludhiana, Punjab, India.
| | - Aundy Kumar
- Division of Plant Pathology, ICAR-Indian Agricultural Research Institute, New Delhi, India.
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Li T, Wen J, Zhang Y, Correll J, Wang L, Pan Q. Reconstruction of an SSR-based Magnaporthe oryzae physical map to locate avirulence gene AvrPi12. BMC Microbiol 2018; 18:47. [PMID: 29855268 PMCID: PMC5984427 DOI: 10.1186/s12866-018-1192-x] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/21/2018] [Accepted: 05/21/2018] [Indexed: 01/30/2023] Open
Abstract
BACKGROUND Pathogen avirulence (Avr) genes can evolve rapidly when challenged by the widespread deployment of host genes for resistance. They can be effectively isolated by positional cloning provided a robust and well-populated genetic map is available. RESULTS An updated, SSR-based physical map of the rice blast pathogen Magnaporthe oryzae (Mo) has been constructed based on 116 of the 120 SSRs used to assemble the last map, along with 18 newly developed ones. A comparison between the two versions of the map has revealed an altered marker content and order within most of the Mo chromosomes. The avirulence gene AvrPi12 was mapped in a population of 219 progeny derived from a cross between the two Mo isolates CHL42 and CHL357. A bulked segregant analysis indicated that the gene was located on chromosome 6, a conclusion borne out by an analysis of the pattern of segregation shown by individual isolates. Six additional PCR-based markers were developed to improve the map resolution in the key region. AvrPi12 was finally located within the sub-telomeric region of chromosome 6, distal to the SSR locus LSM6-5. CONCLUSIONS The improved SSR-based linkage map should be useful as a platform for gene mapping and isolation in Mo. It was used to establish the location of AvrPi12, thereby providing a starting point for its positional cloning.
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Affiliation(s)
- Tonghui Li
- State Key laboratory for Conservation and Utilization of Subtropic Agrobioresurces, Guangdong Provincial Key Laboratory for Crop Molecular Breeding, College of Agriculture, South China Agricultural University, Guangzhou, 510642 China
| | - Jianqiang Wen
- State Key laboratory for Conservation and Utilization of Subtropic Agrobioresurces, Guangdong Provincial Key Laboratory for Crop Molecular Breeding, College of Agriculture, South China Agricultural University, Guangzhou, 510642 China
| | - Yaling Zhang
- State Key laboratory for Conservation and Utilization of Subtropic Agrobioresurces, Guangdong Provincial Key Laboratory for Crop Molecular Breeding, College of Agriculture, South China Agricultural University, Guangzhou, 510642 China
- College of Agronomy, Heilongjiang Bayi Agricultural University, Daqing, 163319 China
| | - James Correll
- Department of Plant Pathology, University of Arkansas, Fayetteville, AR 72701 USA
| | - Ling Wang
- State Key laboratory for Conservation and Utilization of Subtropic Agrobioresurces, Guangdong Provincial Key Laboratory for Crop Molecular Breeding, College of Agriculture, South China Agricultural University, Guangzhou, 510642 China
| | - Qinghua Pan
- State Key laboratory for Conservation and Utilization of Subtropic Agrobioresurces, Guangdong Provincial Key Laboratory for Crop Molecular Breeding, College of Agriculture, South China Agricultural University, Guangzhou, 510642 China
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Sharpee W, Oh Y, Yi M, Franck W, Eyre A, Okagaki LH, Valent B, Dean RA. Identification and characterization of suppressors of plant cell death (SPD) effectors from Magnaporthe oryzae. MOLECULAR PLANT PATHOLOGY 2017; 18:850-863. [PMID: 27301772 PMCID: PMC6638229 DOI: 10.1111/mpp.12449] [Citation(s) in RCA: 32] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/28/2016] [Revised: 06/09/2016] [Accepted: 06/10/2016] [Indexed: 05/04/2023]
Abstract
Phytopathogenic microorganisms, including the fungal pathogen Magnaporthe oryzae, secrete a myriad of effector proteins to facilitate infection. Utilizing the transient expression of candidate effectors in the leaves of the model plant Nicotiana benthamiana, we identified 11 suppressors of plant cell death (SPD) effectors from M. oryzae that were able to block the host cell death reaction induced by Nep1. Ten of these 11 were also able to suppress BAX-mediated plant cell death. Five of the 11 SPD genes have been identified previously as either essential for the pathogenicity of M. oryzae, secreted into the plant during disease development, or as suppressors or homologues of other characterized suppressors. In addition, of the remaining six, we showed that SPD8 (previously identified as BAS162) was localized to the rice cytoplasm in invaded and surrounding uninvaded cells during biotrophic invasion. Sequence analysis of the 11 SPD genes across 43 re-sequenced M. oryzae genomes revealed that SPD2, SPD4 and SPD7 have nucleotide polymorphisms amongst the isolates. SPD4 exhibited the highest level of nucleotide diversity of any currently known effector from M. oryzae in addition to the presence/absence polymorphisms, suggesting that this gene is potentially undergoing selection to avoid recognition by the host. Taken together, we have identified a series of effectors, some of which were previously unknown or whose function was unknown, that probably act at different stages of the infection process and contribute to the virulence of M. oryzae.
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Affiliation(s)
- William Sharpee
- Center for Integrated Fungal Research, Department of Entomology and Plant PathologyNorth Carolina State UniversityRaleighNC27606USA
| | - Yeonyee Oh
- Center for Integrated Fungal Research, Department of Entomology and Plant PathologyNorth Carolina State UniversityRaleighNC27606USA
| | - Mihwa Yi
- Department of Plant PathologyKansas State UniversityManhattanKS66506USA
- Present address:
Noble FoundationArdmoreOK73401USA
| | - William Franck
- Center for Integrated Fungal Research, Department of Entomology and Plant PathologyNorth Carolina State UniversityRaleighNC27606USA
- Present address:
USDA‐ARS Northern Plains Agricultural Research ServiceSidneyMT59270USA
| | - Alex Eyre
- Center for Integrated Fungal Research, Department of Entomology and Plant PathologyNorth Carolina State UniversityRaleighNC27606USA
| | - Laura H. Okagaki
- Center for Integrated Fungal Research, Department of Entomology and Plant PathologyNorth Carolina State UniversityRaleighNC27606USA
- Present address:
Department of Microbiology and ImmunologyUniversity of MinnesotaMN55455USA
| | - Barbara Valent
- Department of Plant PathologyKansas State UniversityManhattanKS66506USA
| | - Ralph A. Dean
- Center for Integrated Fungal Research, Department of Entomology and Plant PathologyNorth Carolina State UniversityRaleighNC27606USA
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Zhang S, Wang L, Wu W, He L, Yang X, Pan Q. Function and evolution of Magnaporthe oryzae avirulence gene AvrPib responding to the rice blast resistance gene Pib. Sci Rep 2015; 5:11642. [PMID: 26109439 PMCID: PMC5387869 DOI: 10.1038/srep11642] [Citation(s) in RCA: 90] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/17/2015] [Accepted: 05/14/2015] [Indexed: 12/12/2022] Open
Abstract
Magnaporthe oryzae (Mo) is the causative pathogen of the damaging disease rice blast. The effector gene AvrPib, which confers avirulence to host carrying resistance gene Pib, was isolated via map-based cloning. The gene encodes a 75-residue protein, which includes a signal peptide. Phenotyping and genotyping of 60 isolates from each of five geographically distinct Mo populations revealed that the frequency of virulent isolates, as well as the sequence diversity within the AvrPib gene increased from a low level in the far northeastern region of China to a much higher one in the southern region, indicating a process of host-driven selection. Resequencing of the AvrPiballele harbored by a set of 108 diverse isolates revealed that there were four pathoways, transposable element (TE) insertion (frequency 81.7%), segmental deletion (11.1%), complete absence (6.7%), and point mutation (0.6%), leading to loss of the avirulence function. The lack of any TE insertion in a sample of non-rice infecting Moisolates suggested that it occurred after the host specialization of Mo. Both the deletions and the functional point mutation were confined to the signal peptide. The reconstruction of 16 alleles confirmed seven functional nucleotide polymorphisms for the AvrPiballeles, which generated three distinct expression profiles.
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Affiliation(s)
- Shulin Zhang
- State Key Laboratory for Conservation and Utilization of Subtropical Agrobioresurces, and Guangdong Provincial Key Laboratory for Microbe Signals and Crop Disease Control, South China Agricultural University, Guangzhou, 510642, China
| | - Ling Wang
- State Key Laboratory for Conservation and Utilization of Subtropical Agrobioresurces, and Guangdong Provincial Key Laboratory for Microbe Signals and Crop Disease Control, South China Agricultural University, Guangzhou, 510642, China
| | - Weihuai Wu
- State Key Laboratory for Conservation and Utilization of Subtropical Agrobioresurces, and Guangdong Provincial Key Laboratory for Microbe Signals and Crop Disease Control, South China Agricultural University, Guangzhou, 510642, China
- Hainan Key Laboratory for Monitoring and Control of Tropical Agricultural pests, Environment and Plant Protection Institute, Chinese Academy of Tropical Agricultural Sciences, Haikou, Hainan 571101, China
| | - Liyun He
- State Key Laboratory for Conservation and Utilization of Subtropical Agrobioresurces, and Guangdong Provincial Key Laboratory for Microbe Signals and Crop Disease Control, South China Agricultural University, Guangzhou, 510642, China
| | - Xianfeng Yang
- State Key Laboratory for Conservation and Utilization of Subtropical Agrobioresurces, and Guangdong Provincial Key Laboratory for Microbe Signals and Crop Disease Control, South China Agricultural University, Guangzhou, 510642, China
| | - Qinghua Pan
- State Key Laboratory for Conservation and Utilization of Subtropical Agrobioresurces, and Guangdong Provincial Key Laboratory for Microbe Signals and Crop Disease Control, South China Agricultural University, Guangzhou, 510642, China
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Choi J, Kim H, Lee YH. Comparative Analysis of the Korean Population of Magnaporthe oryzae by Multilocus Microsatellite Typing. THE PLANT PATHOLOGY JOURNAL 2013; 29:435-9. [PMID: 25288972 PMCID: PMC4174813 DOI: 10.5423/ppj.nt.04.2013.0042] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 04/30/2013] [Revised: 05/25/2013] [Accepted: 05/25/2013] [Indexed: 06/03/2023]
Abstract
Rice blast fungus, Magnaporthe oryzae, inflicts serious damage to global rice production. Due to high variability of this fungal pathogen, resistance of newly-released rice cultivars is easily broken down. To understand the population structure of M. oryzae, we analyzed the genetic diversity of the Korean population using multilocus microsatellite typing. Eleven microsatellite markers were applied to the population of 190 rice isolates which had been collected in Korea for two decades since the 1980's. Average values of gene diversity and allele frequency were 0.412 and 6.5, respectively. Comparative analysis of the digitized allele information revealed that the Korean population exhibited a similar level of allele diversity to the integrated diversity of the world populations, suggesting a particularly high diversity of the Korean population. Therefore, these microsatellite markers and the comprehensive collection of field isolates will be useful genetic resources to identify the genetic diversity of M. oryzae population.
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Affiliation(s)
- Jaehyuk Choi
- Center for Fungal Pathogenesis, Research Institute for Agriculture and Life Sciences, Seoul National University, Seoul 151-921, Korea
| | - Hyojung Kim
- Department of Agricultural Biotechnology, Research Institute for Agriculture and Life Sciences, Seoul National University, Seoul 151-921, Korea
| | - Yong-Hwan Lee
- Center for Fungal Pathogenesis, Research Institute for Agriculture and Life Sciences, Seoul National University, Seoul 151-921, Korea
- Department of Agricultural Biotechnology, Research Institute for Agriculture and Life Sciences, Seoul National University, Seoul 151-921, Korea
- Center for Fungal Genetic Resources, Plant Genomics and Breeding Institute, and Research Institute for Agriculture and Life Sciences, Seoul National University, Seoul 151-921, Korea
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Chuma I, Isobe C, Hotta Y, Ibaragi K, Futamata N, Kusaba M, Yoshida K, Terauchi R, Fujita Y, Nakayashiki H, Valent B, Tosa Y. Multiple translocation of the AVR-Pita effector gene among chromosomes of the rice blast fungus Magnaporthe oryzae and related species. PLoS Pathog 2011; 7:e1002147. [PMID: 21829350 PMCID: PMC3145791 DOI: 10.1371/journal.ppat.1002147] [Citation(s) in RCA: 162] [Impact Index Per Article: 11.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2011] [Accepted: 05/17/2011] [Indexed: 01/22/2023] Open
Abstract
Magnaporthe oryzae is the causal agent of rice blast disease, a devastating problem worldwide. This fungus has caused breakdown of resistance conferred by newly developed commercial cultivars. To address how the rice blast fungus adapts itself to new resistance genes so quickly, we examined chromosomal locations of AVR-Pita, a subtelomeric gene family corresponding to the Pita resistance gene, in various isolates of M. oryzae (including wheat and millet pathogens) and its related species. We found that AVR-Pita (AVR-Pita1 and AVR-Pita2) is highly variable in its genome location, occurring in chromosomes 1, 3, 4, 5, 6, 7, and supernumerary chromosomes, particularly in rice-infecting isolates. When expressed in M. oryzae, most of the AVR-Pita homologs could elicit Pita-mediated resistance, even those from non-rice isolates. AVR-Pita was flanked by a retrotransposon, which presumably contributed to its multiple translocation across the genome. On the other hand, family member AVR-Pita3, which lacks avirulence activity, was stably located on chromosome 7 in a vast majority of isolates. These results suggest that the diversification in genome location of AVR-Pita in the rice isolates is a consequence of recognition by Pita in rice. We propose a model that the multiple translocation of AVR-Pita may be associated with its frequent loss and recovery mediated by its transfer among individuals in asexual populations. This model implies that the high mobility of AVR-Pita is a key mechanism accounting for the rapid adaptation toward Pita. Dynamic adaptation of some fungal plant pathogens may be achieved by deletion and recovery of avirulence genes using a population as a unit of adaptation.
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Affiliation(s)
- Izumi Chuma
- Graduate School of Agricultural Sciences, Kobe University, Kobe, Japan
| | - Chihiro Isobe
- Graduate School of Agricultural Sciences, Kobe University, Kobe, Japan
| | - Yuma Hotta
- Graduate School of Agricultural Sciences, Kobe University, Kobe, Japan
| | - Kana Ibaragi
- Graduate School of Agricultural Sciences, Kobe University, Kobe, Japan
| | - Natsuru Futamata
- Graduate School of Agricultural Sciences, Kobe University, Kobe, Japan
| | | | | | | | | | | | - Barbara Valent
- Department of Plant Pathology, Kansas State University, Manhattan, Kansas, United States of America
| | - Yukio Tosa
- Graduate School of Agricultural Sciences, Kobe University, Kobe, Japan
- * E-mail:
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Wang L, Xu X, Lin F, Pan Q. Characterization of rice blast resistance genes in the Pik cluster and fine mapping of the Pik-p locus. PHYTOPATHOLOGY 2009; 99:900-5. [PMID: 19594308 DOI: 10.1094/phyto-99-8-0900] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/12/2023]
Abstract
Pik-p is carried by cv. K60, which is one of the Japanese differentials widely used in both Japan and China since the 1980s. Its utility and specificity was evaluated with a total of 612 isolates of Magnaporthe oryzae collected from various regions in China in combination with 16 main resistance genes being used in the breeding programs. Pik-p is an independently and dominantly acting gene in the Pik cluster, which conditions differential reactions against many isolates and contains higher resistance in Guangdong, Jiangsu, and Sichuan provinces, China, indicating that this gene could be still used in these regions. A high-resolution genetic map of Pik-p was constructed using genomic position-ready markers. A set of 47 recombinants out of 681 F(2) plants derived from the crosses cv. K60 (resistant) x cv. AS20-1 (susceptible) and x cv. Kasalath (susceptible) was identified in the genetic interval defined by the markers RM5926 and K37 which flank the Pik gene cluster. This set was then genotyped with seven markers known to reside within the interval. The closest markers to Pik-p were K28 (approximately 0.60 centimorgans [cM]) and K39 (approximately 0.07 cM). A further four markers in the K28-K39 interval were developed from an in silico analysis based on the cv. Nipponbare genome sequence, and these all co-segregated with Pik-p. This 0.67-cM region is equivalent to a physical separation in cv. Nipponbare of approximately 126 kb, plus an as-yet-unfilled genomic gap of unknown length. Four nucleotide-binding site leucine-rich repeat-type resistance genes are present in this interval, and these represent good candidates for Pik-p.
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Affiliation(s)
- Ling Wang
- Laboratory of Plant Resistance and Genetics, College of Natural Resources and Environmental Sciences, South China Agricultural University, Guangzhou, China
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