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      Genotype‐by‐sequencing of the plant‐pathogenic fungi Pyrenophora teres and Sphaerulina musiva utilizing Ion Torrent sequence technology

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          Summary

          Genetic and genomics tools to characterize host–pathogen interactions are disproportionately directed to the host because of the focus on resistance. However, understanding the genetics of pathogen virulence is equally important and has been limited by the high cost of de novo genotyping of species with limited marker data. Non‐resource‐prohibitive methods that overcome the limitation of genotyping are now available through genotype‐by‐sequencing ( GBS). The use of a two‐enzyme restriction‐associated DNA ( RAD)‐ GBS method adapted for Ion Torrent sequencing technology provided robust and reproducible high‐density genotyping of several fungal species. A total of 5783 and 2373 unique loci, ‘sequence tags’, containing 16 441 and 9992 single nucleotide polymorphisms ( SNPs) were identified and characterized from natural populations of Pyrenophora teres f. maculata and Sphaerulina musiva , respectively. The data generated from the P. teres f. maculata natural population were used in association mapping analysis to map the mating‐type gene to high resolution. To further validate the methodology, a biparental population of P. teres f. teres, previously used to develop a genetic map utilizing simple sequence repeat ( SSR) and amplified fragment length polymorphism ( AFLP) markers, was re‐analysed using the SNP markers generated from this protocol. A robust genetic map containing 1393 SNPs on 997 sequence tags spread across 15 linkage groups with anchored reference markers was generated from the P. teres f. teres biparental population. The robust high‐density markers generated using this protocol will allow positional cloning in biparental fungal populations, association mapping of natural fungal populations and population genetics studies.

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          Author and article information

          Journal
          Mol Plant Pathol
          Mol. Plant Pathol
          10.1111/(ISSN)1364-3703
          MPP
          Molecular Plant Pathology
          John Wiley and Sons Inc. (Hoboken )
          1464-6722
          1364-3703
          15 December 2014
          August 2015
          : 16
          : 6 ( doiID: 10.1111/mpp.2015.16.issue-6 )
          : 623-632
          Affiliations
          [ 1 ] Department of Plant Pathology North Dakota State University Fargo ND 58108‐6050 USA
          [ 2 ] Department of Computer Science North Dakota State University Fargo ND 58108‐6050 USA
          [ 3 ] Cereal Crops Research Unit USDA‐ARS Fargo ND 58102 USA
          Author notes
          [*] [* ] Correspondence: Email: robert.brueggeman@ 123456ndsu.edu
          Article
          PMC6638358 PMC6638358 6638358 MPP12214
          10.1111/mpp.12214
          6638358
          25346350
          fae5746e-865f-41b2-a5fd-c3fc8de484c8
          © 2014 BSPP AND JOHN WILEY & SONS LTD
          History
          Page count
          Pages: 11
          Funding
          Funded by: USDA‐National Institute of Food and Agriculture (USDA‐NIFA)
          Award ID: 2011‐68002‐30029
          Funded by: USDA‐NIFA‐Regional Integrated Pest Management (USDA‐NIFA‐RIPM)
          Award ID: 2012‐34103‐19771
          Funded by: National Science Foundation CAREER project
          Award ID: 1253987
          Categories
          Technical Advance
          Technical Advance
          Custom metadata
          2.0
          mpp12214
          August 2015
          Converter:WILEY_ML3GV2_TO_NLMPMC version:5.6.4 mode:remove_FC converted:10.06.2019

          Sphaerulina musiva , Pyrenophora teres ,fungi,genotype‐by‐sequencing

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