Open AccessExploiting the Repetitive Fraction of the Wheat Genome for High‐Throughput Single‐Nucleotide Polymorphism Discovery and Genotyping
Author(s) -
Cubizolles Nelly,
Rey Elodie,
Choulet Frédéric,
Rimbert Hélène,
Laugier Christel,
Balfourier François,
Bordes Jacques,
Poncet Charles,
Jack Peter,
James Chris,
Gielen Jan,
Argillier Odile,
Jaubertie JeanPierre,
Auzanneau Jérôme,
Rohde Antje,
Ouwerkerk Pieter B.F.,
Korzun Viktor,
Kollers Sonja,
Guerreiro Laurent,
Hourcade Delphine,
Robert Olivier,
Devaux Pierre,
Mastrangelo AnnaMaria,
Feuillet Catherine,
Sourdille Pierre,
Paux Etienne
Publication year - 2016
Publication title -
the plant genome
Language(s) - English
Resource type - Journals
SCImago Journal Rank - 1.403
H-Index - 41
ISSN - 1940-3372
DOI - 10.3835/plantgenome2015.09.0078
Subject(s) - biology , genotyping , single nucleotide polymorphism , genetics , molecular inversion probe , genome , snp genotyping , dbsnp , sequence tagged site , computational biology , chromosome , genotype , gene mapping , gene
Transposable elements (TEs) account for more than 80% of the wheat genome. Although they represent a major obstacle for genomic studies, TEs are also a source of polymorphism and consequently of molecular markers such as insertion site‐based polymorphism (ISBP) markers. Insertion site‐based polymorphisms have been found to be a great source of genome‐specific single‐nucleotide polymorphism (SNPs) in the hexaploid wheat ( Triticum aestivum L.) genome. Here, we report on the development of a high‐throughput SNP discovery approach based on sequence capture of ISBP markers. By applying this approach to the reference sequence of chromosome 3B from hexaploid wheat, we designed 39,077 SNPs that are evenly distributed along the chromosome. We demonstrate that these SNPs can be efficiently scored with the KASPar (Kompetitive allele‐specific polymerase chain reaction) genotyping technology. Finally, through genetic diversity and genome‐wide association studies, we also demonstrate that ISBP‐derived SNPs can be used in marker‐assisted breeding programs.