title: Exploiting the Repetitive Fraction of the Wheat Genome for High-Throughput Single-Nucleotide Polymorphism Discovery and Genotyping.
abstract: 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 ( 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.
authors.forename: Nelly
authors.initials: N
authors.lastname: Cubizolles
authors.forename: Elodie
authors.initials: E
authors.lastname: Rey
authors.forename: Frédéric
authors.initials: F
authors.lastname: Choulet
authors.forename: Hélène
authors.initials: H
authors.lastname: Rimbert
authors.forename: Christel
authors.initials: C
authors.lastname: Laugier
authors.forename: François
authors.initials: F
authors.lastname: Balfourier
authors.forename: Jacques
authors.initials: J
authors.lastname: Bordes
authors.forename: Charles
authors.initials: C
authors.lastname: Poncet
authors.forename: Peter
authors.initials: P
authors.lastname: Jack
authors.forename: Chris
authors.initials: C
authors.lastname: James
authors.forename: Jan
authors.initials: J
authors.lastname: Gielen
authors.forename: Odile
authors.initials: O
authors.lastname: Argillier
authors.forename: Jean-Pierre
authors.initials: JP
authors.lastname: Jaubertie
authors.forename: Jérôme
authors.initials: J
authors.lastname: Auzanneau
authors.forename: Antje
authors.initials: A
authors.lastname: Rohde
authors.forename: Pieter B F
authors.initials: PB
authors.lastname: Ouwerkerk
authors.forename: Viktor
authors.initials: V
authors.lastname: Korzun
authors.forename: Sonja
authors.initials: S
authors.lastname: Kollers
authors.forename: Laurent
authors.initials: L
authors.lastname: Guerreiro
authors.forename: Delphine
authors.initials: D
authors.lastname: Hourcade
authors.forename: Olivier
authors.initials: O
authors.lastname: Robert
authors.forename: Pierre
authors.initials: P
authors.lastname: Devaux
authors.forename: Anna-Maria
authors.initials: AM
authors.lastname: Mastrangelo
authors.forename: Catherine
authors.initials: C
authors.lastname: Feuillet
authors.forename: Pierre
authors.initials: P
authors.lastname: Sourdille
authors.forename: Etienne
authors.initials: E
authors.lastname: Paux
mesh_terms: D018745:Genome, Plant; D055106:Genome-Wide Association Study; D005838:Genotype; D060005:Genotyping Techniques / Q000379:methods*; D020641:Polymorphism, Single Nucleotide / Q000235:genetics*; D012091:Repetitive Sequences, Nucleic Acid / Q000235:genetics*; D014908:Triticum / Q000145:classification / Q000235:genetics*