Exploiting the Repetitive Fraction of the Wheat Genome for High‐Throughput Single‐Nucleotide Polymorphism Discovery and Genotyping
Year: 2016
Type: article
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.
Source: The Plant Genome
Authors: Nelly Cubizolles, Elodie Rey, Frédéric Choulet, Hélène Rimbert, Christel Laugier, François Balfourier, Jacques Bordes, Charles Poncet, Peter Jack, Chris James, Jan Gielen, Odile Argillier, Jean‐Pierre Jaubertie, Jérôme Auzanneau, Antje Rohde, Pieter B.F. Ouwerkerk, Viktor Korzun, Sonja Kollers, Laurent Guerreiro, Delphine Hourcade, Olivier Robert, Pierre Devaux, Anna‐Maria Mastrangelo, Catherine Feuillet, Pierre Sourdille, Etienne Paux
Institutions: Biogemma (France), Génétique, Diversité, Écophysiologie des Céréales, Institut National de la Recherche Agronomique, Université Blaise Pascal, Centre of the Region Haná for Biotechnical and Agricultural Research, RAGT Seeds (United Kingdom), Syngenta (France), Agri Obtentions (France), Arvalis - Institut du Végétal, Cereal Research Centre, Consiglio per la ricerca in agricoltura e l’analisi dell’economia agraria
Language: English
Subfield: Plant Science
Domain: Life Sciences
SDG: Zero hunger
Open Access status: gold
Estimated APC paid: $3,140
OpenAlex ID: W2417620759