title: Insertion site-based polymorphism markers open new perspectives for genome saturation and marker-assisted selection in wheat.
abstract: In wheat, the deployment of marker-assisted selection has long been hampered by the lack of markers compatible with high-throughput cost-effective genotyping techniques. Recently, insertion site-based polymorphism (ISBP) markers have appeared as very powerful new tools for genomics and genetic studies in hexaploid wheat. To demonstrate their possible use in wheat breeding programmes, we assessed their potential to meet the five main requirements for utilization in MAS: flexible and high-throughput detection methods, low quantity and quality of DNA required, low cost per assay, tight link to target loci and high level of polymorphism in breeding material. Toward this aim, we developed a programme, IsbpFinder, for the automated design of ISBP markers and adapted three detection methods (melting curve analysis, SNaPshot Multiplex System and Illumina BeadArray technology) for high throughput and flexible detection of ISBP or ISBP-derived SNP markers. We demonstrate that the high level of polymorphism of the ISBPs combined with cost-effective genotyping methods can be used to efficiently saturate genetic maps, discriminate between elite cultivars, and design tightly linked diagnostic markers for virtually all target loci in the wheat genome. All together, our results suggest that ISBP markers have the potential to lead to a breakthrough in wheat marker-assisted selection.
authors.affiliation: INRA UBP UMR 1095, Genetics, Diversity & Ecophysiology of Cereals, Clermont Ferrand, France. etienne.paux@clermont.inra.fr
authors.forename: Etienne
authors.initials: E
authors.lastname: Paux
authors.forename: Sébastien
authors.initials: S
authors.lastname: Faure
authors.forename: Frédéric
authors.initials: F
authors.lastname: Choulet
authors.forename: Delphine
authors.initials: D
authors.lastname: Roger
authors.forename: Valérie
authors.initials: V
authors.lastname: Gauthier
authors.forename: Jean-Pierre
authors.initials: JP
authors.lastname: Martinant
authors.forename: Pierre
authors.initials: P
authors.lastname: Sourdille
authors.forename: François
authors.initials: F
authors.lastname: Balfourier
authors.forename: Marie-Christine
authors.initials: MC
authors.lastname: Le Paslier
authors.forename: Aurélie
authors.initials: A
authors.lastname: Chauveau
authors.forename: Mehmet
authors.initials: M
authors.lastname: Cakir
authors.forename: Béatrice
authors.initials: B
authors.lastname: Gandon
authors.forename: Catherine
authors.initials: C
authors.lastname: Feuillet
mesh_terms: D001483:Base Sequence; D002874:Chromosome Mapping; D018744:DNA, Plant / Q000235:genetics; D018745:Genome, Plant; D023281:Genomics / Q000379:methods*; D005838:Genotype; D057166:High-Throughput Screening Assays; D008969:Molecular Sequence Data; D020641:Polymorphism, Single Nucleotide; D017422:Sequence Analysis, DNA / Q000379:methods*; D014908:Triticum / Q000235:genetics*
chemical_list: D018744:DNA, Plant