title: High-throughput single nucleotide polymorphism genotyping in wheat (Triticum spp.).
abstract: Over the past few years, considerable progress has been made in high-throughput single nucleotide polymorphism (SNP) genotyping technologies, largely through the investment of the human genetics community. These technologies are well adapted to diploid species. For plant breeding purposes, it is important to determine whether these genotyping methods are adapted to polyploidy, as most major crops are former or recent polyploids. To address this problem, we tested the capacity of the multiplex technology SNPlex with a set of 47 wheat SNPs to genotype DNAs of 1314 lines that were organized in four 384-well plates. These lines represented different taxa of tetra- and hexaploid Triticum species and their wild diploid relatives. We observed 40 markers which gave less than 20% missing data. Different methods, based on either Sanger sequencing or the MassARRAY genotyping technology, were then used to validate the genotypes obtained by SNPlex for 11 markers. The concordance of the genotypes obtained by SNPlex with the results obtained by the different validation methods was 96%, except for one discarded marker. Furthermore, a mapping study on six markers showed the expected genetic positions previously described. To conclude, this study showed that high-throughput genotyping technologies developed for diploid species can be used successfully in polyploids, although there is a need for manual reading. For the first time in wheat species, a core of 39 SNPs is available that can serve as the basis for the development of a complete SNPlex set of 48 markers.
authors.affiliation: INRA, UR1279 Etude du Polymorphisme des Génomes Végétaux, CEA-IG/Centre National de Génotypage, 2 rue Gaston Crémieux, CP5724, F-91057 Evry, France.
authors.forename: Aurélie
authors.initials: A
authors.lastname: Bérard
authors.forename: Marie Christine
authors.initials: MC
authors.lastname: Le Paslier
authors.forename: Mireille
authors.initials: M
authors.lastname: Dardevet
authors.forename: Florence
authors.initials: F
authors.lastname: Exbrayat-Vinson
authors.forename: Isabelle
authors.initials: I
authors.lastname: Bonnin
authors.forename: Alberto
authors.initials: A
authors.lastname: Cenci
authors.forename: Annabelle
authors.initials: A
authors.lastname: Haudry
authors.forename: Dominique
authors.initials: D
authors.lastname: Brunel
authors.forename: Catherine
authors.initials: C
authors.lastname: Ravel
mesh_terms: D018744:DNA, Plant / Q000235:genetics; D005819:Genetic Markers; D018745:Genome, Plant; D005838:Genotype; D020641:Polymorphism, Single Nucleotide; D011123:Polyploidy; D017422:Sequence Analysis, DNA / Q000379:methods*; D014908:Triticum / Q000235:genetics*
chemical_list: D018744:DNA, Plant; D005819:Genetic Markers