Highly-multiplexed SNP genotyping for genetic mapping and germplasm diversity studies in pea
1 INRA UMRLEG, BP 86510, 21065 Dijon, France
2 GENOTOUL Platform, INRA chemin de Borde-Rouge BP52627 31326 Auzeville, France
3 INRA SGV, UMR SADV, Estrées-Mons BP 50136, 80203 Péronne, France
4 Euralis semences, Domaine de Sandreau, 31700 Mondonville, France
BMC Genomics 2010, 11:468 doi:10.1186/1471-2164-11-468Published: 11 August 2010
Single Nucleotide Polymorphisms (SNPs) can be used as genetic markers for applications such as genetic diversity studies or genetic mapping. New technologies now allow genotyping hundreds to thousands of SNPs in a single reaction.
In order to evaluate the potential of these technologies in pea, we selected a custom 384-SNP set using SNPs discovered in Pisum through the resequencing of gene fragments in different genotypes and by compiling genomic sequence data present in databases. We then designed an Illumina GoldenGate assay to genotype both a Pisum germplasm collection and a genetic mapping population with the SNP set.
We obtained clear allelic data for more than 92% of the SNPs (356 out of 384). Interestingly, the technique was successful for all the genotypes present in the germplasm collection, including those from species or subspecies different from the P. sativum ssp sativum used to generate sequences. By genotyping the mapping population with the SNP set, we obtained a genetic map and map positions for 37 new gene markers.
Our results show that the Illumina GoldenGate assay can be used successfully for high-throughput SNP genotyping of diverse germplasm in pea. This genotyping approach will simplify genotyping procedures for association mapping or diversity studies purposes and open new perspectives in legume genomics.