Highly-multiplexed SNP genotyping for genetic mapping and germplasm diversity studies in pea

BMC Genomics

Research Article

Cécile Donnadieu¹  Amandine Marty²  Isabelle Lejeune-Hénaut³  Françoise Jacquin⁴  Grégoire Aubert⁴  Chrystel Deulvot⁴  Hélène Charrel⁴  Judith Burstin⁴ 

[1] GENOTOUL Platform, INRA chemin de Borde-Rouge, BP52627, 31326, Auzeville, France;GENOTOUL Platform, INRA chemin de Borde-Rouge, BP52627, 31326, Auzeville, France;Euralis semences, Domaine de Sandreau, 31700, Mondonville, France;INRA SGV, UMR SADV, Estrées-Mons, BP 50136, 80203, Péronne, France;INRA UMRLEG, BP 86510, 21065, Dijon, France;

关键词: Mapping Population;    Single Nucleotide Polymorphism;    Germplasm Collection;    Recombinant Inbred Line Population;    Quality Mark;   

DOI  :  10.1186/1471-2164-11-468

 received in 2009-11-18, accepted in 2010-08-11,  发布年份 2010

来源: Springer

【 摘 要 】

BackgroundSingle 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.ResultsWe 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.ConclusionOur 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.

【 授权许可】

Unknown   
© Deulvot et al; licensee BioMed Central Ltd. 2010. This article is published under license to BioMed Central Ltd. This is an Open Access article distributed under the terms of the Creative Commons Attribution License (http://creativecommons.org/licenses/by/2.0), which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited.