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

Publication Overview
TitleHighly-multiplexed SNP genotyping for genetic mapping and germplasm diversity studies in pea
AuthorsDeulvot C, Charrel H, Marty A, Jacquin F, Donnadieu C, Lejeune-Hénaut I, Burstin J, Aubert G
TypeJournal Article
Journal NameBMC genomics
Volume11
Year2010
Page(s)468
CitationDeulvot C, Charrel H, Marty A, Jacquin F, Donnadieu C, Lejeune-Hénaut I, Burstin J, Aubert G. Highly-multiplexed SNP genotyping for genetic mapping and germplasm diversity studies in pea. BMC genomics. 2010; 11:468.

Abstract

BACKGROUND
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.

RESULTS
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.

CONCLUSION
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.

Features
This publication contains information about 388 features:
Feature NameUniquenameType
FVE_SNP2FVE_SNP2genetic_marker
FVE_SNP3FVE_SNP3genetic_marker
FVE_SNP5FVE_SNP5genetic_marker
FVE_SNP6FVE_SNP6genetic_marker
Ga2ox_SNP1Ga2ox_SNP1genetic_marker
Ga2ox_SNP2Ga2ox_SNP2genetic_marker
GAL_SNP2GAL_SNP2genetic_marker
gbsts1_SNP1gbsts1_SNP1genetic_marker
gbsts2_SNP1gbsts2_SNP1genetic_marker
gbsts2_SNP2gbsts2_SNP2genetic_marker
GCSP_SNP1GCSP_SNP1genetic_marker
GCSP_SNP2GCSP_SNP2genetic_marker
Gibbi_SNP3Gibbi_SNP3genetic_marker
GNS2_SNP1GNS2_SNP1genetic_marker
GNS2_SNP2GNS2_SNP2genetic_marker
Gpt_SNP1Gpt_SNP1genetic_marker
Gpt_SNP2Gpt_SNP2genetic_marker
gpt2_SNP2gpt2_SNP2genetic_marker
GTPaseactiv_SNP2GTPaseactiv_SNP2genetic_marker
Hlhrep_SNP3Hlhrep_SNP3genetic_marker
Hlhrep_SNP4Hlhrep_SNP4genetic_marker
Hlhrep_SNP5Hlhrep_SNP5genetic_marker
Hlhrep_SNP6Hlhrep_SNP6genetic_marker
HO1_SNP1HO1_SNP1genetic_marker
Hsp70_SNP2Hsp70_SNP2genetic_marker

Pages

Featuremaps
This publication contains information about 1 maps:
Map Name
pea-CameorxChina-RIL
Properties
Additional details for this publication include:
Property NameValue
Publication ModelElectronic
ISSN1471-2164
eISSN1471-2164
Publication Date2010
Journal AbbreviationBMC Genomics
DOI10.1186/1471-2164-11-468
Elocation10.1186/1471-2164-11-468
Journal CountryEngland
LanguageEnglish
Language Abbreng
Publication TypeJournal Article