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
sbe2_SNP1sbe2_SNP1genetic_marker
sbe2_SNP3sbe2_SNP3genetic_marker
Selbin_SNP2Selbin_SNP2genetic_marker
Selbin_SNP3Selbin_SNP3genetic_marker
Selbin_SNP4Selbin_SNP4genetic_marker
Snrk1_SNP2Snrk1_SNP2genetic_marker
Snrk1_SNP3Snrk1_SNP3genetic_marker
Snrk1_SNP4Snrk1_SNP4genetic_marker
Snrk1_SNP5Snrk1_SNP5genetic_marker
SOD9_SNP1SOD9_SNP1genetic_marker
SOD9_SNP3SOD9_SNP3genetic_marker
SPS_SNP1SPS_SNP1genetic_marker
SPS_SNP2SPS_SNP2genetic_marker
SQEX_SNP2SQEX_SNP2genetic_marker
SS_SNP3SS_SNP3genetic_marker
SS_SNP4SS_SNP4genetic_marker
SS_SNP5SS_SNP5genetic_marker
St100044_SNP3St100044_SNP3genetic_marker
sts1_SNP1sts1_SNP1genetic_marker
sts1_SNP2sts1_SNP2genetic_marker
subt_SNP2subt_SNP2genetic_marker
Sucsyn_SNP1Sucsyn_SNP1genetic_marker
Sugtrans_SNP3Sugtrans_SNP3genetic_marker
SUI1H_SNP2SUI1H_SNP2genetic_marker
sus3_SNP1sus3_SNP1genetic_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