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
PM34like_SNP1PM34like_SNP1genetic_marker
PM34like_SNP2PM34like_SNP2genetic_marker
pore_SNP1pore_SNP1genetic_marker
ppgm_SNP1ppgm_SNP1genetic_marker
ppgm_SNP2ppgm_SNP2genetic_marker
ppgm_SNP3ppgm_SNP3genetic_marker
PPT1_SNP2PPT1_SNP2genetic_marker
PPT1_SNP3PPT1_SNP3genetic_marker
PPT2_SNP2PPT2_SNP2genetic_marker
PPT2_SNP3PPT2_SNP3genetic_marker
ProteasB_SNP2ProteasB_SNP2genetic_marker
PsAAP1_SNP1PsAAP1_SNP1genetic_marker
PsAAP1_SNP3PsAAP1_SNP3genetic_marker
PsAAP1_SNP4PsAAP1_SNP4genetic_marker
PsAAP2_SNP2PsAAP2_SNP2genetic_marker
PsAAP2_SNP3PsAAP2_SNP3genetic_marker
PsAAP2_SNP4PsAAP2_SNP4genetic_marker
PsAS1_SNP2PsAS1_SNP2genetic_marker
PsAS1_SNP3PsAS1_SNP3genetic_marker
PsAS1_SNP5PsAS1_SNP5genetic_marker
PsAS2_SNP1PsAS2_SNP1genetic_marker
PsAS2_SNP3PsAS2_SNP3genetic_marker
PsDmi1_SNP3PsDmi1_SNP3genetic_marker
PsDof1_SNP2PsDof1_SNP2genetic_marker
PsDof1_SNP3PsDof1_SNP3genetic_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