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
PSDof2_SNP1PSDof2_SNP1genetic_marker
PSDof2_SNP2PSDof2_SNP2genetic_marker
PSDof2_SNP3PSDof2_SNP3genetic_marker
PSDof2_SNP4PSDof2_SNP4genetic_marker
Psst70_SNP2Psst70_SNP2genetic_marker
Ptrans_SNP1Ptrans_SNP1genetic_marker
Ptrans_SNP2Ptrans_SNP2genetic_marker
Ptrans_SNP4Ptrans_SNP4genetic_marker
Puttip_SNP1Puttip_SNP1genetic_marker
Puttip_SNP2Puttip_SNP2genetic_marker
Puttip_SNP3Puttip_SNP3genetic_marker
RBBP_SNP3RBBP_SNP3genetic_marker
rbcs_SNP1rbcs_SNP1genetic_marker
rbcs_SNP3rbcs_SNP3genetic_marker
rbcs_SNP4rbcs_SNP4genetic_marker
rfs_SNP1rfs_SNP1genetic_marker
rfs_SNP3rfs_SNP3genetic_marker
rfs_SNP4rfs_SNP4genetic_marker
rgp_SNP1rgp_SNP1genetic_marker
rgp_SNP2rgp_SNP2genetic_marker
rgp_SNP3rgp_SNP3genetic_marker
RNAH_SNP3RNAH_SNP3genetic_marker
RNAH_SNP4RNAH_SNP4genetic_marker
sbe1_SNP3sbe1_SNP3genetic_marker
sbe1_SNP4sbe1_SNP4genetic_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