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
sus3_SNP5sus3_SNP5genetic_marker
sus3_SNP8sus3_SNP8genetic_marker
sut1_SNP1sut1_SNP1genetic_marker
sut1_SNP2sut1_SNP2genetic_marker
sut1_SNP3sut1_SNP3genetic_marker
sym10_SNP2sym10_SNP2genetic_marker
sym10_SNP3sym10_SNP3genetic_marker
sym10_SNP4sym10_SNP4genetic_marker
TE002G22_SNP3TE002G22_SNP3genetic_marker
TE002I21_SNP3TE002I21_SNP3genetic_marker
TE002K12_SNP4TE002K12_SNP4genetic_marker
TE002O11_SNP1TE002O11_SNP1genetic_marker
TE019_SNP2TE019_SNP2genetic_marker
TE019_SNP3TE019_SNP3genetic_marker
TFL1c_SNP2TFL1c_SNP2genetic_marker
TFL1c_SNP4TFL1c_SNP4genetic_marker
ThiorPer_SNP2ThiorPer_SNP2genetic_marker
tip_SNP1tip_SNP1genetic_marker
tip_SNP2tip_SNP2genetic_marker
Tir1_SNP1Tir1_SNP1genetic_marker
Tir1_SNP2Tir1_SNP2genetic_marker
Tir1_SNP3Tir1_SNP3genetic_marker
TNE003F15_SNP3TNE003F15_SNP3genetic_marker
TNE003F15_SNP4TNE003F15_SNP4genetic_marker
Tpe4A_SNP1Tpe4A_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