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
Htrans_SNP1Htrans_SNP1genetic_marker
Htrans_SNP2Htrans_SNP2genetic_marker
Htrans_SNP3Htrans_SNP3genetic_marker
kdsa_SNP3kdsa_SNP3genetic_marker
leukotr_SNP2leukotr_SNP2genetic_marker
MitPhos_SNP2MitPhos_SNP2genetic_marker
MSU515_SNP2MSU515_SNP2genetic_marker
MSU515_SNP3MSU515_SNP3genetic_marker
MSU83_SNP1MSU83_SNP1genetic_marker
MSU83_SNP2MSU83_SNP2genetic_marker
N3like_SNP3N3like_SNP3genetic_marker
NAM_SNP2NAM_SNP2genetic_marker
nin_SNP2nin_SNP2genetic_marker
nin_SNP3nin_SNP3genetic_marker
NIP_SNP1NIP_SNP1genetic_marker
NIP_SNP3NIP_SNP3genetic_marker
non-phosphorylating-GAPDH_SNP2non-phosphorylating-GAPDH_SNP2genetic_marker
NTH1_SNP1NTH1_SNP1genetic_marker
NTH1_SNP3NTH1_SNP3genetic_marker
NTH1_SNP5NTH1_SNP5genetic_marker
NUM1_SNP2NUM1_SNP2genetic_marker
OEE3_SNP2OEE3_SNP2genetic_marker
OPA1_SNP1OPA1_SNP1genetic_marker
OPA1_SNP2OPA1_SNP2genetic_marker
P54_SNP1P54_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