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
polyAbinding_SNP1polyAbinding_SNP1genetic_marker
PPDK_SNP1PPDK_SNP1genetic_marker
PPH_SNP1PPH_SNP1genetic_marker
PPT1_SNP1PPT1_SNP1genetic_marker
PPT2_SNP1PPT2_SNP1genetic_marker
ProteasB_SNP1ProteasB_SNP1genetic_marker
PRTS_SNP2PRTS_SNP2genetic_marker
PsDmi1_SNP1PsDmi1_SNP1genetic_marker
Psst70_SNP1Psst70_SNP1genetic_marker
putprot1_SNP1putprot1_SNP1genetic_marker
RBBP_SNP1RBBP_SNP1genetic_marker
RBPCO_SNP1RBPCO_SNP1genetic_marker
RNAhel_SNP1RNAhel_SNP1genetic_marker
RNAhel_SNP2RNAhel_SNP2genetic_marker
RNAR_SNP1RNAR_SNP1genetic_marker
RNP_SNP1RNP_SNP1genetic_marker
sbe1_SNP1sbe1_SNP1genetic_marker
Selbin_SNP1Selbin_SNP1genetic_marker
SGR_SNP1SGR_SNP1genetic_marker
SLNSLNgenetic_marker
Snrk1_SNP1Snrk1_SNP1genetic_marker
SQEX_SNP1SQEX_SNP1genetic_marker
St100044_SNP2St100044_SNP2genetic_marker
St106463_SNP2St106463_SNP2genetic_marker
subt_SNP1subt_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