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
B2665_SNP1B2665_SNP1genetic_marker
B3006_SNP1B3006_SNP1genetic_marker
BADH_SNP2BADH_SNP2genetic_marker
Bfruct_SNP1Bfruct_SNP1genetic_marker
Bfruct_SNP4Bfruct_SNP4genetic_marker
Bfruct_SNP7Bfruct_SNP7genetic_marker
CABBCABBgenetic_marker
Cabb_SNP1Cabb_SNP1genetic_marker
Cabb_SNP2Cabb_SNP2genetic_marker
Cdk3Cdk3genetic_marker
CE006G18_SNP1CE006G18_SNP1genetic_marker
CE007E18_SNP1CE007E18_SNP1genetic_marker
CE007H08_SNP1CE007H08_SNP1genetic_marker
CE007J22_SNP1CE007J22_SNP1genetic_marker
CE007K12_SNP1CE007K12_SNP1genetic_marker
CE007M24_SNP1CE007M24_SNP1genetic_marker
clp_SNP1clp_SNP1genetic_marker
CNE007I23_SNP1CNE007I23_SNP1genetic_marker
CNE007M06_SNP1CNE007M06_SNP1genetic_marker
CNGC4_SNP1CNGC4_SNP1genetic_marker
CYSK_SNP1CYSK_SNP1genetic_marker
CYSP_SNP1CYSP_SNP1genetic_marker
cystathionineGsynth_SNP1cystathionineGsynth_SNP1genetic_marker
DipeptIV_SNP1DipeptIV_SNP1genetic_marker
DipeptIV_SNP2DipeptIV_SNP2genetic_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