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
DipeptIV_SNP4DipeptIV_SNP4genetic_marker
Dof3_SNP1Dof3_SNP1genetic_marker
Dof4_SNP1Dof4_SNP1genetic_marker
Dof5_SNP1Dof5_SNP1genetic_marker
Dof6_SNP1Dof6_SNP1genetic_marker
Dof7_SNP1Dof7_SNP1genetic_marker
EFGC_SNP1EFGC_SNP1genetic_marker
Enod12B_SNP1Enod12B_SNP1genetic_marker
ENOD7_SNP1ENOD7_SNP1genetic_marker
EST158_SNP1EST158_SNP1genetic_marker
F3153_SNP1F3153_SNP1genetic_marker
F3586_SNP1F3586_SNP1genetic_marker
F4012_SNP2F4012_SNP2genetic_marker
F4023_SNP1F4023_SNP1genetic_marker
F448_SNP1F448_SNP1genetic_marker
FENR1_SNP1FENR1_SNP1genetic_marker
fibrillin_SNP1fibrillin_SNP1genetic_marker
fructose1-6-biphosph_SNP1fructose1-6-biphosph_SNP1genetic_marker
Ga20oxal_SNP1Ga20oxal_SNP1genetic_marker
GAL_SNP1GAL_SNP1genetic_marker
gamma-aminobutyrate-transa_SNP1gamma-aminobutyrate-transa_SNP1genetic_marker
Gibbi_SNP1Gibbi_SNP1genetic_marker
GK15_SNP1GK15_SNP1genetic_marker
GluSTrans_SNP1GluSTrans_SNP1genetic_marker
gpt2_SNP1gpt2_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