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
TNE003A07_SNP1TNE003A07_SNP1genetic_marker
TNE003F15_SNP1TNE003F15_SNP1genetic_marker
tRALs_SNP1tRALs_SNP1genetic_marker
TRPT_SNP1TRPT_SNP1genetic_marker
TUP_SNP1TUP_SNP1genetic_marker
ACCox_SNP1ACCox_SNP1genetic_marker
ACCox_SNP2ACCox_SNP2genetic_marker
ACCox_SNP3ACCox_SNP3genetic_marker
ACCox2_SNP1ACCox2_SNP1genetic_marker
ACCox2_SNP2ACCox2_SNP2genetic_marker
Acetisom_SNP1Acetisom_SNP1genetic_marker
Acetisom_SNP3Acetisom_SNP3genetic_marker
ADH1_SNP1ADH1_SNP1genetic_marker
ADH1_SNP2ADH1_SNP2genetic_marker
AGO1_SNP1AGO1_SNP1genetic_marker
AGO1_SNP2AGO1_SNP2genetic_marker
AGO1_SNP5AGO1_SNP5genetic_marker
agpl1_SNP1agpl1_SNP1genetic_marker
agpl1_SNP2agpl1_SNP2genetic_marker
apyrase_SNP4apyrase_SNP4genetic_marker
Aux1_SNP2Aux1_SNP2genetic_marker
BGAL_SNP1BGAL_SNP1genetic_marker
BGAL_SNP2BGAL_SNP2genetic_marker
CALTL_SNP2CALTL_SNP2genetic_marker
CALTL_SNP3CALTL_SNP3genetic_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