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
P54_SNP2P54_SNP2genetic_marker
PCT_SNP1PCT_SNP1genetic_marker
PCT_SNP2PCT_SNP2genetic_marker
pepC_SNP1pepC_SNP1genetic_marker
pepC_SNP2pepC_SNP2genetic_marker
pepC_SNP3pepC_SNP3genetic_marker
pepC_SNP4pepC_SNP4genetic_marker
pepC_SNP5pepC_SNP5genetic_marker
pepC_SNP6pepC_SNP6genetic_marker
pepC_SNP7pepC_SNP7genetic_marker
pepC_SNP8pepC_SNP8genetic_marker
pepC_SNP9pepC_SNP9genetic_marker
PFK_SNP2PFK_SNP2genetic_marker
PFK_SNP3PFK_SNP3genetic_marker
PFK_SNP4PFK_SNP4genetic_marker
PI_phosphatidylcholine_SNP3PI_phosphatidylcholine_SNP3genetic_marker
PIN1_SNP1PIN1_SNP1genetic_marker
PIN1_SNP2PIN1_SNP2genetic_marker
PIN1_SNP3PIN1_SNP3genetic_marker
pip1_SNP1pip1_SNP1genetic_marker
pip1_SNP3pip1_SNP3genetic_marker
pip2_SNP1pip2_SNP1genetic_marker
pip2_SNP2pip2_SNP2genetic_marker
pip2_SNP3pip2_SNP3genetic_marker
PlcSyn_SNP3PlcSyn_SNP3genetic_marker

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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