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
AAT1_SNP1AAT1_SNP1genetic_marker
abcisind_SNP1abcisind_SNP1genetic_marker
abcisind_SNP2abcisind_SNP2genetic_marker
abi3_SNP1abi3_SNP1genetic_marker
abi3_SNP2abi3_SNP2genetic_marker
acylcoAdehydro_SNP1acylcoAdehydro_SNP1genetic_marker
AGO1AGO1genetic_marker
agps1_SNP1agps1_SNP1genetic_marker
agps1_SNP3agps1_SNP3genetic_marker
agps2_SNP1agps2_SNP1genetic_marker
agps2_SNP3agps2_SNP3genetic_marker
agps2_SNP5agps2_SNP5genetic_marker
AIGP_SNP1AIGP_SNP1genetic_marker
aldo_SNP1aldo_SNP1genetic_marker
aldo_SNP2aldo_SNP2genetic_marker
aldo_SNP3aldo_SNP3genetic_marker
aldo_SNP4aldo_SNP4genetic_marker
anion-exchange_SNP1anion-exchange_SNP1genetic_marker
apyrase_SNP2apyrase_SNP2genetic_marker
Arf1350_SNP1Arf1350_SNP1genetic_marker
ArfB3_SNP1ArfB3_SNP1genetic_marker
ASN2_SNP1ASN2_SNP1genetic_marker
At2g44950_SNP1At2g44950_SNP1genetic_marker
Aux1_SNP1Aux1_SNP1genetic_marker
B2612_SNP1B2612_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
Cross References
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DatabaseAccession
PMID: PubMedPMID:20701750