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
GTPaseactiv_SNP1GTPaseactiv_SNP1genetic_marker
HATPS_SNP2HATPS_SNP2genetic_marker
Hlhrep_SNP1Hlhrep_SNP1genetic_marker
HRIP_SNP1HRIP_SNP1genetic_marker
Hsp70_SNP1Hsp70_SNP1genetic_marker
Kao2_SNP2Kao2_SNP2genetic_marker
kdsa_SNP1kdsa_SNP1genetic_marker
Lb5-10_SNP1Lb5-10_SNP1genetic_marker
leukotr_SNP1leukotr_SNP1genetic_marker
Lhcb3_SNP2Lhcb3_SNP2genetic_marker
MitPhos_SNP1MitPhos_SNP1genetic_marker
MTU04_SNP1MTU04_SNP1genetic_marker
Myb1_SNP1Myb1_SNP1genetic_marker
NAM_SNP1NAM_SNP1genetic_marker
non-phosphorylating-GAPDH_SNP1non-phosphorylating-GAPDH_SNP1genetic_marker
NTRB1_SNP1NTRB1_SNP1genetic_marker
NUM1_SNP1NUM1_SNP1genetic_marker
OEE3_SNP1OEE3_SNP1genetic_marker
OPT_SNP1OPT_SNP1genetic_marker
peptrans_SNP1peptrans_SNP1genetic_marker
peptrans_SNP2peptrans_SNP2genetic_marker
PFK_SNP1PFK_SNP1genetic_marker
PI_phosphatidylcholine_SNP2PI_phosphatidylcholine_SNP2genetic_marker
PIN1PIN1genetic_marker
PlcSyn_SNP1PlcSyn_SNP1genetic_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