High-density linkage map construction and mapping of seed trait QTLs in chickpea (Cicer arietinum L.) using Genotyping-by-Sequencing (GBS)

Publication Overview
TitleHigh-density linkage map construction and mapping of seed trait QTLs in chickpea (Cicer arietinum L.) using Genotyping-by-Sequencing (GBS)
AuthorsVerma S, Gupta S, Bandhiwal N, Kumar T, Bharadwaj C, Bhatia S
TypeJournal Article
Journal NameScientific reports
Volume5
Year2015
Page(s)17512
CitationVerma S, Gupta S, Bandhiwal N, Kumar T, Bharadwaj C, Bhatia S. High-density linkage map construction and mapping of seed trait QTLs in chickpea (Cicer arietinum L.) using Genotyping-by-Sequencing (GBS). Scientific reports. 2015; 5:17512.

Abstract

This study reports the use of Genotyping-by-Sequencing (GBS) for large-scale SNP discovery and simultaneous genotyping of recombinant inbred lines (RILs) of an intra-specific mapping population of chickpea contrasting for seed traits. A total of 119,672 raw SNPs were discovered, which after stringent filtering revealed 3,977 high quality SNPs of which 39.5% were present in genic regions. Comparative analysis using physically mapped marker loci revealed a higher degree of synteny with Medicago in comparison to soybean. The SNP genotyping data was utilized to construct one of the most saturated intra-specific genetic linkage maps of chickpea having 3,363 mapped positions including 3,228 SNPs on 8 linkage groups spanning 1006.98 cM at an average inter marker distance of 0.33 cM. The map was utilized to identify 20 quantitative trait loci (QTLs) associated with seed traits accounting for phenotypic variations ranging from 9.97% to 29.71%. Analysis of the genomic sequence corresponding to five robust QTLs led to the identification of 684 putative candidate genes whose expression profiling revealed that 101 genes exhibited seed specific expression. The integrated approach utilizing the identified QTLs along with the available genome and transcriptome could serve as a platform for candidate gene identification for molecular breeding of chickpea.

Features
This publication contains information about 3,994 features:
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CaGSNP3323CaGSNP3323genetic_marker
CaGSNP3324CaGSNP3324genetic_marker
CaGSNP3325CaGSNP3325genetic_marker

Pages

Projects
This publication contains information about 1 projects:
Project NameDescription
Chickpea-Seed_traits-Verma-2015
Featuremaps
This publication contains information about 1 maps:
Map Name
Chickpea-SBD377/BGD112-RIL-High_density
Properties
Additional details for this publication include:
Property NameValue
Publication ModelElectronic
ISSN2045-2322
eISSN2045-2322
Publication Date2015
Journal AbbreviationSci Rep
DOI10.1038/srep17512
Elocation10.1038/srep17512
LanguageEnglish
Language Abbreng
Publication TypeJournal Article
Journal CountryEngland
Publication TypeResearch Support, Non-U.S. Gov't