A genome-wide SNP scan accelerates trait-regulatory genomic loci identification in chickpea

Publication Overview
TitleA genome-wide SNP scan accelerates trait-regulatory genomic loci identification in chickpea
AuthorsKujur A, Bajaj D, Upadhyaya HD, Das S, Ranjan R, Shree T, Saxena MS, Badoni S, Kumar V, Tripathi S, Gowda CLL, Sharma S, Singh S, Tyagi AK, Parida SK
TypeJournal Article
Journal NameScientific Reports
Volume5
Year2015
Page(s)11166
CitationKujur A, Bajaj D, Upadhyaya HD, Das S, Ranjan R, Shree T, Saxena MS, Badoni S, Kumar V, Tripathi S, Gowda CLL, Sharma S, Singh S, Tyagi AK, Parida SK. A genome-wide SNP scan accelerates trait-regulatory genomic loci identification in chickpea. Scientific Reports. 2015; 5:11166.

Abstract

We identified 44844 high-quality SNPs by sequencing 92 diverse chickpea accessions belonging to a seed and pod trait-specific association panel using reference genome- and de novo-based GBS (genotyping-by-sequencing) assays. A GWAS (genome-wide association study) in an association panel of 211, including the 92 sequenced accessions, identified 22 major genomic loci showing significant association (explaining 23–47% phenotypic variation) with pod and seed number/plant and 100-seed weight. Eighteen trait-regulatory major genomic loci underlying 13 robust QTLs were validated and mapped on an intra-specific genetic linkage map by QTL mapping. A combinatorial approach of GWAS, QTL mapping and gene haplotype-specific LD mapping and transcript profiling uncovered one superior haplotype and favourable natural allelic variants in the upstream regulatory region of a CesA-type cellulose synthase (Ca_Kabuli_CesA3) gene regulating high pod and seed number/ plant (explaining 47% phenotypic variation) in chickpea. The up-regulation of this superior gene haplotype correlated with increased transcript expression of Ca_Kabuli_CesA3 gene in the pollen and pod of high pod/seed number accession, resulting in higher cellulose accumulation for normal pollen and pollen tube growth. A rapid combinatorial genome-wide SNP genotyping-based approach has potential to dissect complex quantitative agronomic traits and delineate trait-regulatory genomic loci (candidate genes) for genetic enhancement in crop plants, including chickpea.
Features
This publication contains information about 310 features:
Feature NameUniquenameType
NIPGR_CaSNP0001NIPGR_CaSNP0001genetic_marker
NIPGR_CaSNP0002NIPGR_CaSNP0002genetic_marker
NIPGR_CaSNP0003NIPGR_CaSNP0003genetic_marker
NIPGR_CaSNP0004NIPGR_CaSNP0004genetic_marker
NIPGR_CaSNP0005NIPGR_CaSNP0005genetic_marker
NIPGR_CaSNP0006NIPGR_CaSNP0006genetic_marker
NIPGR_CaSNP0007NIPGR_CaSNP0007genetic_marker
NIPGR_CaSNP0008NIPGR_CaSNP0008genetic_marker
NIPGR_CaSNP0009NIPGR_CaSNP0009genetic_marker
NIPGR_CaSNP0010NIPGR_CaSNP0010genetic_marker
NIPGR_CaSNP0011NIPGR_CaSNP0011genetic_marker
NIPGR_CaSNP0012NIPGR_CaSNP0012genetic_marker
NIPGR_CaSNP0013NIPGR_CaSNP0013genetic_marker
NIPGR_CaSNP0014NIPGR_CaSNP0014genetic_marker
NIPGR_CaSNP0015NIPGR_CaSNP0015genetic_marker
NIPGR_CaSNP0016NIPGR_CaSNP0016genetic_marker
NIPGR_CaSNP0017NIPGR_CaSNP0017genetic_marker
NIPGR_CaSNP0018NIPGR_CaSNP0018genetic_marker
NIPGR_CaSNP0019NIPGR_CaSNP0019genetic_marker
NIPGR_CaSNP0020NIPGR_CaSNP0020genetic_marker
NIPGR_CaSNP0021NIPGR_CaSNP0021genetic_marker
NIPGR_CaSNP0022NIPGR_CaSNP0022genetic_marker
NIPGR_CaSNP0023NIPGR_CaSNP0023genetic_marker
NIPGR_CaSNP0024NIPGR_CaSNP0024genetic_marker
NIPGR_CaSNP0025NIPGR_CaSNP0025genetic_marker

Pages

Projects
This publication contains information about 1 projects:
Project NameDescription
Chickpea-Yield-Kujur-2015
Featuremaps
This publication contains information about 1 maps:
Map Name
Chickpea-ICC6013/ICC7346-F4
Stocks
This publication contains information about 1 stocks:
Stock NameUniquenameType
ICC6013/ICC7346-F4ICC6013/ICC7346-F4population
Properties
Additional details for this publication include:
Property NameValue
URLhttps://www.ncbi.nlm.nih.gov/pmc/articles/PMC4461920/