An Integrated Genomic Approach for Rapid Delineation of Candidate Genes Regulating Agro-Morphological Traits in Chickpea

Publication Overview
TitleAn Integrated Genomic Approach for Rapid Delineation of Candidate Genes Regulating Agro-Morphological Traits in Chickpea
AuthorsSaxena MS, Bajaj D, Das S, Kujur A, Kumar V, Singh M, Bansal KC, Tyagi AK, Parida SK
TypeJournal Article
Journal NameDNA research : an international journal for rapid publication of reports on genes and genomes
Year2014
CitationSaxena MS, Bajaj D, Das S, Kujur A, Kumar V, Singh M, Bansal KC, Tyagi AK, Parida SK. An Integrated Genomic Approach for Rapid Delineation of Candidate Genes Regulating Agro-Morphological Traits in Chickpea. DNA research : an international journal for rapid publication of reports on genes and genomes. 2014 Oct 21.

Abstract

The identification and fine mapping of robust quantitative trait loci (QTLs)/genes governing important agro-morphological traits in chickpea still lacks systematic efforts at a genome-wide scale involving wild Cicer accessions. In this context, an 834 simple sequence repeat and single-nucleotide polymorphism marker-based high-density genetic linkage map between cultivated and wild parental accessions (Cicer arietinum desi cv. ICC 4958 and Cicer reticulatum wild cv. ICC 17160) was constructed. This inter-specific genetic map comprising eight linkage groups spanned a map length of 949.4 cM with an average inter-marker distance of 1.14 cM. Eleven novel major genomic regions harbouring 15 robust QTLs (15.6-39.8% R(2) at 4.2-15.7 logarithm of odds) associated with four agro-morphological traits (100-seed weight, pod and branch number/plant and plant hairiness) were identified and mapped on chickpea chromosomes. Most of these QTLs showed positive additive gene effects with effective allelic contribution from ICC 4958, particularly for increasing seed weight (SW) and pod and branch number. One robust SW-influencing major QTL region (qSW4.2) has been narrowed down by combining QTL mapping with high-resolution QTL region-specific association analysis, differential expression profiling and gene haplotype-based association/LD mapping. This enabled to delineate a strong SW-regulating ABI3VP1 transcription factor (TF) gene at trait-specific QTL interval and consequently identified favourable natural allelic variants and superior high seed weight-specific haplotypes in the upstream regulatory region of this gene showing increased transcript expression during seed development. The genes (TFs) harbouring diverse trait-regulating QTLs, once validated and fine-mapped by our developed rapid integrated genomic approach and through gene/QTL map-based cloning, can be utilized as potential candidates for marker-assisted genetic enhancement of chickpea.

Features
This publication contains information about 934 features:
Feature NameUniquenameType
NIPGR_CaSSR401NIPGR_CaSSR401genetic_marker
NIPGR_CaSSR402NIPGR_CaSSR402genetic_marker
NIPGR_CaSSR403NIPGR_CaSSR403genetic_marker
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NIPGR_CaSSR406NIPGR_CaSSR406genetic_marker
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NIPGR_CaSSR408NIPGR_CaSSR408genetic_marker
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NIPGR_CaSSR412NIPGR_CaSSR412genetic_marker
NIPGR_CaSSR413NIPGR_CaSSR413genetic_marker
NIPGR_CaSSR414NIPGR_CaSSR414genetic_marker
NIPGR_CaSSR415NIPGR_CaSSR415genetic_marker
NIPGR_CaSSR416NIPGR_CaSSR416genetic_marker
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NIPGR_CaSSR419NIPGR_CaSSR419genetic_marker
NIPGR_CaSSR420NIPGR_CaSSR420genetic_marker
NIPGR_CaSSR421NIPGR_CaSSR421genetic_marker
NIPGR_CaSSR422NIPGR_CaSSR422genetic_marker
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NIPGR_CaSSR424NIPGR_CaSSR424genetic_marker
NIPGR_CaSSR425NIPGR_CaSSR425genetic_marker

Pages

Projects
This publication contains information about 1 projects:
Project NameDescription
Chickpea-Agronomic_traits-Saxena-2014
Featuremaps
This publication contains information about 1 maps:
Map Name
Chickpea-ICC4958/ICC17160-F7-RIL
Stocks
This publication contains information about 1 stocks:
Stock NameUniquenameType
ICC4958/ICC17160-F7-RILICC4958/ICC17160-F7-RILpopulation
Properties
Additional details for this publication include:
Property NameValue
Publication ModelPrint-Electronic
ISSN1756-1663
eISSN1756-1663
Publication Date2014 Oct 21
Journal AbbreviationDNA Res.
Elocationdsu031
Copyright© The Author 2014. Published by Oxford University Press on behalf of Kazusa DNA Research Institute.
LanguageEnglish
Language AbbrENG
Publication TypeJournal Article