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

Overview

Journal DNA Res

Publisher Oxford University Press

Specialties Genetics
Molecular Biology

Date 2014 Oct 23

PMID 25335477

Citations 45

Authors

Maneesha S Saxena

Deepak Bajaj

Shouvik Das

Alice Kujur

Vinod Kumar

Mohar Singh

Kailash C Bansal

Akhilesh K Tyagi

Swarup K Parida

Affiliations

Soon will be listed here.

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.

Citing Articles

Genetic mapping of quantitative trait loci associated with drought tolerance in chickpea (Cicer arietinum L.).

Yadava Y, Chaudhary P, Yadav S, Rizvi A, Kumar T, Srivastava R Sci Rep. 2023; 13(1):17623.

PMID: 37848483 PMC: 10582051. DOI: 10.1038/s41598-023-44990-y.

Marker trait association for biological nitrogen fixation traits in an interspecific cross of chickpea ().

Nagpal S, Sirari A, Sharma P, Singh S, Mandahal K, Singh H Physiol Mol Biol Plants. 2023; 29(7):1005-1018.

PMID: 37649881 PMC: 10462594. DOI: 10.1007/s12298-023-01335-3.

A superior gene allele involved in abscisic acid signaling enhances drought tolerance and yield in chickpea.

Thakro V, Malik N, Basu U, Srivastava R, Narnoliya L, Daware A Plant Physiol. 2022; 191(3):1884-1912.

PMID: 36477336 PMC: 10022645. DOI: 10.1093/plphys/kiac550.

An integrated transcriptome mapping the regulatory network of coding and long non-coding RNAs provides a genomics resource in chickpea.

Jain M, Bansal J, Singh Rajkumar M, Garg R Commun Biol. 2022; 5(1):1106.

PMID: 36261617 PMC: 9581958. DOI: 10.1038/s42003-022-04083-4.

Genome-wide analysis suggests the potential role of lncRNAs during seed development and seed size/weight determination in chickpea.

Khemka N, Singh Rajkumar M, Garg R, Jain M Planta. 2022; 256(4):79.

PMID: 36094579 DOI: 10.1007/s00425-022-03986-0.

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