Genome-wide conserved non-coding microsatellite (CNMS) marker-based integrative genetical genomics for quantitative dissection of seed weight in chickpea

Bajaj, D and Saxena, M S and Kujur, A and Das, S and Badoni, S and Tripathi, S and Upadhyaya, H D and Gowda, C L L and Sharma, S and Singh, S and Tyagi, A K and Parida, S K (2015) Genome-wide conserved non-coding microsatellite (CNMS) marker-based integrative genetical genomics for quantitative dissection of seed weight in chickpea. Journal of Experimental Botany, 66 (5). pp. 1271-1290. ISSN 0022-0957

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Abstract

Phylogenetic footprinting identified 666 genome-wide paralogous and orthologous CNMS (conserved non-coding microsatellite) markers from 5′-untranslated and regulatory regions (URRs) of 603 protein-coding chickpea genes. The (CT)n and (GA)n CNMS carrying CTRMCAMV35S and GAGA8BKN3 regulatory elements, respectively, are abundant in the chickpea genome. The mapped genic CNMS markers with robust amplification efficiencies (94.7%) detected higher intraspecific polymorphic potential (37.6%) among genotypes, implying their immense utility in chickpea breeding and genetic analyses. Seventeen differentially expressed CNMS marker-associated genes showing strong preferential and seed tissue/developmental stage-specific expression in contrasting genotypes were selected to narrow down the gene targets underlying seed weight quantitative trait loci (QTLs)/eQTLs (expression QTLs) through integrative genetical genomics. The integration of transcript profiling with seed weight QTL/eQTL mapping, molecular haplotyping, and association analyses identified potential molecular tags (GAGA8BKN3 and RAV1AAT regulatory elements and alleles/haplotypes) in the LOB-domain-containing protein- and KANADI protein-encoding transcription factor genes controlling the cis-regulated expression for seed weight in the chickpea. This emphasizes the potential of CNMS marker-based integrative genetical genomics for the quantitative genetic dissection of complex seed weight in chickpea.

Item Type: Article
Divisions: RP-Grain Legumes
CRP: CGIAR Research Program on Grain Legumes
Uncontrolled Keywords: Chickpea; Cicer arietinum; CNMS; eQTLs; Microsatellites; Seed weight; SNPs; Transcription factor
Subjects: Mandate crops > Chickpea
Depositing User: Mr Ramesh K
Date Deposited: 27 Jul 2015 07:58
Last Modified: 21 Oct 2016 06:25
URI: http://oar.icrisat.org/id/eprint/8898
Official URL: http://dx.doi.org/10.1093/jxb/eru478
Projects: UNSPECIFIED
Funders: UNSPECIFIED
Acknowledgement: UNSPECIFIED
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