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

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Relation http://oar.icrisat.org/8898/
http://dx.doi.org/10.1093/jxb/eru478
10.1093/jxb/eru478
 
Title Genome-wide conserved non-coding microsatellite (CNMS) marker-based integrative genetical genomics for quantitative dissection of seed weight in chickpea
 
Creator Bajaj, D
Saxena, M S
Kujur, A
Das, S
Badoni, S
Tripathi, S
Upadhyaya, H D
Gowda, C L L
Sharma, S
Singh, S
Tyagi, A K
Parida, S K
 
Subject Chickpea
 
Description 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.
 
Publisher Oxford University Press
 
Date 2015
 
Type Article
PeerReviewed
 
Format application/pdf
 
Language en
 
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Identifier http://oar.icrisat.org/8898/1/J.%20Exp.%20Bot.-2015-Bajaj-1271-90.pdf
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