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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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Title Genome-wide conserved non-coding microsatellite (CNMS) marker-based integrative genetical genomics for quantitative dissection of seed weight in chickpea
 
Creator Bajaj, Deepak
Saxena, Maneesha S.
Kujur, Alice
Das, Shouvik
Badoni, Saurabh
Tripathi, Shailesh
Upadhyaya, Hari D.
Gowda, C. L. L.
Sharma, Shivali
Singh, Sube
Tyagi, Akhilesh K.
Parida, Swarup K.
 
Subject Chickpea
Cicer arietinum
CNMS
eQTLs
microsatellites
seed weight
SNPs
transcription factor
 
Description Accepted date: 31 October 2014
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.
The authors gratefully acknowledge the financial support of the Department
of Biotechnology (DBT), Government of India, through their research
grant (102/IFD/SAN/2161/2013–14) for this research work. AK and SD
acknowledge the CSIR (Council of Scientific and Industrial Research) and
DBT for the award of Senior/Junior Research Fellowships. We thank the
DNA Sequencing Facility, NIPGR for the automated fragment analysis and
sequencing. We are grateful to the editor and reviewers for critically evaluating the manuscript and providing constructive comments for its improvement.
 
Date 2016-01-01T06:08:16Z
2016-01-01T06:08:16Z
2015
 
Type Article
 
Identifier J. Exp. Bot., 66(5): 1271-1290
1460-2431
http://172.16.0.77:8080/jspui/handle/123456789/487
http://jxb.oxfordjournals.org/content/66/5/1271
10.1093/jxb/eru478
 
Language en_US
 
Publisher Oxford University Press