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CNMS: The preferred genic markers for comparative genomic, molecular phylogenetic, functional genetic diversity and differential gene regulatory expression analyses in chickpea

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Title CNMS: The preferred genic markers for comparative genomic, molecular phylogenetic, functional genetic diversity and differential gene regulatory expression analyses in chickpea
 
Creator Bajaj, Deepak
Das, Shouvik
Parida, Swarup K.
 
Subject Chickpea
CNMS
comparative genome mapping
microsatellites
orthologous
paralogous
phylogeny
subfunctionalization
 
Description Accepted date:03 July 2015
The intra/inter-genomic comparative mapping-based phylogenetic footprinting identified 5 paralogous and 656 orthologous genome-wide CNMS markers in the upstream sequences of chickpea genes. These CNMS markers revealed a high-degree of gene-based syntenic relationship between chickpea and Medicago genomes while minimum between chickpea and Vitis genomes. The time of divergence and duplication estimated using CNMS markers highlight the expected phylogenetic relationships between chickpea and six dicot (legume) species as well as occurrence of ancient genome (approximately 53 Mya) with small-scale recent segmental (approximately 10 Mya) duplication events in chickpea. A wider level of functional molecular diversity (14 to 88 percent) and admixed population genetic structure was detected among desi, kabuli and wild genotypes by genic CNMS markers at a genome-wide scale suggesting their utility in large-scale genetic analysis in chickpea. The subfunctionalization at the cis-regulatory element region and TFBS (transcription factor binding site) motif levels in the upstream sequences of CNMS marker-associated orthologous genes than the paralogues was predominant. Functional constraint might have considerable effect on these CNMScontaining regulatory elements controlling consistent orthologous gene expression in dicots. A rapid subfunctionalization based on diverge differential expression of paralogous CNMS marker-associated genes particularly those that underwent recent small-scale segmental duplication events in chickpea was apparent. The differential regulation of expression and subfunctionalization potential of Ultra CNMS marker-associated genes suggest their utility in deciphering the complex gene regulatory function as well as identification and targeted mapping of potential genes/QTLs governing vital agronomic traits in chickpea. The gene-based CNMS markers with desirable inherent genetic attributes like higher degree of comparative genome mapping, functional genetic diversity and differential gene regulatory expression potential can significantly propel the genomics-assisted chickpea crop improvement.
The authors gratefully acknowledge the financial support for
this research study provided by a research grant (102/IFD/
SAN/2161/2013-14) from the Department of Biotechnology
(DBT). SD acknowledges the DBT for Junior Research
Fellowship award.
 
Date 2015-12-31T11:17:14Z
2015-12-31T11:17:14Z
2015
 
Type Article
 
Identifier Journal of Biosciences, 40(3): 579-592
0973-7138
http://172.16.0.77:8080/jspui/handle/123456789/485
http://www.ias.ac.in/listing/articles/jbsc/040/03
 
Language en_US
 
Publisher Indian Academy of Sciences