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Development of genome-wide informative simple sequence repeat markers for large-scale genotyping applications in chickpea and development of web resource

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Title Development of genome-wide informative simple sequence repeat markers for large-scale genotyping applications in chickpea and development of web resource
 
Creator Parida, Swarup K.
Verma, Mohit
Yadav, Santosh K.
Ambawat, Supriya
Das, Shouvik
Garg, Rohini
Jain, Mukesh
 
Subject chickpea
genotyping
molecular diversity
polymorphism
population structure
simple sequence repeat
 
Description Accepted date: 03 August 2015
Development of informative polymorphic simple sequence repeat (SSR) markers at a genome-wide scale is essential for efficient large-scale genotyping applications. We identified genome-wide 1835 SSRs showing polymorphism between desi and kabuli chickpea. A total of 1470 polymorphic SSR markers from diverse coding and non-coding regions of the chickpea genome were developed. These physically mapped SSR markers exhibited robust amplification efficiency (73.9%) and high intra- and inter-specific polymorphic potential (63.5%), thereby suggesting their immense use in various genomics-assisted breeding applications. The SSR markers particularly derived from intergenic and intronic sequences revealed high polymorphic potential. Using the mapped SSR markers, a wider functional molecular diversity (16-94%, mean: 68%), and parentage- and cultivar-specific admixed domestication pattern and phylogenetic relationships in a structured population of desi and kabuli chickpea genotypes was evident. The intra-specific polymorphism (47.6%) and functional molecular diversity (65%) potential of polymorphic SSR markers developed in our study is much higher than that of previous documentations. Finally, we have developed a user-friendly web resource, Chickpea Microsatellite Database (CMsDB; http://www.nipgr.res.in/CMsDB.html), which provides public access to the data and results reported in this study. The developed informative SSR markers can serve as a resource for various genotyping applications, including genetic enhancement studies in chickpea.
This work was financially supported by the core grant
from NIPGR and the Department of Biotechnology,
Government of India, New Delhi, under the Next Generation
Challenge Programme on Chickpea Genomics (grant number
BT/PR12919/AGR/02/676/2009 from 2009 to 2014). RG
acknowledges the INSPIRE Faculty Award from the Department
of Science and Technology, Government of India.
 
Date 2016-01-21T05:51:43Z
2016-01-21T05:51:43Z
2015
 
Type Article
 
Identifier Front. Plant Sc., 6: 645
1664-462X
http://172.16.0.77:8080/jspui/handle/123456789/561
http://journal.frontiersin.org/article/10.3389/fpls.2015.00645/abstract
10.3389/fpls.2015.00645
 
Language en_US
 
Publisher Frontiers Media S.A.