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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 |
Authors: | Parida, Swarup K. Verma, Mohit Yadav, Santosh K. Ambawat, Supriya Das, Shouvik Garg, Rohini Jain, Mukesh |
Keywords: | chickpea genotyping molecular diversity polymorphism population structure simple sequence repeat |
Issue Date: | 2015 |
Publisher: | Frontiers Media S.A. |
Citation: | Front. Plant Sc., 6: 645 |
Abstract: | 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. |
Description: | Accepted date: 03 August 2015 |
URI: | http://172.16.0.77:8080/jspui/handle/123456789/561 |
ISSN: | 1664-462X |
Appears in Collections: | Institutional Publications |
Files in This Item:
File | Description | Size | Format | |
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Jain M_2015_5.pdf | 4.58 MB | Adobe PDF | ![]() View/Open |
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