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Front Plant Sci. 2015 Aug 21;6:645. doi: 10.3389/fpls.2015.00645. eCollection 2015.

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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Functional and Applied Genomics Laboratory, National Institute of Plant Genome Research New Delhi, India.


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;, 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.


chickpea; genotyping; molecular diversity; polymorphism; population structure; simple sequence repeat

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