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Development of genome-wide informative simple sequence repeat markers for molecular diversity analysis in chickpea and development of web resource

By SWARUP KUMAR PARIDA, Mohit eVerma, Santosh eYadav, Supriya eAmbawat, Shouvik eDas, Rohini eGarg and Mukesh eJain


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

Topics: genotyping, polymorphism, population structure, molecular diversity, chickpea, Simple sequence repeat, Plant culture, SB1-1110
Publisher: Frontiers Media S.A.
Year: 2015
DOI identifier: 10.3389/fpls.2015.00645
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