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

Frontiers in Plant Science
Swarup K ParidaMukesh Jain

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, ...Continue Reading

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Citations

Apr 6, 2016·Frontiers in Plant Science·Hari D UpadhyayaSwarup K Parida
Oct 9, 2016·Plant Science : an International Journal of Experimental Plant Biology·Rishi SrivastavaSwarup K Parida
Aug 21, 2019·Frontiers in Plant Science·Rebecca S ZwartJohn P Thompson
Jan 12, 2021·Physiology and Molecular Biology of Plants : an International Journal of Functional Plant Biology·Aparupa NaikJogeswar Panigrahi

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Methods Mentioned

BETA
genotyping
PCR

Software Mentioned

Internet Explorer
STRUCTURE
Apache Tomcat
Mozilla Firefox
CentOs
BLASTN
Primer3
Google Chrome
PowerMarker
Linux

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