Rapid genome-wide location-specific polymorphic SSR marker discovery in black pepper by GBS approach
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Date
2022
Journal Title
Journal ISSN
Volume Title
Publisher
Frontiers in Plant Science
Abstract
Black pepper (Piper nigrum), the “King of Spices,” is an economically important spice
in India and is known for its medicinal and cultural values. SSRs, the tandem repeats
of small DNA sequences, are often polymorphic in nature with diverse applications. For
population structure, QTL/gene discovery, MAS, and diversity analysis, it is imperative
to have their location specificity. The existing PinigSSRdb catalogs ∼70K putative
SSR markers but these are anonymous (unknown chromosomal location), based on
916 scaffolds rather than 26 chromosomes. Under this study, we generated ddRAD
sequence data of 29 black pepper genotypes from all over India, being low-cost and
most efficient technique for the identification of polymorphicmarkers. Themajor limitation
of ddRAD with compromised/non-uniform coverage has been successfully overcome
by taking advantage of chromosome-wise data availability. The latest black pepper
genome assembly was used to extract genome-wide SSRs. A total of 276,230 genomic
SSRs were mined distributed over 26 chromosomes, with relative density of 362.88
SSRs/Mb and average distance of 2.76 Kb between two SSRs. This assembly was
also used to find the polymorphic SSRs in the generated GBS data of 29 black pepper
genotypes utilizing rapid and cost-effective method giving 3,176 polymorphic SSRs, out
of which 2015 were found to be hypervariable. The developed web-genomic resource,
BlackP2MSATdb (http://webtom.cabgrid.res.in/blackp2msatdb/), is the largest and first
reported web resource for genomic and polymorphic SSRs of black pepper, which is
useful to develop varietal signature, coreset, physical map, QTL/gene identification, and
MAS in endeavor of black pepper production.
Description
Keywords
black pepper, diversity, genome, markers, polymorphic, web-resource