Genome-wide chromosome-mapped polymorphic simple sequence repeat markers in black pepper for genetic diversity analysis and marker-assisted breeding.

Authors

Muhammed Azharudheen Thazheyil Pura, Kalpana Singh, Shivakumar Mundagodu Somashekar, Tilak Chandra, Sarika Jaiswal, Ulavappa Basavanneppa Angadi, Mir Asif Iquebal, Muhammed Fayad Abdulkabeer, Sheeja Thotten Elampilay, Dinesh Kumar

Published in

Journal of the science of food and agriculture. Nov 12, 2026. Epub Nov 12, 2026.

Abstract

Black pepper (Piper nigrum), popularly known as the 'King of Spices' and 'Black Gold', is one of the world's oldest and most economically important spices and occupies a prominent position in the global spice trade. Increasing post-pandemic utilization and consumer preference have further emphasized the need to improve its production and Traits of economic importance (value-added traits). Simple sequence repeat (SSR) markers are valuable genomic resources for black pepper research, facilitating genetic analysis, diversity assessment, varietal identification, and marker-assisted breeding. However, the limited availability of SSR markers and their predominantly anonymous or scaffold-based localization, rather than chromosome-level anchoring, restrict their effective utilization. This study therefore aimed to develop chromosome-resolved polymorphic SSR markers from whole-genome resequencing data and establish a centralized resource to facilitate their application in black pepper genetic improvement.
Whole-genome resequencing data from black pepper accessions selected for agronomically important traits were aligned against the chromosomal sequences of the reference genome to identify and quantify repeat-number variation across SSR loci. A total of 150 828 SSR loci were identified across all 26 chromosomes of the analyzed accessions and systematically catalogued in the Black Pepper Polymorphic SSR Database (Bp2SSRdb; https://bp2ssrdb.abrl.in/). To capture accession-specific varietal signatures, two to four markers per chromosome were selected across the complete chromosome set to facilitate accession-level phylogenetic differentiation. A subset of in silico-predicted polymorphic SSR markers, optimized using their flanking sequences, was subsequently validated experimentally. The validated polymorphic markers were associated with or linked to genes encoding proteins involved in disease resistance, amino acid metabolism, cytochrome P450-mediated processes, and other stress-responsive functions, highlighting their potential relevance to growth, stress management, and developmental processes.
The chromosome-resolved SSR resources and experimentally validated polymorphic markers developed in this study provide a robust genomic footprint for marker-assisted breeding and genetic improvement of black pepper. The centralized Bp2SSRDb platform facilitates efficient access to and utilization of these markers, thereby supporting genetic diversity analysis, varietal discrimination, and biotechnological interventions. Together, these resources can accelerate the discovery of novel functional polymorphic loci and provide greater insight into the molecular basis of agronomically important traits, ultimately enabling more targeted and efficient genetic improvement. © 2026 Society of Chemical Industry.

PMID:
43018101
Bibliographic data and abstract were imported from PubMed on 12 Nov 2026.

Read full publication at:
Please sign in to see all details.

Stats

1-terrible, 9-excellent. How would you rate this publication? Sign in in to submit your rating.

Post a comment

You need to be signed in to post comments. You can sign in here.

Comments

There are no comments yet.