biostudies-literatureWimalarathna NAAustrian Science Fund FWFNational Research Council Sri Lankae0305990https://www.ebi.ac.uk/biostudies/studies/S-EPMC11207170biostudies-literatureUnknown19(6)Despite the economic importance of Piper nigrum (black pepper), a highly valued crop worldwide, development and utilization of genomic resources have remained limited, with diversity assessments often relying on only a few samples or DNA markers. Here we employed restriction-site associated DNA sequencing to analyze 175 P. nigrum accessions from eight main black pepper growing regions in Sri Lanka. The sequencing effort resulted in 1,976 million raw reads, averaging 11.3 million reads per accession, revealing 150,356 high-quality single nucleotide polymorphisms (SNPs) distributed across 26 chromosomes. Population structure analysis revealed two subpopulations (K = 2): a dominant group consisting of 152 accessions sourced from both home gardens and large-scale cultivations, and a smaller grPloS oneGenetic diversity and population structure of Piper nigrum (black pepper) accessions based on next-generation SNP markers.PMC11207170NRC 19-062P33143-BWimalarathna NASamuel RChase MWWickramasuriya AMGopallawa BCauz-Santos LABandupriya DSilva TDMetschina DAriyawansa KGSUfalseGenetic diversity and population structure of Piper nigrum (black pepper) accessions based on next-generation SNP markers.Despite the economic importance of Piper nigrum (black pepper), a highly valued crop worldwide, development and utilization of genomic resources have remained limited, with diversity assessments often relying on only a few samples or DNA markers. Here we employed restriction-site associated DNA sequencing to analyze 175 P. nigrum accessions from eight main black pepper growing regions in Sri Lanka. The sequencing effort resulted in 1,976 million raw reads, averaging 11.3 million reads per accession, revealing 150,356 high-quality single nucleotide polymorphisms (SNPs) distributed across 26 chromosomes. Population structure analysis revealed two subpopulations (K = 2): a dominant group consisting of 152 accessions sourced from both home gardens and large-scale cultivations, and a smaller gr2024-01-01T00:00:00Z20242026-06-01T09:22:48.793Z2025-04-05T17:58:00.418ZS-EPMC112071703892402710.1371/journal.pone.0305990