Genotyping-by-Sequencing dataset of 86 diverse rice (Oryza sativa L.) accessions comprising Indonesian local varieties, improved cultivars, and breeding lines

Local Indonesian rice ( Oryza sativa L.) varieties harbor untapped genetic diversity crucial for developing climate-resilient cultivars, yet their high-resolution genomic profiles remain largely undercharacterized. To address this, we present a comprehensive Genotyping-by-Sequencing (GBS) dataset of 86 diverse rice accessions. This panel is uniquely composed of traditional Indonesian varieties, widely cultivated modern improved varieties, elite international reference cultivars, and several advanced breeding lines. Sequencing was performed utilizing a multi-enzyme double digest restriction-site associated DNA sequencing (ddRAD-seq) approach on the Illumina NovaSeq platform, generating approximately 88.6 billion high-quality clean bases. Bioinformatic evaluation revealed robust mapping efficiencies against the Oryza sativa ssp. japonica cv. Nipponbare reference genome, with the majority of accessions exhibiting mapping rates above 94%. Subsequent variant calling and functional annotation successfully identified a high-density, genome-wide panel of single nucleotide polymorphisms (SNPs), highlighting distinct genetic distributions and sequence conservation among the evaluated germplasm. This publicly available genomic dataset provides a foundational resource for the agricultural research community. It will significantly facilitate downstream population genomic analyses, Genome-Wide Association Studies (GWAS), and Quantitative Trait Locus (QTL) mapping, ultimately accelerating molecular breeding and marker-assisted selection (MAS) programs aimed at improving critical agronomic traits and stress tolerance in global rice production.