Whole-Genome Variants Resource of 144 Oryza rufipogon Accessions

Abstract

The global food security crisis highlights the urgent need to improve rice yield and quality. Oryza rufipogon, the wild progenitor of cultivated rice, offers valuable genetic diversity, yet its genome remains underexplored. We conducted whole-genome resequencing (WGS) of 144 O. rufipogon accessions from 13 countries, generating ~400 GB of data using the Illumina NovaSeq 6000 platform. After quality control, 97.58% of reads aligned to the reference genome, achieving 87.97% coverage with 12.47× average depth. We identified a total of 6,183,832 SNPs and 748,493 InDels across 12 chromosomes. Chromosome 1 exhibited the most variants (715,636 SNPs and 91,276 InDels), while chromosome 9 had the fewest (384,000 SNPs and 44,817 InDels). Mutation rates were 67 SNPs and 559 InDels per million base pairs. Notably, 40.75% of SNPs and 46.09% of InDels were found upstream of genes, with 19.13% and 22.26% located downstream, respectively. A transition-to-transversion ratio (Ti/Tv) of 2.72 confirmed the data’s reliability. Our findings offer a comprehensive genomic variation resource for O. rufipogon, supporting future genetic research and rice breeding efforts.