A Whole-Genome Sequence Resource for the Medicinal Rice Landrace Navara.

Abstract

Navara (Oryza sativa L.) is a traditional pigmented rice landrace from Kerala, India, recognized for its nutritional and medicinal importance. However, its genome-wide sequence variation and population-genetic context remain insufficiently characterized. Here, we present a whole-genome sequence resource for a single Navara accession, with particular emphasis on sequence variation in genes associated with anthocyanin and flavonoid biosynthesis. Paired-end whole-genome sequencing generated 58.7 million reads, providing approximately 30× genome coverage. Reference-guided analysis using the well-annotated IRGSP-1.0 genome identified 4,118,622 high-confidence variants, comprising 3,513,668 SNPs and 604,954 INDELs. Among the 19 selected anthocyanin- and flavonoid-related genes, 561 SNPs were identified and characterized according to their genomic context and predicted consequences. Comparison with the Rice3K dataset identified 131 variants in these genes that were not observed in the comparison dataset. Genome-wide principal component analysis placed the sequenced Navara accession closest to the Aus/boro genetic group, while identity-by-state analysis identified Karutha Seenati as the closest accession among those compared using the selected loci. Several variant-containing regions overlapped previously reported rice QTL intervals, providing genomic context for further investigation without implying genetic association or causality. De novo assembly of reference-unmapped reads generated approximately 9.29 Mb of additional sequence, including predicted genes and repetitive elements, while comparison with the PanOryza pangenome indicated that most predicted genes were represented within the broader rice gene pool. Collectively, these datasets provide a reusable genomic resource for comparative genomics, genetic-diversity analysis, marker development, conservation of traditional rice germplasm, and future functional investigation of pigmentation, nutritional, and agronomic traits.