Oryza pan-genomics: A new foundation for future rice research and improvement

The wild rice species in the genus Oryza harbor a large amount of genetic diversity that has been untapped for rice improvement. Pan-genomics has revolutionized genomic research in plants. However, rice pan-genomic studies so far have been limited mostly to cultivated accessions, with only a few close wild relatives. Advances in sequencing technologies have permitted the assembly of high-quality rice genome sequences at low cost, making it possible to construct genus-level pan-genomes across all species. In this review, we summarize progress in current research on genetic and genomic resources in Oryza, and in sequencing and computational technologies used for rice genome and pan-genome construction. For future work, we discuss the approaches and challenges in the construction of, and data access to, Oryza pan-genomes based on representative high-quality genome assemblies. The Oryza pan-genomes will provide a basis for the exploration and use of the extensive genetic diversity present in both cultivated and wild rice populations.