Yaodong Liu

Modern Agricultural Research Center, Cuixi Academy of Biotechnology, Zhuji, 311800, Zhejiang, China
Author    Correspondence author
Rice Genomics and Genetics, 2025, Vol. 16, No. 3   
Received: 30 Apr., 2025    Accepted: 10 Jun., 2025    Published: 28 Jun., 2025

This is an open access article published under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited.

Rice (Oryza sativa) is a staple cereal with immense global importance, yet a single reference genome cannot capture the full genetic diversity underlying key traits. Pan-genomics has emerged as a paradigm to characterize the “pan-genome”-the total genomic repertoire of a species-including core genes shared by all accessions and dispensable genes present in some but absent in others. Here, this study reviews the construction and analysis of rice pan-genomes and the insights they provide into structural variation hotspots across rice subspecies; outlines how the limitations of a single reference genome have driven the development of plant pan-genomics, enabling discovery of extensive genomic variation that was previously hidden; describes strategies for building rice pan-genomes, from early short-read sequencing approaches to recent long-read assemblies and graph-based genome models that integrate diverse accessions (indica, japonica, aus, aromatic, wild relatives). Major types of structural variation-insertions, deletions, inversions, translocations, copy number variations-are defined, and this study surveys computational tools for their detection; synthesizes findings on the distribution of structural variants (SVs) in the rice genome and identify hotspots of variation specific to certain lineages. The functional impact of SVs is discussed, with case studies linking structural variants to agronomic traits (yield, stress tolerance, flowering time) and to gene presence/absence variation affecting gene families (e.g. disease resistance genes). Comparative pan-genome analyses across rice subspecies illuminate how evolutionary forces like domestication bottlenecks, introgression, and selection have shaped genomic differences between indica and japonica rice. Finally, this study highlights emerging applications of rice pan-genome research in germplasm utilization, genome-wide association studies, marker-assisted breeding, and de novo domestication, and discusses future prospects and challenges in integrating multi-omics data and developing pan-genomic resources for sustainable agriculture under climate change.

Rice pan-genome; Structural variation; Genetic diversity; Subspecies; Crop genomics