Rice Genomics and Genetics 2025, Vol.16, No.3, 159-179 http://cropscipublisher.com/index.php/rgg 159 Feature Review Open Access Construction and Analysis of a Rice Pan-genome Reveals Structural Variation Hotspots Across Subspecies Weijie Sun, Yaodong Liu Modern Agricultural Research Center, Cuixi Academy of Biotechnology, Zhuji, 311800, Zhejiang, China Corresponding email: yaodong.liu@cuixi.org Rice Genomics and Genetics, 2025, Vol.16, No.3 doi: 10.5376/rgg.2025.16.0015 Received: 30 Apr., 2025 Accepted: 10 Jun., 2025 Published: 28 Jun., 2025 Copyright © 2025 Sun and Liu, 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. Preferred citation for this article: Sun W.J., and Liu Y.D., 2025, Construction and analysis of a rice pan-genome reveals structural variation hotspots across subspecies, Rice Genomics and Genetics, 16(3): 159-179 (doi: 10.5376/rgg.2025.16.0015) Abstract 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. Keywords Rice pan-genome; Structural variation; Genetic diversity; Subspecies; Crop genomics 1 Introduction Rice is a staple crop for over half the global population, making it central to food security. Advances in rice genomics have brought big improvements in traits like yield, quality, and disease resistance (Shang et al., 2022). One major milestone was the release of the first high-quality genome sequence of Asian rice, which opened the door to better gene discovery and breeding. But rice isn’t a single, uniform crop. Oryza sativa includes two main subspecies-indica and japonica-as well as many subgroups adapted to different climates and growing conditions. Around the world, gene banks have collected more than 780 000 rice accessions. This huge range of genetic material holds the key to traits that can help rice cope with pests, poor soil, and climate stress. However, early studies focused heavily on a few elite varieties like Nipponbare (a japonica type). While these gave researchers a good foundation, it quickly became clear that one variety’s genome doesn’t tell the whole story-some important genes simply aren’t present in every type. That realization shifted the focus toward pan-genomics, which looks at many genomes together. By comparing multiple cultivated and wild types, researchers are now finding new genes and structural differences that were missed before (Zhao et al., 2018). This broader view is helping scientists create better rice varieties faster-something that really matters in today’s changing agricultural landscape. Traditional genome analysis approaches have largely depended on a single reference genome per species. In rice, the use of one reference (e.g. Nipponbare) for read alignment and gene annotation has inherent limitations. A single reference genome does not represent the genetic diversity within the species, as evidenced by the high
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