Rice Genomics and Genetics 2025, Vol.16, No.5, 245-253 http://cropscipublisher.com/index.php/rgg 245 Review Article Open Access The Role of Structural Variants in Rice Domestication and Environmental Adaptation Weijie Sun, Jiawei Li Modern Agricultural Research Center, Cuixi Academy of Biotechnology, Zhuji, 311800, Zhejiang, China Corresponding email: jiawei.li@cuixi.org Rice Genomics and Genetics, 2025, Vol.16, No.5 doi: 10.5376/rgg.2025.16.0021 Received: 12 Jul., 2025 Accepted: 28 Aug., 2025 Published: 09 Sep., 2025 Copyright © 2025 Sun and Li, 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 Li J.W., 2025, The role of structural variants in rice domestication and environmental adaptation, Rice Genomics and Genetics, 16(5): 245-253 (doi: 10.5376/rgg.2025.16.0021) Abstract Structural variants (SVs), as an important form of genomic genetic variation, play a key role in the domestication of rice and its adaptation to complex environments. With the development of third-generation sequencing technology and pan-genomics, an increasing number of studies have revealed the extensive functions of SV in regulating agronomic traits, environmental stress responses, and germplasm diversity. This study systematically reviewed the genetic evidence of SV during the domestication of rice, covering key structural variation events in domestication-related traits such as plant type, flowering period, and grain shedding. At the same time, it explored the functional mechanisms of SV in adaptation to adverse conditions such as drought, salt stress, and cold damage, including regulatory region reconstruction, cis-element changes, and gene replication and deletion processes. This paper further introduces the current mainstream SV detection techniques and their applications in pan-genome construction and functional annotation, with a focus on analyzing how SV regulates gene expression through chromatin accessibility changes, quantitative trait loci (eQTL) reconfiguration, and non-coding RNA networks. Through the analysis of typical cases (such as OsSPL14, OsHKT1;5), this study clarifies the application value of SV in the improvement of rice traits. This study aims to provide theoretical support for a deeper understanding of the functions of structural variations and offer new ideas and strategies for molecular design breeding and precise improvement of rice. Keywords Rice; Structural variation; Domestication; Environmental adaptation; Pan-genome 1 Introduction Rice (Oryza sativa) is almost the daily food supply for more than half of the world's population. It is not an exaggeration to say that it is related to food security (Fornasiero et al., 2022; Li et al., 2025). However, apart from the act of "eating", it is also widely used as a classic model for studying domestication and crop improvement. Ultimately, rice was not a crop that was obedient from the very beginning. Many of the superior traits we see today have actually been gradually domesticated through long-term artificial selection, such as those selected step by step from ancestral materials like common wild rice (Li et al., 2021; Zheng et al., 2021). Behind this, many key genes related to output, stress resistance, and even climate change response have been identified. When it comes to genetic variation, the SNP might be the most familiar to everyone. However, when studying the traits of rice, structural variation (SV) often causes more waves. SV refers to those relatively large genomic variations - some are inserted in a large segment, some are simply missing, duplicated, or even the sequence is changed, such as inversions and translocations (Kou et al., 2020; Zheng et al., 2023). Although they are not the most abundant in the genome, each one may have a domino effect. Studies have found that SV, compared with SNP, often involves larger segments of genetic material. Therefore, they play a more significant role in influencing gene expression, crop trait diversity, and even environmental adaptation (Fuentes et al., 2019; Shang et al., 2022). If it weren't for the rapid upgrading of sequencing technology in recent years, especially the development of pan-genome analysis, many of these structural variations hidden in different species or subpopulations might not have been easily discovered. Nowadays, researchers have identified tens of thousands of SVS in cultivated rice and wild rice, and many of them are linea-specific (Wang et al., 2022). These findings precisely provide a new breakthrough for us to understand the genetic structure of rice and even further guide molecular breeding.
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