Weijie Sun , Jiawei Li

Modern Agricultural Research Center, Cuixi Academy of Biotechnology, Zhuji, 311800, Zhejiang, China
Author    Correspondence author
Rice Genomics and Genetics, 2025, Vol. 16, No. 5   
Received: 12 Jul., 2025    Accepted: 28 Aug., 2025    Published: 23 Oct., 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.

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.

Rice; Structural variation; Domestication; Environmental adaptation; Pan-genome