Rice Genomics and Genetics 2025, Vol.16, No.5, 245-253 http://cropscipublisher.com/index.php/rgg 246 This study will clarify its role in rice domestication, environmental adaptation, and agronomic trait diversity. By integrating high-quality genome assembly, population scale resequencing, and functional genomics, it aims to map the evolutionary patterns of SVs, identify their associations with key traits such as grain size, stress resistance, and plant type, and reveal the genetic mechanisms by which they adapt to different environments. This research not only enables an in-depth understanding of the evolutionary history of rice but also provides valuable resources for breeding programs, allowing for targeted improvement of rice varieties to address future food security challenges. 2 Genetic Evidence of Structural Variants During Rice Domestication 2.1 Key SV events revealed by genome comparisons between wild and cultivated rice The genomic differences between wild rice (Oryza rufipogon) and cultivated rice (Oryza sativa) are far more complex than initially imagined. Especially after using long-read sequencing and whole-genome comparative analysis, researchers found that there were a large number of structural variant (SV) events between the two, and many variant types were concentrated in the regions where transposition factors were active (Shang et al., 2022; Zheng et al., 2023). Especially in wild rice, approximately nearly half (49%) of the SV is unique to it. However, many such variations have been lost during domestication, resulting in the disappearance of approximately 1.76% of the genes in cultivated rice (Kou et al., 2020). Moreover, not only insertions and deletions, but also SVS like inversions and duplications frequently occur. Some of these specific variations, such as the 824 bp deletion in japonica rice related to grain length, were directly linked to important agronomic traits by GWAS analysis. 2.2 Regulatory roles of SVs in domestication-related traits (plant architecture, flowering time, grain shattering, etc.) Domestication has changed many traits of rice, but not every trait change comes from simple mutations. In fact, many regulations that affect plant type, flowering period, grain drop and grain shape are all orchestrated by SV. Especially those SVS that appear in promoters or within genes often directly affect the expression level of genes (Fuentes et al., 2019). For instance, a 17.1 kb tandem repeat at the GL7 locus can make the grains longer. The 1.2kb missing section of qSW5 will affect the width of the grains. In addition, some SVS can cause the plants to become shorter or the shape of the grains to change. The "extent of change" of these structural variations is often much greater than that of ordinary SNPS because they can not only regulate expression but also may reconstruct the regulatory network. Incidentally, some SVS are also associated with traits such as grains being less prone to dropping and tolerance to waterlogging, which also indicates that they were not "supporting roles" in the domestication process. 2.3 Differentiation of major SV loci between the two major Asian rice subspecies (indica andjaponica) Although indica rice and japonica rice, these two subspecies seem to belong to the same genus of rice, when comparing their SV differences, it becomes clear why their ecological adaptations and trait manifestations are so distinct. Many studies have found that there are large inversions, copy number variations and differences in the presence or absence of a certain sequence in their genomes. An inversion of 4.3 Mb in size can almost directly distinguish indica rice fromjaponica rice (Kou et al., 2020). What's more interesting is that these SVS are often concentrated in regions related to domestication, that is, near the genes that regulate yield, quality and stress resistance. Some variations almost only occur in a certain subspecies or are more common in that subspecies, and it is precisely these differences that define the adaptability of indica and japonica to different environments and typical agronomic manifestations. 3 Mechanisms Linking Structural Variants and Environmental Adaptation 3.1 Functional roles of SVs in rice responses to drought, salinity, and cold stresses Often, whether rice can survive drought, saline-alkali conditions or cold is not only determined by the strength of a certain gene, but also by whether there is a structural variation (SV) "working in the dark" behind this gene. In the analysis of a large number of rice genomes, SV often appears in those regions related to adverse conditions, and the density is not low. Sometimes, these SVS can cause regulatory sites to "shift", and sometimes they simply affect the dose of genes or disrupt the coding sequence. Transcription factors such as OsNAC6 and OsMYB6,
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