Rice Genomics and Genetics 2025, Vol.16, No.5, 245-253 http://cropscipublisher.com/index.php/rgg 250 6.3 Transcriptomic regulation by SVs in cold tolerance of japonica rice at high latitudes Whether japonica rice can withstand the cold and achieve stable production in the north is actually influenced by multiple factors, but the variations in the regulated areas are particularly worth mentioning. For example, structural variations in the promoter and coding region of the CTB5 gene have been found to enhance its expression activity under cold stress, thereby improving the cold tolerance level during the seedling stage and reproductive stage (Figure 2) (Guo et al., 2025). This is not an isolated case. In the joint study of pan-transcriptome and eQTL, cold response genes such as OsMAPK3, OsLEA9, and OsWRKY61 also showed significant SV-driven expression differences, including splicing variations and changes at the regulatory level (Lou et al., 2022). These genes seem to have been selectively strengthened during the domestication process of high-latitude japonica rice varieties, which also indicates that the "behind-the-scenes role" of SV in adaptive evolution should not be underestimated. Figure 2CTB5is essential for cold tolerance at the booting stage (Adopted from Guo et al., 2025)
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