Rice Genomics and Genetics 2025, Vol.16, No.5, 245-253 http://cropscipublisher.com/index.php/rgg 247 which are involved in regulating root development and antioxidant defense, are related to these variations. Studies have shown that they can actually enhance drought and salt resistance (Lee et al., 2017). However, not all SVS are positive. Some allelic variations, such as those found on OsWRKY45 or OsDIRP1, may also play a negative role in certain contexts (Tao et al., 2011; Cui et al., 2018). The "adaptability" of different SVS to environmental stresses is likely to depend on the context and the timing of expression. 3.2 Cis-regulatory SVs and their impact on gene expression via regulatory element remodeling The expression level of a gene sometimes does not depend on the gene itself, but rather on whether the cis-type element at its "front gate" has changed. SVS in the promoter region are particularly fond of "tamping", as they reconstruct the original regulatory map. As a result, the expression volume changes, and so do the spatiotemporal patterns (Ding et al., 2021). For instance, a single nucleotide variation in the promoter of the Ghd8 gene can enhance its expression, thereby improving the cold resistance of japonica rice (Figure 1) (Wang et al., 2019). Figure 1 Altered expression of Ghd8affects rice heading date (Adopted from Wang et al., 2019) Image caption: (a–d) Phenotype performances of wild type (WT) and Ghd8 overexpression line (OE) under LD conditions (14.5 h light: 9.5 h dark) (a) and SD conditions (9 h light: 15 h dark) (b). Arrows indicate the first emerging panicle. Heading date of WT and OE in LD (c) and SD (d) conditions. (e,f) The expression of Ghd8 (e) and Hd3a (f). (g–j) Performances of WT and artificial microRNA line (AMI) of Ghd8 in LD (g) and SD (h) conditions. Heading date of WT and AMI plants under LD (i) and SD (j) conditions. (k,1) The expression of Ghd8 (k) and Hd3a (l) in WT and AMI plants. Asterisks ** and * represent significant difference compared to WT by t-test at p < 0.01 and p < 0.05 levels, respectively. Error bars indicate the mean ± SD, with three to five replicates (Adopted from Wang et al., 2019)
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