Rice Genomics and Genetics 2025, Vol.16, No.5, 245-253 http://cropscipublisher.com/index.php/rgg 249 function of these markers can be interfered with or remodeled by SV, thereby affecting gene accessibility and expression activity (Osakabe et al., 2018; Probst, 2022; Sokolova et al., 2022). It is worth noting that regions rich in active markers, such as sequences carrying H3K4me3, tend to be less "tolerant" of structural disturbances. However, SV is more common in heterochromatin (Lyu, 2024). In other words, not all regions are equally "welcoming" to variations. Some places change frequently, while others tend to be more conservative. The way this variation affects chromatin accessibility, nucleosome stability and even participates in the regulation of stress responses cannot be ignored. 5.2 SV-mediated reconstruction of expression quantitative trait loci (eQTLs) Expressing quantitative trait loci (eQTL) has always been an important entry point in the study of expression regulation. But when SV gets involved, things will become a little more complicated. An SV may directly interrupt a control element or make it function again in a different position. This leads to the emergence of new EQtls or the reconfiguration of the original EQtls. In the transcriptome studies of rice, this situation is not uncommon - some genes are jointly regulated by multiple local and remote EQtls, and the complexity of the network far exceeds expectations (Liu et al., 2022). The influence of SV on gene expression is sometimes more intense than that of SNP, especially more obvious in non-coding regions (Chiang et al., 2016). Analyzing eQTL together with phenotypic QTL often enables the identification of those genes that truly "cut" in the regulation of agronomic traits. 5.3 Interactions between SVs and non-coding RNAs (lncRNAs, miRNAs) Non-coding Rnas, such as lncrnas and mirnas, are not simply "non-coding" entities; they are highly active in regulatory networks. However, the expression of these RNA molecules themselves may also be affected by SV. Although direct research in this regard in rice is still advancing, existing evidence suggests that SV may indirectly affect the expression and function of these non-coding Rnas by rewriting chromatin structure or altering regulatory regions (Nunez-Vazquez et al., 2022; Jiang and Berger, 2023). The presence of SV in a gene segment may lead to an earlier or delayed transcriptional initiation of adjacent lncrnas, and may also interfere with miRNA binding sites. This "chain reaction" forms a dynamic regulatory relationship among SV, apparent state and non-coding RNA. It is not merely a one-way regulatory channel but more like a feedback network. Especially in the process of crop adaptation and domestication, this network relationship becomes increasingly important. 6 Case Studies: Representative Applications of SVs in Trait Improvement and Environmental Adaptation 6.1 Structural variation in the OsSPL14 gene and its role in plant architecture improvement The OsSPL14 (also known as IPA1) gene is often mentioned in the regulation of rice plant type. Not every mutation attracts widespread attention, but the point mutation in it unexpectedly disrupted the regulation of OsmiR156, leading to the amplification of OsSPL14 expression. The result is: fewer tillers, thicker stems, larger ears, not only increased yield but also enhanced lodging resistance (Jiao et al., 2010; Wang et al., 2017; Yan et al., 2021). Of course, this kind of variation is essentially a structural variation (SV), but its impact goes far beyond the structural level. Later, researchers attempted to overexpress this favorable allele or introduce it into different background materials through targeted introduction. The results all indicated that this type of SV could directly affect plant type, hormone levels, and even rice quality (Lian et al., 2020). The role of SV in breeding is very directly demonstrated in this case. 6.2 Copy number variation of OsHKT1;5 and its contribution to salt stress tolerance Not all salt tolerance comes from a certain "magic gene", but OsHKT1; 5 is undoubtedly one of the sodium transporters that have been studied more thoroughly at present. Natural variations of this gene, especially changes in copy number, have been found to help plants excrete sodium more effectively, particularly in the aboveground parts (Negrao et al., 2013; Liu et al., 2021). In salt-tolerant varieties like "Nona Bokra", amino acid substitutions at some key sites, along with an increase in gene dosage, ultimately improved the transport capacity of sodium ions. These SVS were not locked at the very beginning but gradually emerged during the actual screening process. For this very reason, they have become important targets in salt-tolerant breeding (Kobayashi et al., 2017).
RkJQdWJsaXNoZXIy MjQ4ODYzNA==