Rice Genomics and Genetics 2025, Vol.16, No.4, 219-236 http://cropscipublisher.com/index.php/rgg 223 are often synergistically controlled by multiple transcription factors, and there are also interactions and cascading relationships among different transcription factors. For instance, miR159-OsNF-YB1-OsbZIP58 constitutes a regulatory pathway that affects endosperm development and starch accumulation. 3.2 Regulatory roles of non-coding RNAs such as miRNAs and lncRNAs Non-coding Rnas play a significant role in gene regulation during plant development. The synthesis of starch in rice endosperm is also influenced by some mirnas and long non-coding Rnas (lncrnas). In recent years, small RNA sequencing has revealed the expression of various mirnas during the grain filling stage and predicted that some mirnas may target starch synthase coding genes (Peng et al., 2013). For instance, miR159 and miR167 are important mirnas involved in the development of rice grains. Among them, miR159 indirectly affects the regulatory network of OsbZIP58 by down-regulating the transcription factor OsNF-YB1, thereby influencing the expression of starch synthesis genes. miR167 has been proven to directly target the OsARF12 transcription factor gene, forming the "MIR167-OSARF12" module, which participates in regulating the grain filling rate and grain weight of rice. Overexpression of OsARF12 can increase starch accumulation in grains, and its phenotype is similar to the effect of inhibiting miR167, indicating that miR167 negatively regulates the starch synthesis process by inhibiting OsARF12. Mir156/157, miR164, miR172, etc. have also been reported to be related to the formation of rice quality: miR156 targets SPL genes to affect grain size and indirectly change starch reservoir capacity, and miR164 may act on the starch synthesis pathway by regulating NAC transcription factors. Overall, the mechanism of action of miRNA is usually to cleave or inhibit target mRNA, thereby precisely controlling the production of corresponding enzymes or regulatory factors and adjusting the rate of starch synthesis in a timely manner at different developmental stages or under different environmental conditions. In contrast, research on the role of lncRNA in starch metabolism is still in its infancy. Some reports indicate that there are hundreds of specifically expressed lncrnas during the development of rice grains, some of which are co-expressed with starch synthase genes. For instance, some studies have identified an endosperm specific lncRNA LncYE1, and it is speculated that it regulates amylose content by influencing the mRNA splicing of key enzymes in starch synthesis. It has also been reported that long non-coding Rnas can act as "sponges" for mirnas. For instance, certain lncrnas competitively bind to miR156, thereby relieving the inhibition of miR156 on target transcription factors and indirectly promoting the synthesis of starch and other storage substances. Although there are not many specific examples, on the whole, non-coding Rnas provide additional dimensions for the multi-level regulation of starch synthesis. They can respond to rapid changes in external signals and integrate into the existing transcriptional regulatory network to achieve precise regulation of starch synthesis. In the future, through high-throughput sequencing and functional analysis, it is expected to discover more regulatory effects of miRNA/lncRNA on starch synthesis, thereby providing new strategies for improving rice quality. 3.3 Effects of epigenetic modifications (DNA methylation, histone modifications) on starch biosynthesis In addition to transcriptional and post-transcriptional regulation, epigenetic modifications also affect the expression of starch synthesis genes, thereby indirectly influencing the quality of rice. Research has found that the DNA methylation level of the starch synthase gene promoter in the endosperm of rice is much lower than that in other tissues, which is conducive to the high-level expression of these genes in the endosperm. Especially, the promoter of the Wx gene has two very close CpG islands, and the methylation level in the endosperm is very low, which is related to the high expression and content of amylose. On the contrary, in some varieties with low amylose content (such as the Wxb allele of japonica rice), the methylation level of the Wx promoter is high, the transcriptional amount decreases, and the synthesis of amylose is also restricted. Studies have found that altering the methylation levels of key gene promoters can, to a certain extent, adjust the composition of starch. For instance, treating pollinated rice ears with demethylating agents can increase the expression of the Wx gene and the content of amylose, which proves that DNA methylation silences the Wx gene (Tang et al., 2022). Recent studies on corn have also shown that the expression levels of starch synthesis-related genes (SSRGs) in endosperm are low when they are highly methylated, and genes with high expression often have low promoter demethylation or low genome methylation. This indicates that there might be a similar mechanism in rice. Environmental factors can also affect starch synthesis through epigenetic pathways. For instance, high
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