Rice Genomics and Genetics 2025, Vol.16, No.4, 199-210 http://cropscipublisher.com/index.php/rgg 203 4.3 Dynamic changes in cell-type specific gene expression during filling stages During the grouting period at different stages, gene expression will also constantly change. In the early stage, genes related to energy, such as those associated with photosynthesis and oxidative phosphorylation, will increase significantly; However, as grouting enters its peak period, the expression of genes controlling glucose metabolism and starch synthesis gradually becomes stronger (Katara et al., 2020). However, the situation is not completely static. For example, micrornas are also involved in regulation. They selectively switch on and off certain genes according to different stages and tissues, such as adjusting hormone balance or controlling starch accumulation (Peng et al., 2013; Yi et al., 2013). Although these changes seem chaotic, it is precisely this "rhythmic chaos" that has driven the grains to develop and mature smoothly in the end. 5 Construction of Gene Regulatory Networks (GRNs) from scRNA-seq Data 5.1 Methods for inferring GRNs from single-cell data Not all single-cell RNA sequencing analyses require sophisticated algorithms, but some commonly used ones nowadays are indeed quite complex, such as graph neural networks (GNNS), graph attention models (like AttentionGRN, GRLGRN), and some deep generative models (like DeepSEM). Their goal is actually quite clear: to figure out which transcription factors control which genes, and also to know that this control is directional and functional (Shu et al., 2021; Gao et al., 2025). However, in the face of such thorny problems as data sparsity, background noise, and inter-cell differences, attention mechanisms, graph convolution, and causal reasoning have to be relied upon to deal with them (Lin and Le, 2022). If it is scRNA-seq data with time sequence, then cyclic autoencoders or causal frameworks can also be used to track the time changes, such as the regulatory changes during the grain filling stage of rice (Chen et al., 2025). 5.2 Key transcription factors and regulatory hubs identified in rice grain filling Although these studies seem to focus more on methods, in fact, they have already been able to help us identify some key regulatory factors and "hub" genes. In other biological systems, systems like TFAP2A and TEAD4 have been identified in this way. This type of method may also reveal the important regulatory nodes during the grain filling period of rice (Wang et al., 2025). Most of these nodes regulate the gene modules related to starch synthesis, hormone signaling, and nutrient transport - these modules play a crucial role in the smooth development of grains. 5.3 Cross-talk between cell-type specific GRNs and hormonal/metabolic pathways The GRN derived from RNA-SEq is not merely about transcription factors and target genes. It also reveals some deep connections - the interaction between the regulatory network and hormones and metabolic signals is actually very frequent. Plant hormones such as auxin, cytokinin and abscisic acid often "disrupt" along with metabolic pathway signals. They jointly regulate gene expression, help grains fill smoothly and improve quality (Mao et al., 2023). This regulatory approach is not static; it adjusts according to changes in the developmental stage or the external environment to ensure that the grains can develop healthily and respond to stress. 6 Functional Insights from Cell-type Specific GRNs in Rice Grain Filling 6.1 GRNs governing starch biosynthesis and storage protein accumulation During the grain filling period, the regulatory networks related to starch synthesis in the endosperm are particularly crucial, and many genes come into play at this stage. For instance, the GIF2 gene encodes the large subunit of ADP-glucose phosphorylase (AGP) and is an important node in the regulatory network. Once GIF2 loses its function, the activity of AGP will decrease, resulting in problems in starch synthesis, and the expression of genes such as starch synthase, branching enzyme, and debranching enzyme will also be affected (Wei et al., 2017). These changes indicate that during the development of grains, the accumulation of starch and stored proteins is actually closely regulated. There is another type of small molecule RNA, such as miR1861 and miR397, which are also involved in the regulatory process. They "fine-tune" starch synthesis by influencing the expression of certain negative regulatory factors, especially when the external environment changes (Teng et al., 2021). 6.2 GRNs controlling nutrient transport and assimilation Not only the endosperm but also the pericarp tissue plays an important role. In the peel, the expression levels of
RkJQdWJsaXNoZXIy MjQ4ODYzNA==