RGG_2025v16n4

Rice Genomics and Genetics 2025, Vol.16, No.4, 199-210 http://cropscipublisher.com/index.php/rgg 208 Huang K., Lu F., Chen P., Jiao G., Lin H., Zhang J., Zhao S., Cao R., Shao G., Sheng Z., Hu S., Tang S., Hu P., and Wei X., 2025, A large-scale gene regulatory network for rice endosperm starch biosynthesis and its application in genetic improvement of rice quality, Plant Biotechnology Journal, 23(7): 2583-2594. https://doi.org/10.1111/pbi.70079 Ishimaru T., Parween S., Saito Y., Masumura T., Kondo M., and Sreenivasulu N., 2021, Laser microdissection transcriptome data derived gene regulatory networks of developing rice endosperm revealed tissue-and stage-specific regulators modulating starch metabolism, Plant Molecular Biology, 108: 443-467. https://doi.org/10.1007/s11103-021-01225-w Islam M., Liu Y., Hassan M., Abraham P., Merlet J., Townsend A., Jacobson D., Buell C., Tuskan G., and Yang X., 2024, Advances in the application of single-cell transcriptomics in plant systems and synthetic biology, Biodesign Research, 6: 29. https://doi.org/10.34133/bdr.0029 Jin S., Xu L., Leng Y., Zhang M., Yang Q., Wang S., Jia S., Song T., Wang R., Tao T., Liu Q., Cai X., and Gao J., 2023, The OsNAC24‐OsNAP protein complex activates OsGBSSI and OsSBEI expression to fine‐tune starch biosynthesis in rice endosperm, Plant Biotechnology Journal, 21: 2224-2240. https://doi.org/10.1111/pbi.14124 Jovic D., Liang X., Zeng H., Lin L., Xu F., and Luo Y., 2022, Single‐cell RNA sequencing technologies and applications: a brief overview, Clinical and Translational Medicine, 12(3): e694. https://doi.org/10.1002/ctm2.694 Katara J., Verma R., Parida M., Ngangkham U., Molla K., Barbadikar K., Mukherjee M., Parameswaran C., Samantaray S., Ravi N., Singh O., and Mohapatra T., 2020, Differential expression of genes at panicle initiation and grain filling stages implied in heterosis of rice hybrids, International Journal of Molecular Sciences, 21(3): 1080. https://doi.org/10.3390/ijms21031080 Kim J., Chae S., Jun K., Pahk Y., Lee T., Chung P., Kim Y., and Nahm B., 2017, Genome-wide identification of grain filling genes regulated by the OsSMF1 transcription factor in rice, Rice, 10: 16. https://doi.org/10.1186/s12284-017-0155-4 Lin Z., and Le O., 2022, Inferring gene regulatory networks from single-cell gene expression data via deep multi-view contrastive learning, Briefings in Bioinformatics, 24(1): bbac586. https://doi.org/10.1093/bib/bbac586 Liu B., Meng S., Yang J., Wu J., Peng Y., Zhang J., and Ye N., 2025, Carbohydrate flow during grain filling: Phytohormonal regulation and genetic control in rice (Oryza sativa), Journal of Integrative Plant Biology, 67: 1086-1104. https://doi.org/10.1111/jipb.13904 Liu C., Ma T., Yuan D., Zhou Y., Long Y., Li Z., Dong Z., Duan M., Yu D., Jing Y., Bai X., Wang Y., Hou Q., Liu S., Zhang J., Chen S., Li D., Liu X., Li Z., Wang W., Li J., Wei X., Ma B., and Wan X., 2022, The OsEIL1‐OsERF115‐target gene regulatory module controls grain size and weight in rice, Plant Biotechnology Journal, 20(8): 1470-1486. https://doi.org/10.1111/pbi.13825 Mao G., Pang Z., Zuo K., Wang Q., Pei X., Chen X., and Liu J., 2023, Predicting gene regulatory links from single-cell RNA-seq data using graph neural networks, Briefings in Bioinformatics, 24(6): bbad414. https://doi.org/10.1093/bib/bbad414 Panda B., Sekhar S., Dash S., Behera L., and Shaw B., 2018, Biochemical and molecular characterisation of exogenous cytokinin application on grain filling in rice, BMC Plant Biology, 18: 89. https://doi.org/10.1186/s12870-018-1279-4 Panigrahi S., Panigrahy M., Kariali E., Dash S., Sahu B., Sahu S., Mohapatra P., and Panigrahi K., 2021, MicroRNAs modulate ethylene induced retrograde signal for rice endosperm starch biosynthesis by default expression of transcriptome, Scientific Reports, 11: 5573. https://doi.org/10.1038/s41598-021-84663-2 Peng T., Sun H., Du Y., Zhang J., Li J., Liu Y., Zhao Y., and Zhao Q., 2013, Characterization and expression patterns of microRNAs involved in rice grain filling, PLoS ONE, 8(1): e54148. https://doi.org/10.1371/journal.pone.0054148 Pérez L., Soto E., Farré G., Juanos J., Villorbina G., Bassie L., Medina V., Serrato A., Sahrawy M., Rojas J., Romagosa I., Muñoz P., Zhu C., and Christou P., 2019, CRISPR/Cas9 mutations in the rice Waxy/GBSSI gene induce allele-specific and zygosity-dependent feedback effects on endosperm starch biosynthesis, Plant Cell Reports, 38: 417-433. https://doi.org/10.1007/s00299-019-02388-z Ram H., Singh A., Katoch M., Kaur R., Sardar S., Palia S., Satyam R., Sonah H., Deshmukh R., Pandey A., Gupta I., and Sharma T., 2020, Dissecting the nutrient partitioning mechanism in rice grain using spatially resolved gene expression profiling, Journal of Experimental Botany, 72(6): 2212-2230. https://doi.org/10.1093/jxb/eraa536 Ren Y., Huang Z., Jiang H., Wang Z., Wu F., Xiong Y., and Yao J., 2021, A Heat stress responsive NAC transcription factor heterodimer plays key roles in rice grain filling, Journal of Experimental Botany, 72(8): 2947-2964. https://doi.org/10.1093/jxb/erab027 Rostom R., Svensson V., Teichmann S., and Kar G., 2017, Computational approaches for interpreting scRNA‐seq data, Febs Letters, 591: 2213-2225. https://doi.org/10.1002/1873-3468.12684

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