Rice Genomics and Genetics 2025, Vol.16, No.3, 159-179 http://cropscipublisher.com/index.php/rgg 178 Beyond abiotic stresses, sustainable agriculture also calls for improved resistance to pests and diseases, potentially reducing the need for chemical inputs. The rice pan-genome contains a vast arsenal of resistance (R) genes and novel allelic variants-far more than any single variety possesses. By exploring this diversity, breeders can pyramid multiple R genes against evolving pathogens, or discover broad-spectrum resistance genes that were hidden in unsequenced germplasm. For example, a pan-genome search might find a wild rice gene that confers resistance to a virulent new rice blast fungus strain; gene editing could then rapidly deploy this resistance into susceptible but high-performing cultivars. Pan-genomics also dovetails with sustainable practices like varietal diversification. Instead of monocultures of a single variety, farmers might plant mixed varietal populations to mitigate risk. Pan-genome analysis helps select varieties that are genetically distinct (carrying complementary resistance genes, for instance) to maximize the benefits of such diversification. Finally, as crop scientists aim for future-proofing crops, they are looking at traits like nitrogen use efficiency, carbon sequestration (root biomass traits), and allelopathy for weed suppression. Many of these traits haven’t been heavily selected in modern breeding but exist in traditional or wild varieties. The pan-genome offers a systematic way to mine genes related to these traits. For example, if deeper roots for drought resilience and carbon sequestration are desired, pan-genome GWAS might identify novel root development regulators present in upland landraces (He et al., 2024). Acknowledgments We sincerely thank Dr. Qian for providing valuable comments and suggestions during the writing of this paper, which were instrumental in improving its quality. Conflict of Interest Disclosure The authors affirm that this research was conducted without any commercial or financial relationships that could be construed as a potential conflict of interest. References Bayer P., Golicz A., Scheben A., Batley J., and Edwards D., 2020, Plant pan-genomes are the new reference, Nature Plants, 6(8): 914-920. https://doi.org/10.1038/s41477-020-0733-0 Daware A., Malik A., Srivastava R., Das D., Ellur R.K., Singh A.K., Tyagi A.K., and Parida S.K., 2023, Rice pangenome genotyping array: an efficient genotyping solution for pangenome-based accelerated genetic improvement in rice, The Plant Journal, 113(1): 26-46. https://doi.org/10.1111/tpj.16028 Guo D., Li Y., Lu H., Zhao Y., Kurata N., Wei X., Wang A., Wang Y., Zhan Q., Fan D., Zhou C., Tian Q., Weng Q., Feng Q., Huang T., Zhang L., Gu Z., Wang C., Wang Z., Wang Z., Huang X., Zhao Q., and Han B., 2025, A pangenome reference of wild and cultivated rice, Nature, 642(7930): 662-671. https://doi.org/10.1038/s41586-025-08883-6 He H., Leng Y., Cao X., Zhu Y., Li X., Yuan Q., Zhang B., He W., Wei H., Liu X., Xu Q., Guo M., Zhang H., Yang L., Lv Y., Wang X., Shi C., Zhang Z., Chen W., Zhang B., Wang T., Yu X., Qian H., Zhang Q., Dai X., Liu C., Cui Y., Wang Y., Zheng X., Xiong G., Zhou Y., Qian Q., and Shang L., 2024, The pan-tandem repeat map highlights multiallelic variants underlying gene expression and agronomic traits in rice, Nature Communications, 15(1): 7291. https://doi.org/10.1038/s41467-024-51854-0 Hickey G., Heller D., Monlong J., Sibbesen J.A., Sirén J., Eizenga J., Paten B., 2020, Genotyping structural variants in pangenome graphs using the vg toolkit, Genome Biology, 21(1): 35. https://doi.org/10.1186/s13059-020-1941-7 Kou Y., Liao Y., Toivainen T., Lv Y., Tian X., Emerson J., Gaut B., Zhou Y., and Purugganan M., 2020, Evolutionary genomics of structural variation in Asian rice (Oryza sativa) domestication, Molecular Biology and Evolution, 37(12): 3507-3524. https://doi.org/10.1093/molbev/msaa185 Li K., Jiang W., Hui Y., Kong M., Feng L., Gao L., Li P., and Lu S., 2021, Gapless indica rice genome reveals synergistic contributions of active transposable elements and segmental duplications to rice genome evolution, Molecular plant, 14(10): 1745-1756. https://doi.org/10.1016/j.molp.2021.06.017 Li X., Dai X., He H., Chen W., Qian Q., Shang L., Guo L., and He W., 2025, Uncovering the breeding contribution of transposable elements from landraces to improved varieties through pan-genome-wide analysis in rice, Frontiers in Plant Science, 16: 1573546. https://doi.org/10.3389/fpls.2025.1573546 Liu C., Peng P., Li W., Ye C., Zhang S., Wang R., Li D., Guan S., Zhang L., Huang X., Guo Z., Guo J., Long Y., Li L., Pan G., Tian B., and Xiao J., 2021, Deciphering variation of 239 elite japonica rice genomes for whole genome sequences-enabled breeding, Genomics, 113(5): 3083-3091. https://doi.org/10.1016/j.ygeno.2021.07.002
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