Molecular Plant Breeding 2025, Vol.16, No.1, 13-23 http://genbreedpublisher.com/index.php/mpb 21 regions. This clustering is indicative of the “domestication syndrome” and explains the phenomenon of “linkage drag” observed in breeding programs. Additionally, the differentiation within the AA genome species, including the transition from wild to cultivated types and the indica-japonica differentiation, has been mapped to specific genomic locations, further elucidating the genetic basis of domestication. The clustered distribution of genetic factors controlling domestication traits has significant implications for rice breeding. Understanding these clusters can help breeders more effectively utilize desirable traits from wild rice, despite the challenges posed by linkage drag. This knowledge can facilitate the development of new rice varieties with improved traits such as yield, disease resistance, and environmental adaptability. Furthermore, the insights gained from the genetic differentiation within the AA genome species can inform evolutionary studies, providing a clearer picture of the domestication process and the genetic mechanisms underlying it. The genetic lessons from rice evolution underscore the complexity of domestication and the intricate interplay of genetic factors involved. The findings from these studies not only enhance our understanding of rice domestication but also offer practical applications for rice breeding programs. By leveraging the genetic information on domestication-related traits, breeders can overcome the challenges of linkage drag and develop superior rice varieties. Continued research in this field will undoubtedly yield further insights, contributing to the advancement of both rice breeding and evolutionary biology. Acknowledgments We extend our sincere thanks to two anonymous peer reviewers for their feedback, whose critical evaluations and constructive suggestions have contributed to the improvement of our manuscript. Funding This work was supported by the grants from the Central Leading Local Science and Technology Development Project (grant nos. 202207AA110010) and the Key and Major Science and Technology Projects of Yunnan (grant nos. 202202AE09002102). 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 Boersma R., Poortvliet P., and Gremmen B., 2018, The elephant in the room: how a technology’s name affects its interpretation, Public Understanding of Science, 28: 218-233. http://dx.doi.org/10.1177/0963662518812295s Delwaide A., Nalley L., Dixon B., Danforth D., Nayga R., Loo E., and Verbeke W., 2015, Revisiting GMOs: are there differences in European consumers’ acceptance and valuation for cisgenically vs transgenically bred rice, PLoS One, 10(5): e0126060. https://doi.org/10.1371/journal.pone.0126060 Egorova A., Chalaya N., Fomin I., Barchuk A., and Gerasimova S., 2022, De novo domestication concept for potato germplasm enhancement, Agronomy, 12(2): 462. https://doi.org/10.3390/agronomy12020462 Fuentes R., Ridder D., Dijk A., and Peters S., 2021, Domestication shapes recombination patterns in tomato, Molecular Biology and Evolution, 39(1): msab287. https://doi.org/10.1093/molbev/msab287 Giovannoni J., 2018, Tomato multiomics reveals consequences of crop domestication and improvement, Cell, 172(1): 6-8. https://doi.org/10.1016/j.cell.2017.12.036 Giordano J., Miller R., Levy B., Goldstein D., and Wapner R., 2019, Have genomic screening advances gone far enough, American Journal of Obstetrics and Gynecology, 220: S4. https://doi.org/10.1016/j.ajog.2018.11.005 Jin J., Huang W., Gao J.P., Yang J., Shi M., Zhu M.Z., Luo D., and Lin H.X., 2008, Genetic control of rice plant architecture under domestication, Nature Genetics, 40: 1365-1369. http://dx.doi.org/10.1038/ng.247 Lin Z., Li X., Shannon L., Yeh C., Wang M., Bai G., Peng Z., Li J., Trick H., Clemente T., Doebley J., Schnable P., Tuinstra M., Tesso T., White F., and Yu J., 2012, Parallel domestication of the Shattering1 genes in cereals, Nature Genetics, 44: 720-724. https://doi.org/10.1038/ng.2281 Hasan S., Furtado A., and Henry R., 2023, Analysis of domestication loci in wild rice populations, Plants, 12(3): 489. https://doi.org/10.3390/plants12030489
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