Rice Genomics and Genetics 2025, Vol.16, No.2, 96-105 http://cropscipublisher.com/index.php/rgg 96 Review Article Open Access Phylogenetic Evolution of Rice: A Comprehensive Review of Domestication Events and Wild Progenitors Zhongxian Li, Zufan Chen, Qifu Zhang Hier Rice Research Center, Hainan Institute of Tropical Agricultural Resources, Sanya, 572025, Hainan, China Corresponding email: qifu.zhang@hitar.org Rice Genomics and Genetics, 2025, Vol.16, No.2 doi: 10.5376/rgg.2025.16.0009 Received: 10 Feb., 2025 Accepted: 25 Mar., 2025 Published: 12 Apr., 2025 Copyright © 2025 Li et al., This is an open access article published under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited. Preferred citation for this article: Li Z.X., Chen Z.F., and Zhang Q.F., 2025, Phylogenetic evolution of rice: a comprehensive review of domestication events and wild progenitors, Rice Genomics and Genetics, 16(2): 96-105 (doi: 10.5376/rgg.2025.16.0009) Abstract This study reviews the phylogenetic process of rice, focusing on the domestication events and the key role of wild ancestors in rice domestication. The study suggests that indica and japonica, the major subspecies of Asian rice, may have been domesticated independently from different wild populations, although some domestication genes such as sh4 may have a single origin. Dynamic processes such as gene flow, gene introgression and hybridization between wild rice and cultivated rice significantly increased the genetic diversity of modern rice varieties. The domestication process of rice has multiple complexities and has been profoundly influenced by multiple gene exchanges between wild and cultivated populations. A thorough understanding of these domestication and evolutionary mechanisms is of great guiding significance for the breeding and conservation of rice varieties in the future. The purpose of this study is to provide theoretical basis and scientific reference for rice breeding and genetic improvement. Keywords Rice domestication; Phylogenetic evolution; Wild progenitors; Genetic diversity; Introgression 1 Introduction Rice (Oryza sativa L.) is now the mainstay of global food production-it supports the daily diet of more than half of the world's population (Zhu et al., 2007; Huang et al., 2012; Huang, 2024). Its presence is particularly felt in Asia: large paddy fields, seasonal rice planting and harvesting have long been integrated into the culture and history of this land (Wei and Huang, 2019). However, how rice became what it is today is no longer a simple agricultural issue. The evolutionary process, domestication path, and relationship with wild rice involved are still under debate today (Molina et al., 2011; Choi et al., 2017). Interestingly, although it is generally believed that rice originated from wild rice (Oryza rufipogon), the research community does not completely agree on the specific location, time, or even number of times (Molina et al., 2011). Some studies have suggested that the two main subspecies of rice, indica (O. sativa indica) and japonica (O. sativa japonica), may not have been domesticated all at once, but rather experienced multiple independent domestication events (Huang et al., 2012; Choi et al., 2017). This view is also supported by some genomic data. The decline in genetic diversity is a phenomenon that has been repeatedly mentioned in rice domestication - some scholars believe that this shows that rice has experienced a serious bottleneck effect (Zhu et al., 2007; Veltman et al., 2018). However, it is precisely these bottlenecks and selection pressures that have gradually allowed it to break away from the wild state and become the staple food we are familiar with. In recent years, with the help of various genomic analysis tools, researchers have gradually clarified the relationship and evolutionary context between rice and wild rice (Gao and Innan, 2008; Wambugu et al., 2015). This study will not stop at a single event or conclusion, but will try to look at the history of rice domestication from multiple perspectives, including genetic background, population history, and phylogenetic information. We hope that by integrating existing research results, we can further understand how this key crop has gradually moved from the wild to the human table, and provide some useful clues for future breeding and food security.
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