Rice Genomics and Genetics 2025, Vol.16, No.2, 96-105 http://cropscipublisher.com/index.php/rgg 99 3.3 Comparative genomics of wild rice and cultivated rice Whole genome sequencing allows us to see the full picture of the genetic differences between wild rice and cultivated rice. Although the traditional view is that indica rice and japonica rice have different origins, studies have found that the two actually share some low genetic diversity regions, which may have been formed by a single selection event and subsequent gene introgression (He et al., 2011). These low-diversity regions are often rich in domestication candidate genes, indicating their important role in the domestication process. In addition, gene regions related to key agronomic traits such as grain size and weight also show signs of selective elimination and positive selection (Kumar et al., 2020). This not only reveals the direction of genetic change, but also reflects the driving force of evolution. Through Bayesian phylogenetic analysis combined with population model support, existing evidence shows that both indica and japonica rice originated from the same wild rice species O. rufipogon, which provides a unified perspective for the overall understanding of rice domestication (Molina et al., 2011). Of course, this model is also constantly being challenged and improved by new data. After all, genetic evolution is never a single-line process. 4 Phylogenetic Relationships and Hybridization Events 4.1 Phylogenetic trees and rice evolution Phylogenetic relationships are key to understanding the evolution and domestication history of rice. Asian rice is mainly divided into indica and japonica, and these two subspecies are actually domesticated from different wild populations of Oryza rufipogon (Sang and Ge, 2007a; 2007b; Huang et al., 2012). Here, genomic analysis revealed significant genetic differences between them (Molina et al., 2011; Choi et al., 2017). However, this is not a simple branching relationship. The study also used a complete set of chloroplast genome sequences to reveal the phylogenetic details of AA genome rice species and highlighted the geographical differentiation of wild rice populations (Wambugu et al., 2015). In fact, these results make it clearer that the evolution of rice is not as linear as we imagined, but rather a combination of multiple lineages and regional variations. 4.2 Hybridization between wild rice and cultivated rice Hybridization is common and important in the evolution of rice. Gene flow between cultivated and wild rice continues, and this gene introgression enriches the genetic background of modern rice (Sang and Ge, 2007a; 2007b; Moner et al., 2018). Interestingly, there was also gene introgression between early independently domesticated varieties, which helped to fix key domestication genes, which is the so-called combination model. The "snowball model" proposed by other studies emphasizes the continued role of gene introgression from local wild populations in ancestral domesticated populations (Sang and Ge, 2007a; 2007b). Moreover, similar continuous hybridization events have been observed in wild rice in Australia, which is very similar to the gene flow during the initial domestication of rice (Moner et al., 2018). This shows that gene exchange has always existed from ancient times to the present, and it is not so simple. 4.3 Impact on genetic diversity Rice domestication has a profound impact on genetic diversity, but the situation is not that simple. In general, domestication reduces genetic diversity, mainly due to selection pressure and population bottlenecks. For example, the nucleotide diversity of indica and japonica rice only retains about 10% to 20% of wild species (Zhu et al., 2007). However, despite the overall reduction in diversity, hybridization and gene introgression events can alleviate this problem and even promote the recovery of genetic diversity. The alleles of early domesticated japonica rice were transferred to populations such as proto-indica and proto-aus through gene introgression, which is critical for maintaining the genetic variation of these populations (Choi et al., 2017). Therefore, the genetic structure of rice is not static, but is constantly affected by gene exchange, showing dynamic diversity. 5 Wild ancestors and Modern Varieties 5.1 Contribution of wild ancestors to modern rice The formation of modern rice varieties is inseparable from their wild ancestors, such as Oryza rufipogon and Oryza nivara. In fact, there is a lot of genetic diversity in the genome structure of cultivated rice, which is mainly
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