Rice Genomics and Genetics 2025, Vol.16, No.2, 96-105 http://cropscipublisher.com/index.php/rgg 97 2 Origin and Evolutionary History of Wild Rice 2.1 Classification and status of wild rice Wild rice plays an important role in understanding the domestication history of rice. They belong to the genus Oryza, whose species have a complex genetic structure and show rich diversity. For example, O. glumaepatula and O. longistaminata are both species carrying AA genomes, but they form different branches within the genome (Wambugu et al., 2015; Moner et al., 2018). Species with AA genomes are most closely related to cultivated rice Oryza sativa and are therefore considered to be the main component of the rice gene pool. In particular, Oryza rufipogon and Oryza nivara are often regarded as the direct wild ancestors of cultivated rice in Asia (Sang and Ge, 2007a; Molina et al., 2011; Huang et al., 2012). However, this taxonomic status also reflects the complex phylogenetic relationship between wild rice. Therefore, the formation process of indica and japonica rice may actually be closely related to the domestication of different wild rice species (Sang and Ge, 2007a; Vaughan et al., 2008; Singh et al., 2017). 2.2 Geographical distribution and habitat Wild rice has a wide distribution range, covering multiple tropical and subtropical continents, especially Asia, Africa and Australia. Their wide distribution is partly due to multiple long-distance dispersals over the past million years (Wambugu et al., 2015). For example, the Yangtze River and Pearl River basins in Asia are generally considered to be the core areas of rice domestication (Molina et al., 2011; Huang et al., 2012), which also makes these places important gathering areas for wild rice. However, wild rice communities in northern Australia show signs of earlier genetic differentiation, belonging to the ancient lineage of the AA genome, showing significant geographical and genetic isolation (Moner et al., 2018). Geographical separation has led to independent evolutionary paths, thus increasing the overall genetic diversity of wild rice. 2.3 Genetic diversity of wild rice The genetic diversity of wild rice is very rich, far exceeding that of modern cultivated rice, and this characteristic is extremely critical for rice domestication and breeding. Studies have found that the frequency of nucleotide variation in wild rice is high, while the genetic diversity of cultivated rice has decreased due to the genetic bottleneck experienced during the domestication process (Zhu et al., 2007; Huang et al., 2012). In addition, there are a large number of different haplotypes in the wild rice population, and there is frequent gene flow between wild species and cultivated species (Figure 1) (Singh et al., 2017; Moner et al., 2018). This gene exchange and diversity provide genetic resource support for improving the stress resistance and adaptability of cultivated rice (Stein et al., 2018). From a phylogenetic perspective, complex gene introgression and selection processes have jointly shaped the genetic relationship between wild rice and cultivated rice (Sang and Ge, 2007a; Vaughan et al., 2008; Singh et al., 2017). 3 Genetic Basis of Rice Domestication 3.1 Key domestication genes Several genes were particularly critical during the domestication of rice, especially in the early stages of cultivation. For example, a special version of the sh4 gene can significantly reduce grain shedding, which is important for maintaining yield. This non-threshing sh4 allele is now almost fixed in all cultivated rice, indicating that it has undergone strong artificial selection (Sang and Ge, 2007a; Zhang et al., 2009). However, the specific details of the selection of important genes such as qSH1 in different rice subspecies are not clear (Zhang et al., 2009). There is also the qSW5 gene, which controls the width of the grain. The loss of the gene causes the grain to hold more starch, thereby increasing yield (Shomura et al., 2008). These genes all indicate that traits that improve harvest efficiency and yield are the focus of selection during the domestication process. However, some exceptions cannot be ignored. For example, different variants of these genes also exist in some wild rice species, indicating that domestication is not simply "having" or "not having" these genes, but is achieved by selecting specific versions.
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