Rice Genomics and Genetics 2025, Vol.16, No.2, 96-105 http://cropscipublisher.com/index.php/rgg 100 passed down from these wild rice species (Sang and Ge, 2007a; Huang et al., 2012; Singh et al., 2017). However, the process of rice domestication is not just a simple selection. Important traits such as reducing grain shedding are controlled by the sh4 gene, which is clearly pointed out in the study (Sang and Ge, 2007a; 2007b). Indica and japonica rice seem to be very different, but in fact, the genetic differences are largely derived from their respective wild ancestors. Especially for indica rice, when it spread to South Asia and Southeast Asia, it also hybridized with local wild rice, which also affected its evolutionary trajectory (Huang et al., 2012; Choi et al., 2017). However, not all wild rice participated in domestication, and the specific participating populations need to be further subdivided. 5.2 Application in modern breeding programs Modern breeding work is increasingly dependent on these wild rice species. In fact, using the beneficial genes carried by wild rice is an effective means to improve the disease resistance, drought tolerance and yield of cultivated rice (Yang et al., 2012; Singh et al., 2017; Stein et al., 2018). Speaking of which, wild rice populations from Australia are particularly valued because of their unique genetic background, and are even considered to have an important impact on global rice food security (Moner et al., 2018). Of course, such utilization is not always smooth. For example, when transferring domestication genes fromjaponica rice to indica rice, there were also problems with gene compatibility. However, this work is generally of great significance to modern variety improvement (Molina et al., 2011; Yang et al., 2012). In fact, this hybridization and gene transfer has always been one of the important methods of rice improvement. 5.3 Protection of wild rice genetic resources Protecting wild rice genetic resources is the basis for maintaining continuous rice improvement. With more and more artificial selection, the genetic diversity of cultivated rice is decreasing, which makes the protection of wild rice populations more important (Sang and Ge, 2007b; Moner et al., 2018). At present, the collection and sequencing of wild rice genomes is in progress, which not only helps to understand their evolutionary history, but also provides valuable resources for breeding (Yang et al., 2012; Stein et al., 2018). However, wild rice populations are not static. For example, in wild rice in Australia, genes have been introgressing new mutations, which reminds us to continue to monitor these resources to ensure better use in the future (Moner et al., 2018). Conservation work is not only about preservation, but also about paving the way for future germplasm innovation. 6 Domestication Bottleneck and Genetic Variation 6.1 Loss of genetic diversity during domestication After domestication, the genetic diversity of rice has decreased significantly, as can be seen from multiple studies. For example, compared with its wild ancestors Oryza rufipogon and Oryza nivara, the nucleotide diversity of cultivated rice (Oryza sativa) is only 10% to 20% of that of wild rice (Zhu et al., 2007). This reduction indicates that the domestication process has experienced a serious genetic bottleneck. African rice (Oryza glaberrima) has encountered a similar situation, with its genetic diversity only retaining about 30% of that of its wild ancestor O. barthii (Li et al., 2011; Nabholz et al., 2014). However, there are exceptions. Although the overall diversity of some rice varieties has decreased, they still perform well in certain regions. In general, the sharp decline in genetic diversity has a negative impact on the adaptability and stress resistance of rice. 6.2 Genetic variation in local varieties and improved varieties Although overall genetic diversity has decreased due to domestication, there is still a lot of genetic variation in local varieties and modern improved varieties of rice. Local varieties are mostly the result of long-term selection by farmers, and thus retain more genetic diversity. For example, local varieties show rich differences in grain shape, size and aroma, and these variations provide a basis for the preservation of genetic diversity (Ray et al., 2013). Studies in South Korea have shown that the nucleotide diversity of local varieties is even higher than that of weedy rice (Tong et al., 2017), which shows that traditional varieties are still an important source of genetic resources (Figure 2). This type of diversity is very important for breeding and improvement, and can inject more potential into modern varieties.
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