Rice Genomics and Genetics 2025, Vol.16, No.2, 96-105 http://cropscipublisher.com/index.php/rgg 102 japonica rice was locked in southern China (Huang et al., 2012). However, it is worth noting that this process was not smooth sailing. A serious genetic bottleneck occurred during the domestication process, resulting in the genetic diversity of cultivated rice being far less than that of its wild ancestor (Zhu et al., 2007; Gao and Innan, 2008). 7.2 Genetic insights into cultivated rice subspecies When we look at indica and japonica rice, we find that they are genetically distinct, which has led to different views on whether they were domesticated independently or have a common origin. The latest multi-locus and population model analyses reveal that although the two are genetically different, there is actually gene flow between them, indicating that the evolutionary history of the two subspecies is quite complex, and they even partially share the same ancestral population (Gao and Innan, 2008; Molina et al., 2011). Whole-genome studies have also found a number of selection pressures and gene introgression events that have affected the genetic composition of modern rice varieties (Zhao et al., 2010; Choi and Purugganan, 2018; Stein et al., 2018). In particular, artificial breeding and cultural exchanges have played a significant role in shaping these genetic characteristics (Huang et al., 2012; Veltman et al., 2018). 7.3 Impact of modern breeding It is of great significance to apply the genetic understanding of domestication and evolution of cultivated rice to modern breeding. By understanding the genetic diversity and population structure of rice, we can better locate important genetic regions and improve key traits such as yield, disease resistance and stress tolerance (Zhao et al., 2010; Stein et al., 2018). For example, the release of whole genome assemblies and new haplotypes, such as the genome of the “IR 8 miracle rice”, has become a valuable tool for breeding improvement (Stein et al., 2018). In addition, understanding the phenomena of gene introgression and hybridization not only helps us to utilize the genetic resources of wild relatives, but also broadens the genetic base of cultivated rice and makes it more adaptable to changing environmental conditions (Garris et al., 2005; Choi and Purugganan, 2018). 8 Challenges and Future Directions 8.1 Complex genetic history The genetic background of rice is actually very complex, which is related to the independent domestication of indica and japonica rice from different wild ancestors. What's more troublesome is that there has been gene introgression between the two subspecies and their wild relatives, which makes the genetic relationship more confusing (Sang and Ge, 2007a; Zou et al., 2008; Stein et al., 2018). The rapid species differentiation within the genus Oryza has brought a large number of genetic changes and new genetic elements over millions of years, which undoubtedly makes the reconstruction of phylogeny very difficult (Zou et al., 2008; Stein et al., 2018). However, these rapid differentiations have also led to contradictions in genetic lineages, increasing the difficulty of understanding the evolutionary relationships of the genus Oryza (Zou et al., 2008). Therefore, it is difficult to clarify the entire evolutionary process by relying solely on traditional methods. 8.2 Technical limitations in genomic research Although genomic technology is advancing, phylogenetic research on rice still faces many technical difficulties. In particular, genomes rich in highly repetitive sequences and structural variations are particularly difficult to assemble and annotate (Li et al., 2014; Stein et al., 2018). Short-read sequencing technology often cannot assemble a complete genome, resulting in the masking of some phylogenetic signals. Although long-read sequencing technology has improved, such as in the genome assembly of the "IR 8 miracle rice", its high cost and technical barriers limit its popularity (Stein et al., 2018). In addition, to accurately compare and compare diverse rice materials, it is necessary to rely on advanced bioinformatics tools and huge computing resources, which is a practical obstacle for many research teams (Li et al., 2014). 8.3 Socioeconomic and cultural impacts The domestication and cultivation of rice are inseparable from the socioeconomic and cultural background, which directly affects the research direction and the promotion of new technologies. As the staple food of more than half
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