Rice Genomics and Genetics 2025, Vol.16, No.3, 159-179 http://cropscipublisher.com/index.php/rgg 172 genomics forward-not only by capturing more genetic variation, but also by turning that variation into meaningful insights. It’s a good example of how using multiple genomes together can make a real difference in trait analysis, especially in crops like rice where population diversity is high. 7.3 Case 3: pan-genome study in wild rice Wild rice carries a treasure trove of genes that modern cultivated rice has either lost or never had. A notable example comes from a 2025 study by Guo and his team (Figure 2) (Guo et al., 2025). They assembled a pan-genome from 145 high-quality rice genomes-129 from wild Oryza rufipogon and 16 from cultivated O. sativa. Compared to the traditional Nipponbare reference genome, this new dataset added 3.87 gigabases of fresh sequences, mostly from wild rice. Much of it came from repeated DNA regions like those near centromeres and telomeres, along with duplicated genes. In total, over 69 000 genes were annotated. About 29 000 were shared across all samples (core genes), while roughly 13 700 were unique to wild rice. Many of these wild-specific genes are tied to stress resistance-useful traits for dealing with pests, diseases, or harsh environments. One striking detail: wild rice contains far more disease resistance (R) genes than cultivated varieties. This suggests that domestication may have unintentionally weeded out valuable genes or failed to tap into them at all. The study also highlighted key genes linked to deep root systems and perennial growth-traits that have largely disappeared in today's annual rice crops. Another important takeaway came from comparing the wild and cultivated genomes. The patterns of variation supported the idea that Asian rice was domesticated just once, with the two main subspecies, indica and japonica, diverging later. The team identified nearly 14 000 structural differences between these two types, helping to explain their evolutionary paths. Interestingly, japonica showed signs of a stronger genetic bottleneck, having lost more wild traits than indica. Today, this wild rice pan-genome serves as a valuable tool for breeders. It offers a treasure trove of genes-especially those for stress tolerance and disease resistance-that could be used to improve modern rice through crossbreeding or gene editing. This case clearly shows the importance of keeping wild relatives in the picture when working to expand and improve crop diversity. 7.4 Case 4: application in marker-assisted selection One practical outcome of rice pan-genome research is the development of more effective genotyping tools. A notable example is the Rice Pan-genome Genotyping Array (RPGA), a high-density SNP array designed to detect not just common variants but also those missing from the reference genome (Nipponbare) but found in other rice varieties. Daware et al. (2023) compiled roughly 80 000 markers for this array, including probes aimed at dispensable genomic regions uncovered through pan-genome studies. Using this tool, researchers genotyped a diverse set of rice accessions. The results were quite revealing. When performing GWAS with the RPGA, they identified 42 QTLs associated with grain size and weight-8 of which had been completely missed using only the reference genome. One particularly interesting locus involved a gene absent in Nipponbare: a WD40 repeat-containing protein on chromosome 7. This gene, found only in some rice lines, was linked to longer grain length and was confirmed through QTL mapping to have a real impact on the trait. Beyond discovery, the RPGA also proved useful for practical breeding tasks. It successfully distinguished population structures, tested hybridity in crosses, and helped build dense linkage maps. For breeders using marker-assisted selection (MAS), having markers tied to presence/absence variants is especially valuable. For example, if a beneficial gene from a wild rice donor is missing in elite lines, the RPGA can track its introgression during backcrossing. Overall, this case shows how pan-genomic knowledge can be translated into breeding tools. Instead of relying only on a single reference, breeders can now tap into a broader range of genetic diversity-including structural variants-to make more informed selection decisions and improve rice varieties more effectively.
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