Rice Genomics and Genetics 2025, Vol.16, No.2, 96-105 http://cropscipublisher.com/index.php/rgg 98 3.2 The role of quantitative trait loci (QTL) in domestication QTL is actually a key genetic factor regulating various morphological and physiological traits of rice, and they play an important role in domestication. A large number of studies have found QTLs related to domestication, such as those that control grain abscission, seed dormancy and plant morphology (Cai and Morishima, 2002; Li et al., 2006). These QTLs often appear in clusters, especially in the comparison between wild and cultivated rice. The existence of these clusters suggests the correlation between traits and also reflects the coordinated adjustment of these traits by natural selection (Cai and Morishima, 2002). It is worth noting that some QTLs with particularly large effects, such as the one on chromosome 7, significantly affect yield and plant structure (Li et al., 2006). The concentrated distribution of these QTLs may be the genetic basis of the "domestication syndrome" and also explain the phenomenon of "linkage drag" in breeding. However, the effects of some QTLs are not always directly apparent. Sometimes they are affected by other genes and show complex genetic interactions. Figure 1 (A) A haplotype network of Rc gene along with its pericarp color, in total four haplotypes were formed, Rc-H3 was the ancestral haplotype of wild rice; (B) Haplotype based phylogenetic tree of Rc gene was constructed using 179 diverse rice genotypes and were separated into four major distinct groups (Adopted from Singh et al., 2017) Image caption: (A) The size of each circle is proportional to haplotype (allele) frequency. To determine the origin and dispersal of these mutations in Rc gene we examined in total 179 diverse rice genotypes. Color-coding represents different population groups (Red-Wild rice, Blue-Indica, Black-Aus, Green-Aromatic, and Magenta-Japonica); (B) Color-coding represents different varietal groups (Cyan-Pro-Indica, Orange-Pro-Aus, Red-Mid-Gangetic, Blue-Indica, Black-Aus, Green-Aromatic, and Magenta-Japonica) (Adopted from Singh et al., 2017)
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