Rice Genomics and Genetics 2024, Vol.15, No.2, 83-93 http://cropscipublisher.com/index.php/rgg 86 3 Insights from Genetics and Genomics of Domestication 3.1 Key genetic changes associated with domestication The domestication of rice is a complex process involving significant genetic changes. Recent studies have provided valuable insights into the genetic and genomic alterations that occurred during the domestication of rice. One of the key genetic changes associated with rice domestication is the reduction in seed shattering and seed dormancy, which are crucial for effective harvesting and cultivation. Quantitative trait locus (QTL) analysis has identified several loci associated with these traits, including a cluster of QTLs on chromosome 7, which can significantly improve the plant architecture and panicle structure of cultivated rice (Li et al., 2006). This suggests that selection for high yield played a crucial role in the fixation of beneficial mutations. Whole-genome studies have shown that the two main subspecies of rice, indica and japonica, originated from genetically distinct gene pools within their wild ancestor, Oryza rufipogon, indicating multiple domestication events. However, the presence of common domestication alleles in all cultivated varieties suggests limited introgression of key domestication genes between different gene pools (Kovach et al., 2007; Wei et al., 2012). Gene introgression from wild relatives has also played an important role in rice domestication. For instance, the Pi-cd blast resistance gene found in japonica varieties was introgressed from the southern wild rice, highlighting the importance of gene flow from wild species in enhancing the disease resistance of cultivated rice (Fujino et al., 2019). Additionally, whole-genome analyses have identified numerous structural variations and loss/gain of genes that differentiate cultivated rice from its wild ancestors. These genetic changes are associated with phenotypic and physiological adaptations, such as improved photosynthetic and oxidative phosphorylation systems, enabling cultivated rice to thrive in diverse environments (Zhang et al., 2016). 3.2 The role of selective breeding in shaping modern rice varieties Selective breeding has played a crucial role in the domestication and evolution of modern rice varieties. The domestication process involved both natural and artificial selection, leading to significant genetic changes that distinguish cultivated rice (Oryza sativa) from its wild ancestors. Recent studies have highlighted the impact of selective breeding on the genetic diversity and structure of rice populations (Chen et al., 2019). For example, analyses of genome-wide polymorphism patterns in rice have shown that selective breeding has resulted in the introgression of beneficial traits from different subspecies, creating genetic mosaics that enhance the adaptability and productivity of cultivated rice. This genetic introgression is evident in the genetic coherence around key domestication genes in different subgroups, indicating that ancient farmers exchanged genetic material to improve crop traits (Chen et al., 2019). Quantitative Trait Locus (QTL) analysis has further elucidated the genetic basis of domestication traits. Studies involving crosses between cultivated rice and wild species such as O. nivara have identified QTLs associated with reduced seed shattering, decreased seed dormancy, and synchronized seed maturation-traits essential for effective harvesting and cultivation. These findings emphasize the role of selective breeding in fixing beneficial mutations, thereby improving yield and enhancing plant architecture, such as fewer erect tillers and more branched panicles. Genomic sequencing and analysis of a large number of wild and cultivated rice varieties have provided insights into the genomic characteristics of domestication. For instance, selective sweeps identified in the genomes of indica and japonica rice varieties have pinpointed regions that underwent strong selection during domestication. These selective sweeps are associated with traits conferring advantages in agricultural environments, such as disease resistance and improved grain quality (Yuan et al., 2017). Combining genome-wide association studies (GWAS) with genomic scans has also highlighted the interaction between artificial and natural selection. These approaches effectively identify valuable alleles from both cultivated and wild species, which can be used in breeding programs aimed at improving rice varieties. The accumulation and appropriate sampling of germplasm collections are crucial for expanding the pool of useful alleles, potentially leading to the re-domestication of rice varieties for sustainable food production.
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