Rice Genomics and Genetics 2024, Vol.15, No.4, 178-189 http://cropscipublisher.com/index.php/rgg 182 region in the evolutionary history of rice. The release of a complete long-read assembly of IR 8 ‘Miracle Rice’ further emphasizes the significance of East Asia in modern rice research and breeding (Stein et al., 2018; Chen et al., 2019). In Africa, the domestication of Oryza glaberrima, the African rice, presents a different narrative. Unlike the centric domestication observed in Asian rice, African rice is believed to have undergone a non-centric, multiregional domestication process. Genetic analyses of Oryza glaberrima and its progenitor Oryza barthii suggest that domestication traits such as seed non-shattering were selected from multiple genotypes across different geographical regions in West and Central Africa. This multiregional origin hypothesis is supported by the genetic structure and phylogeographic analysis of domestication-related genes (Lu, 2023). 5.2 Archaeological evidence of domestication Archaeological evidence plays a pivotal role in tracing the domestication history of Oryza species. Excavations and studies of ancient rice remains have provided crucial data on the early cultivation and domestication practices. For instance, the presence of domesticated rice grains in ancient archaeological sites across South and East Asia corroborates the genetic findings and helps establish a timeline for the domestication events. These findings are essential for understanding the transition from wild to cultivated rice and the spread of domesticated varieties across different regions (Chen et al., 2019; Choi et al., 2019). 5.3 Genetic markers of domestication Genetic markers have been instrumental in identifying the domestication signatures in Oryza species. Genome sequencing and analysis have revealed specific mutations and genetic variations associated with domestication traits such as seed shattering, plant architecture, and flowering time. For example, the study of genome-wide variations in Oryza sativa and Oryza glaberrima has identified key domestication genes and their evolutionary trajectories. These genetic markers not only provide insights into the domestication processes but also offer potential targets for future rice breeding programs aimed at improving crop resilience and yield (Stein et al., 2018; Chen et al., 2019; Choi et al., 2019; Lu, 2023). 6 Evolution of CultivatedOryza Species 6.1 Key domestication traits The domestication of Oryza species, particularly Oryza sativa, has been marked by the selection of key traits that distinguish cultivated varieties from their wild counterparts. These traits include reduced shattering, increased grain size, and changes in plant architecture. The analysis of 3 010 diverse Asian cultivated rice genomes revealed significant genetic variation and identified numerous single nucleotide polymorphisms (SNPs) and structural variations that contribute to these domestication traits (Figure 2) (Wang et al., 2018). The genome-wide analysis presented in Figure 2 offers valuable insights into the genetic diversity and domestication history of Oryza sativa, highlighting the complexity of its genomic composition in relation to geographical distribution and environmental adaptation. This analysis reveals over 10 000 new full-length protein-coding genes and a wide range of presence/absence variations (PAVs), which are crucial for the adaptation and survival of rice in diverse environments. Additionally, it demonstrates the complex structural variations within the rice species and evidence of multiple independent domestication events, indicating that the domestication and evolution of rice are diverse and region-specific processes. The presence of selfish genetic elements, such as the toxin-antidote system, has been shown to play a role in reproductive isolation and the maintenance of domestication traits by preventing gene flow from wild to cultivated varieties (Yu et al., 2018).
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