Rice Genomics and Genetics 2024, Vol.15, No.3, 94-105 http://cropscipublisher.com/index.php/rgg 96 markers often exhibit higher sequence divergence compared to cpDNA, making them useful for resolving relationships at both inter- and intraspecific levels. Random amplified polymorphic DNA (RAPD) markers and cleaved amplified polymorphic sequence (CAPS) analysis have also been employed to study nuclear DNA polymorphisms in Oryza, aiding in the classification and phylogenetic analysis of different species (Buso et al., 2001). Next-generation sequencing (NGS) technologies have revolutionized phylogenetic studies by enabling the sequencing of entire genomes or large genomic regions. These technologies facilitate the identification of numerous genetic markers across the genome, providing high-resolution data for phylogenetic analysis. NGS has been particularly useful in identifying variable regions within the chloroplast genome and developing universal cpDNA markers for phylogenetic studies (Yang et al., 2017). The application of NGS has also allowed for the comprehensive analysis of nuclear and organellar genomes, enhancing our understanding of the evolutionary history and relationships among Oryzaspecies. 3.2 Phylogenetic relationships among Oryza species The primary gene pool of Oryza includes species that are closely related to the cultivated rice, Oryza sativa, and can readily interbreed with it. Phylogenetic studies using cpDNA and nuclear DNA markers have shown that species within the primary gene pool, such as O. rufipogon and O. nivara, share a close evolutionary relationship with O. sativa (Buso et al., 2001). These species are often used in breeding programs to introduce desirable traits into cultivated rice. Secondary and tertiary gene pool species are more distantly related to O. sativa and exhibit greater genetic divergence. These species include O. glumaepatula, O. alta, O. grandiglumis, and O. latifolia, which belong to the O. officinalis complex (Buso et al., 2001). Phylogenetic analyses have indicated that these species diverged from the primary gene pool species approximately 20 million years ago. The secondary and tertiary gene pool species are valuable for studying the broader evolutionary history of the Oryza genus and for identifying novel genetic resources for rice improvement. 3.3 Evolutionary divergence and speciation Molecular clock estimates have been used to date the divergence times of various Oryza species. These estimates are based on the accumulation of genetic mutations over time and provide insights into the timing of speciation events. For example, the divergence of American diploid and tetraploid species from the primary gene pool species has been estimated to have occurred around 20 million years ago (Buso et al., 2001). Such estimates are crucial for understanding the evolutionary timeline and the factors driving speciation in the Oryza genus. Divergence of Oryza sativa and Oryza glaberrima: The wild progenitors of Oryza sativa and Oryza glaberrima diverged from a common ancestor approximately 2~3 million years ago. This divergence occurred due to geographical and ecological isolation, leading to the development of distinct gene pools in Asia and Africa. Oryza sativa was domesticated from its wild relatives Oryza nivara and Oryza rufipogon in the Yangtze River basin of China around 8 000 ~ 9 000 years ago. Oryza glaberrima was domesticated from its wild ancestor Oryza barthii in the Niger River basin of West Africa around 3 000~3 500 years ago. Adam et al. (2023) found significant differences in genomic structure between Asian rice and African rice, particularly in regions related to panicle structure. The results showed that Oryza glaberrima had fewer branches, while Oryza sativa exhibited complex panicle shapes and more branches (Figure 1). Formation of Oryza nivara and Oryza rufipogon: The common ancestor of Oryza nivara and Oryza rufipogon diverged from other Oryza species approximately 2~3 million years ago. This divergence was driven by geographical isolation and ecological differentiation, leading to the establishment of distinct genetic lineages. Xu et al. (2020) found the differences in flowering times between O. rufipogon and O. nivara contribute significantly to reproductive isolation. O. nivara flowers much earlier than O. rufipogon, maintaining species divergence despite potential hybrid viability.
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