Rice Genomics and Genetics 2024, Vol.15, No.3, 106-120 http://cropscipublisher.com/index.php/rgg 108 3 Phylogenetic Relationships and Classification 3.1 Molecular phylogenetics of Oryza Molecular phylogenetics has significantly advanced our understanding of the evolutionary relationships within the genus Oryza. The genus comprises 27 species, providing a rich source of genetic diversity for rice improvement (Mussurova et al., 2020). High-quality genome assemblies, such as those produced for Oryza rufipogon using SMRT sequencing, have enabled detailed comparative genomic analyses (Mahajan and Kapoor, 2019; Li et al., 2020). These studies have identified numerous genomic variants and lineage-specific expansions of gene families that contribute to reproductive isolation and adaptation to diverse environments. The development of platinum standard reference genome sequences (PSRefSeq) for all Oryza species sets a new benchmark for integrating wild relatives into crop improvement programs (Mussurova et al., 2020). 3.2 Classification systems The classification of Oryza species is based on morphological and genetic criteria. As more genetic and morphological data become available, the classification system of Oryza species continues to evolve. Traditional classification systems have relied on morphological traits, such as plant stature, leaf shape, and spikelet structure. Advances in genomics have allowed for more precise classifications based on genetic data. For instance, the construction of pan-genomes across all Oryza species has provided a comprehensive framework for understanding the genetic diversity within the genus (Huang et al., 2021). This approach has revealed the presence of numerous dispensable genes and large-effect mutations that are crucial for agronomic traits (Li et al., 2020; Huang et al., 2021). Modern classification systems incorporate both genetic and morphological data, leading to a more accurate representation of the evolutionary relationships within the genus. The current classification system divides the Oryza genus into two main groups: the AA genome group, which includes most diploid species and is particularly important in rice breeding due to its reservoir of many beneficial alleles (Zhang et al., 2022). And the BB, CC, EE, and FF genome groups, which contain the polyploid species. This genomic classification has practical implications for rice breeding, as it helps breeders select compatible species for hybridization and gene transfer. 3.3 Evolutionary history and speciation The evolutionary history of the Oryza genus is marked by complex processes of speciation, adaptation, and genome evolution. Phylogenetic studies suggest that the genus originated in Asia around 15 million years ago, with subsequent radiation into diverse ecological niches across the tropics and subtropics (Mahajan and Kapoor, 2019). Speciation within Oryza has been driven by both allopatric and sympatric mechanisms, resulting in the rich genetic diversity observed today. The evolutionary history of Oryza is marked by significant events such as polyploidization and speciation. Cultivated rice varieties are diploid, but there is growing interest in the domestication of wild allotetraploid species like Oryza alta, which offers advantages in genome buffering and environmental robustness (Yu et al., 2021). The speciation process within Oryza has been driven by various factors, including reproductive isolation mechanisms and selection pressures. For example, the lineage-specific expansion of gene families in Oryza rufipogon has played a role in the evolution of mating systems and adaptation to different habitats (Li et al., 2020). Understanding these evolutionary processes is essential for harnessing the genetic potential of wild Oryza species for rice improvement (Li et al., 2020). 4 Geographical Migration and Domestication 4.1 Historical perspectives on rice migration The migration and domestication of rice have been pivotal in shaping its genetic diversity and adaptability. The genus Oryza, which includes both wild and cultivated species, has a rich evolutionary history spanning 15 million years, contributing to the genetic reservoir available for rice improvement (Mussurova et al., 2020). The migration of rice can be traced back to the earliest agricultural practices. Initially domesticated in Asia, rice gradually spread worldwide through human migration, trade routes, and cultural exchanges.
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