Rice Genomics and Genetics 2024, Vol.15, No.3, 94-105 http://cropscipublisher.com/index.php/rgg 95 2 Historical Overview of Oryza Classification 2.1 Traditional morphological classification The traditional classification of Oryza species was primarily based on morphological characteristics such as plant height, leaf shape, and flower structure. This method, while useful, often led to ambiguities due to the phenotypic plasticity of plants and the influence of environmental factors on their morphology. Early taxonomists grouped Oryza species into complexes based on these visible traits, which sometimes resulted in misclassification and confusion regarding the evolutionary relationships among species (Wang et al., 1992). 2.2 Transition to molecular classification The advent of molecular techniques revolutionized the classification of Oryza species. Molecular markers such as RFLPs (Restriction Fragment Length Polymorphisms), SSRs (Simple Sequence Repeats), and ISSRs (Inter Simple Sequence Repeats) provided more reliable and precise tools for phylogenetic studies. These methods allowed researchers to analyze genetic diversity and relationships at the DNA level, leading to more accurate classifications. For instance, ISSR polymorphism has been used to determine genetic diversity and phylogenetic relationships, revealing that the genus Oryza may have evolved following a polyphyletic pathway (Joshi et al., 2000). Similarly, SSR markers from mitochondrial and chloroplast genomes have provided new insights into the phylogenetic relationships among Oryza species (Nishikawa et al., 2005). 2.3 Major milestones inOryza phylogenetic research Several key studies have marked significant milestones in the phylogenetic research of Oryza species. One such study used sequences from nuclear genes and MITE insertions to reconstruct the phylogeny of the A-genome group, providing evidence for the monophyletic origin of most species within this group (Zhu and Ge, 2005). Another important study utilized AFLP markers to fingerprint 23 Oryza species, suggesting a common ancestry and polyphyletic evolution within the genus. Additionally, the use of nuclear and mitochondrial DNA sequences has helped resolve the phylogenetic relationships among medaka fishes of the genus Oryzias, indicating the necessity for systematic taxonomic revisions (Takehana et al., 2005). Recent advancements in phylogenomics have further refined our understanding of Oryza evolution. For example, a comprehensive phylogenomic analysis of AA-genome species by Zhu et al. (2014) using over 60 kb of nuclear genes and intergenic regions successfully resolved their phylogenetic relationships and divergence times. Another study highlighted the genetic conservation, turnover, and innovation across the genus Oryza by analyzing 13 reference genomes, providing a detailed view of genome evolution and species diversification (Stein et al., 2018). These molecular approaches have not only clarified the evolutionary history of Oryza species but also identified potential genetic resources for crop improvement, such as new haplotypes for disease resistance (Stein et al., 2018). The integration of molecular data with traditional morphological classification continues to enhance our understanding of the complex phylogenetic relationships within the genus Oryza. 3 Molecular Phylogenetics of Oryza 3.1 DNA markers and genomic tools used in phylogenetic studies Chloroplast DNA (cpDNA) markers have been extensively used in phylogenetic studies of the Oryza genus due to their maternal inheritance and relatively conserved nature. Studies have utilized various cpDNA regions to resolve phylogenetic relationships among Oryza species. For instance, the trnL-trnF and trnK/matK regions have been commonly employed, although their resolution at lower taxonomic levels can be limited (Bouillé et al., 2011). Additionally, cpDNA restriction patterns have been used to distinguish between different Oryza species, revealing significant diversity within species with histories of introgression and allotetraploidization. The use of noncoding cpDNA sequences has also been highlighted for their variability and utility in phylogenetic and phylogeographic studies (Shaw et al., 2014). Nuclear DNA markers, such as internal transcribed spacer (ITS) sequences of ribosomal DNA, have been used alongside cpDNA markers to provide a more comprehensive understanding of phylogenetic relationships. These
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