Rice Genomics and Genetics 2024, Vol.15, No.3, 94-105 http://cropscipublisher.com/index.php/rgg 94 Systematic Review Open Access Phylogenetic Patterns and Classification of Oryza Species: A Molecular Perspective Xuanjun Fang Hainan Institute of Tropical Agricultural Resources, Sanya, 572025, Hainan, China Corresponding email: xuanjunfang@hitar.org Rice Genomics and Genetics, 2024, Vol.15, No.3 doi: 10.5376/rgg.2024.15.0011 Received: 10 Apr., 2024 Accepted: 11 May, 2024 Published: 22 May, 2024 Copyright © 2024 Fang, This is an open access article published under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited. Preferred citation for this article: Fang X.J., 2024, Phylogenetic patterns and classification of Oryza species: a molecular perspective, Rice Genomics and Genetics, 15(3): 94-105 (doi: 10.5376/rgg.2024.15.0011) Abstract This study explores the phylogenetic patterns and classification of Oryza species from a molecular perspective, offering key findings and insights. Major studies have found that traditional morphological methods have been enhanced by molecular techniques, such as DNA markers and next-generation sequencing (NGS), refining our understanding of Oryza phylogenetics, independent domestication in Asia and Africa has led to distinct genetic differences. Molecular evidence identifies key domestication genes and genomic signatures, shedding light on evolutionary adaptations, and that the distribution and genetic diversity of Oryza species have been shaped by natural dispersal and human-mediated migration. This study provides a detailed understanding of the phylogenetic system of the Oryza genus, providing profound insights into the evolutionary history and genetic diversity of rice species. Leveraging molecular phylogenetic insights can enhance taxonomy, conservation, and breeding, contributing to sustainable global rice agriculture. Keywords Oryza genus; Phylogenetics; Molecular classification; Domestication genes; Genetic diversity 1 Introduction The genus Oryza, commonly known as rice, is of paramount importance both economically and scientifically. It comprises 23 species, including two domesticated species, Oryza sativa and Oryza glaberrima, which are staple foods for over half of the world's population (Joshi et al., 2000). The genus is also a model system for studying molecular evolution, given its diverse genome types and the evolutionary history spanning millions of years (Stein et al., 2018). Understanding the phylogenetic relationships within the Oryza genus is crucial for crop improvement, conservation of genetic resources, and elucidating the mechanisms of plant evolution (Zhu et al., 2014; Joshi et al., 2000). Molecular phylogenetics has revolutionized our understanding of evolutionary relationships by utilizing DNA sequences to reconstruct the tree of life. In the context of Oryza, various molecular approaches have been employed to resolve phylogenetic relationships. These include the analysis of nuclear genes, mitochondrial and chloroplast DNA sequences, and inter simple sequence repeat (ISSR) polymorphisms (Nishikawa et al., 2005; Zhu et al., 2014; Joshi et al., 2000). Phylogenomic analyses using large datasets, such as 53 nuclear genes and 16 intergenic regions, have provided high-resolution insights into the evolutionary history of Oryza species (Zhu et al., 2014). Additionally, the use of simple sequence repeats (SSR) and their flanking regions has offered new perspectives on the genetic diversity and phylogenetic relationships within the genus (Nishikawa et al., 2005). This study aims to synthesize the current knowledge on the phylogenetic patterns and classification of Oryza species from a molecular perspective. The primary objectives are to compile and analyze the various molecular approaches used in phylogenetic studies of the Oryza genus, evaluate the effectiveness of these methods in resolving phylogenetic relationships and understanding genome evolution, and identify gaps in the current research and suggest future directions for comprehensive phylogenetic studies. By achieving these objectives, this study expects to provide a cohesive understanding of the molecular phylogenetics of Oryza, which will be instrumental for future research and practical applications in rice breeding and conservation.
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