Genomics and Applied Biology 2024, Vol.15, No.1, 54-63 http://bioscipublisher.com/index.php/gab 54 Research Analysis Open Access Genomic Diversity and Evolutionary Mechanisms in the Oryza Genus: A Comparative Analysis Jianquan Li, Fu Jiong Hainan Institute of Tropical Agricultural Resources, Sanya, 572025, China Corresponding email: hitar@hitar.org Genomics and Applied Biology, 2024, Vol.15, No.1 doi: 10.5376/gab.2024.15.0008 Received: 02 Jan., 2024 Accepted: 06 Feb., 2024 Published: 18 Feb., 2024 Copyright © 2024 Li and Jiong, 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: Li J.Q., and Jiong F., 2024, Genomic diversity and evolutionary mechanisms in the Oryza genus: a comparative analysis, Genomics and Applied Biology, 15(1): 54-63 (doi: 10.5376/gab.2024.15.0008) Abstract The genus Oryza encompasses a diverse array of species that exhibit significant genomic variation and evolutionary complexity. This systematic study synthesizes current research on the genomic diversity and evolutionary mechanisms within the Oryza genus, providing a comprehensive comparative analysis. Studies have revealed that polyploidy plays a crucial role in the diversification and evolution of Oryza, with homoeologous genomic regions experiencing both independent and parallel evolution. Genetic diversity and phylogenetic relationships within the genus have been elucidated using various molecular markers, such as inter simple sequence repeat (ISSR) polymorphism and chloroplast DNA sequences, highlighting the polyphyletic evolution and extensive gene family expansions. Comparative genomic analyses have shown that different Oryza species have experienced dissimilar amplification histories of retrotransposons, leading to remarkable differences in genome sizes. Additionally, gene duplication events, including whole genome duplications and segmental duplications, have contributed to the structural and functional evolution of Oryza genomes. The rapid diversification of AA-genome species, driven by lineage-specific expansions and contractions of gene families, has facilitated adaptations to diverse ecological niches. The genomic diversity and evolutionary mechanisms in the Oryza genus are shaped by a complex interplay of polyploidy, transposable elements, gene duplications, and natural selection. This study underscores the importance of comparative genomic studies in understanding the evolutionary dynamics and potential for crop improvement within the Oryza genus. Keywords Genus Oryza; Genomic diversity; Evolutionary mechanisms; Comparative genomics; Inter-species comparison Rice (Oryza sativa L) is a staple food for over half of the world's population and serves as a model organism for plant biology research. The genus Oryza includes two domesticated species, O. sativa and O. glaberrima, and 22 wild species, representing a significant reservoir of genetic diversity that is crucial for crop improvement and food security (Zhang et al., 2014). The wild species of Oryza, with their untapped genetic potential, are essential for breeding programs aimed at enhancing disease resistance, stress tolerance, and yield. The advent of genomics has revolutionized plant research, providing comprehensive insights into genome structure, function, and evolution. The sequencing of the rice genome, particularly the high-quality map-based sequence of O. sativa ssp. japonica 'Nipponbare', has been a landmark achievement, offering a valuable resource for comparative genomic studies and agricultural productivity improvements. Genomic tools such as bacterial artificial chromosome (BAC) libraries, genome-wide association studies (GWAS), and whole-genome sequencing have facilitated the identification of genetic variations and their association with important agronomic traits (Sakai et al., 2014). These advancements enable the exploration of genetic diversity and evolutionary mechanisms within the Oryza genus, providing a foundation for future crop improvement efforts. This systematic study aims to explore the genomic diversity within the Oryza genus by analyzing various genomic resources and studies. By examining the genetic architecture of both cultivated and wild rice species, we seek to understand the extent of genetic variation and its implications for rice breeding and conservation. The research will cover the construction and analysis of BAC libraries, genome-wide association mapping, and the sequencing of multiple rice genomes to provide a comprehensive overview of the genetic diversity present in the Oryzagenus.
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