Rice Genomics and Genetics 2024, Vol.15, No.4, 164-177 http://cropscipublisher.com/index.php/rgg 164 Systematic Review Open Access Functional and Structural Insights from the Oryza Genome: Implications for Crop Enhancement Yumin Huang1 , Jianquan Li2 1 School of Life Science, Xiamen University, Xiamen, 361102, Fujian, China 2 Hainan Institute of Tropical Agricultural Resources, Sanya, 572025, Hainan, China Corresponding email: hym@xmu.edu.cn Rice Genomics and Genetics, 2024, Vol.15, No.4 doi: 10.5376/rgg.2024.15.0017 Received: 07 Jul., 2024 Accepted: 10 Aug., 2024 Published: 18 Aug., 2024 Copyright © 2024 Huang and Li, 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: Huang Y.M., and Li J.Q., 2024, Functional and structural insights from the Oryza genome: implications for crop enhancement, Rice Genomics and Genetics, 15(4): 164-176 (doi: 10.5376/rgg.2024.15.0017) Abstract The Oryza genus holds immense genetic diversity critical for global food security. This study synthesizes recent advances in the structural and functional genomics of Oryza, highlighting their implications for crop enhancement. Key insights include the identification of genes and quantitative trait loci (QTLs) associated with yield, stress resistance, and nutritional quality, facilitated by high-throughput sequencing technologies and comprehensive genomic databases. Emerging genomic tools, such as CRISPR/Cas9 and genomic selection, have enabled precise genetic modifications and accelerated breeding programs aimed at developing resilient, high-yielding rice varieties. The integration of genomics with other omics approaches provides a holistic understanding of the biological processes underlying agronomic traits. However, the deployment of these technologies necessitates addressing ethical, regulatory, and social considerations. This study underscores the potential of leveraging Oryza genomics to meet future food security challenges and emphasizes the need for continued research and innovation in rice breeding. Keywords Oryza genome; Crop enhancement; Genetic diversity; Structural variations; Functional genomics; CRISPR/Cas9 1 Introduction Rice (Oryza sativa L.) is a fundamental staple food crop, feeding more than half of the global population and playing a crucial role in global food security. The genus Oryza, which includes both cultivated and wild rice species, serves as a model system for studying molecular evolution and genetic diversity (Hechanova et al., 2021; Zhang et al., 2022). Understanding the Oryza genome is essential for improving rice varieties to meet the challenges posed by biotic and abiotic stresses, climate change, and the increasing food demands of a growing population. The genetic diversity within the Oryza genus, including structural variations (SVs) and gene copy number variations (gCNVs), has been pivotal in the evolution, domestication, and improvement of rice (Kong et al., 2019; Chen et al., 2023). Over the past decade, significant advancements have been made in rice functional genomics, with over 2000 genes controlling important agronomic traits being cloned and partially characterized (Li et al., 2018). High-quality genome assemblies and pan-genome analyses have revealed hidden genomic variations and provided valuable resources for rice breeding and functional genomics research (Zhang et al., 2022). Studies have also focused on the regulatory mechanisms of complex traits, such as salt stress tolerance and grain yield, using advanced genomic tools like CRISPR/Cas9 and miRNA sequencing (Kong et al., 2019; Usman et al., 2020; Chen et al., 2023). Additionally, the development of genome-wide marker sets and introgression libraries has facilitated the efficient use of wild rice species for varietal improvement (Hechanova et al., 2021). This study aims to synthesize the current knowledge on the functional and structural aspects of Oryza genomes, providing a comprehensive overview of key findings in genomic research. It emphasizes the implications of these discoveries for crop improvement and identifies gaps that need to be addressed in ongoing research. By integrating and analyzing existing literature, this study offers valuable insights for researchers and practitioners in the fields of plant genomics and breeding. It is hoped that this study will contribute to the development of more resilient and productive rice varieties, thereby supporting global food security and sustainable agriculture.
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