Rice Genomics and Genetics 2024, Vol.15, No.4, 164-177 http://cropscipublisher.com/index.php/rgg 166 Comparative genomics has revealed significant insights into the genetic diversity and evolutionary history of rice. High-confidence assemblies of genomes, such as those of Oryza sativa and Oryza brachyantha, have enabled detailed comparative analyses, revealing significant chromosomal rearrangements and gene duplications that contribute to phenotypic diversity and adaptability (Liao et al., 2018). Pangenomic studies, which integrate genomic data from multiple rice accessions, have highlighted the extensive structural variations (SVs) that contribute to genetic diversity within the species. These studies enable the identification of candidate SVs associated with important agronomic traits, thereby enhancing the potential for targeted breeding and crop improvement (Zanini et al., 2021). Additionally, the functional impact map of genetic variants (GVs) in rice provides a valuable resource for prioritizing causal variants in mapping populations, further aiding in the functional characterization of genetic diversity (Zhao et al., 2021). 2.2 Chromosomal organization and structure Karyotyping and chromosome mapping have been essential tools in studying the structural organization of Oryza genomes. These techniques have helped identify the number, size, and shape of chromosomes, facilitating the mapping of genes and QTLs associated with important traits. Detailed chromosomal maps have been developed for several Oryza species, highlighting regions of structural diversity and evolutionary significance (Stein et al., 2018). In the study of Song et al. (2021), the gap-free reference genomes of 'ZS97' and 'MH63' have provided a global view of centromere architecture, revealing conserved centromere-specific satellite motifs and structural variants that affect gene copy numbers. These insights are crucial for elucidating the mechanisms of chromosomal behavior and stability, which are fundamental to rice breeding and genetic studies. Structural variations, including inversions, duplications, deletions, and translocations, are prevalent in Oryza genomes and have significant implications for genetic diversity and adaptation. Studies have shown that these variations can affect gene expression and contribute to the domestication process. For instance, the identification of large inversions and translocations in indica and japonica rice varieties has provided insights into the evolutionary mechanisms underlying rice domestication (Kou et al., 2020). 2.3 Transposable elements and repeat sequences Transposable elements (TEs) and repeat sequences are abundant in the Oryza genome and play a pivotal role in shaping genome structure and evolution. TEs are classified into different types based on their mechanism of transposition, with long terminal repeat (LTR) retrotransposons being the most prevalent. The distribution of these elements varies across different Oryza species, contributing to genomic diversity and complexity (Dai et al., 2022). The impact of transposable elements and repeat sequences on genome evolution is profound, influencing gene regulation, genome stability, and adaptation. The functional impact map of genetic variants in rice has demonstrated that large-effect GVs in both coding and regulatory regions are subject to selection pressures, which may be driven by the activity of TEs and repeat sequences (Zhao et al., 2021). These elements contribute to the generation of genetic diversity and the evolution of new traits, underscoring their significance in the ongoing adaptation and improvement of rice varieties. By integrating these structural and functional insights from the Oryza genome, researchers can better understand the genetic basis of important traits and develop strategies for crop enhancement, ultimately contributing to global food security. 3 Functional Genomics of Oryza 3.1 Gene annotation and functional prediction Gene annotation and functional prediction are critical steps in understanding the biology of Oryza species. Various gene families have been identified in Oryza, each with distinct functions contributing to the plant's growth, development, and stress responses. For instance, the Dof transcription factor family regulates various stresses and developmental processes in Oryza, with evolutionary analyses revealing significant structural and functional diversity across different species (Tabassum et al., 2022). Similarly, the MIR gene, specific to the Oryza genus, plays a crucial role in iron deficiency response, highlighting the importance of specific gene families
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