Genomics and Applied Biology 2024, Vol.15, No.1, 54-63 http://bioscipublisher.com/index.php/gab 61 Despite the significant advancements, there are limitations and shortcomings in the current research. One major limitation is the sample size. Many studies have focused on a limited number of accessions or species, which may not fully capture the genomic diversity present within the entire Oryza genus. For example, the study on genome size variation included only 166 accessions from 16 non-AA genome Oryza species, which may not be representative of the entire genus. Another limitation lies in the analysis methods. While advanced sequencing technologies have been employed, there are still challenges in accurately assembling and annotating complex genomes, particularly those with high levels of repetitive elements and structural variations. The reliance on single reference genomes for comparative analyses may also overlook the extensive genomic and allelic diversity within the genus. Additionally, the detection of linkage disequilibrium and marker-trait associations may be influenced by the choice of markers and the resolution of genome-wide scans (Li et al., 2020). Future research should focus on addressing these limitations by leveraging the development of genomics technology and exploring new prospects for rice genome research. The integration of high-quality de novo assemblies and long-read sequencing technologies can provide more comprehensive and accurate genomic data, facilitating the discovery of novel genetic elements and structural variations. Expanding the sample size to include a broader range of Oryza species and accessions will enhance the understanding of genomic diversity and its role in rice evolution and adaptability. Moreover, the establishment of comprehensive genomic databases, such as OryzaGenome, can serve as valuable resources for genotype-phenotype association studies and functional analyses. Future research should also focus on the functional characterization of identified genes and genomic elements, particularly those involved in stress responses, reproductive processes, and disease resistance. The application of integrated genomic approaches and comparative phylogenomics will further elucidate the molecular mechanisms underlying rice evolution and provide new opportunities for crop improvement and conservation of wild rice germplasm. 7 Concluding Remarks The genus Oryza, encompassing both domesticated and wild rice species, has been extensively studied to understand its genomic diversity and evolutionary mechanisms. Key research achievements include the identification of significant genetic conservation, turnover, and innovation across the genus. For instance, the study of 13 reference genomes has highlighted rapid species diversification and the emergence of novel elements such as transposons and new coding and noncoding genes. Additionally, the analysis of molecular diversity and linkage disequilibrium patterns in various Oryza germplasm accessions has provided insights into the genetic structure and evolutionary processes within the genus. The development of comprehensive genomic resources, such as the Rice TE database (RiTE-db), has facilitated the annotation and comparative analysis of transposable elements across multiple Oryza species. Furthermore, the sequencing and analysis of wild and cultivated rice genomes have shed light on the domestication processes and heterosis in rice, revealing genome-wide signatures and the origin of cultivated rice. The Oryza Map Alignment Project (OMAP) has also contributed significantly by establishing a genus-wide comparative framework, highlighting the impact of structural variations on genome diversity. The application of genomic research in rice breeding has profound implications for the future of agriculture. The comprehensive genomic resources developed for the Oryza genus provide a valuable foundation for leveraging genetic diversity from wild relatives to improve cultivated rice varieties. For example, the construction of bacterial artificial chromosome (BAC) libraries representing the 10 genome types of Oryza has enabled the exploration of agriculturally important genes from wild species. These resources are crucial for maintaining a safe and secure food supply in the face of global challenges such as climate change and population growth. Moreover, the integration of genomic and phenotypic data in databases like OryzaGenome facilitates genotype-phenotype association studies, which are essential for understanding the functional and structural
RkJQdWJsaXNoZXIy MjQ4ODYzMg==