Plant Gene and Traits 2024, Vol.15, No.4, 184-194 http://genbreedpublisher.com/index.php/pgt 190 Additionally, the use of CRISPR/Cas systems in plants, including rice, has demonstrated significant improvements in yield, stress tolerance, and biofortification, underscoring its potential for crop improvement. Future research should focus on optimizing CRISPR delivery systems and exploring its integration with other genomic tools to maximize its utility in Oryzagenomics. Figure 3 Major application areas of CRISPR-Cas-based technologies beyond genome editing (Adopted from Adli, 2018) Image caption: While WT Cas9 enables genome editing through its guidable DNA cleavage activity, catalytically impaired Cas9 enzymes have been repurposed to achieve targeted gene regulation, epigenome editing, chromatin imaging, and chromatin topology manipulations. Furthermore, the catalytically impaired nickase Cas9 enzyme has been used as a platform for base editing without double strand breaks. In addition to DNA-targeting Cas proteins, novel RNA-targeting CRISPR/Cas systems have been described as well (Adopted from Adli, 2018) 7.2 Opportunities for integrating molecular markers with other genomic technologies Integrating molecular markers with other genomic technologies presents a promising avenue for advancing Oryza genomics. The combination of CRISPR/Cas9 with high-throughput sequencing technologies can facilitate the identification and validation of novel molecular markers (Wang et al., 2017). Moreover, the integration of CRISPR-based epigenome editing tools can provide insights into the regulatory mechanisms governing gene expression, thereby aiding in the discovery of epigenetic markers (Nakamura et al., 2021). The use of CRISPR in conjunction with transcriptomics and proteomics can also enhance our understanding of gene function and interaction networks, leading to the identification of functional markers associated with important agronomic traits (Adli, 2018; Manghwar et al., 2020). By leveraging these integrated approaches, researchers can develop more comprehensive marker-assisted selection strategies, ultimately accelerating the breeding of improved rice varieties. 7.3 Challenges and prospects for future research inOryzagenomics Despite the significant advancements in molecular marker research, several challenges remain in the field of Oryza genomics. One major challenge is the efficient and precise delivery of CRISPR/Cas9 components into plant cells, which is crucial for achieving high editing efficiencies and minimizing off-target effects (Leisen et al., 2020). Additionally, the complexity of the rice genome, with its high degree of genetic diversity and polyploidy, poses challenges for marker development and validation (Wang et al., 2017). Future research should focus on addressing these challenges by developing more efficient delivery methods, such as nanoparticle-based systems, and by employing advanced bioinformatics tools for accurate marker identification and validation (Manghwar et al.,
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