Plant Gene and Traits 2024, Vol.15, No.4, 184-194 http://genbreedpublisher.com/index.php/pgt 189 et al., 2011). Moreover, the integration of SSR markers into genetic maps has facilitated the identification of genetic linkages and the construction of detailed phylogenetic trees (Martina et al., 2022). These studies have also highlighted the importance of SSR markers in marker-assisted selection and breeding programs, as they provide valuable information on genetic relationships and trait inheritance. Overall, the use of SSR markers in phylogenetic studies has enhanced our understanding of the genetic architecture and evolutionary history of the genus Oryza. 6 Advancements in Molecular Marker Technologies 6.1 Next-generation sequencing (NGS) and its impact on marker discovery The advent of next-generation sequencing (NGS) has revolutionized the field of genomics, providing unprecedented capabilities for the discovery and genotyping of genetic markers. NGS technologies enable the rapid sequencing of millions of DNA fragments simultaneously, which has significantly reduced the cost and time required for genome-wide studies (Davey et al., 2011; Satam et al., 2023). This high-throughput approach is particularly beneficial for both model and non-model organisms, facilitating the discovery of genetic markers even in species with no existing genomic data. Techniques such as restriction-site-associated DNA sequencing (RAD-seq) and reduced-representation libraries (RRLs) have been developed to reduce the complexity of target genomes, making marker discovery more efficient and cost-effective. Moreover, NGS has expanded the scope of genomics research, enabling studies on rare genetic diseases, cancer genomics, microbiome analysis, and population genetics. 6.2 High-throughput genotyping platforms High-throughput genotyping platforms have emerged as powerful tools for large-scale genetic analysis, allowing researchers to genotype thousands of samples simultaneously. These platforms leverage the advancements in NGS technologies to provide detailed information on genetic variations across populations (Dijk et al., 2014). For instance, targeted multiplex NGS techniques enable the simultaneous resequencing of multiple genomic regions from numerous individuals, enhancing the efficiency of population genomic studies (Hancock‐Hanser et al., 2013). Such platforms are particularly useful for non-model organisms, where traditional genotyping methods may be less effective (Cross et al., 2016). The integration of high-throughput genotyping with NGS has also facilitated the development of novel applications in clinical diagnostics, agrigenomics, and forensic science, further broadening the impact of these technologies (Pabinger et al., 2013). 6.3 Integration of multi-omics data for enhanced phylogenetic and classification accuracy The integration of multi-omics data, including genomics, transcriptomics, proteomics, and metabolomics, has significantly enhanced the accuracy of phylogenetic and species classification studies. By combining data from multiple molecular levels, researchers can obtain a more comprehensive understanding of the evolutionary relationships and genetic diversity within and between species (Kumar and Kocour, 2017). NGS technologies play a crucial role in this integration, providing the high-throughput sequencing capabilities needed to generate large-scale multi-omics datasets. For example, the use of both mitochondrial and nuclear DNA sequencing has improved the resolution of phylogeographic studies, allowing for more precise identification of genetic structure and evolutionary history (Hancock‐Hanser et al., 2013). Additionally, the application of NGS in systematics and population genetics has demonstrated the potential of multi-omics approaches to uncover novel insights into the genetic and biological significance of various species (Cross et al., 2016). 7 Future Directions in Molecular Marker Research for Oryza 7.1 Potential of CRISPR-based and other emerging molecular tools The advent of CRISPR/Cas9 technology has revolutionized genome editing, offering unprecedented precision and efficiency in genetic manipulation. This technology holds immense potential for advancing molecular marker research in Oryza genomics. CRISPR/Cas9 allows for targeted modifications at specific genomic loci, facilitating the study of gene function and the development of new molecular markers (Figure 3) (Zhang et al., 2014; Adli, 2018). Recent advancements in CRISPR technology, such as the development of high-fidelity variants and base editors, further enhance its applicability by reducing off-target effects and enabling precise nucleotide changes.
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