Rice Genomics and Genetics 2024, Vol.15, No.4, 164-177 http://cropscipublisher.com/index.php/rgg 171 fromwild Oryza species into cultivated rice, enhancing traits such as grain size and drought resistance (Zhang et al., 2022). Additionally, retrotransposon-based markers have been used to study genetic diversity and stress-induced genomic instabilities in rice (Chadha, 2021). Integrating genomic selection into breeding programs involves the use of genome-wide markers to predict the performance of breeding lines. This approach enhances the efficiency and accuracy of selecting high-yielding and stress-resistant rice varieties. By leveraging genomic selection, breeders can make more informed decisions, ultimately leading to the development of improved rice cultivars with enhanced agronomic traits. Studies have shown that integrating GS with other breeding technologies can significantly enhance the efficiency of selecting high-yielding and stress-tolerant rice varieties. For instance, a study demonstrated the use of GS in predicting root system architecture and above-ground agronomic traits, showing the potential of GS to accelerate breeding cycles (Sharma et al., 2021). Another research highlighted the effectiveness of GS models incorporating functional markers and genotype-by-environment interactions in improving predictive abilities for rice breeding (Xu et al., 2021). 5.3 High-throughput phenotyping and genotyping High-throughput phenotyping technologies have greatly advanced the study of rice genetics and breeding. These technologies allow for the rapid and accurate measurement of plant traits under various environmental conditions, facilitating the identification of phenotypic variations linked to genetic markers. Advances in imaging and sensor technologies have enabled detailed phenotyping of traits such as plant height, biomass, and root architecture (Chen et al., 2019). These technologies include imaging systems, remote sensing, and automated phenotyping platforms, which enable the rapid assessment of large populations of rice plants. Such advancements are crucial for understanding the phenotypic variation and its genetic basis, thereby facilitating the selection of superior genotypes. Genotyping platforms have evolved to offer high-throughput and cost-effective solutions for analyzing genetic variation in rice. Techniques such as next-generation sequencing (NGS) and single nucleotide polymorphism (SNP) arrays are widely used to genotype large populations. These platforms provide comprehensive data on genetic diversity, which is essential for mapping quantitative trait loci (QTL) and conducting genome-wide association studies (GWAS). The integration of high-throughput genotyping with phenotyping data accelerates the identification of genes associated with important traits, thereby enhancing the efficiency of rice breeding programs. The integration of advanced genomic tools and technologies, including CRISPR/Cas systems, marker-assisted selection, genomic selection, and high-throughput phenotyping and genotyping, is transforming rice breeding. These innovations are paving the way for the development of superior rice varieties with improved yield, stress resistance, and other desirable traits, ultimately contributing to global food security. 6 Case Studies of Genomic Applications in Crop Enhancement 6.1 Disease resistance breeding Disease resistance in rice has been significantly enhanced through genomic insights and technologies. The identification of resistance genes and QTLs has been pivotal. For instance, the study by Kim et al. (2019) focused on utilizing the CRISPR/Cas9 system to target mutations in the rice Os8N3 gene to enhance resistance against Xanthomonas oryzae pv. oryzae (Xoo), the pathogen responsible for bacterial blight in rice (Figure 4). By editing the Os8N3 gene, researchers successfully produced mutants with enhanced disease resistance in the Japanese rice variety Kitaake. These mutants exhibited significant resistance to Xoo in the T1, T2, and T3 generations and did not contain transgenic DNA (T-DNA). Additionally, the study demonstrated that these mutants showed no significant differences in agronomic traits, such as pollen development, compared to non-transgenic control plants. This research not only confirmed the effectiveness of the CRISPR/Cas9 system in precise gene editing but also provided a successful example of using gene editing technology to improve crop disease resistance.
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