Molecular Plant Breeding 2024, Vol.15, No.4, 155-166 http://genbreedpublisher.com/index.php/mpb 159 phenotypes in sugarcane. Similarly, Oz et al. (2021) applied CRISPR/Cas9-mediated multi-allelic targeted editing to convert inferior alleles into superior ones through targeted nucleotide replacement, thereby successfully conferring herbicide tolerance to sugarcane. These advancements contribute significantly to sugarcane improvement and present an efficient, replicable method for enhancing crops via targeted nucleotide substitutions. This technology not only enhances the efficiency of genetic modifications but also reduces the time required to develop cultivars with optimal traits. 4.3 Integrative genomics approaches Integrative genomics, which combines genomic, transcriptomic, and metabolomic data, provides a comprehensive approach to understanding the biological functions and interactions within sugarcane. This holistic view is essential for elucidating the complex metabolic pathways and regulatory networks involved. Souza et al. (2019) demonstrated that the integration of these diverse data types could resolve the putative homo(eo)logs in the sugarcane genome, which are crucial for trait development and adaptation. Furthermore, the gene space assembly of SP80-3280 by Souza et al. (2019) provides insights into the regulatory elements involved in sucrose synthesis, showcasing the power of integrative approaches in functional genomics. By combining data from various genomic platforms, researchers can achieve a more detailed and accurate picture of the genetic underpinnings of important agronomic traits in sugarcane. 5 Genetics and Gene Mapping in Sugarcane 5.1 Genetic linkage maps Genetic linkage maps are critical tools in understanding the genomic organization of complex polyploid organisms like sugarcane, which has a highly complicated genetic structure due to its autopolyploid nature and interspecific hybrid origins. Recent advances have significantly improved the resolution and utility of these maps for trait association studies. For instance, a comprehensive linkage map using AFLP, SSR, and TRAP markers was developed, revealing insights into the homologous chromosome groupings and their association with phenotypic traits in sugarcane cultivars (Andru et al., 2011). With the rapid development of next-generation sequencing technology, the comprehensive linkage genetic map of sugarcane developed using single nucleotide polymorphism (SNP) markers is being increasingly applied (Yadav et al., 2021). These maps facilitate the identification of linkage disequilibrium patterns and provide a foundation for marker-assisted selection and breeding strategies. 5.2 QTL mapping Quantitative Trait Loci (QTL) mapping is a powerful genetic tool used to associate specific genomic regions with phenotypic traits. This method is particularly effective in sugarcane due to its ability to handle the complexities arising from its genome structure. For instance, multiple QTLs influencing sugar yield and related traits have been identified, demonstrating significant associations that are invaluable for breeding programs aimed at enhancing sugar production (Ming et al., 2002). Costa et al. (2016) utilized a comprehensive interval mapping approach, employing SNP markers across various ploidy levels, to develop a genetic linkage map of sugarcane that includes AFLP and SSR markers. They also identified QTLs affecting critical agronomic traits in sugarcane, thereby providing genetic information for molecular assisted selection and breeding in sugarcane. In another study, the construction of a genetic linkage map and QTL analysis identified quantitative trait loci (QTLs) associated with resistance to red rot disease in sugarcane and identified candidate genes related to plant defense responses (Banerjee et al., 2023). In recent years, many researchers have utilized QTL mapping to identify QTLs and associated candidate genes related to traits such as sugarcane yield, sugar and disease resistance (Singh et al., 2013; Ukoskit et al., 2019; Lu et al., 2023). The mapping of these QTLs helps in understanding the genetic basis of complex traits and assists in the development of sugarcane varieties with optimized traits. 5.3 Marker-assisted selection Marker-Assisted Selection (MAS) leverages molecular markers linked to desirable traits to accelerate the breeding process. In sugarcane, MAS has been enhanced by the development and validation of markers such as EST-SSRs, which are associated with sugar-related traits. The identification and use of these markers allow for more precise
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