Molecular Plant Breeding 2024, Vol.15, No.4, 155-166 http://genbreedpublisher.com/index.php/mpb 160 selection of phenotypes with favorable genetic profiles, significantly improving the efficiency of breeding programs (Ukoskit et al., 2019). Moreover, the integration of functional markers into linkage maps enables breeders to directly target genes involved in key metabolic pathways, thereby streamlining the development of superior sugarcane varieties. 6 Implications for Sugarcane Breeding and Agriculture 6.1 Breeding for disease resistance Recent advancements in sugarcane genomics have provided significant insights into disease resistance, which are crucial for breeding programs. The identification of the rust resistance gene (Bru1) through map-based cloning techniques exemplifies the potential of genomic strategies to overcome the challenges posed by the highly polyploid nature of the sugarcane genome (Islam et al., 2021). Additionally, genomic selection has shown promise in predicting genetic values for disease resistance traits, with studies demonstrating correlations between observed and predicted values, thus validating the feasibility of genomic selection in sugarcane breeding (Islam et al., 2021). Lu et al. (2023) investigated the symptoms of sugarcane mosaic disease (SMD) in offspring through natural infection and artificial infection with a mixture of sugarcane mosaic virus (SCMV) and sorghum mosaic virus (SrMV) (Figure 2). 110 pathogen response genes and 69 transcription factors were identified in the QTL interval, and 9 key genes were predicted. Genome-wide association studies (GWAS) revealed the dominant role of alleles from the wild species Saccharum spontaneumin conferring resistance to sugarcane orange rust (SOR) in modern sugarcane varieties. Six quantitative trait loci (QTLs) associated with this resistance were identified, which can effectively predict disease resistance, thereby paving the way for efficient marker-assisted breeding strategies (Dijoux et al., 2024). These genetic insights enable breeders to develop disease-resistant cultivars more efficiently, ensuring sustainable crop production. 6.2 Improving yield and sugar content Genetic discoveries aimed at improving yield and sugar content have been crucial in enhancing sugarcane productivity. GWAS have identified multiple marker-trait associations (MTAs) for key yield components such as stalk height, stalk number, and cane yield, which can be utilized in marker-assisted selection to improve these traits (Barreto et al., 2019; Meena et al., 2022; Wang et al., 2023; Saavedra-Díaz et al., 2024). Furthermore, advancements in genomic selection techniques, such as genomic estimated breeding values (GEBVs), have significantly improved the accuracy of predicting complex traits like tonnes of cane per hectare (TCH) and commercial cane sugar (CCS), potentially doubling the rate of genetic gain in breeding programs (Hayes et al., 2021; Satpathy et al., 2022). Genetic engineering and genome editing technologies, such as CRISPR/Cas9, have opened new avenues for directly manipulating genes associated with yield and sugar content (Khan et al., 2019). These genomic tools facilitate the accumulation of favorable alleles, resulting in increased yield and sucrose accumulation in sugarcane cultivars. 6.3 Adaptation to environmental stresses The adaptation of sugarcane to abiotic stresses, such as drought and heat is critical for maintaining productivity in the face of climate change. Meena et al. (2022) have highlighted the role of next-generation sequencing and genome-editing technologies in identifying and harnessing genes associated with stress tolerance. For instance, the establishment of a monoploid reference sequence has provided a comprehensive understanding of the sugarcane genome, enabling the identification of genes involved in stress responses (Garsmeur et al., 2018). Additionally, the integration of functional genomics and gene expression profiling has resulted in the delineation of gene networks that contribute to stress tolerance, paving the way for the development of stress-resilient sugarcane varieties. These advancements ensure that sugarcane can thrive under adverse environmental conditions, securing its role as a major crop for sugar and bioenergy production. By leveraging these genetic insights and biotechnological tools, sugarcane breeding programs can achieve significant improvements in disease resistance, yield, sugar content, and environmental stress adaptation, ultimately enhancing the sustainability and productivity of sugarcane agriculture.
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