Decoding the Mystery of Sugarcane Genome-Based Breeding: Current Advancements, Strategies, and Future Challenges

Sugarcane serves as one of the world's most crucial economic crops, with fundamental importance to global sugar production and the sustainable biofuel industry. To meet the rising global demands and tackle various biotic and abiotic stresses, there is an urgent necessity to enhance the sugarcane breeding programme. Deciphering the intricate sugarcane genomes and integrating valuable agronomic traits into elite cultivars are vital to sustainable crop improvement. We review the major challenges in genomics-enabled sugarcane improvement, including genome complexity, polyploidy, and the limitation of traditional breeding methods. We discuss recent advancements in sugarcane genomic research, with a particular focus on cutting-edge strategies and algorithms for polyploid genome assembly, the key features and characteristics of newly assembled sugarcane genomes, and the development of graph-based pangenomes to capture genomic diversity. Our review highlights genomics-based sugarcane breeding from three perspectives: the history of conventional breeding, advanced breeding strategies empowered by genomic resources, and the emerging era of big data-driven crop improvement. These advancements provide powerful tools to accelerate sugarcane breeding and genetic improvement. Over the past decades, sugarcane genomics has made significant progress, including the assembly of high-quality reference genomes, the generation of comprehensive multi-omics datasets, and the development of precision genetic engineering tools. These advancements enable targeted manipulation of key alleles to improve yield, stress tolerance, and other important agronomic traits. Finally, this review summarises key breakthroughs in sugarcane gene-editing technologies and offers future perspectives on how these innovations are reshaping crop enhancement strategies.