Molecular Plant Breeding 2024, Vol.15, No.4, 155-166 http://genbreedpublisher.com/index.php/mpb 156 from the latest research efforts in sugarcane genomics, emphasizing developments in genome sequencing, functional genomics, and the emerging applications of these technologies in sugarcane breeding and agricultural practices. By examining these advancements, the study seeks to highlight the transformative potential of genomic science in overcoming the genetic complexities of sugarcane, paving the way for more targeted and efficient breeding strategies. 2 Complexity of the Sugarcane Genome 2.1 Genetic composition Sugarcane (Saccharum spp.) is an interspecific hybrid primarily derived from Saccharum officinarum and Saccharum spontaneum. The genetic composition of sugarcane is notably complex due to these interspecific hybridizations, which have endowed sugarcane with genes from both progenitor species. Saccharum officinarum, known for its high sugar content, and Saccharum spontaneum, which contributes robustness and disease resistance, combine to create the genetically diverse and highly adaptable modern sugarcane varieties. This hybrid vigor or heterosis is pivotal for the enhanced productivity and resilience seen in current sugarcane cultivars (Grivet and Arruda, 2001; Sharma et al., 2018; Thirugnanasambandam et al., 2018). 2.2 Polyploidy and aneuploidy The sugarcane genome is characterized by a high degree of polyploidy and aneuploidy, making it one of the most complex genomes in the plant kingdom (D’Hont et al., 1996; Grivet and Arruda, 2002). Polyploidy refers to the condition of having more than two complete sets of chromosomes, which in the case of sugarcane can be as high as 12x (12 sets). Aneuploidy, the presence of an abnormal number of chromosomes in a cell, further complicates genetic studies and breeding because it leads to variable gene expression levels and phenotypic diversity. These characteristics pose significant challenges in sequencing efforts and in the assembly of a coherent genome sequence, which are critical for advanced genetic research and breeding programs. The highly polyploid and aneuploid nature of the sugarcane genome results in a massive genome size, approximately 10 Gb, filled with repetitive sequences and multiple gene copies, which complicates genetic mapping and trait association studies (Hoang et al., 2017; Riaño-Pachón and Mattiello, 2017; Yang et al., 2018). 2.3 Implications of complexity The complexity of the sugarcane genome has profound implications on breeding and genetic research. Many important traits for sugarcane improvement are polymorphic in the progenitor species and are influenced by gene dosage in hybrid breeding programs (Healey et al., 2024). Traditional breeding methods are often insufficient to address and utilize the full genetic potential of sugarcane due to the difficulty in tracking and selecting for specific traits governed by multiple genes with variable expression. However, the advent of genomic selection and marker-assisted breeding has begun to unlock the potential for more targeted and efficient breeding strategies. Despite these advances, the intricate nature of the genome still requires sophisticated, high-throughput genotyping technologies to accurately select desirable traits. Moreover, the polyploidy and aneuploidy of sugarcane necessitate innovative approaches in genetic transformation, gene editing, and biotechnological interventions to achieve desired improvements in crop yield, disease resistance, and stress tolerance. Understanding and manipulating such a complex genetic architecture remain a central challenge and focus of contemporary genomic research in sugarcane (Wang et al., 2017). The genomic complexity of sugarcane not only defines the current limits of genetic research and breeding but also highlights the necessity for advanced genetic tools and more refined genomic resources to improve sugarcane cultivation and productivity effectively. 3 Recent Advancements in Sugarcane Genome Sequencing and Assembly 3.1 High-throughput sequencing technologies The advent of NGS technologies has significantly impacted sugarcane genomics, a crop known for its complex polyploid genome. High-throughput sequencing (HTS) technologies, such as Illumina and PacBio, have enabled the generation of large volumes of sequencing data, facilitating the assembly of sugarcane genomes with greater accuracy and depth (Trujillo-Montenegro et al., 2021). Additionally, the integration of PacBio Iso-Seq with
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