Plant Gene and Trait 2024, Vol.15, No.2, 62-72 http://genbreedpublisher.com/index.php/pgt 67 validated in other populations to support sugarcane breeding programs with the introgression of favorable alleles and marker-assisted selection (Barreto et al., 2019). The study of the CIPK gene family in sugarcane revealed that duplicated genes play various roles in response to different stresses, such as abscisic acid (ABA), polyethylene glycol (PEG), and sodium chloride (NaCl). This indicates that gene duplications contribute to the plant's ability to adapt to environmental stresses, which is crucial for its survival and productivity (Panchy et al., 2016). 5.3 Comparative analysis of sugarcane with other crops Comparative genomic studies have shown that sugarcane shares a high degree of gene content and collinearity with other crops like sorghum and rice. For example, the analysis of three sugarcane homo/homeologous regions suggested independent polyploidization events of Saccharum officinarum and Saccharum spontaneum. These regions presented a high degree of conservation of gene content and synteny with sorghum and rice orthologous regions, although they were invaded by transposable elements (Yang et al., 2020). The study of whole genome duplications (WGDs) across various angiosperms, including sugarcane, revealed that WGDs are a major driving force in species diversification. These duplications provide evolutionary potential for generating novel functions and contribute to the complexity and diversity of plant genomes (Ren et al., 2018). Gene duplications in sugarcane have led to significant evolutionary advancements and trait diversifications. These duplications not only enhance the plant's adaptability to environmental stresses but also contribute to its agronomic traits, making sugarcane a vital crop for sugar and biofuel production (Panchy et al., 2016). 6 Technological Advances in Genetic Research 6.1 Next-generation sequencing (NGS) and its impact on gene duplication studies Next-Generation Sequencing (NGS) has revolutionized the field of genomics, providing unprecedented insights into the complex genome of sugarcane. The large and polyploid nature of the sugarcane genome, which includes sub-genomes fromSaccharum officinarum and S. spontaneum, has historically posed significant challenges for genetic research (Augustine et al., 2015). However, advancements in NGS technologies have facilitated the sequencing and assembly of these complex genomes, enabling more detailed studies of gene duplication events. For instance, the sequencing of 317 euchromatic BACs and the generation of a reference set of 1,400 manually-annotated protein-coding genes have provided a robust framework for understanding gene duplication in sugarcane (Setta et al., 2014). Additionally, long-read sequencing technologies have supported the generation of a more complete set of sugarcane gene transcripts, which is crucial for transcript profiling and understanding the functional implications of gene duplications (Thirugnanasambandam et al., 2018). 6.2 Bioinformatics approaches to analyzing gene duplication Bioinformatics tools and approaches are essential for analyzing the vast and complex data generated by NGS. In sugarcane, bioinformatics has been pivotal in elucidating the allelic expression and genomic behaviors of duplicated genes. For example, the study of the HP600 and Centromere Protein C (CENP-C) genes revealed the presence of these genes in different homeologous chromosome groups with varying ploidies, highlighting the complexity of gene duplication in sugarcane. Furthermore, bioinformatics analyses have enabled the identification of non-redundant enzyme-encoding genes in key metabolic pathways, such as sucrose and starch metabolism, and the exploration of sequence structural variations and sRNA landscapes associated with duplicated regions (Setta et al., 2014). These approaches are critical for integrating physical and genetic data, thereby enhancing our understanding of gene duplication and its evolutionary significance in sugarcane. 6.3 Emerging technologies and their applications in sugarcane genomics Emerging technologies continue to push the boundaries of sugarcane genomics, offering new opportunities to study gene duplication and its impact on trait diversity. The development of advanced genome assembly strategies, including the sequencing of BAC clones that cover the gene space of related species like sorghum, has made the sugarcane genome more tractable (Thirugnanasambandam et al., 2018). Additionally, the use of small RNA collections and RNA-seq libraries has provided valuable insights into gene expression patterns and the regulatory roles of duplicated genes (Setta et al., 2014). These technological advancements are not only enhancing our understanding of sugarcane genetics but also contributing to the development of molecular tools for breeding and
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