Plant Gene and Trait 2024, Vol.15, No.2, 62-72 http://genbreedpublisher.com/index.php/pgt 63 2 Gene Duplication 2.1 Fundamentals of gene duplication processes Gene duplication is a fundamental process in the evolution of genomes, particularly in plants. It involves the creation of one or more copies of a gene within the genome. These duplications can occur through various mechanisms, including whole-genome duplications (WGDs), segmental duplications, tandem duplications, and transposon-mediated duplications (Rensing, 2014; Panchy et al., 2016; Barreto et al., 2019). WGDs, in particular, have been a significant driver of plant evolution, leading to the retention of numerous duplicate genes that contribute to genetic diversity and complexity (Zhang et al., 2022). The fate of duplicated genes can vary; they may be retained and acquire new functions (neofunctionalization), divide the original function (subfunctionalization), or become nonfunctional pseudogenes (Rensing, 2014; Panchy et al., 2016). 2.2 Role of gene duplication in plant evolution and adaptation Gene duplication has played a crucial role in the evolution and adaptation of plants. Duplicated genes can provide raw material for evolutionary innovation, allowing plants to develop new traits and adapt to changing environments (Rensing, 2014; Panchy et al., 2016). For instance, gene duplications have been linked to the development of novel floral structures, disease resistance, and stress adaptation (Rensing, 2014; Panchy et al., 2016). In sugarcane, a highly polyploid and aneuploid crop, gene duplications have contributed to its complex genome and the evolution of important agronomic traits (Panchy et al., 2016). The retention of duplicated genes in sugarcane has facilitated the development of traits such as increased yield, improved stress tolerance, and enhanced disease resistance (Panchy et al., 2016). 2.3 Methods for identifying gene duplications in sugarcane Identifying gene duplications in sugarcane involves a combination of genomic, transcriptomic, and genetic mapping approaches. Comparative genomic analyses can reveal conserved gene content and collinearity with related species, such as sorghum and rice, which helps in identifying duplicated regions (Panchy et al., 2016). Techniques such as Bacterial Artificial Chromosome (BAC) sequencing and the construction of physical and linkage maps are also employed to elucidate the genomic architecture and allelic interactions in sugarcane (Panchy et al., 2016). Additionally, genome-wide association studies (GWAS) and the analysis of simple sequence repeat (SSR) markers can be used to detect marker-trait associations and identify candidate genes involved in important traits (Barreto et al., 2019). These methods collectively enhance our understanding of the complex polyploid genome of sugarcane and facilitate the identification of gene duplications that contribute to its trait diversity and evolution. 3 The Role of Gene Duplication in Sugarcane Evolution and Trait Diversity 3.1 Sugarcane genetic diversity and evolution Sugarcane (Saccharumspp.) is a vital crop for sugar and biofuel production, characterized by its complex genetic architecture and significant genetic diversity. The genetic diversity within sugarcane is a crucial factor for breeding programs aimed at improving yield and stress resistance. This diversity is largely attributed to the polyploid nature of sugarcane, which includes contributions from its progenitor species, Saccharum officinarum andSaccharum spontaneum(Barreto et al., 2016; Singh et al., 2020; Tolera et al., 2023). 3.2 Genetic architecture of sugarcane The genetic architecture of sugarcane is highly intricate due to its polyploidy and the presence of sub-genomes from its progenitor species. Modern sugarcane varieties are interspecific hybrids that combine the high sugar content of S. officinarum with the hardiness and disease resistance of S. spontaneum (Figure 1) (Thirugnanasambandam et al., 2018; Zhang et al., 2018). The genome of sugarcane is characterized by a high degree of polymorphism and genetic variability, which is essential for the crop's adaptability and productivity (Singh et al., 2020). Advances in sequencing technologies have facilitated the assembly of sugarcane genomes, providing valuable resources for genetic research and breeding (Thirugnanasambandam et al., 2018; Yang et al., 2020).
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