Journal of Energy Bioscience 2025, Vol.16, No.1, 13-20 http://bioscipublisher.com/index.php/jeb 16 5 Population Structure and Evolutionary Dynamics 5.1 Genetic clustering of germplasm Some studies have shown that sugarcane materials can be divided into several independent subpopulations based on genetic diversity analysis. Xiong et al. ’s 2022 study of 196 Saccharummaterials showed that the researchers could identify 3 to 8 genetic subgroups through model clustering, principal component analysis and phylogenetic analysis. This clustering is helpful for understanding the genetic relationship and diversity of S. officinarum, S. spontaneumand their hybrids. Xiong et al. (2022) demonstrated that the results of this study could not only be used in the management of germplasm resources, but also in breeding, especially in the identification of species-specific alleles for species identification and breeding selection. 5.2 Historical gene flow and hybridization patterns Mahadevaiah et al. (2021) demonstrated that the complex hybridization nature of sugarcane mainly stems from the interspecific and intergenus hybridization between S. officinarumand S. spontaneum, and these hybridization events formed modern sugarcane varieties with highly diverse genetic background. Gene penetration analysis showed that the contribution of S. spontaneum chromosome fragment was decreasing in modern sugarcane varieties, while the proportion of S. officinarumwas increasing, reflecting the breeding trend of improving target traits through artificial selection (Li et al., 2024). Meng et al. ’s study in 2019 found a new tetraploid S. spontaneum with a basic chromosome number of x=10, which provided a new perspective on the genome evolution and polyploidy event of Saccharum. 5.3 Adaptive evolution in cultivated sugarcane The whole genome sequencing of sugarcane varieties by Li et al. (2024) has identified several SNP markers related to important agronomic traits. These genetic variations are important factors for sugarcane to adapt to different environmental conditions and increase yield. Yang et al. ’s study in 2018 identified selective sweep regions and candidate genes related to environmental factors, suggesting that adaptive evolution played a key role in the domestication and improvement of sugarcane. 6 Case Study: Phylogenetic Analysis of Sugar-Rich Cultivars 6.1 Study context and sample description This case study focused on sugar-rich sugarcane varieties, and selected relevant cases of diverse sugarcane germplasm resources for analysis. Yang et al. (2018) and Xiong et al. (2022) believed that sugarcane was a polyploid crop with complex genetic structure. A 2018 study by Yang et al. sequenced 307 sugarcane germplasm material and revealed nearly 5 million sequence variants, a finding that is helpful in understanding the genetic makeup of sugar-rich varieties (Figure 2). Xiong et al. ’s 2022 study analyzed 196 Saccharummaterials, including multiple species and hybrids, to assess the genetic diversity and population structure of sugarcane. 6.2 Methodology and tree construction Li et al. (2024) believe that whole genome sequencing and SNP detection are important techniques for identifying genetic variation associated with sugar content and other agronomic traits. In related studies, researchers often use model-based cluster analysis, principal component analysis and phylogenetic tree construction. Xiong et al. (2022) also used these methods to analyze the genetic structure and diversity of sugarcane. Evans et al. (2019) and Zhou et al. (2022) used mitochondrial sequencing to study sugarcane phylogeny because the mitochondrial genome structure was simple and easy to handle. 6.3 Key findings and breeding implications Vilela et al. (2017) and Yang et al. (2018) found that ancient and modern sugarcane hybrids had different genetic compositions and hybridization processes, reflecting the genetic contributions of different ancestral species. Xiong et al. (2022) and Li et al. (2024) identified specific SSR alleles and SNP markers related to traits such as sucrose content, which provided important molecular tools for sugarcane breeding. According to the study of Mahadevaiah et al. (2021) and Li et al. (2024), these findings illustrate that modern sugarcane varieties have
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