International Journal of Molecular Ecology and Conservation, 2025, Vol.15, No.1, 1-8 http://ecoevopublisher.com/index.php/ijmec 4 way of photosynthesis by adding new genes, but by changing the use of existing genes, that is, changing their functions (Ming et al., 2015). This method allows pineapples to save water, which is very important for arid areas (Ming et al., 2015; Zhu and Ming, 2019). 5.3 How did pineapple’s disease resistance evolve? Pineapple's disease resistance also evolved over a long period of time. Some genes were gradually “eliminated” because they were not helpful in fighting diseases, and some repeated gene structures also appeared. For example, someone found a repeated “protease inhibitor” gene that may help pineapples resist pests (Chen et al., 2019). In addition, there are many types of genes such as WRKY, and there are complex interactions between them, which may also be one of the reasons why pineapples have enhanced disease resistance (Xie et al., 2018). 6 Population Genomics and Phylogenetics of Pineapple Varieties 6.1 Genetic relationships among different pineapple cultivars The genes of different pineapple varieties are quite different. Studies have found that there are two species and five variants in the genus Anine, and there is a clear genetic separation between them. But in many cultivated varieties, most of the differences in appearance and traits are due to somatic mutations, not the result of long-term breeding (VanBuren, 2018). Common varieties such as “Smooth Cayenne” and “Queen” have traces of ancient genes in their genes, as well as new genes that have been mixed in recently. This shows that the evolution and domestication process of pineapples is quite complicated (Chen et al., 2019). 6.2 New discoveries brought by whole genome research By measuring the whole genome of pineapples, such as the two varieties “F153” and “MD2”, scientists found that they did not experience ancient whole genome duplication events like some plants (Ming et al., 2015). In other words, the genes of pineapples are not changed through large-scale duplication. These studies also found many changes in gene structure that are useful for domestication, as well as some genes that may have been “selected”, which played a significant role in pineapple's adaptation to the environment (Figure 2) (Chen et al., 2019; Feng et al., 2024). Figure 2 Putative domestication sweep around a bromelain inhibitor gene that helps control fruit ripening (Adopted from Chen et al., 2019)
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