International Journal of Molecular Ecology and Conservation, 2025, Vol.15, No.6, 286-293 http://ecoevopublisher.com/index.php/ijmec 288 3.4 Implications for crop improvement and climate adaptation Understanding the operating logic of the CAM mechanism in pineapple is not just a "paper talk" for agriculture. Studying this mechanism provides a new direction for improving C₃ crops in the future - if key genes and regulatory modules can be "transplanted" into ordinary crops, they may perform better in drought environments. At present, researchers are focusing on finding the core regulatory network that affects CAM expression. In the future, if these regulatory strategies can be integrated into C₃ plants, it is expected to improve their water use efficiency and drought resistance (Wai et al., 2017). At the same time, pineapple research also reminds us that in addition to genes themselves, epigenetic mechanisms may also play a potential role in responding to climate change and maintaining stable food production (Niechayev et al., 2019; Shi et al., 2021). 4 Chromosome Rearrangement Phenomenon in Pineapple Evolution 4.1 Evidence of large-scale rearrangement of pineapple chromosomes At the genomic level, pineapple chromosomes are not immutable. Studies have found that its chromosomes have undergone multiple rearrangements, which have had a profound impact on its evolutionary path. Some gene families, such as WRKY and MYB, expand their number through segmental duplication. This kind of "gene copy-reuse" mechanism enables some genes to acquire new functions (Xie et al., 2018). Compared with other monocots, pineapple has fewer genome duplication events, and it still retains a simple structure of 7 chromosomes. This stability suggests that pineapple has taken a different genome evolutionary route from other crops (Hu et al., 2021). 4.2 Functional effects of chromosome rearrangement on gene regulation Changes in chromosome structure not only change the location of genes, but also reshape their expression patterns. For example, some members of gene families such as MYB and MADS-box have been given new functions after segmental duplication, such as participating in stress response or controlling flowering process (Liu et al., 2017). Analysis of the expression of these genes in different tissues and developmental stages also showed that their expression changes are the direct product of chromosome rearrangement. These structural changes not only promote functional diversification, but also provide a regulatory basis for plants to adapt to different environmental conditions (Pan et al., 2022). 4.3 Comparison with other monocots: evolutionary implications When scientists compare pineapple to other monocots like rice, they find big differences. Many cereal crops went through several full-genome duplications, but pineapple did not. Its chromosomes are more like those of early monocots. Pineapple also kept many gene families and developed unique ways to control gene activity. These traits make pineapple stand out from other monocots in both how its genome looks and how it works. 5 Gene Duplication Clusters and Functional Diversification 5.1 Mechanisms of gene duplication in pineapple Gene duplication is an important means of plant evolution and functional expansion. In pineapple, multiple gene families have expanded in this way. For example, the bZIP transcription factor family currently has 57 members, divided into 11 subgroups, of which 27 genes are generated by 17 fragment duplications (Liu et al., 2020). The expansion path of the WRKY gene family is similar, mainly relying on fragment duplication (Xie et al., 2018); the CPK gene family has recorded 7 similar duplication events (Zhang et al., 2020). These phenomena together reveal that gene duplication plays an important role in promoting pineapple's adaptation to the environment and evolutionary path. 5.2 Functional significance of gene duplication in metabolism, stress response and developmental regulation The duplicated genes are not useless "redundant parts". On the contrary, many of them play a key role in actual function. For example, AcobZIP24 in the bZIP family is significantly enhanced in expression when pineapple is subjected to adverse environments, suggesting that it may play a regulatory role in adversity response. WRKY genes are also sensitive to external stress and plant hormone signals, and participate in the regulation of multiple
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