International Journal of Molecular Evolution and Biodiversity, 2025, Vol.15, No.1, 40-50 http://ecoevopublisher.com/index.php/ijmeb 43 3.4 Reticulate evolution and hybridization in ananas Although species within the genus Ananas are generally intercrossable, natural hybridization is limited due to geographic isolation. Cultivars such as ‘Smooth Cayenne’ and ‘Queen’ carry genome segments derived from multiple wild lineages, consistent with hybridization among distinct wild populations during domestication. The ‘Singapore Spanish’ cultivar, by contrast, is almost entirely derived from a single ancestral population. Chen et al. (2019) proposed a mixed domestication model: some cultivated groups were domesticated mainly through clonal propagation from a single origin (a one-step process), while others experienced a phase of sexual reproduction, during which genetic material from different lineages was introduced. Further evidence comes from the genome of the wild species A. bracteatus CB5, whose comparative analysis reveals a mosaic of genomes from three different Ananas species (Feng et al., 2022). 4 Evolutionary Trajectories of Key Traits in Pineapple 4.1 CAM photosynthesis and metabolic adaptation Pineapple developed CAM photosynthesis in a way that is different from C4 grasses. In grasses, new enzymes came from gene duplications. In pineapple, existing genes changed how they are used. These changes happened through gene regulation. The pineapple genome has not gone through a recent whole-genome duplication. Important CAM enzymes like phosphoenolpyruvate carboxylase and malate dehydrogenase are mostly single-copy or belong to small gene groups. Many CAM genes in pineapple leaves turn on and off in a daily rhythm. This allows the plant to take in and fix CO₂ at night. Also, photosynthetic tissues (green leaves) and non-photosynthetic ones (white leaves) show different levels of CHH methylation, which is linked to CAM gene expression (Yow et al., 2023). Because there is no recent genome duplication, the pineapple genome is simpler. It uses time-based gene activity to support CAM function. This helps the plant save water but leads to slower growth compared to C3 plants. CAM in pineapple evolved alongside other traits, like thick leaves with big vacuoles (for storing malate) and stomata that open at night. 4.2 Reproductive biology: flowering and compatibility Pineapple has some unique reproductive traits. It often produces fruit without pollination (parthenocarpy). Wild types usually have flowers that can't self-pollinate, so they outcross. For example, A. comosus var. bracteatus is self-incompatible, but some cultivated types can self-pollinate. Chen et al. (2019) found four possible self-incompatibility (SI) genes in the wild genome F153. These genes are missing or not working in the cultivated variety CB5. Pineapple does not flower at a steady time. Flowering can be triggered by cold or drought stress (Yow et al., 2023). Studies show that cold affects plant hormone signals, like ethylene and ABA. Genes related to vernalization and flowering (like FT-like and VIN3-like) act differently in various genotypes. The B-box transcription factor gene AcBBX5 has been shown to promote flowering in pineapple (Ouyang et al., 2022). The AcBBX gene family in pineapple (19 members) displays some degree of diversification, though gene duplications are limited. Flowering time regulation can be achieved through expression changes in a few key regulators such as AcBBX5. 4.3 Fruit development and quality trait evolution Pineapple fruit is made up of many flowers joined together. During domestication, fruit traits changed to meet human taste. Cultivated pineapples have more sugar than wild ones. Genes that manage sugar metabolism and transport were affected by selection. For example, areas in the genome with sucrose synthase and sugar transporter genes show signs of selection. These genes may help the fruit store more sugar (Chen et al., 2019). In pineapple hybrids, researchers found QTLs linked to shell (rind) color. The gene AcCCD4, which breaks down carotenoids, is a likely candidate (Nashima et al., 2023). Some cultivars have special AcCCD4 alleles that slow down this breakdown. Another gene, AcMYB266, helps make the fruit peel red. Overexpression of this gene turns the peel red (Zhang et al., 2024).
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