International Journal of Molecular Evolution and Biodiversity, 2025, Vol.15, No.1, 40-50 http://ecoevopublisher.com/index.php/ijmeb 46 seed-grown crops, which often have hundreds. This may be because pineapple mostly reproduces asexually, so it doesn’t need as many defense genes. There’s no clear sign that these genes expanded a lot recently. Usually, there is one gene per lineage. Some pineapple varieties show different numbers of these genes. For example, one gene on chromosome group LG12 appears several times in resistant types but only once in sensitive ones. WRKY transcription factors also play a role in stress response. Pineapple has around 54 WRKY genes (Wai et al., 2024), spread across groups I, II (a-e), and III. These genes have different roles. For example, AcWRKY31 (Group III) helps defend against pests, while AcWRKY28 (Group II) helps with heat or drought. The NAC gene family has about 73 members. These genes help control stress response, plant growth, and aging. 6.4 Metabolic pathway genes and secondary metabolites Pineapple makes proteases, which are enzymes that break down proteins. These come from a small group of C1A peptidase genes. They fall into two types: fruit-type and stem-type. The fruit-type (e.g., AcCP1) is from a single gene. The stem-type likely came from gene duplications and shows different traits, like isoelectric points. Pineapple also has protease inhibitors like cystatins. These are encoded by a few genes, though some duplicated over time. This shows an evolutionary balance between proteases and inhibitors (Chen et al., 2019). Pineapple's smell comes from esters, terpenes, and aldehydes. These are made by gene families like acetyltransferases, terpene synthases, and alcohol dehydrogenases. The BAHD acetyltransferase family is active in ripe fruit. One member, AcAAT, helps make key esters like ethyl butyrate. Pineapple has about a dozen TPS (terpene synthase) genes. Some of them evolved under positive selection, which may increase aroma diversity. Pineapple has key genes for anthocyanin pigment production (e.g., DFR, ANS, UFGT), usually one copy each. But regulators like AcMYB266 can change skin color from green to red by changing gene activity or mutating (Zhang et al., 2024). Enzymes like ACC synthase and ACC oxidase, which make ethylene, have evolved under pressure to meet flowering and ripening needs in pineapple. 7 Case Study: Domestication and Genetic Improvement of Pineapple 7.1 Origin and domestication of pineapple Pineapple was domesticated by the indigenous peoples of tropical America before the time of Columbus, and its domestication process appears to have been a “single-step” event (Chen et al., 2019). Wild populations of Ananas in the Paraguay-Paraná river basin are considered the ancestors of cultivated pineapple (A. comosus). Cultivated pineapple exhibits characteristics of reduced genetic diversity, consistent with a model of a single domestication origin followed by clonal propagation. Most cultivated varieties share a common genomic foundation, particularly those in the “Spanish group,” which are almost entirely derived from a single wild lineage (supporting the single-step domestication hypothesis). In fact, some varietal groups, such as “Smooth Cayenne” and “Queen,” carry genomic segments from other wild pineapple populations. Traits selected during domestication include: increased fruit size, high sugar content, reduced flesh fiber, development of seedless fruit, and the loss of sexual reproduction capability. The domestication process achieved a transition from sexual reproduction to complete reliance on clonal propagation through suckers and slips. 7.2 Genomic features selected in cultivated pineapple In cultivated pineapple, genetic diversity is lower than in wild types. Some parts of the genome are very different from wild alleles. Chen et al. (2019) found 25 possible domestication sweep regions in the pineapple genome. These regions range in size from 150 kb to 1.2 Mb. The strongest sweep is on chromosome 5. It includes several genes that control fruit growth and fiber traits. Another important region is on chromosome 10. It has a gene for sugar transport and another gene that helps control how the fruit grows (Figure 2).
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