International Journal of Molecular Evolution and Biodiversity, 2025, Vol.15, No.1, 40-50 http://ecoevopublisher.com/index.php/ijmeb 48 like fruit weight, sugar level (measured by Brix), sourness, and flesh color (Nashima et al., 2023). One major QTL that controls peel color was found in a gene called AcCCD4. This gene helps break down pigments, so it affects whether the peel looks yellow or orange. Another QTL related to vitamin C was found on chromosome 7. It includes a gene that helps make vitamin C, called a galacturonate reductase. A separate GWAS study looked at 89 pineapple types, including wild and farmed ones. This study found DNA markers linked to traits like plant height and when the plant flowers (Nashima et al., 2024). The company Del Monte used genetic engineering to make a pink-fleshed pineapple. They did this by turning off the AcCCD4 gene, which lets lycopene (a pink pigment) build up in the fruit. Another gene, AcMYB266, was found to control red peel color. Breeders can use this gene to cross red-skinned ornamental types with common yellow-fleshed ones. Then, they can use DNA markers to pick out new plants that have both red skin and good fruit traits (Zhang et al., 2024). 8 Implications for Future Phylogenomics and Evolutionary Research 8.1 Pineapple as a model for phylogenomics of monocotyledonous plants Pineapple occupies a key phylogenetic position as an outgroup to commelinid monocots such as grasses and palms (Xu et al., 2018). Its genome serves as a valuable reference point for comparative analyses aimed at inferring the ancestral genome content and chromosomal structure of monocots. The Ananas genome has already been used to identify conserved non-coding sequences across monocots. Due to its relatively small genome and extensive functional annotations (e.g., the PGD database), pineapple is gradually becoming an important model for evolutionary genomics of monocots, following rice and banana. Future studies may include sequencing more Bromeliaceae genomes (some projects are already underway, such as the Aechmea fasciata genome), which will uncover the genomic basis of epiphytism, CAM (Crassulacean Acid Metabolism) evolution, and other lineage-specific innovations in Bromeliaceae (Li et al., 2022). 8.2 Genetic diversity and conservation of wild ananas species Cultivated pineapple includes only a small part of the genetic diversity found in the Ananas genus (Chen et al., 2019). Some wild species like A. macrodontes (previously called Pseudananas) grow in tough environments such as dry savannas. These plants may carry useful genes that help them survive heat and drought. Another wild species, A. bracteatus, is known for its strong leaf fibers and its resistance to certain soil diseases. These traits could be helpful in breeding pineapples that produce both fruit and fiber, or in improving root strength. By sequencing and genotyping wild species, scientists can find special gene variants and structural differences. For example, if a wild plant has a gene that naturally protects it from pineapple mealybug wilt-associated virus, breeders can try to introduce that gene into new pineapple varieties. Conservation genomics can also help explain how wild Ananas species are related and how their genes move between populations. Feng et al. (2022) found that A. bracteatus CB5 has genes from different sources, so it’s important to protect more than one group of this species. Gene editing can be used to improve wild pineapples that resist disease but have small fruit, such as A. ernestii. By changing just a few key genes, scientists can make these wild plants produce sweeter or larger fruits, creating new pineapple-like crops. 8.3 Integrated omics and systems biology studies in pineapple Combining DNA methylation maps with gene expression data can help scientists understand how genes control complex traits like CAM metabolism and flowering. Researchers have already used chromatin accessibility methods, such as DNase-seq or ATAC-seq, on pineapple leaves. These tests give clues about which genes are turned on or off by the plant's internal clock. In the future, the same methods can be used to study fruit growth, stress response, and other traits (Sharma et al., 2017). Some important traits, like sugar buildup or the start of flowering, are controlled by transcription factors and DNA patterns. Looking at these elements together will help us understand them better.
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