International Journal of Molecular Evolution and Biodiversity, 2025, Vol.15, No.1, 40-50 http://ecoevopublisher.com/index.php/ijmeb 47 Figure 2 Putative domestication sweep around a bromelain inhibitor gene that helps control fruit ripening (Adopted from Chen et al., 2019) Image caption: a: top: heat maps showing the distribution of domestication sweeps (top 5% πw/πc) for the four cultivars; Bottom: a putative swept region at the end of LG03 containing AccBI1 and AccBI2. πw/πc across all cultivars is plotted using a sliding window of 0.5 Mb with 0.1 Mb shift; b: genetic distance (FST) between the smooth cayenne, queen, singapore spanish and mordilona-related clusters for the 6.5 Mb of LG03. Mean FST values are plotted in sliding windows of 50 kbwith 25 kb step size; c: Tajima’s D values for the four combined cultivar clusters (var. comosus) and wild (var. microstachys); Mean Tajima’s D values are plotted in sliding windows of 50 kb with a step size of 25 kb; d: left: pineapple fruit at select stages from a fruit ripening series (stages 1, 2, 7 and 8); right: maximum likelihood phylogeny of bromelain genes with log2 transformed RPKMs of expression in fruit, flower, leaf and root tissue (Adopted from Chen et al., 2019) Cultivated pineapples have accumulated numerous nonsynonymous mutations in genes related to disease resistance, consistent with the loss of trait-specific adaptive selection pressures. A typical feature of asexually propagated crop genomes is the accumulation of deleterious mutations (genetic load), due to the absence of purifying effects of sexual recombination in each generation. In pineapple, a large number of mildly deleterious variants are retained in a heterozygous state (Yow et al., 2022). The domestication process by humans may have driven these mutations to drift toward higher frequencies. Currently, more than 48% of the genes in the pineapple genome are observed to carry putatively heterozygous deleterious variants. 7.3 Breeding and genetic improvement of modern pineapple In the past, pineapple breeding mainly relied on picking parent plants, doing hand pollination, collecting seeds, and then testing the new plants made from cuttings. This whole process usually takes many years. Now, with the pineapple genome and many SNP markers available, scientists can use genetic tools to speed up the work. Researchers have used an F1 mapping population to find important regions (QTLs) in the genome linked to traits
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