Polyploidy, the presence of three or more homologous chromosome sets, is a well-reported, often difficult-to-study, phenomenon widespread in plants. Polyploidization can impact plant metabolism through changes in morphology, cell size, stress tolerance, gene expression patterns, and epigenomic landscape. The effects of polyploidization have significant implications for plant metabolism, diversity, and survival. The combination of ever-improving research techniques and the high prevalence of polyploidy in angiosperms provides exciting research possibilities. My work uses genomic, transcriptomic, and metabolomic analyses to investigate three crops: blueberry, cherry, and strawberry. The first chapter reviews aspects of polyploidy that are favorable for environmental resilience, including the fate of duplicated genes, the effects of genomic shock, and the prominent occurrence of polyploidization events at times of ecological transition. The second chapter investigates resistance to anthracnose fruit rot in tetraploid northern highbush blueberry. This work identifies four genomic markers and one metabolic marker with properties consistent with a quercetin rhamnoside that are significantly associated with resistance and investigates the metabolic reaction of a blueberry fruit upon infection. The third chapter identified the maternal and paternal contributors of tetraploid sour cherry as tetraploid ground cherry and diploid sweet cherry, respectively. The fourth chapter examined the effects of growing conditions and hybridization direction on subgenome expression dominance in interspecific Fragaria hybrids. I found that neither growing nor germination conditions determine which subgenome exhibits homoeolog expression bias with consistent bias direction across all germination and growth conditions tested. Subgenome expression patterns were consistent among reciprocal hybrids as well. The fifth chapter reflects on the projects I completed and looks ahead to questions I would be interested to investigate in the future. Together, these chapters represent both basic and applied research projects involving the dynamics of polyploidy and polyploid crops.
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