Using multi-omics approaches to study flowering time and fruit development in perennial fruit species

Perennial fruiting plants coordinate their reproductive activities with seasonal changes in the temperate climates, with a pattern of bud set, dormancy establishment, fulfillment of chilling, flowering, fruit set, and fruit ripening. These processes have been optimized for the production of orchard plants that reliably produce quality fruit for human consumption. The understanding of molecular controls of dormancy in fruit trees has grown rapidly in the past decade, however, the complex mechanisms remain largely unknown. This dissertation presents my findings on genetic and epigenetic changes in Prunus species from dormancy to flowering using transcriptomics and epigenomics approaches. First, I compared the gene expression patterns in peach (Prunus persica) and apricot (Prunus armeniaca) with different CR over flower bud dormancy release. Two distinctive patterns were identified: genes induced in endodormancy are associated with chromatin reprogramming and reproduction pathways, while genes induced in ecodormancy are associated with pollen development. The indication of epigenetic regulation induced in endodormancy encouraged me to investigate the role of non-coding RNAs in dormancy release. I identified 250 microRNAs, over 60,000 small RNAs, and 789 long non-coding RNAs in the peach genome. The expression profiles suggested that small RNA and microRNA are more likely to respond to the shift of environmental temperature rather than dormancy phase transition. Long non-coding RNAs and microRNA miR2275 associated with pollen development are significantly upregulated at ecodormancy, indicating that pollen development is initiated at ecodormancy. Next, I analyzed the changes of histone H3K27me3 and DNA methylation over peach bud dormancy. Unlike small RNAs, H3K27me3 patterns primarily shifted at endodormancy under cold conditions, while DNA methylation levels shifted at the transition of endodormancy to ecodormancy. Although DNA methylation changes were poorly correlated with gene expression changes, genes associated with chromatin remodeling and oxidation-reduction may be under the regulation of DNA methylation. Finally, I assembled a reference genome and studied the gene expression during berry development in an evergreen blueberry (Vaccinium darrowii) with low CR which provides a breeding resource for decreasing CR in southern highbush blueberries to facilitate blueberry production in southern climates.