CHARACTERIZING MORPHOLOGICAL AND GENETIC VARIATION IN PRUNUS AND MALUS TO UNDERSTAND FLOWERING TIME REGULATION IN ROSACEOUS TREES

The Rosaceae plant family is one of the most economically important families for fruit crop production. Members include domesticated apple (Malus × domestica Borkh.) and sweet and sour cherry (Prunus avium and P. cerasus, respectively). Bloom time is an agronomically significant trait in these species since flowering quality directly translates to yield. If bloom time is too early or too late, the economic losses may be severe. A possible strategy to maximize flowering and fruit set in either scenario is to understand the genetic basis of bloom time and use this information to create cultivars with bloom times customized to certain climates. The genes and processes of flower development they affect are well-studied in model species, which has aided our understanding in species with similar floral phenology. However, the control of flowering time in fruit trees, which exhibit perennial growth and dormancy phases, is poorly understood. In the first chapter of this dissertation, the entire flowering process is reviewed for rosaceous fruit trees from molecular, physiological, and genetic perspectives. Gaps in our knowledge are identified and future directions of the field are described. In chapter two, I characterize the morphology of diverse Malus accessions showing extreme bloom time variation and speculate on the potential regulatory mechanisms considering the results. Chapter three describes the construction of a valuable resource for genomics-assisted breeding: a chromosome-scale genome of P. cerasus cv. Montmorency, which is the predominant sour cherry cultivar grown in the United States. In chapter four, I holistically compare floral biology in a bloom time segregating population of sour cherry for several years to identify where siblings deviate in their developmental journeys. Using this information, the ‘Montmorency’ genome is used to identify molecular changes underlying the bloom time differences with RNA-sequencing, differential expression comparisons, and network analysis. Moreover, I identify genomic variation associated with a late-blooming QTL haplotype, k, on Prunus chromosome 4. These variants are then intersected with the differential expression comparisons to obtain a set of high-quality candidate genes for the basis of late bloom in this segregating population of sour cherry. This work allows a better understanding of the molecular and genetic control of flower development and bloom time in trees and lays a strong foundation for future work. This knowledge will inform researchers and fruit tree breeders on ways to modify, select for, or engineer desired bloom times to maximize crop yields. They will also provide insight into how temperate fruit trees may respond to a changing climate.