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Historic breeding populations often have limited pedigree notation and genomic data associated with them. A prime example of this is the Plum Collection of over 150 cultivars introduced by Luther Burbank between the 1880’s-1920’s which consisted of many different Prunus species, the most prominent of which were combinations of the diploid species P. salicina, P. simonii, P. americana, and the hexaploid species P. domestica. The primary goals of this study were to locate as many of Burbank’s introductions as possible and to investigate their pedigrees and genetic diversity. Fifty-three cultivars were located at three California sites; the USDA-ARS-National Clonal Germplasm Repository at the Wolfskill Experimental Orchard , Luther Burbank Home & Gardens, Gold Ridge Experiment Farm, and at numerous scion exchanges held by the California Rare Fruit Growers. These taxa were analyzed using genotyping by sequencing (GBS) which retrieved over 24,000 SNPs spread over eight chromosomes with degrees of heterozygosity that ranged from 5.33% - 30.90%, with an average of 13.28%. The transition/transversion rates of SNPs retrieved were 60.99% and 33.73% respectively The remaining SNPs are indels.SNP data were visualized using Identity by Descent (IBD) heatmaps, dendrograms, kinship matrices, and phylogenetic admixture plots. Eight distinct kinship groups emerged as significant using approximately unbiased bootstrapping on a dendrogram. Phylogenetic admixture analyses optimized at K=4 corresponded to P. salicina, P. simonii, European plums (P. domestica and P. cerasifera), and North American plums (P. americana and P. rivularis). The heatmap visualized shared rare alleles. Combined with phylogenetic admixture, the IBD analyses show how the taxa are related to each other. Lastly, fruits scored for exocarp color, mesocarp color, free or cling-stone endocarps, and general shape were compared to genotypic data using genome-wide association studies (GWAS) and integrated haplotype scoring (iHS). Using Bonferroni-corrected and false discovery rate (FDR) p-values as a threshold of significance at alpha=0.05, GWAS showed exocarp color significantly correlated to a SNP on chromosome 2. Mesocarp color showed SNPs on chromosomes 2 and 3 that surpassed significance thresholds for association at FDR alpha=0.15. Similarly, free and cling-stone endocarps have a prominent, non-significant SNP on chromosome 7, and shape appears to be a multi-genic trait with SNP areas of interest on chromosomes 1, 3, 4,and 6. These results await confirmation in a larger sample. The iHS showed areas of improvement via long haplotypes on chromosomes 2, 4, and 7. Traits being selected against, as indicated by short haplotypes, were detected on chromosomes 1, 2, 3, 5, and 6. Taken together, these analyses provide new insights into the identities among Burbank’s Prunus introductions and the potential of these valuable genetic resources for further development in the horticultural industry.

In the United States and Canada, rapid growth in production and sales of alcoholic or “hard” cider has brought about a rapid increase in the number of acres planted with high-tannin apple (Malus ×domestica) cultivars, mostly of English and French origin. These cultivars, valued for the “mouthfeel” they confer to alcoholic cider, are often prone to “biennial” bearing, which is largely caused by seed-derived gibberellins suppressing floral bud formation, and thus return bloom. Crop load management, via bloom or fruitlet thinning, is often used to mitigate biennial bearing, as are bloom-promoting plant growth regulator (PGR) sprays. Four field experiments assessed the innate bearing habit, response to thinning, and response to bloom-promoting PGR sprays of seven high-tannin cider cultivars, as well as the effects of crop load on fruit maturity and juice quality. In a three-year hand-thinning experiment conducted in Lyndonville, NY (Chapter 2), biennial bearing index (BBI) correlated negatively with cumulative yield both within and among cultivars: ‘Chisel Jersey’, ‘Dabinett’, and ‘Harry Masters Jersey’ had low BBI and high cumulative yield overall, while ‘Michelin’ had higher BBI and somewhat lower cumulative yield; ‘Brown Snout’, ‘Binet Rouge’, and ‘Geneva Tremlett’s Bitter’ were highly biennial and unproductive overall. Hand-thinning reduced BBI over three years, but rarely achieved comparable or greater cumulative yields over three years. Fourth-year bloom data indicate that, had treatments been re-imposed, thinning would result in comparable or improved cumulative yield, and lower BBI, for four of seven cultivars. This experiment, and an identical experiment performed in the low-crop “off” year only on a different set of trees, indicate that thinning in the “off” year is not effective at promoting return bloom. The same two experiments found that crop load correlated negatively with polyphenol (i.e., tannin) content, soluble solid (i.e., sugar) content, titratable acidity, and nitrogen content, of juice over three years, for all seven cultivars (Chapter 3). The relationship between maturity and crop load was cultivar-specific. A concurrent three-year experiment (Chapter 4) found that PGRs were not effective at promoting return bloom in any of the same seven cultivars. Likewise, a two-year experiment (Chapter 4) conducted in Lansing, NY found that PGR sprays had no appreciable bloom-promoting effect either compared to or in combination with hand-thinning, in ‘Chisel Jersey’ or ‘Brown Snout’, but that crop load did have a significant negative effect on return bloom. A survey of commercial cidermakers in the United States and Canada (Chapter 5) found that biennial bearing affects apple supply for a majority of cidermakers growing their own high-tannin fruit, but only affects a minority of non-grower cidermakers working with high-tannin cider cultivars. Thinning and other horticultural practices to promote annual bearing were not commonly performed by high-tannin cider apple growers. The most mentioned cultivars by both apple growers and cideries who only purchase fruit or juice were the reputedly annual ‘Dabinett’ and the notoriously biennial ‘Kingston Black’. Inconsistent supply was the leading reason given by cidermakers who choose not to use high-tannin fruit in their cider. The work presented in this thesis demonstrates: the efficacy of hand thinning in certain high-tannin cider cultivars at promoting annual bearing, improved cumulative yields, improved juice quality, and overall tannin yield; the long-term profitability of thinning in high-density cider orchards for some cultivars; and the need for further research to identify effective midsummer PGR strategies that can be used with fruit thinning to promote return bloom in biennial high-tannin cider cultivars. Thinning to 9 fruit/cm2 TCSA can improve long-term productivity in ‘Brown Snout’, ‘Chisel Jersey’, ‘Dabinett’, and ‘Harry Masters Jersey’, and can improve long-term tannin production in all seven cultivars described in this thesis.

Olives (Olea europaea L.) produce abundant flowers, but only a small subset persist as fruits. We hypothesize that the low fruit set to flower ratio is due to the short ovule longevity. Ethylene inhibition is hypothesized to prolong olive inflorescence longevity, extending the effective pollination period (EPP) and improving yield. The objective of this research is to determine whether applying exogenous aminoethoxyvinglglycine (AVG, an ethylene inhibitor) during bloom will decrease ethylene generation and increase the EPP, fruit set and yield. A 264 ppm ReTain™ (a.i. Aminoethoxyvinylglycine) sprayed at bloom on Arbequina olives and monitored through the end of bloom significantly reduced ethylene production but did not affect visual bloom senescence or pollen tube growth, measured by pollen tube width. At harvest, fruit yield was measured, and the oil analyzed. ReTain™ bloom application did not delay flower senescence or improve pollen tube growth. It significantly reduced ethylene generation and mildly increased fruit yield, but the yield increase was not significant. The collective results show that ReTain™ can significantly and strongly decrease ethylene generation in Arbequina olive flowers, but not extend flower longevity, improve fruit set or yield. Heavy rain, accompanied by low temperatures, during the bloom may be the reason why the flower longevity was not extended, resulting in decreased fruit set.

The state of Virginia was analyzed to establish its suitability for grape culture. This investigation occurred in two phases: a small scale analysis that encompassed the entire state, and a large scale analysis which focused on site selection at the local level. After identifying regions across the state in terms of their viticulture potential, a study area was chosen from within the highest ranking region. This study area was the focus for the local-scale site potential analysis. First, to delineate regions across Virginia that had greater or lesser viticulture potential from a physical and climatological basis, weather station data were collected for minimum winter temperatures, maximum summer temperatures, precipitation, length of growing season, and day versus night temperature differentials. In addition, elevation and slope models were constructed to complement the climatic variables in identifying areas that contained factors most conducive to grape production. To validate this regional assessment, the history of fruit industries within the state are outlined geographically to display the evolution of the fruit industries, and to establish the factors which have shaped the current fruit landscape. Secondly, at the local scale, a Geographic Information System (GIS) approach was used to identify sites at the county scale that had greater or lesser viticulture potential from a physical basis. Composite maps, constructed by individual counties in the state, were produced from a series of physical databases. The individual databases (sources and resolution in parentheses) included land-use (Virginia Gap Analysis; 30meter2 resolution), slope, aspect, and elevation (USGS 1:24,000 Digital Elevation Model; 30meter2), and soils data (USGS Digital Line Graph (DLG-3)). Each physical feature layer was given a numerical classification, then all layers were combined to produce a 0 to 100 scale in the final, composite image. Given this model of potential vineyard suitability, existing fruit operations in select counties were geo-located on each feature layer using a Global Positioning System (GPS: 1-2meter accuracy). Actual data on occurrences of frosts, minimum winter temperatures, and other site variables were collected from these fruit operations and surrounding weather stations as a sample to validate the model. A strong correlation between areas containing characteristics of current fruit acreage--namely apple--and sites high in potential for viticulture according to the model. Studying the history of geographic distribution of apple and grape industries across the state reinforces the regional assessment of viticulture potential, formulated by the climatic and topographic analysis. Employment of GIS approach at the local site scale was shown to be an effective tool for site selection at the local scale with certain caveats. In addition, the evaluation procedure integrating GIS and GPS technologies allows us to visually assess the distribution pattern of each of the factors employed individually; and, in turn, physically identify and locate areas of viticulture potential created from the combination of those factors.