UC Davis

Many cultivars of almond (Prunus dulcis Mill. D. A. Webb) suffer from a disorder known as non-infectious bud failure in which preformed meristematic tissue becomes necrotic during dormancy, then fails to emerge in the following growing season. Non-infectious bud failure is a noteworthy disorder in perennial crops due to its miotic inheritance through asexual propagation and variance in severity between genetic clones. While the cause of the disorder is unknown, previous research has shown possible connections between DNA methylation and symptoms of the disorder. Non-infectious bud failure has been mitigated through propagation from basal epicormic buds, which show reduced non-infectious bud failure in clonal progeny relative to the axillary canopy buds typically used for propagation. In this dissertation, we explored several possibilities of detecting differences in DNA methylation and expression to develop potential biomarkers for non-infectious bud failure in almonds. First, we explored variation in DNA methylation between epicormic and axillary shoots that may provide insight into the spread and origins of non-infectious bud failure. We hypothesized that shoots derived from different tissues (epicormic and axillary buds) and growing environments would have distinct genome-wide patterns of DNA methylation. We sampled leaf tissue from epicormic and axillary canopy shoots from two almond varieties at four locations, then used whole-genome enzymatic methyl-sequencing to determine global methylation levels and differentially methylated regions between tissues. We found no significant differences in genome-wide methylation levels between different shoot types, locations, and varieties. Epicormic and axillary shoots displayed 23 differentially-methylated regions in one variety and 45 in the other, with no overlap in these regions between varieties. In addition, we identified 4546 regions that appeared differentially methylated between varieties; however, DNA polymorphism may account for some of these differences. In pairwise comparisons between locations, we identified 312 regions, with overlapping regions between some, but not all, locations. The remarkable stability of DNA methylation patterns across tissues and locations motivates further investigation into possible perturbations of these patterns by non-infectious bud failure and related genetic disorders in perennial plants. Next, we explored differences in DNA methylation and RNA expression between trees displaying different severities of non-infectious bud failure. To do so, we developed a new haplotype-phased reference assembly for the variety “Carmel”. One parent of Carmel, “Texas” has no history of bud failure symptoms, while its other parent, “Nonpareil” does. We then scored Carmel trees in a commercial orchard for non-infectious bud failure severity, then sampled leaf tissue from those trees. We used enzymatic methyl-seq to measure whole-genome DNA methylation and perform differential methylation analysis and we used 3` TAG RNA sequencing to measure gene expression between the levels. Our results show 20 regions of differential methylation between the two haplotypes. Additionally, 2083 genes were differentially expressed between the two haplotypes, with the expression of certain genes highly correlated with bud failure level. Three of these DMRs fall within 5000 base pairs of the differentially expressed genes. These areas of variation in methylation and expression data may indicate candidate genes for non-infectious bud failure, and may aid in the development of future diagnostic tools. Finally, we describe a successful program for zinnia breeding. Zinnias (Z. Elegans) have emerged as an important crop for many California organic growers. Due to their cold intolerance, zinnias cannot be refrigerated for extended periods of time. Therefore, production cannot be easily moved to locations that require long transportation times, which has resulted in localized production. However, most zinnia seed currently in production has been bred for conventional systems. Additionally, very few resources exist on the methods and strategies for improving zinnias for cut flower production. After evaluating available germplasm, we made 463 crosses, then selected 85 to evaluate in a single field season. Using a modified synthetic breeding strategy, we performed selection on color, petal doubling, stem length and flower size for five years. We introduce two new cultivars, ZP.23.225 and ZC.23.227, that have been bred specifically for organic systems and addressing new and emerging market demands. ZP.23.225 is a zinnia with a light pink color and a small flower head but maintains agronomic vigor. ZC.23.227 is an orange “cactus” type zinnia with good field performance and an exceptionally large flower head. These varieties were developed through the Student Organic Plant Breeding and Education program at the University of California, Davis.