Phenotypic and Genetic Studies of Grapevine

Abstract

Plant breeding is the science of altering a plant's genetics to attain a desired phenotype. In this dissertation, I explore what phenotypes to measure when breeding for downy mildew resistance and improved floral scent and how to measure these phenotypes accurately and efficiently. Traditionally, downy mildew resistance has been measured by visually rating sporulation and hypersensitive response on leaves or leaf discs. However, such manual ratings become intractable when dealing with thousands of samples. Therefore, to measure sporulation on leaf discs, I developed a computer vision system that reduced phenotyping time by more than 90% when compared to manual ratings, and also was found to work well for phenotyping leaf trichomes. If phenotypes are collected in the vineyard, spatial variation from inoculum, soil, and microclimate might have an effect on these phenotypes. Testing this assumption, spatial processes explained some variance in vineyard phenotypes, but accounting for the spatial variance might not lead to significantly more accurate phenotypes. Quantitative phenotyping of floral scent for large numbers of grapevines using headspace analysis is not economically feasible, so I evaluated the robustness of a hexane extraction followed by gas chromatography-mass spectrometry to identify floral volatiles and found that it was robust regardless of extraction time when flowers were sampled from the same inflorescence. After obtaining phenotypes and genotypes of vines, quantitative trait loci are found, traditionally using one phenotype at a time. In our case, understanding how sporulation, HR, and leaf trichomes affected each other was of interest, in addition to how genetic markers affected the phenotypes, so I used Bayesian networks to explore these interactions. In one of two F1 families studied, HR had a positive effect on sporulation, and leaf trichomes had a negative effect on both HR and sporulation, suggesting that leaf trichome density can be selected for in breeding for downy mildew disease resistance. A breeding project was started with the intention of creating a dwarf grapevine with an attractive floral scent. With a complementary interest to understand what volatile compounds were responsible for the various floral scents in grapevine, a diverse set of genotypes from various Vitis spp. were phenotyped for floral scent and volatiles, and it was found that similar scents were generated from different sesquiterpene profiles. Overall, this dissertation spans key concepts in the science of plant breeding, from parental selection and hybridization, to phenotyping by computer vision and chemical analysis, to statistical analyses of interacting phenotypes, genotypes, and spatial variability, with the findings possibly enhancing grapevine breeding strategies and execution.