Patterns of genomic and phenomic diversity in apple and grape

Abstract

Apples and grapes are two long-lived perennial crops which are economically valuable but whose genomic and phenomic diversity has not yet been fully described and exploited. In this thesis, there were two main objectives: to characterize the genetic basis of several traits in apple and to estimate the degree to which wild relatives have been exploited in modern grape breeding. To achieve these objectives, I first describe variation in apple leaf morphology and demonstrate that comprehensive morphometric analyses of leaf shape can capture hidden, heritable phenotypes. Next, I performed a genome-wide association study using historical data from a diverse apple collection. I identified numerous genotype-phenotype associations, including an amino acid substitution in the transcription factor NAC18.1 that is a strong functional candidate for fruit firmness and harvest date. I also assessed ancestry in some of the most widely grown commercial hybrid grape cultivars. Over one third of hybrids derived approximately half of their ancestry from wild Vitis and half from the domesticated grape Vitis vinifera, suggesting hybrid grape breeding is in its infancy. Finally, I conclude by describing the potential of using genomics to improve perennial crops through introgression of valuable traits from wild relatives, such as disease resistance. Genetic mapping in wild relatives is difficult since genomic tools are often ill-suited to wild-relatives and phenotyping is an expensive and difficult process. However, there is an urgent need to immediately begin the collection and characterization of wild relatives to enable introgression of these valuable traits using genomics-assisted breeding. Overall, the results of this thesis lead to the following conclusions: comprehensive morphometric techniques capture heritable variation, novel genomic insights can be generated using historical phenotype data from gene banks, hybrid grape breeding is still in its infancy, and wild relatives should be exploited for genomics-assisted breeding of perennial crops.