The genus Vitis (grapevine) contains about 70 species, including domesticated grapevine (Vitis vinifera L.). Since its domestication about 11,000 years ago, humans have generated thousands of domesticated grapevine cultivars exhibiting large phenotypic diversity, likely owing to the use of grapes in wine. Advances in genome sequencing technologies have allowed plant geneticists to disentangle the genetic basis of many of these diverse, complex traits and have led to the production of many Vitis genomes to aid in this effort. In this dissertation, I utilized modern genomic resources in Vitis to investigate the genetic mechanisms that influence various phenotypes within Vitis species (V. vinifera and V. riparia Michx.) and to generate a new genomic resource. In Chapter 1, I reviewed the history of Vitis and domesticated grapevine, as well as the current state of genetic research in Vitis that I have built upon in this dissertation. In Chapter 2, I investigated the genetic basis of the Witch’s Broom bud sports in domesticated grapevine, which are shoots that randomly arise on otherwise normal grapevine plants—presumably through somatic mutations—and exhibit dwarf phenotypes and reduced fertility. To do so, I sequenced two independent cases of the Witch’s Broom bud sport alongside their wild-type counterparts and identified putative causal genetic variants. I also characterized the phenotypes of the two cases, which revealed that these bud sports display developmental defects early on within the developing buds and that these independent cases display distinct phenotypes. In Chapter 3, I investigated the molecular genetic basis of mite domatia (hereafter, “domatia”) in V. riparia, which are tiny structures the plants form on the undersides of their leaves that mediate a mutualism with beneficial mites by providing them shelter in return for protection. These mites protect against small herbivores and pathogenic fungi, including significant grapevine pests like powdery mildew. Using transcriptome sequencing of two V. riparia genotypes with heritable distinct investments into domatia, I was able to identify key molecular genetic pathways involved in domatia development and intraspecific variation in domatia traits. This work, coupled with comparing leaf shapes between the two genotypes, also demonstrated a strong potential link between domatia traits and overall leaf development in V. riparia. In Chapter 4, I assembled and annotated the genome of the Dakapo variety of grapevine, a teinturier (“dyer”) variety that produces pigmented berry flesh (unlike most grapevine varieties). This high-quality genome assembly and the accompanying annotations will support future work on berry flesh color and anthocyanin production, as well as other work genetic research in domesticated grapevine. In Chapter 5, I described future directions for these research projects. Overall, the work described in this dissertation has provided unique insights into grapevine biology and generated new genomic resources, which will greatly facilitate future research in grapevine and other plant systems.
Read
