ADVANCING THE DISCOVERY OF CAUSAL ALLELES CONTROLLING AGRICULTURAL PHENOTYPES IN APPLE (MALUS DOMESTICA)

Abstract

The apple is an economically and culturally important fruit crop grown in temperate regions around the world. The apple stands to benefit greatly from modern genomics, including the application of genomics informed breeding and gene editing technologies. However, the discovery of the DNA sequences, or causal alleles, that control apple phenotypes remains as a key barrier to the rapid advancement of genomics informed breeding and gene editing in apple. The objective of this thesis is to advance the current state of knowledge in the areas of apple phenomics and genomics by leveraging the wealth of phenotypic and genetic diversity in Canada’s Apple Biodiversity Collection (ABC). The present thesis presents a series of studies aimed at quantifying multiple apple phenotypes and revealing the identity of causal alleles that control them. Specifically, this research aims to provide a detailed comparison of the phenotypic differences between domesticated and wild apples, and to make contributions toward the discovery of causal alleles controlling apple phenotypes. In chapter 1, I compare the domestic apple to its wild progenitor by analysing 10 key agricultural phenotypes. This analysis reveals significant differences in key agricultural phenotypes between the two species. For example, domesticated apples contain 68% less phenolic content than their wild counterparts, on average. This investigation suggests that domesticated apples have significantly diverged from their primary wild progenitor species, and that wild apples may offer important germplasm for breeding in the future. In chapter 2, I use a pool-sequencing genomics approach to scan the genome for regions that control ripening time, phenolic content, and fruit softening. This investigation identifies a number of regions in the genome that are likely to harbour causal alleles. For instance, the analysis in chapter three identifies a region upstream of a well-known transcription factor gene NAC18.1 as being potentially causal for ripening time. In chapter 4, a genome wide association study is conducted using high depth DNA sequence data from 97 diverse samples from the ABC with the aim of discovering the causal allele for ripening time in apple. Results from chapter 4 delimit a narrow region of the genome on chromosome 3 probable to harbour the causal allele for ripening time, and illustrate some challenges associated with generating gene editing targets from association studies. Finally, a reference panel is generated for future genotype imputation in the ABC population. Chapter 5 summarises the findings of this thesis and provides context and prospective directions for enabling gene editing technologies in apple in the near future. Causal allele discovery in apple will remain challenging moving forward, however the research presented here represents key steps towards identifying causal alleles for a few key phenotypes and provides a foundation for unlocking the full mapping potential of Canada’s ABC.