The genetic basis of apple quality

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Genomics is emerging as a key tool to help build a future of environmentally sustainable agriculture that leads to a safe and secure food supply. The development of genomics tools relies primarily on the discovery of relationships between genotypes and phenotypes, which is accomplished by performing genetic mapping. The proposed research involves genetic mapping in apples (Malus domestica), one of the world's most widely grown fruit crops and Canada's leading fruit in both volume and value. I propose to discover genetic markers that predict apple quality that Canadian apple breeders will then use to perform genomics-assisted breeding: they will screen offspring at the seedling stage using the markers we discover and discard those predicted to have poor quality. Apples take nearly a decade to grow to maturity and evaluate, and breeding apples using traditional phenotypic evaluations is therefore extremely time-consuming and expensive. Marker-assisted selection thus holds particular promise in apples because it can dramatically increase the efficiency and reduce the costs of generating desirable apples that require less chemical input to grow. To enable genomics-assisted breeding in apples, I established the Apple Biodiversity Collection (ABC) an orchard with over 1000 apple varieties that serves as the most diverse and arguably most powerful genetic mapping population of apples in the world. The ABC was planted in 2013 specifically for the purposes of genetic mapping and is emerging from juvenility over the next few years. It is the foundation of my proposed NSERC Discovery research. It is my long-term objective to exhaustively catalogue all of the genetic variation present in the ABC. Here I propose to sequence the DNA of the 1000+ apple varieties and extract as many genetic markers from these data by developing novel bioinformatics tools. However, the challenge in genetically mapping fruit quality traits clearly lies in the collection of the phenotype data. Therefore, a primary activity in this proposal involves the development and use of automated, high-throughput phenotyping devices and metabolomic/proteomic assays to query as much of the apple's phenome as possible. In addition, I also propose to evaluate the apple's wild ancestor in Central Asia to determine if it is worth exploiting its functional genetic variation for future apple improvement. The proposed research will not only result in markers that accelerate the improvement of apple quality through breeding, but it will also generate innovative bioinformatics tools that improve the power of genetic mapping in other non-model organisms. Thus, the proposed project promises to benefit stakeholders along the entire Canadian apple value chain, from grower to consumer, and to help accelerate the impact of genomics in several fields including agriculture, biofuels and forestry.