Genome to phenome mapping and marker-assisted breeding in apples

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A future of environmentally sustainable agriculture that leads to a safe and secure food supply requires sustained breeding programmes that respond to evolving pests and pathogens, global climate change and the demand for alternative biofuel sources. Genomics holds the promise to significantly accelerate the breeding of improved cultivars with desirable traits through marker-assisted breeding and genomic selection. As the costs of DNA sequencing continue to rapidly drop, we are entering an era where genotyping and sequencing costs are often not the limiting step for enabling genotype-to-phenotype mapping. Rather, the major barriers limiting the use of DNA sequence data for crop improvement are the availability of genomic and bioinformatic tools that are user-friendly and useful across a diverse range of agricultural systems, and accurate measures of species' phenomes. My research programme aims to overcome these barriers by developing genomic and phenomic tools that can be leveraged to reduce the amount of time and money required to breed novel cultivars that require less chemical input. A population of over 1000 diverse apple cultivars forms the basis of my research programme. This population will be extensively genotyped and phenotyped with the aim of uncovering novel genotype-phenotype relationships. Not only will this programme provide novel insights into apple biology, but it will provide a launching point for future breeding efforts aimed at producing cultivars with commercial appeal that require less chemical input.