Tools and Techniques for Allele Mining in Apple

Apple (genus: Malus) is an important fruit tree grown in 95 countries around the world. There are over 10,000 known domesticated apple cultivars and over 45 species of apple. These cultivars and species are highly diverse, with distinct fruit flavors, textures, colors, and sizes. They also have distinct tree traits, including growth habits, disease resistance, and abiotic stress responses. The development of new apple cultivars is driven by consumer preferences and adaptation to environmental changes. Breeding new apple cultivars with improved quality traits is a laborious process. The highly heterozygous nature of apples coupled with a long juvenile phase makes the evaluation, selection, and subsequent release of the new cultivar a process that can extend well over a decade. Allele mining is a strategy to uncover allelic variations underlying important traits in apple. Various techniques including whole-genome sequencing and single nucleotide polymorphism discovery are utilized. Downstream analysis of variations, including insertions, deletions, and polymorphisms can be used to determine the genetic cause and variations underlying the trait of interest. Creation of genetic markers that can distinguish between those allelic differences can be applied to traditional breeding programs for marker-assisted selection. Knowledge, identification, and characterization of causal genes can be directly applied to targeted genetic improvement of apples. The use of genetic engineering to target traits of interest can directly be applied to improve existing cultivars. Apple transformation and tissue culture protocols are well established, and genome-editing techniques are already being used in apples. Key genes and causal variations involved in apple fruit quality and tree quality have already been identified. In this chapter, we present an overview of tools, techniques, and resources available for allele mining in apple. Furthermore, we explore allelic mining studies of important horticultural traits in apple and summarize the genetic identification and causal variation behind these traits.