Commercial apple breeding is dominated by a very small number of cultivars. Pre-breeding projects aim to enrich the utilized genepool with genetically distinct material, including wild species and old/local cultivars. This material has great potential, especially in breeding programmes focused on resistance to various pests and diseases, or on cultivation in marginal production areas requiring improved habitat adaptation. For most of the wild species, only a few accessions have however been evaluated, thereby probably overlooking many potentially valuable gene sources.
Molecular tools are consistently being developed for assisting commercial breeding of apple and numerous other crops. These tools are of course useful also for pre-breeding and have been implemented, e.g. for identification of accessions in germplasm collections and determination of pedigree relationships. Similarly, an increasing number of methods are becoming available for efficient identification of valuable genes and development of markers for choosing suitable parents and for early selection in seedling populations. Several apple genome sequences have been published, both of domestic apples (Peace et al. 2019) and, more recently, also of M. robusta 5 (Karlström et al. 2025), M. baccata ‘jackii’ (Pfeifer et al. 2025b) and M. fusca PI 589975 (Mansfeld et al. 2023).
While the molecular tool development looks very promising, there is also the matter of acquiring data on large sets of genotypes in order to identify sources of valuable genes and enable in-depth genetic analyses. Ideally, such data should be collected during a period of several years at multiple sites on repeated sets of carefully chosen genotypes representing both wild species and domestic cultivars. Such experiments are, however, exceedingly expensive and require several years for planning, planting and growing the material before it can be evaluated.