U.S. heirloom apple cultivars are an underutilized and threatened resource, that DNA fingerprinting can help save and remobilize. These heirlooms are old cultivars that were named, clonally propagated, and distributed more than a century ago. Many heirloom cultivars have great historical value, some are still grown commercially, and others could be reintroduced to enhance rural prosperity and diversify options for consumers. While some heirloom cultivars are ancestors of modern cultivars, many others could be valuable for future breeding. However, most heirlooms have been long neglected, and thousands once documented are already extinct. Before more heirlooms disappear forever, mystery trees need to be distinguished from known cultivars, identified, and adequately preserved. Leaf samples for more than 2000 apple trees in collections, national heritage sites, old orchards, and backyards across the U.S. were crowdsourced from about 150 “MyFruitTree” submitters and DNA fingerprinted using KASP genotyping with 48 SNPs. The cultivar identity or uniqueness of each tree was determined by comparing obtained DNA profiles to a previously developed dataset of several thousand apple cultivars and individuals. Trees with replicates were prioritized into five categories according to several criteria for likelihood of representing heirloom cultivars. After removing duplicate samples, poor genotypic data, and non-apple samples, about 60% (1202) of samples were identified as cultivars and most were heirlooms. Of the unidentified samples, 85% (665) were unique, and 15% (118) of the samples represented replicated trees. We found five “Priority 1” trees (filled cultivar pedigree gaps or from three U.S. regions) and four “Priority 2” trees (detected in two regions). Hundreds more trees likely representing unknown heirlooms were also identified in single regions. Collaborators across the country, including historians and citizen scientists, can now closely examine the highest priority trees to uncover their historic cultivar names, while ensuring they are propagated so that they are preserved and valued once again. As more old apple trees are DNA fingerprinted, it is expected that current “unique” DNA profiles will be replicated in the same or other regions. Replicated trees must represent propagated, valued, and likely named cultivars, increasing the opportunities to rediscover lost heirlooms.
