What’s that apple? Cultivar identification of apple trees in the U.S. via SNP-based DNA profiling

Authors: PEACE, CAMERON - Washington State University; LEE, D - Washington State University; HOWARD, NICHOLAS - Fresh Forward Breeding & Marketing; Volk, Gayle

Submitted to: Meeting Abstract
Publication Type: Abstract Only
Publication Acceptance Date: 2/17/2025
Publication Date: N/A
Citation: N/A

Interpretive Summary: N/A

Technical Abstract: Apple cultivar name and unique identity matters. Misidentification and unlabeled trees are common, impeding utilization for cultivation and breeding and hindering long-term preservation. Many thousands of apple cultivars exist in the U.S., with more being imported or created each year. 16,350 are documented as once being grown in North America, but most are very rare, perhaps a quarter represent synonyms, up to a thousand are estimated to be lost but still alive somewhere, and more than 5000 are suspected to now be extinct. Focusing on the U.S. genepool, the “MyFruitTree” endeavor at Washington State University provides the public with an objective basis for cultivar identification via DNA profiling. The RosBREED and FruitBreedomics projects provided the technological and dataset foundations. Those projects’ several thousand unique DNA profiles have since been expanded by crowdsourced DNA profiling of apple trees from cultivar collection managers, park and forest managers, old orchard owners, lost apple hunters, historians, breeders, researchers, commercial growers, and other apple tree owners and enthusiasts. Two levels of genotyping are offered. “Simple DNA testing” is cheapest, quickest, uses 48 SNPs via KASP, readily determines identity vs. uniqueness, and suits trees suspected to be cultivars. “Full DNA testing” uses genotyping platforms for thousands of SNPs (8K then 20K Illumina arrays, now a 5-10K SNP set via Flex-Seq) and definitively establishes parentage, pedigree, and/or ancestry. Comparisons of tested trees are made to a “Reference Panel” of thousands of DNA profiles of named cultivars and thousands more “Accessory Profiles”. For trees with evidence of intentional cultivation, cultivar identities are usually determined – and if not become the focus of nationwide collaborative activities to discover their historical cultivar names. While contributing to genetics research advances and germplasm preservation, MyFruitTree also supports the U.S. public’s fascination with the diversity and histories of apple cultivars.