DNA profiling with the 20K apple SNP array reveals Malus domestica hybridization and admixture in M. sieversii, M. orientalis, and M. sylvestris genebank accessions

Abstract

The USDA-ARS National Plant Germplasm System (NPGS) apple collection in Geneva, NY, USA maintains accessions of the primary Malus domestica (Suckow) Borkh. progenitor species M. sieversii (Ledeb.) M. Roem., M. orientalis Uglitzk., and M. sylvestris (L.) Mill. Many of these accessions originated from seeds that were collected from wild populations in the species' centers of diversity. Some of these accessions have fruit phenotypes that suggest recent M. domestica hybridization, which if true would represent crop contamination of wild species populations and mislabeled species status of NPGS accessions. Pedigree connections and admixture between M. domestica and its progenitor species can be readily identified with apple SNP array data, despite such arrays not being designed for these purposes. To investigate species purity, most (463 accessions) of the NPGS accessions labeled as these three progenitor species were genotyped using the 20K apple SNP array. DNA profiles obtained were compared with a dataset of more than 5000 unique M. domestica apple cultivars. Only 212 accessions (151 M. sieversii, 26 M. orientalis, and 35 M. sylvestris) were identified as "pure" species representatives because their DNA profiles did not exhibit genotypic signatures of recent hybridization with M. domestica. Twenty-one accessions (17 M. sieversii, 1 M. orientalis, and 3 M. sylvestris) previously labeled as wild species were instead fully M. domestica. Previously unrealized hybridization and admixture between wild species and M. domestica was identified in 230 accessions (215 M. sieversii, 9 M. orientalis, and 6 M. sylvestris). Among these species-mislabeled accessions, 'Alexander', 'Gold Reinette', 'Charlamoff', 'Rosmarina Bianca', and 'King of the Pippins' were the most frequently detected M. domestica parents or grandparents. These results have implications for collection management, including germplasm distribution, and might affect conclusions of previous research focused on these three progenitor species in the NPGS apple collection. Specifically, accessions received from the NPGS for breeding and genomics, genetics, and evolutionary biology research might not be truly representative of their previously assigned species.

Keywords: Central Asia; crop wild relatives; cultivar; genetic diversity; genotype.

Figure 1

Example of newly detected presence of recent M. domestica ancestry in accessions previously labeled as pure wild progenitor species. (A). Extended shared haplotypes of ‘Alexander’ present in the M. domestica-M. sieversii hybrid accession PI 613979; (B) Extended shared haplotypes of ‘Alexander’ present in the M. domestica-M. sieversii hybrid accession PI 650959.

Figure 2

Map of M. sieversii collection sites for NPGS apple collection genotyped with a 20K SNP array. The subsequently determined proportions of pure M. sieversii, pure M. domestica, and hybrid/admixed individuals investigated from each site are overlaid as pie charts (small pie chart: 1-10 individuals; medium pie chart: 11-50 individuals; large pie chart: 51-135 individuals).

Figure 3

Malus fruit images from the USDA-NPGS apple collection (A) PI 657117 collected from Kazakhstan Site 12, determined to be pure M. sieversii; (B) PI 682787 collected from Kazakhstan Site 12, determined to be a hybrid between M. sieversii and M. domestica ‘King of the Pippins’; (C) Accession PI 589676, M. domestica ‘King of the Pippins’.

Figure 4

Malus fruit images from the USDA-NPGS apple collection (A) Three accessions collected in Kazakhstan determined to be pure M. sieversii; (B) Three accessions collected in Kazakhstan determined to be M. sieversii-M. domestica hybrids with ‘Rosmarina Bianca’ as a parent; (C) Two accessions collected as M. sieversii in Kazakhstan with genotype matching the United Kingdom National Fruit Collection accession 1951197, ‘Rosmarina Bianca’.