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

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

Submitted to: Frontiers in Plant Science
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: 9/21/2022
Publication Date: 10/13/2022
Citation: Volk, G.M., Peace, C.P., Henk, A.D., Howard, N.P. 2022. DNA profiling with the 20K apple SNP array reveals Malus domestica hybridization and admixture in M. sieversii, M. orientalis, and M. sylvestris genebank accessions. Frontiers in Plant Science. 13. Article e1015658. https://doi.org/10.3389/fpls.2022.1015658.
DOI: https://doi.org/10.3389/fpls.2022.1015658

Interpretive Summary: The USDA National Plant Germplasm System (NPGS) maintains a large collection of apple cultivars and Malus wild species that are used for breeding and research projects around the world. It is important that materials in the collection are identified correctly so that recipients of NPGS apple genetic resources can make accurate conclusions from the results they obtain. The NPGS has significant collections of apple crop wild relatives M. sieversii, M. orientalis, and M. sylvestris, all of which are progenitors to the domesticated apple, M. domestica. Seeds of the crop wild relatives were mostly obtained through exploration and exchange programs between 1989 and 2002. Herein, 463 of the trees representing these crop wild relatives were genotyped using the 20K SNP array genotyping platform to determine if taxa were correctly identified or if they exhibited signs of admixture with M. domestica. Only 45% of the genotyped accessions were found to be true species representatives, necessitating a relabeling of NPGS materials and database updates to reflect the true identities of Malus crop wild relatives in the NPGS.

Technical 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 admixture, which if true would represent crop contamination of wild species populations and mislabeled species status of NPGS accessions. Pedigree connections and admixture among 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 admixture 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 interspecific hybridization (or 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 genomics, evolutionary biology, and breeding programs might not be truly representative of their previously assigned species.