DataSheet_2_DNA profiling with the 20K apple SNP array reveals Malus domestica hybridization and admixture in M. sieversii, M. orientalis, and M. sylvestris genebank accessions.pdf

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.

美国农业部农业研究局（USDA-ARS）位于美国纽约州日内瓦市的国家植物种质资源库（National Plant Germplasm System, NPGS）苹果种质圃，保存有栽培苹果（Malus domestica (Suckow) Borkh.）的3个核心祖先种种质：塞威士苹果（M. sieversii (Ledeb.) M. Roem.）、东方苹果（M. orientalis Uglitzk.）以及森林苹果（M. sylvestris (L.) Mill.）。此类种质多数源自采自各物种多样性中心野生种群的种子。部分种质的果实表型显示其近期发生过与栽培苹果的杂交事件，若确证此类杂交，则意味着野生物种种群受到栽培作物的基因污染，同时也会导致NPGS该批种质被错误标注物种身份。尽管苹果单核苷酸多态性（Single Nucleotide Polymorphism, SNP）阵列并非专为该类分析设计，但借助其数据可便捷鉴定栽培苹果与其祖先种之间的系谱关联与基因渐渗现象。
为探究物种纯度，研究人员对该3类祖先种标注的NPGS种质中的大部分（463份）开展了20K苹果SNP阵列基因分型。将获得的DNA分型结果与包含5000余份独特栽培苹果品种的数据集进行比对后发现：仅212份种质（151份塞威士苹果、26份东方苹果、35份森林苹果）可被鉴定为"纯种"野生祖先种，因其DNA分型未呈现与栽培苹果近期杂交的基因型特征。另有21份此前被标注为野生种的种质（17份塞威士苹果、1份东方苹果、3份森林苹果）实际完全属于栽培苹果。在230份种质（215份塞威士苹果、9份东方苹果、6份森林苹果）中，研究人员发现了此前未被认知的野生种与栽培苹果之间的杂交与基因渐渗事件。在这批被错误标注物种的种质中，"Alexander（亚历山大苹果）"、"Gold Reinette（金雷诺特苹果）"、"Charlamoff（查拉莫夫苹果）"、"Rosmarina Bianca（白迷迭香苹果）"以及"King of the Pippins（皮平之王苹果）"是被最频繁检测到的栽培苹果亲本或祖亲本。
此类研究结果对种质资源圃的管理（包括种质分发）具有重要参考价值，同时可能会影响此前基于该库内这3类祖先种种质开展的相关研究结论。具体而言，若从该库获取用于育种、基因组学、遗传学及进化生物学研究的种质，其可能并不符合此前被标注的物种身份。