The cultivated strawberry (Fragaria ×ananassa) arose through a hybridization of two wild American octoploid strawberry species in a French garden in the 1750’s. Since then, breeders have developed improved cultivars adapted to different growing regions. Diverse germplasm is crucial to meet the challenges strawberry breeders will continue to address. The USDA-ARS National Clonal Germplasm Repository (NCGR) in Corvallis, Oregon maintains the U.S. strawberry collection. Recent developments in high-throughput genotyping for strawberry can provide new insights about the diversity and structure of the collection, germplasm management, and future breeding strategies. Genotyping was conducted on 539 F. ×ananassa accessions using either the iStraw35 or FanaSNP 50 K Axiom array. Data for markers shared by the two arrays were curated for call quality, missing data, and minor allele frequency resulting in 4033 markers for structure assessment, diversity analysis, pedigree confirmation, core collection development, and the identification of haplotypes associated with desirable traits. The F. ×ananassa collection was equally diverse across the different geographic regions represented. K-means clustering, sNMF, and UPGMA hierarchal clustering revealed seven to nine sub-populations associated with different geographic breeding centers. Two 100 accession core collections were created. Pedigree linkages within the collection were confirmed. Finally, accessions containing disease resistance-associated haplotypes for FaRCa1, FaRCg1, FaRMp1, and FaRPc2 were identified. These new core collections will allow breeders and researchers to more efficiently utilize the F. ×ananassa collection. The core collections and other accessions of interest can be requested for research from the USDA-ARS NCGR via the Germplasm Resources Information Network (https://www.ars-grin.gov/).

中文翻译：

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探索美国国家栽培草莓收藏的多样性和遗传结构

栽培草莓 (Fragaria ×ananassa) 是 1750 年代法国花园中两种野生美洲八倍体草莓品种的杂交产生的。从那时起，育种者开发了适应不同种植区域的改良品种。多样化的种质对于迎接草莓育种者将继续应对的挑战至关重要。位于俄勒冈州科瓦利斯的 USDA-ARS 国家克隆种质资源库 (NCGR) 维护着美国草莓的收藏。草莓高通量基因分型的最新进展可以为收集的多样性和结构、种质管理和未来育种策略提供新的见解。使用 iStraw35 或 FanaSNP 50 K Axiom 阵列对 539 个 F. ×ananassa 种质进行基因分型。两个阵列共享的标记数据针对通话质量进行了整理，缺失数据和次要等位基因频率导致 4033 个标记用于结构评估、多样性分析、谱系确认、核心收集开发以及与理想性状相关的单倍型鉴定。F. ×ananassa 的集合在所代表的不同地理区域中同样多样化。K-means 聚类、sNMF 和 UPGMA 层次聚类揭示了与不同地理育种中心相关的七到九个亚群。创建了两个 100 加入核心收藏。确认了收藏中的谱系联系。最后，鉴定了包含 FaRCa1、FaRCg1、FaRMp1 和 FaRPc2 的抗病相关单倍型的种质。这些新的核心馆藏将使育种者和研究人员能够更有效地利用 F. ×ananassa 馆藏。