Exploring the diversity and genetic structure of the U.S. National Cultivated Strawberry Collection

The cultivated strawberry (Fragaria ×ananassa) arose through a hybridization of two wild American octoploid strawberry species in a French garden in the 1750s. 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/).