The USDA cucumber (Cucumis sativus L.) collection: genetic diversity, population structure, genome-wide association studies and core collection development

Authors: WANG, X - Cornell University; BAO, K - Cornell University; REDDY, UMESH - West Virginia State University; BAI, Y - Cornell University; HAMMAR, S - Michigan State University; JIAO, C - Cornell University; WEHNER, T - North Carolina State University; MADERA, A - University Of Wisconsin; Weng, Yiqun; GRUMET, R - Michigan State University; FEI, Z - Cornell University

Submitted to: Horticulture Research
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: 8/8/2018
Publication Date: 10/1/2018
Citation: Wang, X., Bao, K., Reddy, U.K., Bai, Y., Hammar, S.A., Jiao, C., Wehner, T.C., Madera, A.R., Weng, Y., Grumet, R., Fei, Z.J. 2018. The USDA cucumber (Cucumis sativus L.) collection: genetic diversity, population structure, genome-wide association studies and core collection development. Horticulture Research. 5(64):1-13. https://doi.org/10.1038/s41438-018-0080-8.
DOI: https://doi.org/10.1038/s41438-018-0080-8

Interpretive Summary: Germplasm collection is a crucial resource to conserve natural genetic diversity and provide a source of novel traits essential for sustained crop improvement. Optimal collection, preservation and utilization of these materials depends upon knowledge of the genetic variation present within the collection. In this study, we use the high throughput genotyping by sequencing technology to characterize 1234 cucumber lines in the United States National Plant Germplasm System collection. Over 23000 high quality molecular markers (SNPs) were identified, which were used to study the genetic diversity, population structure, phylogenetic relationships of the NPGS cucumber collection. These results complement NPGS descriptive information regarding geographic origin and phenotypic characterization of these lines. We identified genome regions significantly associated with thirteen horticulturally important traits including disease resistances and fruit quality traits. A molecularly informed, publicly accessible core collection of 395 accessions was developed, which represents more than 96% of the genetic variation presented in the NPGS. Work from this project gains insight into the diversity present and genetic relationships among accessions within the collection, which provides a valuable resource for cucumber breeders, geneticists in genetic analysis, gene discovery, crop improvement and germplasm preservation, which will eventually benefit cucumber growers and the industry.

Technical Abstract: Germplasm collections are a crucial resource to conserve natural genetic diversity and provide a source of novel traits essential for sustained crop improvement. Optimal collection, preservation and utilization of these materials depends upon knowledge of the genetic variation present within the collection. Here we use the high throughput genotyping-by-sequencing (GBS) technology to characterize the United States National Plant Germplasm System (NPGS) collection of cucumber (Cucumis sativus L.). The GBS data, derived from 1,234 cucumber accessions, provided more than 23K high quality single nucleotide polymorphisms (SNPs) that are well distributed at high density in the genome (~1 SNP/10.6 kb). The SNP markers were used to characterize genetic diversity, population structure, phylogenetic relationships, linkage disequilibrium, and population differentiation of the NPGS cucumber collection. These results, providing detailed genetic analysis of the U.S. cucumber collection, complement NPGS descriptive information regarding geographic origin and phenotypic characterization. We also identified genome regions significantly associated with thirteen horticulturally important traits through genome-wide association studies (GWAS). Finally, we developed a molecularly-informed, publicly accessible core collection of 395 accessions that represents at least 96% of the genetic variation present in the NPGS. Collectively, the information obtained from the GBS data enabled deep insight into the diversity present and genetic relationships among accessions within the collection, and will provide a valuable resource for genetic analysis, gene discovery, crop improvement and germplasm preservation.