Browse Articles

Article|01 Oct 2018|OPEN
The USDA cucumber (Cucumis sativus L.) collection: genetic diversity, population structure, genome-wide association studies, and core collection development
Xin Wang1 , Kan Bao1 , Umesh K. Reddy2 , Yang Bai1 , Sue A. Hammar3 , Chen Jiao1 , Todd C. Wehner4 , Axel O. Ramírez-Madera5 , Yiqun Weng5,6 and Rebecca Grumet3 , , Zhangjun Fei,1,7 ,
1Boyce Thompson Institute, Cornell University, Ithaca, NY 14853, USA
2Gus R. Douglass Institute and Department of Biology, West Virginia State University, Institute, Virginia, WV 25112, USA
3Department of Horticulture, Michigan State University, East Lansing, MI 48824, USA
4Horticultural Science Department, North Carolina State University, Raleigh, NC 27695, USA
5Horticulture Department, University of Wisconsin, Madison, WI 53706, USA
6USDA-ARS Vegetable Crops Research Unit, Madison, WI 53706, USA
7USDA-ARS Robert W. Holley Center for Agriculture and Health, Ithaca, NY 14853, USA
*Corresponding author. E-mail: grumet@msu.edu,zf25@cornell.edu

Horticulture Research 5,
Article number: 64 (2018)
doi: https://doi.org/10.1038/s41438-018-0080-8
Views: 963

Received: 05 Jun 2018
Revised: 07 Aug 2018
Accepted: 08 Aug 2018
Published online: 01 Oct 2018

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 1234 cucumber accessions, provided more than 23 K 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 13 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 analyses, gene discovery, crop improvement, and germplasm preservation.