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

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.

FLOWERING LOCUS T Improves Cucumber Adaptation to Higher Latitudes

“…**, P , 0.01 (Student's t test). distribution of the three types of URs is consistent with genome-wide phylogenetic studies (Lv et al, 2012;Qi et al, 2013;Wang et al, 2018b) that distinguished Eurasian and East-Asian populations, indicating that CsFT UR variation associated with flowering time was one of the selective signatures during domestication of Eurasian and East-Asian cucumbers.…”

A fast, simple, high efficient and one-step generation of composite cucumber plants with transgenic roots by Agrobacterium rhizogenes-mediated transformation

“…Over the past decade, genomics sequencing of cucumber has been completed (Huang et al 2009). Furthermore, root-specific transcriptome, proteome, EST (expressed sequence tags), large scale cDNA sequencing studies, GWAS (genome-wide association studies) in cucumber have been completed and conducted (Du et al 2010;Li et al 2012;Ma et al 2018;Qi et al 2012;Wang et al 2018;Xu et al 2017;Yuan et al 2016;Zheng et al 2019). Efficient transformation methods are the prerequisite for the functional annotations of such numbers of candidate genes and assist the development and improvement of elite cucumber cultivars.…”

The major‐effect quantitative trait locus Fnl7.1 encodes a late embryogenesis abundant protein associated with fruit neck length in cucumber

“…Interestingly, we also found that five accessions from East Asian were assigned to group 1, and eight accessions from Eurasian were assigned to group 3. The exception was likely the result of cucumber germplasm exchange between the two geographical regions (Wang et al , ). Despite the low numbers of accessions included, we found that the Indian accessions had relative higher genetic and phenotypic diversity levels.…”