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Cucumbers are an important economic vegetable crop that is used for fresh or processing purposes worldwide. In this study, we used 264 accessions that consisted of world-wide wild germplasms and advanced breeding lines in order to understand the genetic diversity and the genetic correlation among the germplasm collection. A genotyping-by-sequencing (GBS) approach was applied to obtain dense genome-wide markers coverage (&gt;12,082 SNPs) to construct a high-density haplotype map. Various population stratification methods were performed, and three subgroups were divided based on the genetic diversity, which reflected their geographic regions. According to the phylogenetic analysis, the breeding lines were separated from wild germplasms, and the two distinct groups were divided within the breeding lines. One of the groups mainly consisted of East-Asian varieties, which showed the unique homogenous genotype patterns. Using this germplasm collection, three important horticultural traits of cucumbers—powdery mildew resistance, spine color, and fruit stalk-end color—were evaluated and used to conduct the genome-wide association study (GWAS). All of the significant SNPs and two novel candidate genes (Csa5G453160 and Csa5G471070) for the powdery mildew were identified in chromosome 5 from the natural population, which is where reported major QTLs from various bi-parental population are located. Furthermore, two candidate genes, Csa1G006300 and Csa3G824850, and four candidate genes, Csa2G368270, Csa3G236570, Csa5G175680, and Csa6G448170, were identified for the spine color and the fruit stalk-end color, respectively. These results are expected to be helpful to develop molecular markers of the horticultural traits in cucumbers.

agronomy

Assessment of the Genetic Diversity of the Breeding Lines and a Genome Wide Association Study of Three Horticultural Traits Using Worldwide Cucumber (Cucumis spp.) Germplasm Collection