2019 ASHS Annual Conference

A genotyping-by-sequencing (GBS) was conducted for diverse commercial F1 hybrid varieties to identify genome-wide single nucleotide polymorphisms(SNPs) in cucumber(Cucumis sativus L.). A total of 91 F1 varieties consisting 9 cultivar groups of Korean, China, Japan, and South Asia were selected for GBS. After reads filtering process, a total of 112,322 SNPs was identified and used for hierarchical clustering, principle component analysis, and population structure analysis of 91 F1 varieties. The results showed that varieties could be divided into 9 major clusters depending on their cultivar group. A subset of non-synonymous 192 SNPs that are evenly distributed in the genome and the polymorphic information content (PIC) values higher than 0.3 was selected for variety identification of 55 F1 hybrids consisting three major Korean cultivar groups(Baekdadagi-gae, Nakhap-gae, and Gasi-gae). The analysis of hierarchical clustering using the subset of 192 SNPs showed all 55 varieties could be distinguished from each other by their unique SNP genotypes. The SNP set developed in this study has potential for application to the SNP-based barcoding for variety identification, F1 seed purity test, and marker-assisted backcross not only in 91 varieties but in diverse resources for cucumber breeding.