Cucumber (Cucumis sativus L.) fruit has characteristic taste and aroma, the important organoleptic qualities influencing consumer preference and marketability. Profiling of metabolites conferring bitterness and aroma is required to improve cucumber fruit quality and produce preferred fruit. In this study, we profiled cucurbitacins responsible for bitterness and volatile compounds using fruit of 69 cucumber genotypes with different fruit shape, color, and origin and provided qualitative and quantitative information of metabolites involved in the organoleptic quality. Among six types of cucurbitacis (CuA-E, I), only CuC was detected in six inbreds while most genotypes didn’t contain them. It means bitterness has been lost in modern cucumber cultivars with domestication process. The 69 genotypes were classified into four clusters according to the profiles of cucurbitacins and volatile compounds. Clusters 2 and 3 accumulated the highest and lowest volatile contents, respectively. Clusters 1 and 4 were discriminated by minor volatiles rather than major ones, suggesting they have distinct background flavor. Clusters 1 and 4 also showed different phenotypes such as length and color, implying a relationship between fruit phenotype and background flavor. However, the clustering was inconsistent with cultivar types or origins. It suggests independent domestication for bitterness and flavor has been conducted for cultivars in different origins. We further examined hybridization effect on metabolite compositions using 15 F1 hybrids from selected inbreds. Total volatile compound (TVC) content was reduced in the F1 hybrids, especially due to decrease in total alcohol content affecting increase in ratio of aldehyde to TVC. These findings will contribute to improvements of cucumber organoleptic qualities and will provide useful information for selecting cucumber materials to produce preferred fruit.
