Univariate and multivariate QTL analyses provide insights into genetic architecture of variation of key volatile aroma compounds in cucumber (Cucumis sativus L.)

Key message Univariate and multivariate (PC-based) QTL analyses in multiple segregating populations and environments identify 284 QTL and 52 PC-QTL for 24 volatile aroma compounds in cucumber, including two environmentally stable QTL clusters, each harboring 26 and 25 QTL for major C 6 /C 9 alcohols and aldehydes, respectively. Abstract Consumers enjoy cucumber for its refreshing sensation, which is primarily associated with volatile organic compounds (VOCs) produced by the lipoxygenase biosynthesis pathway. However, our knowledge of cucumber flavor genetics remains limited. Here, we report QTL mapping of VOCs in multiple segregating populations grown under greenhouse and open-field conditions. VOC abundance exhibited highly quantitative inheritance with strong environmental effects and low broad‐sense heritability. Transgressive segregation and underdominance were observed for most VOCs. Univariate QTL analysis identified 284 QTL for 24 VOCs, averaging 17 QTL for the six most abundant and aromatically significant VOCs. Both additive and dominance effects contributed significantly to VOC variation. Consistent with the strong correlation among many VOCs, 154 of the 284 QTL were co-localized into 15 distinct clusters. Multivariate principal component (PC)-based QTL analysis identified 52 PC-QTL that captured the maximum covariances among VOCs. Results from both methods were highly congruent, including the identification of two population-independent and environmentally stable QTL clusters, each harboring 26 and 25 QTL for major C 6 /C 9 alcohols and aldehydes, respectively. The cos 2 and loading patterns of PCs mapped to these QTL clusters suggested closely linked loci rather than pleiotropic effects. Analysis of sequence variation and expression of annotated genes inside the two clusters identified several transcription factor genes as potential candidates. This study reveals a complex genetic architecture of VOC variation in cucumber. We discuss the results in the context of allele effects, segregation distortion, the association between QTL clustering and the LOX pathway, and implications for cucumber breeding for flavor enhancement.