The fruit surface is an important tissue that serves many functions including protection from abiotic and biotic stresses which can impact fruit development, post-harvest quality and subsequent storage. Variation in fruit surface properties has been observed among species, cultivars, and developmental stages. Genetic factors driving this natural variation are not well characterized in cucumber (Cucumis sativus). Morphological changes in the fruit epidermal properties of two breeding lines of cucumber were quantified in fruits ranging in age from anthesis (0 days post-pollination (dpp)) to maturity (~30 dpp). Pickling type ‘Gy14’, and Chinese fresh market type Chinese Long ‘9930’ (CL9930) were chosen for this study based on epidermal properties differences and the availability of genomic resources. Thin sections from the mid-region of fruits were stained with red lipid stain Sudan IV and viewed using light microscopy. Measurements were taken for cuticle thickness and depth of cuticular intercalations between epidermal cells, epidermal cell height and width, and number and diameter of lipid droplets. These features increased in size coinciding with overall fruit growth, exhibiting rapid increase between 4 and 12 dpp and plateauing at ~16 dpp. Fruits from a genotyped Gy14xCL9930 recombinant inbred line (RIL) population were phenotyped at 16 dpp for epidermal traits for use in a quantitative trait loci (QTL) study. Strong QTL co-localized on chromosome 1 for epidermal cell height, cuticle thickness, intercalation depth, and diameter of lipid droplets. Fine mapping with SSR and KASP markers, transcriptomic analyses, and gene expression profiling identified transcription factor CsSHINE1/WIN1 as a source of natural variation for cucumber fruit epidermal traits. To explore additional sources of variation, a genome wide association study (GWAS) was done using the cucumber diversity panel, which varied greatly for cuticle thickness and lipid droplet number and size. GWAS identified several QTL that correspond with prior candidate genes for cuticle or lipid biosynthesis as well as suggesting new candidate genes of interest. Persistence of lipid droplets in number and size as fruits approached maturity indicated lipid droplets may have additional roles other than substrate transport for cuticular deposition. A protocol was devised to isolate and purify lipid droplets from cucumber fruit peel. Lipid droplets were analyzed using mass spectrometry and their contents shown to vary with genotype, developmental state, and environment.
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