Comparative Transcriptome Sequencing of Cucumber Cultivars with Different Hypocotyl Length

Cucumber (Cucumis sativus L.; 2n = 2x = 14), which belongs to the Cucurbitaceae, is one of the agriculturally and economically important vegetable crops around the world. It's appropriate hypocotyl length is beneficial for establishing strong seedlings before transplanting. However, little knowledge is known about the molecular mechanism underlying hypocotyl elongation in the seedling traits. In our study, comparative analysis of hypocotyl transcriptome between long hypocotyl (B80) cultivar and short hypocotyl (JSH) cultivar would unravel novel genetic regulatory mechanisms involved in hypocotyl elongation. Using BGISEQ-500 platform, about 23.74 M reads per sample was averagely generated. The average mapping ratio with reference genome is 95.12% and the average mapping ratio with gene is 58.58%. A total of 20, 861 genes were detected, among them, 1089 differentially expressed genes (DEGs) were detected between the two samples including 646 up-regulated genes and 443 down-expressed genes and Kyoto Encyclopedia of Genes and Genomes (KEGG) analysis revealed that the main activated genes in hypocotyl development were predominately involved in metabolic processes, biosynthesis of secondary metabolite pathways, catalytic activity, binding protein and other cellular components. In addition, the majority of related transcription factors (TFs) such as MYB, MYB related genes, and AP2-EREBP were identified in transcriptome. Multiple candidate cucumber genes in the hypocotyl development related pathways were also discovered. In all, these results offer specific genotype-dependent genes for genetic research of hypocotyl elongation in cucumber.