Comprehensive analysis of NAC transcription factors and their expression during fruit spine development in cucumber (Cucumis sativus L.)

Abstract

The cucumber (<i>Cucumis sativus</i> L.) is an important vegetable crop worldwide, and fruit trichomes or spines are an important trait for external fruit quality. The mechanisms underlying spine formation are not well understood, but the plant-specific NAC family of transcription factors may play important roles in fruit spine initiation and development. In this study, we conducted a genome-wide survey and identified 91 <i>NAC</i> gene homologs in the cucumber genome. Clustering analysis classified these genes into six subfamilies; each contained a varying number of <i>NAC</i> family members with a similar intron-exon structure and conserved motifs. Quantitative real-time PCR analysis revealed tissue-specific expression patterns of these genes, including 10 and 12 that exhibited preferential expression in the stem and fruit, respectively. Thirteen of the 91 <i>NAC</i> genes showed higher expression in the wild-type plant than in its near-isogenic trichome mutant, suggesting their important roles in fruit spine development. Exogenous application of four plant hormones promoted spine formation and increased spine density on the cucumber fruits; several <i>NAC</i> genes showed differential expression over time in response to phytohormone treatments on cucumber fruit, implying their essential roles in fruit-trichome development. Among the <i>NAC</i> genes identified, 12 were found to be targets of 13 known cucumber micro-RNAs. Collectively, these findings provide a useful resource for further analysis of the interactions between <i>NAC</i> genes and genes underlying trichome organogenesis and development during fruit spine development in cucumber.