Expression changes of miRNA-regulated genes associated with the formation of the leafy head in cabbage

Abstract

The vegetative development of cabbage (Brassica oleracea var. capitata) passes through seedling, rosette, folding and heading stages. Leaves that form the rosette are large and mostly flat. In the following developmental stages, the plants produce leaves that curve inward to produce the leafy head. Many microRNAs and their target genes have been described participating in leaf development and leaf curvature. The aim of this study is to investigate the role of miRNA-regulated genes in the transition from the rosette to the heading stage. We compared the miRNA and gene abundances between emerging rosette and heading leaves. To remove transcripts (miRNAs and genes) whose regulation was most likely associated with plant age rather than the change from rosette to heading stage, we utilized a non-heading collard green (B. oleracea var. acephala) morphotype as control. This resulted in 33 DEMs and 1 998 DEGs with likely roles in the transition from rosette to heading stage in cabbage. Among these 1 998 DEGs, we found enriched GO terms related to DNA-binding transcription factor activity, transcription regulator activity, iron ion binding, and photosynthesis. We predicted the target genes of these 33 DEMs and focused on the subset that was differentially expressed (1 998 DEGs) between rosette and heading stage leaves to construct miRNA-target gene interaction networks. Our main finding is a role for miR396b-5p targeting two Arabidopsis thaliana orthologues of GROWTH REGULATING FACTORs 3 (GRF3) and 4 (GRF4) in pointed cabbage head formation.

Keywords

• Brassica oleracea var. capitata
• RNA sequencing
• miRNA-target gene network
• leafy head formation