Mining of genes and pathways associated with endoplasmic reticulum stress in Brassica campestris via RNA-Seq

This study elucidates endoplasmic reticulum (ER) stress response mechanisms in Brassica campestris at the gene level using high-throughput transcriptome analysis. The productivity of Brassica campestris is severely limited by adverse environmental conditions that trigger ER stress and disrupt cellular homeostasis. However, the molecular mechanisms underlying ER stress responses in B. campestris remain poorly understood. In this study, tunicamycin (TM) and tauroursodeoxycholic acid (TUDCA; TU) were applied to induce and alleviate ER stress, respectively, followed by transcriptome profiling through high-throughput RNA sequencing. A total of 11,728 differentially expressed genes (DEGs) were identified across distinct pairwise comparisons. These DEGs were significantly enriched in GO terms related to oxidative stress response, protein processing in the ER, unfolded protein binding, and protein folding, as well as activated pathways associated with ROS signaling, calcium signaling, and flavonoid biosynthesis. Hierarchical clustering analysis grouped these DEGs into five clusters, of which C1 showed higher expression associated with TM and TU, C2 showed downregulation during ER stress, and C3 showed higher expression in TM treatment. Among DEGs, 351 transcription factors (TFs) were identified under ER stress, with the most abundant families being bZIP (57), NAC (83), MYB (113), HSF (26), and WRKY (72). Weighted gene co-expression network analysis (WGCNA) further identified three co-expression modules (green, brown, and turquoise) comprising 60 key genes, including four unique genes (BraC03g015140, BraC05g046930, BraC08g032210, and BraC09g046280), and 56 hub genes overlapping with DEGs. The identified 60 candidate genes are involved in protein quality control, chaperone activity, ubiquitin-mediated degradation, redox regulation, vesicle trafficking, and metabolic adjustment. Therefore, this study provides a comprehensive transcriptional landscape of ER stress responses in B. campestris, identifies key regulatory genes for functional validation, and offers valuable insights into improving stress resilience in Brassica crops.