Non-heading Chinese cabbage (Brassica campestris (syn. Brassica rapa) ssp. chinensis) (NHCC) is an important vegetable crop with economic benefits and is widely cultivated worldwide. Heat stress disrupts intracellular homeostasis, resulting in significant growth inhibition of buds and roots, severe retardation of growth and development, and even death. However, there are relatively few studies on the molecular response mechanism of NHCC to heat stress. In this study, RNA sequencing (RNA-seq) technology was employed to investigate the transcriptome data of the heat-tolerant variety “SHI” and the heat-sensitive variety “aijiaohuang” (“AJH”) under high temperature. Differentially expressed genes (DEGs), including transcription factors (TFs), genes related to hormone synthesis, and genes related to protein processing in the endoplasmic reticulum, were identified in both varieties. The combination of multi-sample RNA-seq data and weighted gene co-expression network analysis (WGCNA) identified four key modules, namely the darkgreen module, the yellow module, the blue module, and the turquoise module, and core genes within them, including MYB-related, HSP20 and DBB etc., were mined. Our findings suggest that protein processing in the endoplasmic reticulum, photosynthesis, and plant hormone signaling are crucial for “SHI"’s response to heat stress and some candidate genes such as MYB-related, HSP20 and DBB were identified. We validated our results with qRT-PCR, reinforcing the reliability of our data. These insights deepen our understanding of the physiological and molecular bases of NHCC heat tolerance and identify key genes for further molecular investigation. The online version contains supplementary material available at 10.1186/s12870-025-07120-6.

Background: Auxin, a plant hormone, plays diverse roles in the modulation of plant growth and development. The transport and signal transduction of auxin are regulated by various factors involved in shaping plant morphology and responding to external environmental conditions. The auxin signal transduction is primarily governed by the following two gene families: the auxin response factor (ARF) and auxin/indole-3-acetic acid (AUX/IAA). However, a comprehensive genomic analysis involving the expression profiles, structures, and functional features of the ARF and AUX/IAA gene families in Vaccinium bracteatum has not been carried out to date. Results: Through the acquisition of genomic and expression data, coupled with an analysis using online tools, two gene family members were identified. This groundwork provides a distinguishing characterization of the chosen gene families in terms of expression, interaction, and response in the growth and development of plant fruits. In our genome-wide search of the VaARF and VaIAA genes in Vaccinium bracteatum, we identified 26 VaARF and 17 VaIAA genes. We analyzed the sequence and structural characteristics of these VaARF and VaIAA genes. We found that 26 VaARF and 17 VaIAA genes were divided into six subfamilies. Based on protein interaction predictions, VaIAA1 and VaIAA20 were designated core members of VaIAA gene families. Moreover, an analysis of expression patterns showed that 14 ARF genes and 12 IAA genes exhibited significantly varied expressions during fruit development. Conclusion: Two key genes, namely, VaIAA1 and VaIAA20, belonging to a gene family, play a potentially crucial role in fruit development through 26 VaARF-IAAs. This study provides a valuable reference for investigating the molecular mechanism of fruit development and lays the foundation for further research on Vaccinium bracteatum.