Integrating WGCNA and PPI network to screen heat stress-responsive hub genes of Pinellia ternata

Abstract

Abstract Background Pinellia ternata (Thunb.) Breit. is a heat-sensitive herb. Heat damage can lead to leaf senescence and even death, but the impact on underground parts is not significant when the ambient temperature exceeds 30℃. P. ternata has a diversity of leaf types, however, the response strategies of different leaf types to high temperatures have not been thoroughly analyzed. This study aims to explore hub genes response to heat stress shared in two main leaf types of P. ternata based on integrated network analysis for improving planting measures. Results The ultrastructure, physiological indices, and photosynthetic fluorescence parameters were investigated, which indicated that the leaves of P. ternata were able to prevent the damage of photosynthetic structures, averted the accumulation of ROS, and sustained photosynthetic physiological responses under moderate heat stress. Serious heat stress activated the antioxidant enzyme activity systems to provide protective effects. However, the structure and function of chloroplasts in P. ternata leaves were adversely affected. By analyzing the transcriptome data, we obtained a total of 20,875 DEGs. Furthermore, weighted gene co-expression network analysis (WGCNA) was performed to explore the main modules related to heat stress, and 6,183 DEGs were obtained in five candidate modules. Among them, 1,000 DEGs could be annotated by the Uniprot and STRING databases, and a protein-protein interaction (PPI) network was constructed based on these DEGs. In this network, we identified 54 hub genes, and these genes were mainly related to thermal stimulation (HSPs, HSFs, and molecular chaperones) and photosynthesis (Photosystem I chlorophyll a/b-binding protein, Chlorophyll a-b binding protein et al.). Conclusion The response mechanisms to high-temperature treatment of two leaf types of P. ternata were analyzed at physiological, subcellular, and molecular levels. The results indicate that these two germplasms shared a common strategy in response to heat stress, and hub genes obtained provide valuable genetic resources for molecular resistance breeding in P. ternata.