Integrated transcriptomic and proteomic analyses provide insight into the global stress responses in two soybean cultivars differing in chilling tolerance. (PRJCA029648)

Soybean (Glycine max (L.) Merr.) is an important globally economical crop due to its high protein, oil content and nutritional value. Cold stress is one of the most critical abiotic factors limiting soybean growth and productivity. However, the molecular mechanisms of the cold stress in soybean remain insufficiently explored compared to those of other crops. This study investigates two soybean cultivars, HH43 and HX3, which exhibit significant differences in cold tolerance and originate from colder and warmer regions of China, respectively. Through comprehensive morphological, biochemical, transcriptomic, and proteomic analyses, we found that HX3 superior cold tolerance compared to HH43, exhibiting delayed wilting, higher relative water content, reduced oxidative damage, and greater antioxidant enzyme activities under chilling stress. A series of cold stress related transcription factors, such as CAMTA1, CAMTA2, WRKY33, WRKY40, ATAF1, ERF72, and bZIP29, along with their target genes, were identified as potential regulators of cold tolerance mechanisms in soybeans through WGCNA and GENIE3 network construction. We summarize the multi-complex pathways related to signal transduction, transcriptional regulation, and stress tolerance, ultimately leading to chilling tolerance difference between HH43 and HX3, including various hormonal pathways like jasmonic acid, abscisic acid, ethylene, salicylic acid and circadian clock, interacting with key transcription factors and modulating gene expression in response to stress. These findings provide important insights into breeding cold-tolerant soybean cultivars, offering strategies to improve soybean resilience in colder climates.