Multi-omics reveal the regulation mechanism in response to freezing tolerance in Dendrobium catenatum

Main conclusion Freezing-tolerant Dendrobium catenatum cultivar responds to freezing stress by activating antioxidant enzyme systems and non-enzymatic systems including AsA and flavonoid biosynthetic pathways. Dendrobium catenatum (also named Dendrobium officinale) is a rare traditional Chinese medicinal plant, and has developed into 10 billion-grade industry by artificial breeding. Freezing stress is a devastating abiotic stress that hinders the growth and yield of D. catenatum. However, the cold response molecular mechanisms of D. catenatum are nearly unknown. Here, multi-omics including metabolomics, transcriptomics, and proteomics analyses were conducted under − 9 °C freezing stress using two varieties of D. catenatum, namely freezing-tolerant Jingpin Tianmushan (TMS) and freezing-sensitive Jingpin 6A2B (6A2B). TMS had significantly high levels of antioxidant enzymes including CAT, SOD, APX, and MDHAR, as well as high contents of the metabolites including quercetin, rutin, galacturonic acid, and ascorbic acid (AsA), compared to 6A2B. Rutin and AsA contents were positively related to the expression levels of the hub genes, including Dc4CL4/DcF3’H3 and DcGalUR1/DcGalUR2/DcGGP2/DcL-GalDH, which associate with freezing-responsive regulators comprising AP2/ERF, ARF, bHLH, bZIP, MYB, and ZF-HD members by co-expression network analysis. These results provide insights into the underlying freezing-tolerant molecular mechanism and promote freezing-resistant breeding of D. catenatum.