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Background  Glyceollins are isoflavonoid-derived pathogen-inducible defense metabolites (phytoalexins) from soybean ( Glycine max  L. Merr) that have important roles in providing defense against pathogens. They also have impressive anticancer and neuroprotective activities in mammals. Despite their potential usefulness as therapeutics, glyceollins are not economical to synthesize and are biosynthesized only transiently and in low amounts in response to specific stresses. Engineering the regulation of glyceollin biosynthesis may be a promising approach to enhance their bioproduction, yet the transcription factors (TFs) that regulate their biosynthesis have remained elusive. To address this, we first aimed to identify novel abiotic stresses that enhance or suppress the elicitation of glyceollins and then used a comparative transcriptomics approach to search for TF gene candidates that may positively regulate glyceollin biosynthesis.    Results  Acidity stress (pH 3.0 medium) and dehydration exerted prolonged (week-long) inductive or suppressive effects on glyceollin biosynthesis, respectively. RNA-seq found that all known biosynthetic genes were oppositely regulated by acidity stress and dehydration, but known isoflavonoid TFs were not. Systemic acquired resistance (SAR) genes were highly enriched in the geneset. We chose to functionally characterize the NAC (NAM/ATAF1/2/CUC2)-family TF  GmNAC42–1  that was annotated as an SAR gene and a homolog of the  Arabidopsis thaliana  (Arabidopsis) indole alkaloid phytoalexin regulator  ANAC042 . Overexpressing and silencing  GmNAC42–1  in elicited soybean hairy roots dramatically enhanced and suppressed the amounts of glyceollin metabolites and biosynthesis gene mRNAs, respectively. Yet, overexpressing  GmNAC42–1  in non-elicited hairy roots failed to stimulate the expressions of all biosynthesis genes. Thus,  GmNAC42–1  was necessary but not sufficient to activate all biosynthesis genes on its own, suggesting an important role in the glyceollin gene regulatory network (GRN). The GmNAC42–1 protein directly bound the promoters of biosynthesis genes  IFS2  and  G4DT  in the yeast one-hybrid (Y1H) system.    Conclusions  Acidity stress is a novel elicitor and dehydration is a suppressor of glyceollin biosynthesis. The TF gene  GmNAC42–1  is an essential positive regulator of glyceollin biosynthesis. Overexpressing  GmNAC42–1  in hairy roots can be used to increase glyceollin yields > 10-fold upon elicitation. Thus, manipulating the expressions of glyceollin TFs is an effective strategy for enhancing the bioproduction of glyceollins in soybean.    Electronic supplementary material  The online version of this article (10.1186/s12864-019-5524-5) contains supplementary material, which is available to authorized users.

The NAC family transcription factor GmNAC42–1 regulates biosynthesis of the anticancer and neuroprotective glyceollins in soybean