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Background  The NAC (NAM, ATAF1/ATAF2, and CUC2) transcription factors belong to a large family of plant-specific transcription factors in monocot and dicot species. These transcription factors regulate the expression of stress tolerance-related genes that protect plants from various abiotic stresses, including drought, salinity, and low temperatures.    Results  In this study, we identified the  CaNAC46  transcription factor gene in  Capsicum annuum . Its open reading frame was revealed to comprise 921 bp, encoding a protein consisting of 306 amino acids, with an isoelectric point of 6.96. A phylogenetic analysis indicated that CaNAC46 belongs to the ATAF subfamily. The expression of  CaNAC46  was induced by heat, cold, high salt, drought, abscisic acid, salicylic acid, and methyl jasmonate treatments. Thus, CaNAC46 may be important for the resistance of dry pepper to abiotic stresses. A subcellular localization analysis confirmed that CaNAC46 is localized in the nucleus. The overexpression of  CaNAC46  improved the tolerance of transgenic  Arabidopsis thaliana  plants to drought and salt stresses. The  CaNAC46 -overexpressing lines had longer roots and more lateral roots than wild-type lines under prolonged drought and high salt stress conditions. Additionally, CaNAC46 affected the accumulation of reactive oxygen species (ROS). Moreover, CaNAC46 promoted the expression of  SOD ,  POD ,  RD29B ,  RD20 ,  LDB18 ,  ABI ,  IAA4 , and  P5CS . The malondialdehyde contents were higher in  TRV2-CaNAC46  lines than in wild-type plants in response to drought and salt stresses. Furthermore, the expression levels of stress-responsive genes, such as  ABA2 ,  P5CS ,  DREB ,  RD22 ,  CAT , and  POD , were down-regulated in  TRV2-CaNAC46  plants.    Conclusions  Under saline and drought conditions, CaNAC46 is a positive regulator that activates ROS-scavenging enzymes and enhances root formation. The results of our study indicate CaNAC46 is a transcriptional regulator responsible for salinity and drought tolerance and suggest the abiotic stress-related gene regulatory mechanisms controlling this NAC transcription factor are conserved between  A. thaliana  and pepper.    Supplementary Information  The online version contains supplementary material available at 10.1186/s12870-020-02764-y.

The NAC-type transcription factor CaNAC46 regulates the salt and drought tolerance of transgenic Arabidopsis thaliana