Integrated Genomic and Functional Analyses Identify FaNAC6 as a Candidate Regulator of Drought and Salinity Responses in Strawberry (Fragaria × ananassa)

Abstract

NAC proteins are a large family of plant transcription factors that play a key role in growth, development and responses to abiotic stress (drought, salinity). Various genomic studies across several species have identified NAC genes with specific responses to cold, drought and salinity. This study conducts a comprehensive genomic and transcriptomic analysis of FaNAC genes in strawberry (Fragaria × ananassa) to elucidate their role in response to drought and salinity. Using RNA-seq and validation by RT-qPCR, thirty-five FaNAC genes were identified that showed differential expression under both stress conditions. Their expression profiles were highly specific to tissue and stimulus type: some were induced in leaves and roots under both conditions, whilst others showed restricted induction. This suggests a specialised regulatory network rather than a uniform response. Phylogenetically, the FaNAC genes showed high homology with Arabidopsis orthologues and conserved collinearity between subgenomes. The promoters contained cis elements associated with hormones and stress, particularly ABA and MeJA. FaNAC6 was selected for its strong induction in leaves and roots in response to drought and salinity, as well as under oxidative stress and ABA. Its overexpression in Nicotiana benthamiana increased stress tolerance, improving photosynthesis and water-use efficiency, and was associated with the upregulation of genes involved in photosystems, electron transport and carbon fixation. Overall, FaNAC6 emerges as a promising candidate for further evaluation in strawberry breeding strategies to improve drought and salinity resilience.