Genome-wide analysis of cowpea NAC transcription factor family elucidating the genetic & molecular relationships that interface stress and growth regulatory signals

Abstract

Being a key transcriptional mediator of stress and growth responses, NAC transcription factors hold the paramount potential to develop climate-smart pulse crops. Despite their seminal role, they are yet unexplored in many important orphan legumes like cowpea. The recent availability of a comprehensive reference genome motivated us to investigate and assess the functional importance of the remarkable NAC family in cowpea for sustainable crop research. This study identified 130 NAC proteins in cowpea, namely VuNAC01-130, classified into 8 phylogenetic groups. 27 cowpea-specific members were clustered as a distinct clade with no close orthologs from other species, implicating novel functions. VuNAC proteins carried multipartite nuclear signals and unique transactivation regions with conserved patterns. 18 proteins were associated with non-NAC chimeric domains. The genes owned a unique promoter architecture encompassing pyrimidine-rich elements. The family manifested prominent segmental and tandem chromosomal duplication resulting in numerous stress-responsive members and large paralogous groups. The promoter and interactome analysis revealed multi-tier regulation through light, hormone, and transcription factors (NAC/MYB/WRKY/ERF and Dof/TCP), suggesting a cross-talk between stress and growth-regulating signals. Besides, the TFs were associated with metabolic processes such as trehalose and folate synthesis, carbohydrate transport, lipid signaling, and electron transfer. Comparatively, ATAF-like members (Group Ia) would be the most promising candidates to develop climate-smart crops with improved stress adaptation and agronomic traits by translational approach, due to their predicted functional versatility.