Genome-wide analysis of NAC transcription factors in grain amaranth reveals structural diversity and regulatory features

Grain amaranth (Amaranthus hypochondriacus) is a climate-resilient pseudo-cereal with high nutritional value and stress tolerance. NAC transcription factors (TFs) are key regulators in plant development and environmental responses. Here, we performed a comprehensive genome-wide analysis of 70 NAC genes (AhypNACs), classified into 24 phylogenetic subfamilies. Gene structure analysis showed exon variation (1-7), and chromosomal mapping revealed uneven distribution, with 32 segmental, 5 tandem, and 32 transposed duplications. Promoter analysis identified diverse cis-regulatory elements linked to light, hormone signaling, and stress response. miRNA analysis suggested Ahyp-miR164a targets four NAC genes, indicating post-transcriptional control. Comparative genomics showed both conserved and lineage-specific expansions among Oryza sativa, Beta vulgaris, Arabidopsis thaliana, and Chenopodium quinoa. Transcriptome analysis across seven tissues and five stress conditions identified several condition-specific and multi-stress-responsive NAC genes, with AhypNAC17, AhypNAC23, and AhypNAC24 showing strong induction. RT-qPCR validation under drought stress confirmed early and sustained upregulation of AhypNAC23 and AhypNAC24, and downregulation of AhypNAC03 and AhypNAC70, supporting their functional roles in drought adaptation. This study provides key insights into the structural diversity, evolutionary patterns, and stress-regulatory roles of NAC TFs in A. hypochondriacus, laying the foundation for genetic improvement of stress-resilient cultivars.