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

Abstract

Abstract 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.