Genome-wide identification and expression analysis of the CeARF gene family in tigernut (Cyperus esculentus L.)

Auxin response factors (ARFs) function as central transcriptional regulators within the auxin signal cascade and coordinate diverse developmental and stress-responsive processes. This study conducted a genome-wide survey of the CeARF gene family in tigernut (Cyperus esculentus L.), integrating identification of family members with analyses of physicochemical properties, subcellular localization, phylogenetic relationships, gene structures, conserved motifs, and cis-acting element prediction. Seedlings were subjected to salt stress, and transcript levels were quantified through fluorescence-based assays. Analysis of physicochemical properties indicated that CeARF proteins were subcellularly localized in the nucleus. Phylogenetic analysis revealed that CeARF proteins were distributed in three subfamilies. Conserved domain assessment showed that all 14 CeARF proteins contained B3 and Auxin_resp domains, and most also contained Aux/IAA domains. Genomic mapping indicated a dispersed distribution of the 14 CeARF genes rather than placement across all 12 chromosomes. Gene structure analysis showed intron-containing architectures with clear variation in intron number among genes. Further analysis revealed that the 14 CeARF genes contained five classes of endogenous hormone-responsive elements. Salt stress experiments demonstrated consistent down-regulation of five ARF genes across examined tissues.