Genome-wide characterization and temperature-responsive expression profiling of the NF-X1-type zinc-finger gene family in upland cotton

NF-X1-type Zinc finger (ZF) proteins are important regulatory factors involved in transcriptional control and stress-responsive signaling in plants. However, their evolutionary features and potential functions in upland cotton ( Gossypium hirsutum L.) remain largely unclear. In this study, we systematically interrogated genome-wide identification and comprehensive characterization of NF-X1-type ZF genes in G. hirsutum using integrated bioinformatic and transcriptomic analyses. Four NF-X1-type ZF genes were identified and found to be distributed across the A and D sub-genomes. Phylogenetic analysis showed that these proteins are closely related to homologs from dicotyledonous species, especially those in the Malvaceae lineage, suggesting strong evolutionary conservation. The identified proteins were predicted to be large, hydrophilic, and alkaline, with conserved motifs, domains, and exon-intron structures between homologous gene pairs. Promoter study demonstrated multiple cis-acting elements linked with hormonal signaling, light responses, and regulation of abiotic stresses. Structural prediction indicated conserved conformations dominated by random coil regions, and model validation supported their reliability. Transcriptomic analysis showed tissue-specific and stress-responsive expression patterns, with GhChrA09G0713 and GhChrD09G0661 showing relatively higher expression across multiple tissues and stress treatments. Notably, qRT-PCR validation demonstrated that GhChrA09G0713 and GhChrD09G0661 were significantly induced by both heat (42 °C) and cold (4 °C) stress, although with distinct temporal expression profiles. GhChrA09G0713 exhibited sustained upregulation under both temperature treatments, whereas GhChrD09G0661 showed a rapid response to heat stress and stronger induction during prolonged cold exposure. Overall, this study provides a comprehensive overview of NF-X1-type ZF genes in cotton and offers a basis for future functional dissection of their roles in developmental programs and environmental stress tolerance.