Identification and Characterization of Circadian Clock Genes and Their Transcriptional Responses to Aluminum Stress in Peanut (Arachis hypogaea L.)

The circadian clock is an endogenous timekeeping system that coordinates plant growth, development, metabolism, and responses to environmental stimuli. Although circadian regulation has been implicated in multiple abiotic stress responses, its potential involvement in aluminum (Al) stress adaptation in peanut (Arachis hypogaea L.) remains poorly understood. A genome-wide analysis was performed to identify and characterize circadian clock genes in peanut and investigate their transcriptional responses to Al stress. A total of 74 circadian clock genes from Arabidopsis thaliana were used as reference sequences to identify homologous genes in the peanut genome. A total of 71 encoding circadian clock proteins were identified and comprehensively characterized through analyses of chromosomal distribution, conserved domains, motif composition, transmembrane regions, subcellular localization, phylogenetic relationships, functional annotation, and protein interaction networks. Transcriptome data (RNA-seq accession PRJNA525247) from Al-sensitive ZH2 (Zhonghua 2) and Al-tolerant 99-1507 peanut cultivars were further analyzed to evaluate gene expression patterns under Al stress. The identified genes were unevenly distributed across all 20 peanut chromosomes and exhibited diverse structural features and predicted biological functions. Phylogenetic analysis demonstrated a high degree of evolutionary conservation between peanut and Arabidopsis circadian clock genes. Functional annotation indicated that many identified genes are associated with transcriptional regulation, light perception, signal transduction, phytohormone signaling, and stress-responsive pathways. Comparative transcriptome analysis revealed distinct expression profiles between the Al-sensitive and Al-tolerant cultivars, with several genes, including homologs of XAP5, PIF3, GIGANTEA (GI), FLOWERING LOCUS T (FT), and AGL15, displaying cultivar-dependent responses to Al treatment, where these were upregulated in ZH2 but downregulated in 99-1507. These findings provide the first comprehensive overview of the circadian clock genes in peanut and suggest that circadian regulatory pathways may contribute to transcriptional responses associated with Al stress adaptation. This study establishes a valuable genomic resource for future functional characterization of circadian clock genes and supports molecular breeding efforts for rhythmic traits for Al tolerance in cultivated peanuts.