Comprehensive Genome-Wide Identification and Expression Analysis of the CCR4-Associated Factor 1 Gene Family in Common Bean (Phaseolus vulgaris L.) Under Abiotic Stresses

Abstract

CCR4-associated factor 1 (CAF1), a key component of the CCR4-NOT complex, plays a central role in transcriptional regulation and mRNA degradation in several plants. Despite its importance, no studies have yet explored the molecular phylogeny and expression patterns of the CAF1 gene in the stress response in common beans. Through genome-wide analysis, 27 PvCAF1 genes were identified, with gene sizes ranging from 108 to 618 amino acids and predicted molecular weights between 25.7 and 116.1 kDa. Phylogenetic analysis classified the PvCAF1 genes into four distinct groups, and their chromosomal distribution revealed that PvCAF1 genes were mostly located on chromosome 2, with 15 genes. Gene structure analysis showed that 74% of the PvCAF1 genes were intronless, while others exhibited varied exon-intron arrangements. Gene duplication analysis identified nine duplication events, with Ka/Ks ratios indicating purifying selection. Synteny analysis showed that PvCAF1 genes have the highest homology with those in Solanum lycopersicum and Arabidopsis thaliana. Cis-regulatory elements (CREs) identified in the promoters of these genes revealed that growth and development regulatory elements, particularly light-responsive elements, were the most abundant (73.36%). Stress-responsive CREs such as drought inducibility (MYB) and low-temperature responsiveness (LTR) were also found. Protein-protein interaction analysis highlighted 32 key nodes with high interaction degrees. Expression analysis of PvCAF1 genes under different growth conditions, such as in the presence of drought (PEG), salinity (NaCl), ABA, and IAA, demonstrated the upregulation of PvCAF1 genes, indicating their involvement in response to stimuli. PvCAF1-22 and PvCAF1-23 showed the highest expression under PEG and NaCl treatments, peaking at 4.9-fold and 7.2-fold at 24 h, respectively. PvCAF1-27 responded most strongly to IAA and PEG, reaching 6.1-fold at 48 and 24 h. These findings support the importance of PvCAF1 in developing drought and salinity-tolerant bean varieties, enhancing crop productivity in changing environmental conditions.