Decoding drought resilience: a comprehensive exploration of the cotton Eceriferum (CER) gene family and its role in stress adaptation

Abstract Background The cuticular wax serves as a primary barrier that protects plants from environmental stresses. The Eceriferum (CER) gene family is associated with wax production and stress resistance. Results In a genome-wide identification study, a total of 52 members of the CER family were discovered in four Gossypium species: G. arboreum, G. barbadense, G. raimondii, and G. hirsutum. There were variations in the physicochemical characteristics of the Gossypium CER (GCER) proteins. Evolutionary analysis classified the identified GCERs into five groups, with purifying selection emerging as the primary evolutionary force. Gene structure analysis revealed that the number of conserved motifs ranged from 1 to 15, and the number of exons varied from 3 to 13. Closely related GCERs exhibited similar conserved motifs and gene structures. Analyses of chromosomal positions, selection pressure, and collinearity revealed numerous fragment duplications in the GCER genes. Additionally, nine putative ghr-miRNAs targeting seven G. hirsutum CER (GhCER) genes were identified. Among them, three miRNAs, including ghr-miR394, ghr-miR414d, and ghr-miR414f, targeted GhCER09A, representing the most targeted gene. The prediction of transcription factors (TFs) and the visualization of the regulatory TF network revealed interactions with GhCER genes involving ERF, MYB, Dof, bHLH, and bZIP. Analysis of cis-regulatory elements suggests potential associations between the CER gene family of cotton and responses to abiotic stress, light, and other biological processes. Enrichment analysis demonstrated a robust correlation between GhCER genes and pathways associated with cutin biosynthesis, fatty acid biosynthesis, wax production, and stress response. Localization analysis showed that most GCER proteins are localized in the plasma membrane. Transcriptome and quantitative reverse transcription-polymerase chain reaction (qRT-PCR) expression assessments demonstrated that several GhCER genes, including GhCER15D, GhCER04A, GhCER06A, and GhCER12D, exhibited elevated expression levels in response to water deficiency stress compared to control conditions. The functional identification through virus-induced gene silencing (VIGS) highlighted the pivotal role of the GhCER04A gene in enhancing drought resistance by promoting increased tissue water retention. Conclusions This investigation not only provides valuable evidence but also offers novel insights that contribute to a deeper understanding of the roles of GhCER genes in cotton, their role in adaptation to drought and other abiotic stress and their potential applications for cotton improvement.