Genome-wide identification and expression analysis of the CLC gene family in blueberry (Vaccinium corymbosum) under salt stress

Objective CLC proteins play pivotal roles in plant responses to salt stress; however, the salt stress expression patterns and molecular regulatory networks of the CLC family in blueberry (Accinium corymbosum) remain largely unknown. This study performed a genome-wide identification of the blueberry CLC gene family and systematically analyzed their expression profiles under salt stress, aiming to lay a foundation for elucidating the molecular mechanisms by which CLCs mediate Cl^– homeostasis and regulate salt tolerance in blueberry.

Method Bioinformatics methods were used to analyze the physicochemical properties, gene structures, conserved motifs, scaffold locations, collinearity relationships, cis-acting elements in promoter regions, and phylogenetic relationships in VcCLCs family. Differentially expressed genes were screened based on transcriptome data, and RT-qPCR was used to analyze the expression patterns under salt stress.

Result (1) 19 genes encoding CLC family members were identified from the genomic data and unevenly distributed across 12 scaffolds. Phylogenetic analysis classified them into four subfamilies, with significant variations in gene structure and conserved motif composition among the members of different subfamilies. (2) Analysis of promoter cis-acting elements and upstream transcription factor prediction revealed that VcCLCs promoters contain multiple regulatory elements related to growth and development, phytohormones, and stress responses. Their expression is likely regulated by transcription factors such as ERF, NAC, and WRKY. (3) Based on the salt-stress transcriptome analysis of roots from the salt-tolerant cultivar ‘Duke’ and the salt-sensitive cultivar ‘Sweetheart’, three common differentially expressed genes were identified and designated as VcCLCc1, VcCLCc2, and VcCLCf2. RT-qPCR results demonstrated that these three genes were significantly upregulated in ‘Duke’ roots under salt stress but were notably downregulated in ‘Sweetheart’ roots, indicating their potential involvement in blueberry salt-stress responses.

Conclusion This study elucidates the core characteristics of the CLC gene family in blueberry and identifies key genes responsive to salt stress, providing candidate genes and a theoretical foundation for understanding the molecular mechanisms of Cl^– homeostasis maintenance under salt stress.