Genome-wide identification and expression pattern analysis of the chloride channel gene family in potato (Solanum tuberosum L.) under salt stress

TL;DR

This study identifies and analyzes chloride channel genes in potato and their role in responding to salt stress.

Contribution

The study provides the first comprehensive characterization of the potato chloride channel gene family under salt stress.

Findings

Seven StCLC genes were identified and classified into three clusters based on structure and phylogeny.

StCLC genes showed significant upregulation in roots under salt stress, indicating their role in salt tolerance.

Promoter analysis revealed 35 cis-acting elements linked to stress response and hormone regulation.

Abstract

Chloride channel (CLC) proteins are crucial anion channels that play a vital role in plant adaptation to abiotic stresses. Potato (Solanum tuberosum L.) is a major global staple crop; however, the CLC gene family in potato (StCLC) remains poorly characterized, and its specific functions in salt tolerance are unclear. This study aimed to systematically identify and characterize the StCLC gene family and analyze its expression patterns under salt stress.

Using bioinformatics methods based on the potato genome, transcriptome, and qRT-PCR data, we analyzed the protein structures, physicochemical properties, phylogenetic relationships, gene structures, conserved domains, chromosomal locations, collinearity, GO annotations, and promoter cis-acting elements of StCLC members.

Seven StCLC genes (StCLC1–7) were identified and unevenly distributed across four chromosomes. Based on protein structures and phylogenetic relationships with Arabidopsis thaliana CLCs, the seven StCLCs were classified into three clusters. Gene structure analysis revealed that StCLC genes contain 6–9 exons, and Motifs 6, 7, 8, and 9 were conserved across all seven StCLC proteins, suggesting their functional importance. Collinearity analysis indicated that the StCLC family has its own collinear genes and shares a close evolutionary relationship with the tomato (Solanum lycopersicum L) CLC family. GO annotation indicated that CLCs are primarily involved in chloride ion transport. Thirty-five cis-acting regulatory elements were identified in the promoter regions, predominantly associated with light response, abiotic stress, hormone regulation, and growth and development, implying potential roles in various physiological processes. RNA-seq data showed distinct expression patterns of StCLC genes across different tissues, indicating tissue-specific expression. Furthermore, qRT-PCR results demonstrated that under NaCl treatment, the expression levels of all seven StCLC genes, including StCLC3 and StCLC6, were significantly upregulated in roots, suggesting their active involvement in the response to salt stress.

These findings elucidate the structural, evolutionary, and functional diversity of the StCLC gene family and highlight its important role in salt stress response, thereby providing a theoretical foundation for the genetic improvement of salt tolerance in potato.

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