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

Huiling Gong^1*Hang Wang¹Jie Chen¹Leonce Dusengemungu²Zaiping Feng¹

• ¹School of Life Sciences and Engineering, Lanzhou University of Technology, Lanzhou, China
• ²Agriculture and Animal Resources Development Board, Rwanda Development Board, Kigali, Rwanda

Chloride channel (CLC) proteins are a class of important anion channel proteins in organisms and play a crucial role in plant adaptation to abiotic stresses. They are particularly significant in salt tolerance mechanisms: CLC proteins can regulate the selective uptake of ions, fine-tune stress signaling cascades, and alleviate salt stress-induced physiological damage by supporting osmoregulation. Despite the global importance of potato (Solanum tuberosum L.) as a staple crop, the CLC gene family in this species remains underexplored. This study aimed to systematically identify and characterize the potato CLC (StCLC) gene family and analyze its expression patterns in response to salt stress. Using bioinformatics approaches, seven StCLC genes were identified and designated as StCLC1–7 based on their chromosomal locations. These seven genes were unevenly distributed on four chromosomes. The seven StCLCs were classified into three clusters based on their protein structures and phylogenetic relationships with Arabidopsis thaliana.The StCLCs consisted of six to nine exons, and Motifs 6, 7, 8, and 9 were distributed among the seven StCLC members.The potato StCLC family has collinear genes of its own and may share a common ancestor with tomato (Solanum lycopersicum L).Thirty-five cis-acting regulatory elements were identified, which are mainly associated with light response, abiotic stress, hormones and growth and development. RNA-seq data indicated different expression patterns of StCLCs genes in different tissues. In addition, the results of Quantitative real-time PCR (qRT-PCR) showed that under NaCl treatment, the expression levels of 7 genes including StCLC3 and StCLC6 were significantly upregulated in roots. These findings elucidate the structural diversity, evolutionary characteristics, and functional diversity of the StCLC gene family, as well as the important role of StCLC genes in responding to salt stress, thereby providing a theoretical basis for the genetic improvement of salt tolerance in potatoes.