Genome-wide identification of the CLC gene family in tomato (Solanum lycopersicum) and functional analysis of SlCLC8 in salt stress tolerance

•A total of eight SlCLC genes were identified in tomato genome version.•SlCLC genes can response to salt stress treatments.•The silencing of SlCLC8 gene reduced the salt tolerance of tomato. When plants under salt stress, the intracellular ion concentration and osmotic pressure increase, which inhibits normal growth, development and life processes, and even leads to plant wilting and death. CLC (chloride channel protein) is a kind of anion channel protein that widely exists in plant cell membrane or organelle membrane. CLC proteins participate in the transmembrane transport of anions and plays an active role in plant tolerance to salt stress. In this study, we analysed the response and function of tomato CLC family genes in salt stress tolerance. Bioinformatics analysis showed that the promoter of SlCLC gene contained the most cis-acting elements related to abiotic stress response. Transcriptome data analysis and quantitative reverse transcription-polymerase chain reaction (qRT-PCR) results showed that SlCLC8 may be the key gene for salt stress resistance in this family. After salt stress treatment, the SlCLC8-silenced tomato plants showed higher wilting and oxidative stress, and significantly reduced salt tolerance compared with the control plants. Therefore, SlCLC8 is a positive regulator of tomato salt tolerance. In summary, this study elucidated the evolutionary patterns and functional differences of the tomato CLC gene family, and deepened the understanding of the regulatory mechanisms of salt stress tolerance in plants.