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Genome-wide analysis of chloride channel-encoding gene family members and identification of CLC genes that respond to Cl−/salt stress in upland cotton

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Abstract

Chloride channels (CLCs) are kinds of anion transport protein family members that are mainly distributed in cell endomembrane systems of prokaryotic and eukaryotic organisms and mediate anion (Cl−, as a representative) transport and homeostasis. Some CLC genes have been reported to be involved in Cl−/salt tolerance of plants exposed to NaCl stress. Through BLAST in cotton database, a total of 22 CLCs were identified in genomes A and D in upland cotton (Gossypium hirsutum L.), and except for GhCLC6 and GhCLC17, they formed highly similar homologous genes pairs. According to the prediction in PlantCARE database, many cis-acting elements related to abiotic stress responses, including ABREs, AREs, GT-1s, G-boxes, MYBs, MYCs, etc., were found in the promoters of GhCLCs. qRT-PCR revealed that most GhCLC gene expression was upregulated in the roots and leaves of cotton seedlings under salt stress, and those of homologous GhCLC4/15, GhCLC5/16, and GhCLC7/18 displayed more obvious expression. Furthermore, according to leaf virus-induced gene silencing (VIGS) assay and compared with the salt-stressed GhCLC4/15- and GhCLC7/18-silenced cotton plants, the salt-stressed GhCLC5/16-silenced plants displayed relatively better growth with significant increases in both Cl− content and Cl−/NO3− ratio in the roots and drop of the same parameters in the leaves. These results indicate that homologous GhCLC5/16, with the highest NaCl−induced upregulation of expression and the maximum number of MYC cis-acting elements, might be the key members contributing to cotton Cl−/salt tolerance by regulating the transport, interaction and homeostasis of Cl− and NO3−.

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Acknowledgements

This work was supported by the National Natural Science Foundation of China (31671604), and Postgraduate Research & Practice Innovation Program of Jiangsu Province (KYCX19_0614).

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Authors and Affiliations

  1. Lab of Plant Stress Biology, College of Life Sciences, Nanjing Agricultural University, Nanjing, China

    Xun Liu, Boyi Pi, Jianwei Pu, Cong Cheng, Jiajia Fang & Bingjun Yu

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  1. Xun Liu
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  2. Boyi Pi
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  3. Jianwei Pu
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  4. Cong Cheng
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  5. Jiajia Fang
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  6. Bingjun Yu
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Contributions

BY and XL conceived and designed experiments; XL, BP and JP performed the experiments; XL, BP, CC and JF analysed the data; XL and BY wrote the manuscript. All authors read and approved the manuscript.

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Correspondence to Bingjun Yu.

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Liu, X., Pi, B., Pu, J. et al. Genome-wide analysis of chloride channel-encoding gene family members and identification of CLC genes that respond to Cl−/salt stress in upland cotton. Mol Biol Rep 47, 9361–9371 (2020). https://doi.org/10.1007/s11033-020-06023-z

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