Genome-wide identification and analysis of the CNGC gene family in upland cotton under multiple stress conditions

Abstract Background The cyclic nucleotide-gated channel (CNGC) gene family plays a significant role in the uptake of both essential and toxic cations, and has a role in enhancing tolerance to various forms of abiotic stresses as well as the modulation of the heavy metal toxicity to plant through the absorption of heavy metals. Results A complete genome-wide identification and functional characterization of the cotton CNGC genes was carried out, in which 55, 28, and 29 CNGC genes were identified in Gossypium hirsutum, G. raimondii, and G. arboreum, respectively. The protein encoded by the CNGC genes exhibited GRAVY value below zero, indicating their hydrophilic property. CNGC genes were unevenly distributed in 19 out of 26 chromosomes, in which the highest density were observed on Ah05, with 8 genes. High gene coverage was observed among the diploid cotton species, with CNGC genes mapped on all A chromosomes and on 11 out of 13 of D chromosomes. The majority of CNGC proteins were localized in the endoplasmic reticulum, nucleus, and plasma membrane. Gene expression analysis revealed the up-regulation of Gh_A01G0520 (CNGC4) and Gh_D13G1974 (CNGC5) across various forms of abiotic stresses. Moreover, down-regulation of Gh_A01G0520 (CNGC4) and Gh_D13G1974 (CNGC5) in CNGC s silenced plants caused the significantly reduced ability to tolerate drought and salt stresses. All CNGCs silenced plants were recorded to have significantly low content of antioxidants but relatively higher content of oxidant, including MDA and H2O2. Furthermore, SPAD, CMS (cell membrane stability), ELWL (excised leaf water loss), SDW (shoot dry matter weight), and RDW (root dry matter weight) were all lower in CNGCs silenced plants compared with the wild type plants. Conclusion Significant reduction in antioxidant content and negative effects of physiological and morphological characters in CNGCs silenced plants has revealed the novel role of CNGC genes in enhancing cell integrity under abiotic stress conditions. These results provide vital information that will expand our understanding of the CNGC gene family in cotton and other plants, thus promoting the integration of these genes in the development of the environmental resilient plants.