Insight between the epigenetics and transcription responding of cotton hypocotyl cellular elongation under salt-alkaline stress

Authors: RUI, CUN - Chinese Academy Of Agricultural Sciences; ZHANG, YUEXIN - Chinese Academy Of Agricultural Sciences; FAN, YAPENG - Chinese Academy Of Agricultural Sciences; HAN, MINGGE - Chinese Academy Of Agricultural Sciences; DAI, MAOHUA - Chinese Academy Of Agricultural Sciences; WANG, QINQIN - Chinese Academy Of Agricultural Sciences; CHEN, XIUGUI - Chinese Academy Of Agricultural Sciences; LU, XUKE - Chinese Academy Of Agricultural Sciences; WANG, DELONG - Chinese Academy Of Agricultural Sciences; WANG, SHUAI - Chinese Academy Of Agricultural Sciences; GAO, WENWEI - Xinjiang Agricultural University; Yu, John; YE, WUWEI - Chinese Academy Of Agricultural Sciences

Submitted to: Frontiers in Plant Science
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: 10/18/2021
Publication Date: 11/11/2021
Citation: Rui, C., Zhang, Y., Fan, Y., Han, M., Dai, M., Wang, Q., Chen, X., Lu, X., Wang, D., Wang, S., Gao, W., Yu, J., Ye, W. 2021. Insight between the epigenetics and transcription responding of cotton hypocotyl cellular elongation under salt-alkaline stress. Frontiers in Plant Science. 12. Article 772123. https://doi.org/10.3389/fpls.2021.772123.
DOI: https://doi.org/10.3389/fpls.2021.772123

Interpretive Summary: The growth of cotton plants is threatened by adverse stress such as alkaline toxicity in the soil. This abiotic stress causes a profound yield loss to cotton production in areas where farmland is environmentally contaminated. While high intracellular pH value is known to inhibit the cell extension of plant root hairs, the molecular mechanism of cotton tolerance to the stress remains elusive. In this study, we developed a cytosine methylome map of cotton hypocotyl and used it to investigate cotton response to methylation for regulating cell elongation under alkaline stress. Detailed analysis of DNA methylation and gene transcription reveals a regulatory mechanism of gene promoter methylation in response to alkaline stress during cotton hypocotyl elongation. Such methylation is found to regulate cell extension actively at the seed germination stage. Regulation of DNA methylation under stress environment is likely related to plant hormone signal transduction. The study provides new insight for plant biologists to understand and further study the regulation mechanism of plant abiotic stress response. Ultimately the information and resources obtained from the study will facilitate cotton breeders in developing tolerant cotton cultivars that can be grown under an adverse alkaline soil environment.

Technical Abstract: Gossypium barbadense is a cultivated cotton not only known for producing superior fiber but also for its salt and alkaline resistance. Here, we used Whole Genome Bisulfite Sequencing (WGBS) technology to map the cytosine methylation of the whole genome of the G. barbadense hypocotyl at single base resolution. We obtained 352,498,262, 386,850,350 and 462,494,704 reads from control check (CK), alkaline (Alk) and salt (Sal) stresses, respectively. The methylation sequencing results showed that the mapping rates of the three samples were 75.32%, 77.54%, and 77.94%, respectively. In addition, the Bisulfite Sequence (BS) conversion rate was 99.78%. Approximately 71.03%, 53.87%, and 6.26% methylation was identified at CG, CHG and CHH sequence contexts, respectively. A comprehensive analysis of DNA methylation and transcriptome data showed that the methylation level of the promoter region was correlated with the gene expression level. Saline-alkaline stress was related to the methylation changes of many genes, including transcription factors (TFs) and transposable elements (TEs). We explored the regulatory mechanism of DNA methylation in response to salt and alkaline stress during cotton hypocotyl elongation. Our data sheds light into the relationship of methylation regulation at the germination stage of G. barbadense hypocotyl cell elongation and salt-alkali stress, and between G. barbadense salt-alkaline tolerance and cell elongation. The results of this research helps us to understand the growth regulation mechanism of G. barbadense in response to abiotic stress.