Cotton transcriptome analysis reveals novel biological pathways that eliminate reactive oxygen species (ROS) under sodium bicarbonate (NaHCO3) alkaline stress

Authors: FAN, YAPENG - Chinese Academy Of Agricultural Sciences; LU, XUKE - Chinese Academy Of Agricultural Sciences; CHEN, XIUGUI - Chinese Academy Of Agricultural Sciences; WANG, JUNJUAN - Chinese Academy Of Agricultural Sciences; WANG, DELONG - Chinese Academy Of Agricultural Sciences; WANG, SHUAI - Chinese Academy Of Agricultural Sciences; GUO, LIXUE - Chinese Academy Of Agricultural Sciences; RUI, CUN - Chinese Academy Of Agricultural Sciences; ZHANG, YUEXIN - Chinese Academy Of Agricultural Sciences; CUI, RUIFENG - Chinese Academy Of Agricultural Sciences; WANG, QINQIN - Chinese Academy Of Agricultural Sciences; Yu, John; YE, WUWEI - Chinese Academy Of Agricultural Sciences

Submitted to: Genomics
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: 2/25/2021
Publication Date: 3/6/2021
Citation: Fan, Y., Lu, X., Chen, X., Wang, J., Wang, D., Wang, S., Guo, L., Rui, C., Zhang, Y., Cui, R., Wang, Q., Yu, J., Ye, W. 2021. Cotton transcriptome analysis reveals novel biological pathways that eliminate reactive oxygen species (ROS) under sodium bicarbonate (NaHCO3) alkaline stress. Genomics. 113(3):1157-1169. https://doi.org/10.1016/j.ygeno.2021.02.022.
DOI: https://doi.org/10.1016/j.ygeno.2021.02.022

Interpretive Summary: Alkaline toxicity presents a profound abiotic stress that threatens the growth of cotton plants. One of the primary toxic chemical compounds, called sodium bicarbonate, increasingly accumulates in contaminated farmland. Little is known about biological pathways and genetic factors of the cotton plants in response to the toxicity and tolerance mechanisms. The lack of information hinders the progress of plant breeding for cotton cultivars that can be grown in adverse soil environments. This study screened large numbers of differentially expressed genes (DEGs) through transcriptome analysis of cotton roots and leaves. Candidate genes and biological pathways were found for the first time known for cotton to tolerate the sodium bicarbonate toxicity. Regulation of secondary metabolites to eliminate the toxicity by the identified genes and pathways provides insights into how tolerant cotton plants cope with such abiotic stress. The new knowledge and resources are valuable for cotton breeders to develop elite cotton cultivars tolerant to this alkaline stress. They are also useful for plant biologists to further study the mechanisms of plant abiotic stress response.

Technical Abstract: Alkaline stress is one of the abiotic threats to cotton production. Though RNA-Seq analyses have been conducted to investigate genome-wide gene expression in response to alkaline stress in plants, the response of sodium bicarbonate (NaHCO3) stress-related genes in cotton has not been reported. To explore the mechanisms of cotton response to this alkaline stress, we used next-generation sequencing (NGS) technology to study transcriptional changes of cotton under NaHCO3 alkaline stress. A total of 18,230 and 11,177 differentially expressed genes (DEGs) were identified in cotton roots and leaves, respectively. Gene ontology (GO) analysis indicated the enrichment of DEGs involved in various stimuli or stress responses. Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway analysis showed that DEGs associated with plant hormone signal transduction, amino acid biosynthesis, and biosynthesis of secondary metabolites were regulated in response to the NaHCO3 stress. We further analyzed genes enriched in secondary metabolic pathways and found that secondary metabolites were regulated to eliminate the reactive oxygen species (ROS) and improve the cotton tolerance to the NaHCO3 stress. In this study, we learned that the toxic effect of NaHCO3 was more profound than that of NaOH at the same pH. Thus, Na+, HCO3- and pH had a great impact on the growth of cotton plant. The novel biological pathways and associated candidate genes for cotton tolerance to NaHCO3 stress identified from the study would be useful in the genetic improvement of the alkaline tolerance in cotton.