Transcriptome analysis reveals cotton (Gossypium hirsutum) genes that are differentially expressed in cadmium (Cd) stress tolerance

Authors: HAN, MINGGE - Chinese Academy Of Agricultural Sciences; LU, XUKE - Chinese Academy Of Agricultural Sciences; Yu, John; CHEN, XIUGUI - Chinese Academy Of Agricultural Sciences; WANG, XIAOGE - Chinese Academy Of Agricultural Sciences; MALIK, WAQAR-AFZAL - 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; CHEN, CHAO - Chinese Academy Of Agricultural Sciences; CUI, RUI-FENG - Chinese Academy Of Agricultural Sciences; YANG, XIAOMIN - Chinese Academy Of Agricultural Sciences; YE, WUWEI - Chinese Academy Of Agricultural Sciences

Submitted to: International Journal of Molecular Sciences
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: 3/19/2019
Publication Date: 3/24/2019
Citation: Han, M., Lu, X., Yu, J., Chen, X., Wang, X., Malik, W., Wang, J., Wang, D., Wang, S., Guo, L., Chen, C., Cui, R., Yang, X., Ye, W. 2019. Transcriptome analysis reveals cotton (Gossypium hirsutum) genes that are differentially expressed in cadmium (Cd) stress tolerance. International Journal of Molecular Sciences. 20(6):1479. https://doi.org/10.3390/ijms20061479.
DOI: https://doi.org/10.3390/ijms20061479

Interpretive Summary: Cadmium (Cd) is one of many heavy pollutants affecting farmland. It has the strongest toxicity among soil metals, and threatens human health, and plant growth as an abiotic stress. While some accessions of cotton germplasm exhibit Cd tolerance, the molecular mechanisms remain unknown. In this study, we conducted transcriptome analysis of Cd tolerance on an Upland cotton type called Han242. By treating Han242 with Cd stress for 9 hours, we identified 4,627 differentially expressed genes (DEGs) in cotton roots, 3,203 in stems and 3,673 in leaves. Analysis of the DEGs showed that they were mainly involved in the oxidation-reduction process and metal ion binding. The genes in calcium signal transduction and phytohormone signal pathway also played an important role in the cotton tolerance to Cd stress. The Cd tolerance genes are useful for the repair of heavy metal contaminated soil through cotton molecular breeding. This study provided valuable information for the use of specific cotton accessions to remediate soil polluted with heavy metals.

Technical Abstract: Cadmium (Cd), one of the most common heavy metals, causes great pollution to farmland. Cd has been recognized with the strongest toxicity among soil metals, threatening the health of human beings and the growth of crop plants. The molecular mechanism of Cd tolerance in cotton remains unknown. The transcriptome analysis was carried out on Upland cotton Han242 at trefoil stage with 4 mM Cd stress treatment for 9 hours. We identified 4,627 differentially expressed genes (DEGs) in cotton roots, 3,203 in stems and 3,673 in leaves. Many genes expressed under Cd stress, such as heavy metal transporter genes (ABC, CDF, HMA, IRT, ZIP, etc.), annexin genes, heat shock protein (HSP) genes, heavy metals transport/detoxification super-family genes and phosphatase 2C protein family genes, and auxin factors genes. Gene ontology analysis showed that these DEGs were mainly involved in the oxidation-reduction process and metal ion binding. The Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway enrichment mainly in carbon metabolism, mitogen-activated protein kinase (MAPK), calcium (Ca) signaling pathways and plant hormone signaling pathways, and more interestingly that the DEGs enriched in two pathways, namely, the influenza A pathway and pyruvate pathway. Through the transcriptome analysis of cotton under Cd stress, we have obtained a large number of Cd tolerance genes, which provide the key genes for the repair of heavy metal contaminated soil through cotton molecular breeding. The serine/threonine protein kinase in the MAPK pathway. Besides, the DEGs in Ca signal transduction and phytohormone signals (ABA, IAA, SA, etc.) pathway played an important role in the cotton tolerance to Cd stress. This study provided valuable information for the use of cotton to remediate the soil polluted with heavy metals.