Skip to main content
SpringerLink
Log in

RNA-seq analysis reveals a key role of brassinolide-regulated pathways in NaCl-stressed cotton

  • Original paper
  • Published:
Biologia Plantarum

Abstract

Brassinolide (BL) alleviates salt injury in cotton seedlings; however, little is known about the molecular mechanisms of this response. In this study, digital gene expression analysis was performed to better understand the regulatory pathways of BL in NaCl-stressed cotton (Gossypium hirsutum L.). Compared with control plants (CK), a total of 1 162 and 7 659 differentially expressed genes (DEGs) were detected in the leaves and roots of NaCl-treated plants, respectively. Most of the DEGs in NaCl-treated plants, compared to CK, were regulated by BL. Moreover, expression patterns of DEGs in BL+NaCl treated plants were similar to those in CK plants; however, the responses of DEGs in the leaves and roots of NaCl-treated plants to BL differed. In the roots, BL-regulated DEGs were involved in protein biosynthesis, whereas in the leaves, BL promoted photosynthesis in NaCl-stressed cotton. BL treatment also significantly increased the overall biomass, chlorophyll a + b content in leaves, and the protein content in roots in NaCl-stressed cotton. The downregulation of stress-responsive genes in BL+NaCl-stressed leaves was also found. These results suggest that BL can alleviate NaCl injury in cotton plants.

This is a preview of subscription content, log in via an institution to check access.

Access this article

Log in via an institution

Price excludes VAT (USA)
Tax calculation will be finalised during checkout.

Instant access to the full article PDF.

Institutional subscriptions

Similar content being viewed by others

Abbreviations

BL:

brassinolide

BRs:

brassinosteroids

Chl:

chlorophyll

CK:

control

DEG:

differentially expressed gene

EBR:

epibrassinolide

GO:

gene ontology

KEGG:

Kyoto encyclopedia of genes and genomes

L:

leaf

RT-qPCR:

reverse transcriptase quantitative polymerase chain reaction

R:

root

References

  • Anders, S., Huber, W.: Differential expression analysis for sequence count data. — Genome Biol. 11: 1–12, 2010.

    Article  Google Scholar 

  • Anuradha, S., Rao, S.S.R.: Application of brassinosteroids to rice seeds (Oryza sativa L.) reduced the impact of salt stress on growth, prevented photosynthetic pigment loss and increased nitrate reductase activity. — Plant Growth Regul. 40: 29–32, 2003.

    Article  CAS  Google Scholar 

  • Bajguz, A., Hayat, S.: Effects of brassinosteroids on the plant responses to environmental stresses. — Plant Physiol. Biochem. 47: 1–8, 2009.

    Article  CAS  PubMed  Google Scholar 

  • Clouse, S.D., Sasse, J.: Brassinosteroids: essential regulators of plant growth and development. — Annu. Rev. Plant Biol. 49: 427–451, 1998.

    Article  CAS  Google Scholar 

  • Dhaubhadel, S., Krishna, P.: Identification of differentially expressed genes in brassinosteroid-treated Brassica napus seedlings. — J. Plant Growth Regul. 27: 297–300, 2008.

    Article  CAS  Google Scholar 

  • Divi, U.K., Krishna, P.: Brassinosteroid: a biotechnological target for enhancing crop yield and stress tolerance. — New Biotechnol. 36: 131–136, 2009.

    Article  Google Scholar 

  • Dobrikova, A.G., Vladkova, R.S., Rashkov, G.D., Todinova, S.J., Krumova, S.B., Apostolova, E.L.: Effects of exogenous 24-epibrassinolide on the photosynthetic membranes under non-stress conditions. — Plant Physiol. Biochem. 80: 75–82, 2014.

    Article  CAS  PubMed  Google Scholar 

  • Fariduddin, Q., Yusuf, M., Ahmad, I., Ahmad, I.: Brassinosteroids and their role in response of plants to abiotic stress. — Biol. Plant. 58: 9–17, 2014.

    Article  CAS  Google Scholar 

  • Goetz, M., Godt, D.E., Roitsch, T.: Tissue-specific induction of the mRNA for an extracellular invertase isoenzyme of tomato by brassinosteroids suggests a role for steroid hormones in assimilate partitioning. — Plant J. 22: 515–522, 2000.

    Article  CAS  PubMed  Google Scholar 

  • Hershkovitz, V., Sela, N., Taha-Salaime, L., Liu, J., Rafael, G., Kessler, C., Aly, R., Levy, M., Wisniewski, M., Droby, S.: De-novo assembly and characterization of the transcriptome of Metschnikowia fructicola reveals differences in gene expression following interaction with Penicillium digitatum and grapefruit peel. — BMC Genomics 14: 168–181, 2013.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Janeczko, A., Oklestkova, J., Pociecha, E., Koscielniak, J., Mirek, M.: Physiological effects and transport of 24-epibrassinolide in heat-stressed barley. — Acta. Physiol. Plant. 33: 1249–1259, 2011.

    Article  CAS  Google Scholar 

  • Kanehisa, M., Araki, M., Goto, S., Hattori, M., Hirakawa, M., Itoh, M., Katayama, T., Kawashima, S., Okuda, S., Tokimatsu, T., Yamanishi, Y.: KEGG for linking genomes to life and the environment. — Nucl. Acids Res. 36: 480–484, 2008.

    Article  Google Scholar 

  • Kosmas, S.A., Argyrokastritis, A., Loukas, M.G., Eliopoulos, E., Tsakas, S., Kaltsikes, P.J.: Isolation and characterization of drought-related trehalose 6-phosphate-synthase gene from cultivated cotton (Gossypium hirsutum L). — Planta 223: 329–339, 2006.

    Article  CAS  PubMed  Google Scholar 

  • Krumova, S., Zhiponova, M., Dankov, K., Velikova, V., Balashev, K., Andreeva, T., Russinova, E., Taneva, S.: Brassinosteroids regulate the thylakoid membrane architecture and the photosystem II function. — J. Photochem. Photobiol. B. 126: 97–104, 2013.

    Article  CAS  PubMed  Google Scholar 

  • Li, B., Dewey, C.: RSEM: accurate transcript quantification from RNA-Seq data with or without a reference genome. — BMC Bioinformatics 12: 323, 2011.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Li, F., Fan, G., Wang, K., Sun, F., Yuan, Y., Song, G., Li, Q., Ma, Z., Lu, C., Zou, C., Chen, W., Liang, X., Shang, H., Liu, W., Shi, C., Xiao, G., Gou, C., Ye, W., Xu, X., Zhang, X., Wei, H., Li, Z., Zhang, G., Wang, J., Liu, K., Kohel, R.J., Percy, R.G., Yu, J.Z., Zhu, Y.X., Wang, J., Yu, S.: Genome sequence of the cultivated cotton Gossypium arboretum. — Nat. Genet. 46: 567–574, 2014.

    Article  CAS  PubMed  Google Scholar 

  • Liu, B., Yue, Y.M., Li, R., Shen, W.J., Wang, K.L.: Plant leaf chlorophyll content retrieval based on a field imaging spectroscopy system. — Sensors 14: 19910–19925, 2014.

    Article  PubMed  PubMed Central  Google Scholar 

  • Livak, K.J., Schmittgen, T.D.: Analysis of relative gene expression data using real-time quantitative PCR and the 2-ΔΔCt method. — Methods 25: 402–408, 2001.

    Article  CAS  PubMed  Google Scholar 

  • Mao, X., Cai, T., Olyarchuk, J.G., Wei, L.: Automated genome annotation and pathway identification using the KEGG Orthology (KO) as a controlled vocabulary. — Bioinformatics 21: 3787–3793, 2005.

    Article  CAS  PubMed  Google Scholar 

  • Mortazavi, A., Williams, B.A., McCue, K., Schaeffer, L., Wold, A.: Mapping and quantifying mammalian transcriptomes by RNA-Seq. — Nat. Methods. 5: 621–628, 2008.

    Article  CAS  PubMed  Google Scholar 

  • Peng, Z., He, S., Gong, W., Sun, J., Pan, Z., Xu, F., Lu, Y., Du, X.: Comprehensive analysis of differentially expressed genes and transcriptional regulation induced by salt stress in two contrasting cotton genotypes. — BMC Genomics 15: 760, 2014.

    Article  PubMed  PubMed Central  Google Scholar 

  • Sharma, I., Ching, E., Saini, R., Bhardwaj, S., Pati, P.K.: Exogenous application of brassinosteroid offers tolerance to salinity by altering stress responses in rice variety Pusa Basmati-1. — Plant Physiol. Biochem. 69: 17–26, 2013.

    Article  CAS  PubMed  Google Scholar 

  • Shu, H., Guo, S., Gong, Y., Ni, W.: [Effects of brassinolide on leaf physiological characteristics and differential gene expression profiles of NaCl-stressed cotton.] — Chin. J. appl. Ecol. 27: 150–156, 2016. [In Chin.]

    CAS  Google Scholar 

  • Shu, H., Ni, W., Guo, S., Gong, Y., Shen, X., Zhang, X., Xu, P., Guo, Q.: Root-applied brassinolide can alleviate the NaCl injuries on cotton. — Acta Physiol. Plant. 37: 75, 2015.

    Article  Google Scholar 

  • Storey, J.D., Tibshirani, R.: Statistical significance for genomewide studies. — Proc. nat. Acad. Sci. USA. 100: 9440–9445, 2003.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Wang, K., Wang, Z., Li, F., Ye, W., Wang, J., Song, G., Yue, Z., Cong, L., Shang, H., Zhu, S., Zou, C., Li, Q., Yuan, Y., Lu. C., Wei. H., Gou, C., Zheng, Z., Yin, Y., Zhang, X., Liu, K., Wang, B., Song, C., Shi, N., Kohel, R.J., Percy, R.G., Yu, J.Z., Zhu, Y.X., Wang, J., Yu, S.: The draft genome of a diploid cotton Gossypium raimondii. — Nat. Genetics 44: 1098–1103, 2012.

    Article  CAS  PubMed  Google Scholar 

  • Wu, C.Y., Trieu, A., Radhakrishnan, P., Kwok, S.F., Harris, S., Zhang, K., Wang, J., Wan, J., Zhai, H., Takatsuto, S., Matsumoto, S., Fujioka, S., Feldmann, K.A., Pennella, R.I.: Brassinosteroids regulate grain filling in rice. — Plant Cell 20: 2130–2145, 2008.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Xu, P., Liu, Z., Fan, X., Gao, J., Zhang, X., Zhang, X., Shen, X.: De novo transcriptome sequencing and comparative analysis of differentially expressed genes in Gossypium aridum under salt stress. — Gene 525: 26–34, 2013.

    Article  CAS  PubMed  Google Scholar 

  • Yao, D., Zhang, X., Zhao, X., Liu, C., Wang, C., Zhang, Z., Zhang, C., Wei, Q., Wang, Q., Yan, H., Li, F., Su, Z.: Transcriptome analysis reveals salt-stress-regulated biological processes and key pathways in roots of cotton (Gossypium hirsutum L.). — Genomics 98: 47–55, 2011.

    Article  CAS  PubMed  Google Scholar 

  • Young, M.D., Wakefield, M.J., Smyth, G.K., Oshlack, A.: Gene ontology analysis for RNA-seq: accounting for selection bias. — Genome Biol. 11: 1–12, 2010.

    Article  Google Scholar 

  • Zhang, T., Hu, Y., Jiang, W., Fang, L., Guan, X., Chen, J., Zhang, J., Saski, CA., Scheffler, B.E., Stelly, D.M., Hulse-Kemp, A.M., Wan, Q., Liu, B., Liu, C., Wang, S., Pan, M., Wang, Y., Wang, D., Ye, W., Chang, L., Zhang, W., Song, Q., Kirkbride, R.C., Chen, X., Dennis, E., Llewellyn, D.J., Peterson, D.G., Thaxton, P., Jones, D.C., Wang, Q., Xu X., Zhang, H., Wu, H., Zhou, L., Mei, G., Chen, S., Tian, Y., Xiang, D., Li, X., Ding, J., Zuo, Q., Tao, L., Liu, Y., Li, J., Lin, Y., Hui, Y., Cao, Z., Cai, C., Zhu, X., Jiang, Z., Zhou, B., Guo, W., Li, R., Chen, Z.J.: Sequencing of allotetraploid cotton (Gossypium hirsutum L. acc.TM-1) provides a resource for fiber improvement. — Nat. Biotechnol. 33: 531–537, 2015.

    Article  CAS  PubMed  Google Scholar 

Download references

Author information

Authors and Affiliations

  1. Key Laboratory of Cotton and Rapeseed, Ministry of Agriculture, Institute of Industrial Crops, Jiangsu Academy of Agricultural Sciences, Nanjing, 210014, P.R. China

    H. M. Shu, S. Q. Guo, Y. Y. Gong, L. Jiang, J. W. Zhu & W. C. Ni

Authors
  1. H. M. Shu
    View author publications

    You can also search for this author in PubMed Google Scholar

  2. S. Q. Guo
    View author publications

    You can also search for this author in PubMed Google Scholar

  3. Y. Y. Gong
    View author publications

    You can also search for this author in PubMed Google Scholar

  4. L. Jiang
    View author publications

    You can also search for this author in PubMed Google Scholar

  5. J. W. Zhu
    View author publications

    You can also search for this author in PubMed Google Scholar

  6. W. C. Ni
    View author publications

    You can also search for this author in PubMed Google Scholar

Corresponding author

Correspondence to W. C. Ni.

Additional information

Acknowledgments: This work was funded by the National Natural Science Foundation of China (31201139), the National Transgenic Program (2016ZX08005-001), and the Jiangsu Agricultural Science and Technology Innovation Funds (CX (13) 5011).

Electronic supplementary material

Rights and permissions

Reprints and permissions

About this article

Check for updates. Verify currency and authenticity via CrossMark

Cite this article

Shu, H.M., Guo, S.Q., Gong, Y.Y. et al. RNA-seq analysis reveals a key role of brassinolide-regulated pathways in NaCl-stressed cotton. Biol Plant 61, 667–674 (2017). https://doi.org/10.1007/s10535-017-0736-5

Download citation

  • Received:

  • Revised:

  • Accepted:

  • Published:

  • Issue Date:

  • DOI: https://doi.org/10.1007/s10535-017-0736-5

Additional key words

Search

Navigation