Hostname: page-component-586b7cd67f-g8jcs Total loading time: 0 Render date: 2024-11-25T14:22:48.408Z Has data issue: false hasContentIssue false
  • English
  • Français

Foxtail millet WRKY genes and drought stress

Part of: AGS Millet Collection

Published online by Cambridge University Press:  02 November 2016

L. ZHANG ,
H. SHU ,
A. Y. ZHANG ,
B. L. LIU ,
G. F. XING ,
J. A. XUE ,
L. X. YUAN ,
C. Y. GAO  and
R. Z. LI
L. ZHANG
Affiliation:
Institute of Molecular Agriculture & Bioenergy, Shanxi Agricultural University, Taigu 030801, China
H. SHU
Affiliation:
Program of Molecular Medicine, University of Massachusetts Medical School, Massachusetts 01605, USA
A. Y. ZHANG
Affiliation:
Institute of Millet, Shanxi Academy of Agricultural Sciences, Changzhi 046011, China
B. L. LIU
Affiliation:
Institute of Molecular Agriculture & Bioenergy, Shanxi Agricultural University, Taigu 030801, China
G. F. XING
Affiliation:
Institute of Molecular Agriculture & Bioenergy, Shanxi Agricultural University, Taigu 030801, China
J. A. XUE
Affiliation:
Institute of Molecular Agriculture & Bioenergy, Shanxi Agricultural University, Taigu 030801, China
L. X. YUAN
Affiliation:
Institute of Molecular Agriculture & Bioenergy, Shanxi Agricultural University, Taigu 030801, China
C. Y. GAO
Affiliation:
Institute of Molecular Agriculture & Bioenergy, Shanxi Agricultural University, Taigu 030801, China
R. Z. LI*
Affiliation:
Institute of Molecular Agriculture & Bioenergy, Shanxi Agricultural University, Taigu 030801, China
*
*To whom all correspondence should be addressed. Email: [email protected]
Get access Rights & Permissions [Opens in a new window]

Summary

Foxtail millet (Setaria italica (L.) P. Beauv.) is a naturally stress-tolerant plant, a major reserve crop and a model for panicoid grasses. The recent completion of the S. italica genome facilitates identification and characterization of WRKY transcription factor family proteins that are important regulators of major plant processes, including growth, development and stress response. The present study identified 103 WRKY transcription factor-encoding genes in the S. italica genome. The genes were named SiWRKY1–SiWRKY103 according to their order on the chromosomes. A comprehensive expression analysis of SiWRKY genes among four different tissues was performed using publicly available RNA sequencing data. Eighty-four SiWRKY genes were more highly expressed in root tissue than in other tissues and nine genes were only expressed in roots. Additionally, real-time quantitative polymerase chain reaction was performed to comprehensively analyse the expression of all SiWRKY genes in response to dehydration. Results indicated that most SiWRKY genes (over 0.8) were up-regulated by drought stress. In conclusion, genome-wide identification and expression profiling of SiWRKY genes provided a set of candidates for cloning and functional analyses in plants’ response to drought stress.

Type
Crops and Soils Research Papers
Information
The Journal of Agricultural Science , Volume 155 , Issue 5 , July 2017 , pp. 777 - 790
Check for updates
Copyright
Copyright © Cambridge University Press 2016 

Access options

Get access to the full version of this content by using one of the access options below. (Log in options will check for institutional or personal access. Content may require purchase if you do not have access.)

Footnotes

†

The first two authors contributed equally to this paper.

References

REFERENCES

Bennetzen, J. L., Schmutz, J., Wang, H., Percifield, R., Hawkins, J., Pontaroli, A. C., Estep, M., Feng, L., Vaughn, J. N., Grimwood, J., Jenkins, J., Barry, K., Lindquist, E., Hellsten, U., Deshpande, S., Wang, X., Wu, X., Mitros, T., Triplett, J., Yang, X., Ye, C. Y., Mauro-Herrera, M., Wang, L., Li, P., Sharma, M., Sharma, R., Ronald, P. C., Panaud, O., Kellogg, E. A., Brutnell, T. P., Doust, A. N., Tuskan, G. A., Rokhsar, D. & Devos, K. M. (2012). Reference genome sequence of the model plant Setaria . Nature Biotechnology 30, 555–561.Google Scholar
Cochrane, G., Alako, B., Amid, C., Bower, L., Cerdeño-Tárraga, A., Cleland, I., Gibson, R., Goodgame, N., Jang, M., Kay, S., Leinonen, R., Lin, X., Lopez, R., McWilliam, H., Oisel, A., Pakseresht, N., Pallreddy, S., Park, Y., Plaister, S., Radhakrishnan, R., Rivière, S., Rossello, M., Senf, A., Silvester, N., Smirnov, D., Ten Hoopen, P., Toribio, A., Vaughan, D. & Zalunin, V. (2013). Facing growth in the European Nucleotide Archive. Nucleic Acids Research 41, D30–D35.Google Scholar
Ding, Z. J., Yan, J. Y., Li, C. X., Li, G. X., Wu, Y. R. & Zheng, S. J. (2015). Transcription factor WRKY46 modulates the development of Arabidopsis lateral roots in osmotic/salt stress conditions via regulation of ABA signaling and auxin homeostasis. Plant Journal 84, 56–69.Google Scholar
Eulgem, T., Rushton, P. J., Robatzek, S. & Somssich, I. E. (2000). The WRKY superfamily of plant transcription factors. Trends in Plant Science 5, 199–206.Google Scholar
Gallou, A., Declerck, S. & Cranenbrouck, S. (2012). Transcriptional regulation of defence genes and involvement of the WRKY transcription factor in arbuscular mycorrhizal potato root colonization. Functional and Integrative Genomics 12, 183–198.Google Scholar
Ghosh, D. & Xu, J. (2014). Abiotic stress responses in plant roots: a proteomics perspective. Frontiers in Plant Science 5, 6.Google Scholar
Golldack, D., Lüking, I. & Yang, O. (2011). Plant tolerance to drought and salinity: stress regulating transcription factors and their functional significance in the cellular transcriptional network. Plant Cell Reports 30, 1383–1391.Google Scholar
Goodstein, D. M., Shu, S. Q., Howson, R., Neupane, R., Hayes, R. D., Fazo, J., Mitros, T., Dirks, W., Hellsten, U., Putnam, N. & Rokhsar, D. S. (2012). Phytozome: a comparative platform for green plant genomics. Nucleic Acids Research 40, D1178–D1186.Google Scholar
Jiang, Y. & Deyholos, M. K. (2009). Functional characterization of Arabidopsis NaCl inducible WRKY25 and WRKY33 transcription factors in abiotic stresses. Plant Molecular Biology 69, 91–105.Google Scholar
Jiang, Y., Liang, G. & Yu, D. (2012). Activated expression of WRKY57 confers drought tolerance in Arabidopsis . Molecular Plant 5, 1375–1388.Google Scholar
Krzywinski, M. I., Schein, J. E., Birol, I., Connors, J., Gascoyne, R., Horsman, D., Jones, S. J. & Marra, M. A. (2009). Circos: an information aesthetic for comparative genomics. Genome Research 19, 1639–1645.Google Scholar
Langmead, B. & Salzberg, S. L. (2012). Fast gapped-read alignment with Bowtie 2. Nature Methods 9, 357–359.Google Scholar
Luo, X., Bai, X., Sun, X., Zhu, D., Liu, B., Ji, W., Cai, H., Cao, L., Wu, J., Hu, M., Liu, X., Tang, L. & Zhu, Y. (2013). Expression of wild soybean WRKY20 in Arabidopsis enhances drought tolerance and regulates ABA signalling. Journal of Experimental Botany 64, 2155–2169.Google Scholar
Marchive, C., Mzid, R., Deluc, L., Barrieu, F., Pirrello, J., Gauthier, A., Corio-Costet, M. F., Regad, F., Cailleteau, B., Hamdi, S. & Lauvergeat, V. (2007). Isolation and characterization of a Vitis vinifera transcription factor, VvWRKY1, and its effect on responses to fungal pathogens in transgenic tobacco plants. Journal of Experimental Botany 58, 1999–2010.Google Scholar
Muthamilarasan, M. & Prasad, M. (2015). Advances in Setaria genomics for genetic improvement of cereals and bioenergy grasses. Theoretical and Applied Genetics 128, 1–14.Google Scholar
Muthamilarasan, M., Bonthala, V. S., Khandelwal, R., Jaishankar, J., Shweta, S., Nawaz, K. & Prasad, M. (2015). Global analysis of WRKY transcription factor superfamily in Setaria identifies potential candidates involved in abiotic stress signaling. Frontiers in Plant Science 6, 910.Google Scholar
Mukhtar, M. S., Deslandes, L., Auriac, M. C., Marco, Y. & Somssich, I. E. (2008). The Arabidopsis transcription factor WRKY27 influences wilt disease symptom development caused by Ralstonia solanacearum . Plant Journal 56, 935–947.Google Scholar
Okay, S., Derelli, E. & Unver, T. (2014). Transcriptome-wide identification of bread wheat WRKY transcription factors in response to drought stress. Molecular Genetics and Genomics 289, 765–781.Google Scholar
Pepke, S., Wold, B. & Mortazavi, A. (2009). Computation for ChIP-seq and RNA-seq studies. Nature Methods 6, S22–S32.Google Scholar
Puranik, S., Sahu, P. P., Mandal, S. N., Suresh, B. V., Parida, S. K. & Prasad, M. (2013). Comprehensive genome-wide survey, genomic constitution and expression profiling of the NAC transcription factor family in foxtail millet (Setaria italica L.). PLoS ONE 8, e64594. http://dx.doi.org/10.1371/journal.pone.0064594 Google Scholar
Qiu, Y. P. & Yu, D. Q. (2009). Over-expression of the stress-induced OsWRKY45 enhances disease resistance and drought tolerance in Arabidopsis . Environmental and Experimental Botany 65, 35–47.Google Scholar
Rushton, P. J., Torres, J. T., Parniske, M., Wernert, P., Hahlbrock, K. & Somssich, I. E. (1996). Interaction of elicitor-induced DNA-binding proteins with elicitor response elements in the promoters of parsley PR1 genes. EMBO Journal 15, 5690–5700.CrossRefGoogle ScholarPubMed
Rushton, P. J., Somssich, I. E., Ringler, P. & Shen, Q. J. (2010). WRKY transcription factors. Trends in Plant Science 15, 247–258.Google Scholar
Saeed, A. I., Bhagabati, N. K., Braisted, J. C., Liang, W., Sharov, V., Howe, E. A., Li, J., Thiagarajan, M., White, J. A. & Quackenbush, J. (2006). TM4 microarray software suite. Methods in Enzymology 411, 134–193.Google Scholar
Shiu, S. H. & Bleecker, A. B. (2003). Expansion of the receptor-like kinase/pelle gene family and receptor-like proteins in Arabidopsis . Plant Physiology 132, 530–543.Google Scholar
Song, Y., Jing, S. J. & Yu, D. Q. (2009). Overexpression of the stress-induced OsWRKY08 improves osmotic stress tolerance in Arabidopsis . Chinese Science Bulletin 54, 4671–4678.Google Scholar
Suyama, M., Torrents, D. & Bork, P. (2006). PAL2NAL: robust conversion of protein sequence alignments into the corresponding codon alignments. Nucleic Acids Research 34, (Suppl. 2), W609–W612.Google Scholar
Tang, H., Bowers, J. E., Wang, X., Ming, R., Alam, M. & Paterson, A. H. (2008). Synteny and collinearity in plant genomes. Science 320, 486–488.CrossRefGoogle ScholarPubMed
Tao, Z., Liu, H. B., Qiu, D. Y., Zhou, Y., Li, X. H., Xu, C. G. & Wang, S. P. (2009). A pair of allelic WRKY genes play opposite roles in rice-bacteria interactions. Plant Physiology 151, 936–948.Google Scholar
Tripathi, P., Rabara, R. C., Langum, T. J., Boken, A. K., Rushton, D. L., Boomsma, D. D., Rinerson, C. I., Rabara, J., Reese, R. N., Chen, X., Rohila, J. S. & Rushton, P. J. (2012). The WRKY transcription factor family in Brachypodium distachyon . BMC Genomics 13, 270.Google Scholar
Tripathi, P., Rabara, R. C. & Rushton, P. J. (2014). A systems biology perspective on the role of WRKY transcription factors in drought responses in plants. Planta 239, 255–266.Google Scholar
Ülker, B. & Somssich, I. E. (2004). WRKY transcription factors: from DNA binding towards biological function. Current Opinion in Plant Biology 7, 491–498.Google Scholar
Voorrips, R. E. (2002). MapChart: software for the graphical presentation of linkage maps and QTLs. Journal of Heredity 93, 77–78.Google Scholar
Wang, Y. N., Dang, F. F., Liu, Z. Q., Wang, X., Eulgem, T., Lai, Y., Yu, L., She, J. J., Shi, Y. L., Lin, J. H., Chen, C. C., Guan, D. Y., Qiu, A. & He, S. L. (2013). CaWRKY58, encoding a group I WRKY transcription factor of Capsicum annuum, negatively regulates resistance to Ralstonia solanacearum infection. Molecular Plant Pathology 14, 131–144.Google Scholar
Wang, L. N., Zhu, W., Fang, L. C., Sun, X. M., Su, L. Y., Liang, Z. C., Wang, N., Londo, J. P., Li, S. H. & Xin, H. P. (2014). Genome-wide identification of WRKY family genes and their response to cold stress in Vitis vinifera . BMC Plant Biology 14, 103.Google Scholar
Wei, K. F., Chen, J., Chen, Y. F., Wu, L. J. & Xie, D. X. (2012). Molecular phylogenetic and expression analysis of the complete WRKY transcription factor family in maize. DNA Research 19, 153–164.Google Scholar
Xie, Z., Zhang, Z. L., Zou, X., Huang, J., Ruas, P., Thompson, D. & Shen, Q. J. (2005). Annotations and functional analyses of the rice WRKY gene superfamily reveal positive and negative regulators of abscisic acid signaling in aleurone cells. Plant Physiology 137, 176–189.Google Scholar
Xiong, W., Xu, X., Zhang, L., Wu, P., Chen, Y., Li, M., Jiang, H. & Wu, G. (2013). Genome-wide analysis of the WRKY gene family in physic nut (Jatropha curcas L.). Gene 524, 124–132.Google Scholar
Yan, H. R., Jia, H. H., Chen, X. B., Hao, L. L., An, H. L. & Guo, X. Q. (2014). The cotton WRKY transcription factor GhWRKY17 functions in drought and salt stress in transgenic Nicotiana benthamiana through ABA signaling and the modulation of reactive oxygen species production. Plant Cell Physiology 55, 2060–2076.Google Scholar
Yang, P. Z., Chen, C. H., Wang, Z. P., Fan, B. F. & Chen, Z. X. (1999). A pathogen- and salicylic acid-induced WRKY DNA-binding activity recognizes the elicitor response element of the tobacco class I chitinase gene promoter. Plant Journal 18, 141–149.Google Scholar
Zhang, Y. & Wang, L. (2005). The WRKY transcription factor superfamily: its origin in eukaryotes and expansion in plants. BMC Evolutionary Biology 5, 1.Google Scholar
Zhang, G., Liu, X., Quan, Z., Cheng, S., Xu, X., Pan, S. K., Xie, M., Zeng, P., Yue, Z., Wang, W. L., Tao, Y., Bian, C., Han, C. L., Xia, Q. J., Peng, X. H., Cao, R., Yang, X. H., Zhan, D. L., Hu, J. C., Zhang, Y. X., Li, H., Li, H., Li, N., Wang, J. Y., Wang, C. C., Wang, R., Guo, T., Cai, Y. J., Liu, C. Z., Xiang, H. T., Shi, Q. X., Huang, P., Chen, Q. C., Li, Y. G., Wang, J., Zhao, J. H. & Wang, J. (2012). Genome sequence of foxtail millet (Setaria italica) provides insights into grass evolution and biofuel potential. Nature Biotechnology 30, 549–554.Google Scholar
Zhou, Q. Y., Tian, A. G., Zou, H. F., Xie, Z. M., Lei, G., Huang, J., Wang, C. M., Wang, H. W., Zhang, J. S. & Chen, S. Y. (2008). Soybean WRKY-type transcription factor genes, GmWRKY13, GmWRKY21, and GmWRKY54, confer differential tolerance to abiotic stresses in transgenic Arabidopsis plants. Plant Biotechnology Journal 6, 486–503.Google Scholar
Zou, C. S., Jiang, W. B. & Yu, D. Q. (2010). Male gametophyte-specific WRKY34 transcription factor mediates cold sensitivity of mature pollen in Arabidopsis . Journal of Experimental Botany 61, 3901–3914.Google Scholar
Supplementary material: File

Zhang supplementary material

Table S1

Download Zhang supplementary material(File)
File 23.3 KB
Supplementary material: File

Zhang supplementary material

Table S2

Download Zhang supplementary material(File)
File 110.6 KB
Supplementary material: File

Zhang supplementary material

Table S4

Download Zhang supplementary material(File)
File 46.1 KB
Supplementary material: File

Zhang supplementary material

Table S5

Download Zhang supplementary material(File)
File 14.2 KB
Supplementary material: File

Zhang supplementary material

Table S3

Download Zhang supplementary material(File)
File 38.4 KB