Skip to main content Accessibility help

Foxtail millet WRKY genes and drought stress

  • L. ZHANG (a1), H. SHU (a2), A. Y. ZHANG (a3), B. L. LIU (a1), G. F. XING (a1), J. A. XUE (a1), L. X. YUAN (a1), C. Y. GAO (a1) and R. Z. LI (a1)...


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.


Corresponding author

*To whom all correspondence should be addressed. Email:


Hide All

The first two authors contributed equally to this paper.



Hide All
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, 555561.
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, D30D35.
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, 5669.
Eulgem, T., Rushton, P. J., Robatzek, S. & Somssich, I. E. (2000). The WRKY superfamily of plant transcription factors. Trends in Plant Science 5, 199206.
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, 183198.
Ghosh, D. & Xu, J. (2014). Abiotic stress responses in plant roots: a proteomics perspective. Frontiers in Plant Science 5, 6.
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, 13831391.
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, D1178D1186.
Jiang, Y. & Deyholos, M. K. (2009). Functional characterization of Arabidopsis NaCl inducible WRKY25 and WRKY33 transcription factors in abiotic stresses. Plant Molecular Biology 69, 91105.
Jiang, Y., Liang, G. & Yu, D. (2012). Activated expression of WRKY57 confers drought tolerance in Arabidopsis . Molecular Plant 5, 13751388.
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, 16391645.
Langmead, B. & Salzberg, S. L. (2012). Fast gapped-read alignment with Bowtie 2. Nature Methods 9, 357359.
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, 21552169.
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, 19992010.
Muthamilarasan, M. & Prasad, M. (2015). Advances in Setaria genomics for genetic improvement of cereals and bioenergy grasses. Theoretical and Applied Genetics 128, 114.
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.
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, 935947.
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, 765781.
Pepke, S., Wold, B. & Mortazavi, A. (2009). Computation for ChIP-seq and RNA-seq studies. Nature Methods 6, S22S32.
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.
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, 3547.
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, 56905700.
Rushton, P. J., Somssich, I. E., Ringler, P. & Shen, Q. J. (2010). WRKY transcription factors. Trends in Plant Science 15, 247258.
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, 134193.
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, 530543.
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, 46714678.
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), W609W612.
Tang, H., Bowers, J. E., Wang, X., Ming, R., Alam, M. & Paterson, A. H. (2008). Synteny and collinearity in plant genomes. Science 320, 486488.
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, 936948.
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.
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, 255266.
Ülker, B. & Somssich, I. E. (2004). WRKY transcription factors: from DNA binding towards biological function. Current Opinion in Plant Biology 7, 491498.
Voorrips, R. E. (2002). MapChart: software for the graphical presentation of linkage maps and QTLs. Journal of Heredity 93, 7778.
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, 131144.
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.
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, 153164.
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, 176189.
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, 124132.
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, 20602076.
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, 141149.
Zhang, Y. & Wang, L. (2005). The WRKY transcription factor superfamily: its origin in eukaryotes and expansion in plants. BMC Evolutionary Biology 5, 1.
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, 549554.
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, 486503.
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, 39013914.

Related content

Powered by UNSILO
Type Description Title
Supplementary materials

Zhang supplementary material
Table S1

 Excel (23 KB)
23 KB
Supplementary materials

Zhang supplementary material
Table S2

 Word (111 KB)
111 KB
Supplementary materials

Zhang supplementary material
Table S4

 Excel (46 KB)
46 KB
Supplementary materials

Zhang supplementary material
Table S5

 Excel (14 KB)
14 KB
Supplementary materials

Zhang supplementary material
Table S3

 Word (38 KB)
38 KB

Foxtail millet WRKY genes and drought stress

  • L. ZHANG (a1), H. SHU (a2), A. Y. ZHANG (a3), B. L. LIU (a1), G. F. XING (a1), J. A. XUE (a1), L. X. YUAN (a1), C. Y. GAO (a1) and R. Z. LI (a1)...


Full text views

Total number of HTML views: 0
Total number of PDF views: 0 *
Loading metrics...

Abstract views

Total abstract views: 0 *
Loading metrics...

* Views captured on Cambridge Core between <date>. This data will be updated every 24 hours.

Usage data cannot currently be displayed.