Genome wide identification of AGC kinase genes and their expression in response to heat and cold stresses in barley


  • Zohreh HAJIBARAT Department of Plant Sciences and Biotechnology, Faculty of Life Sciences and Biotechnology, Shahid Beheshti University, Tehran, Iran
  • Abbas SAIDI Department of Plant Sciences and Biotechnology, Faculty of Life Sciences and Biotechnology, Shahid Beheshti University, Tehran, Iran



AGC kinase protein, protein model, synteny, gene duplication


AGC kinases are highly conserved regulators in a variety of cellular processes such as differentiation, proliferation, and growth.  They are known to play important roles in stress and hormonal responses, including ROS signaling. AGC kinases are the main class of protein kinases in plants, having central functions in different stages of plant growth. In the present study, the analysis of phylogenetic relationships, gene structures, chromosomal locations, synteny analysis, gene ontology, subcellular localization, and gene expression of AGC kinase identified 28 AGC kinase genes in barley. Phylogenetic tree grouped them into seven subfamilies, as supported by exon-intron organization. Gene duplication and synteny indicated that tandom and block duplication events played an essential role in the expansion of AGC kinase gene families in barley. The Real-time quantitative reverse transcription PCR (qRT-PCR) analysis performed for HvAGC kinase gene were largely expressed in different tissues of roots, stems, and leaves in Azaran and Jolgeh cultivars under heat and cold stresses. The results of chromosomal localization showed that the AGC kinases were located on all chromosomes of barley except chromosome 1. Genome evolution of species was surveyed using identification of orthologous and paralogous genes. Identifying overlaps between orthologous clusters can enable us to study the function and evolution of proteins in different species. To our knowledge, this is the first detailed report of using AGC kinases for bioinformatics analysis in barley. Results revealed a broad understanding of the AGC kinase gene family in barley, which will be valuable for improving barley varieties’ response  to heat and cold stresses. Also, HvNDR6.2 gene can utilized as molecular markers under cold stress in the three organs.


Altenhoff, A.M. & Dessimoz, C. (2009). Phylogenetic and functional assessment of orthologs inference projects and methods. PLoS Computational Biology, 5(1), p.e1000262.

Altschul, S.F., Gish, W., Miller, W., Myers, E.W. & Lipman, D.J. (1990). Basic local alignment search tool. Journal of Molecular Biology, 215(3), 403-410.

Bradley D. & Beltrao, P. (2019). Evolution of protein kinase substrate recognition at the active site. PLoS Biology, 17(6), p.e3000341.

Cheung, J., Estivill, X., Khaja, R., MacDonald, J.R., Lau, K., Tsui, L.C. & Scherer, S.W. (2003). Genome-wide detection of segmental duplications and potential assembly errors in the human genome sequence. Genome Biology, 4(4), 1-10.

Christensen, S.K., Dagenais, N., Chory, J. & Weigel, D. (2000). Regulation of auxin response by the protein kinase PINOID. Cell, 100(4), 469-478.

Dhonukshe, P., Huang, F., Galvan-Ampudia, C.S., Mähönen, A.P., Kleine-Vehn, J., Xu, J., Quint, A., Prasad, K., Friml, J., Scheres, B. & Offringa, R. (2010). Plasma membrane-bound AGC3 kinases phosphorylate PIN auxin carriers at TPRXS (N/S) motifs to direct apical PIN recycling. Development, 137(19), 3245-3255.

Galván-Ampudia, C.S. & Offringa, R. (2007) Plant evolution: AGC kinases tell the auxin tale. Trends in Plant Science, 12(12), 541-547.

Hergovich, A. (2016). The roles of NDR protein kinases in hippo signalling. Genes, 7(5), 21.

Huang, F., Kemel Zago, M., Abas, L., van Marion, A., Galván-Ampudia, C.S. & Offringa, R. (2010). Phosphorylation of conserved PIN motifs directs Arabidopsis PIN1 polarity and auxin transport. The Plant Cell, 22(4), 1129-1142.

Kong, W., Tan, S., Zhao, Q., Lin, D.L., Xu, Z.H., Friml, J. & Xue, H.W. (2021). mRNA surveillance complex PELOTA–HBS1 regulates phosphoinositide-dependent protein kinase1 and plant growth. Plant Physiology, 186(4), 2003-2020.

Krupnick, J.G. & Benovic, J.L. (1998). The role of receptor kinases and arrestins in G protein–coupled receptor regulation. Annual Review of Pharmacology and Toxicology, 38(1), 289-319.

Kyoko, K., Ohno, S., Serji, M., Ichiro, Y. & Koichi, S. (1989) A novel yeast gene coding for a putative protein kinase. Gene, 76(1), 177-180.

Oyama, T., Shimura, Y. & Okada, K. (2002). The IRE gene encodes a protein kinase homologue and modulates root hair growth in Arabidopsis. The Plant Journal, 30(3), 289-299.

Petersen, L.N., Ingle, R.A., Knight, M.R. & Denby, K.J. (2009). OXI1 protein kinase is required for plant immunity against Pseudomonas syringae in Arabidopsis. Journal of Experimental Botany, 60(13), 3727-3735.

Pislariu, C.I. & Dickstein, R. (2007). An IRE-like AGC kinase gene, MtIRE, has unique expression in the invasion zone of developing root nodules in Medicago truncatula. Plant Physiology, 144(2), 682-694.

Rentel, M.C., Lecourieux, D., Ouaked, F., Usher, S.L., Petersen, L., Okamoto, H., Knight, H., Peck, S.C., Grierson, C.S., Hirt, H. & Knight, M.R. (2004). OXI1 kinase is necessary for oxidative burst-mediated signalling in Arabidopsis. Nature 427(6977), 858-861.

Robert, H.S. & Offringa, R. (2008). Regulation of auxin transport polarity by AGC kinases. Current Opinion in Plant Biology, 11(5),495-502.

Saidi, A. & Hajibarat, Z. (2020a). Computational study of environmental stress-related transcription factor binding sites in the promoter regions of maize auxin response factor (ARF) gene family. Notulae Scientia Biologicae, 12(3), 646-657.

Saidi, A., Hajibarat, Z. & Hajibarat, Z. (2020b). Identification of responsive genes and analysis of genes with bacterial-inducible cis-regulatory elements in the promoter regions in Oryza sativa L.. Acta agriculturae Slovenica, 116(1), 115-123.

Saidi, A., Hajibarat, Z. & Hajibarat, Z. (2021a). Phylogeny, gene structure and GATA genes expression in different tissues of Solanaceae species. Biocatalysis and Agricultural Biotechnology,102015.

Saidi, A., Hajibarat, Z. & Ahmadikhah, A. (2021b). Computational analysis of responsive transcription factors involved in drought and salt stress in rice. Journal of Applied Biotechnology Reports, 8(4), 406-413. doi:10.30491/jabr.2020.243913.1272

Thimm, O., Bläsing, O., Gibon, Y., Nagel, A., Meyer, S., Krüger, P., Selbig, J., Müller, L.A., Rhee, S.Y. & Stitt, M. (2004). MAPMAN: a user‐driven tool to display genomics data sets onto diagrams of metabolic pathways and other biological processes. The Plant Journal, 37(6), 914-939.

Toda, T., Cameron, S., Sass, P. & Wigler, M. (1988). SCH9, a gene of Saccharomyces cerevisiae that encodes a protein distinct from, but functionally and structurally related to, cAMP-dependent protein kinase catalytic subunits. Genes & Development, 2(5), 517-527.

Voorrips, R.E. (2002). MapChart: software for the graphical presentation of linkage maps and QTLs. Journal of Heredity, 93(1), 77-78.

Wang, L., Yin, H., Qian, Q., Yang, J., Huang, C., Hu, X. & Luo, D. (2009). NECK LEAF 1, a GATA type transcription factor, modulates organogenesis by regulating the expression of multiple regulatory genes during reproductive development in rice. Cell Research, 19(5), 598-611.

Waterhouse, A., Bertoni, M., Bienert, S., Studer, G., Tauriello, G., Gumienny, R., Heer, F.T., de Beer, T.A.P., Rempfer, C., Bordoli, L. & Lepore, R. (2018). SWISS-MODEL: homology modelling of protein structures and complexes. Nucleic Acids Research, 46(W1), W296-W303.

Xue, Y.J., Tao, L. & Yang, Z.M. (2008). Aluminum-induced cell wall peroxidase activity and lignin synthesis are differentially regulated by jasmonate and nitric oxide. Journal of Agricultural and Food Chemistry, 56(20), 9676-9684.

Yang, S., Zhang, X., Yue, J.X., Tian, D. & Chen, J.Q. (2008). Recent duplications dominate NBS-encoding gene expansion in two woody species. Molecular Genetics and Genomics, 280(3), 187-198.

Zhang, Y. & Friml, J. (2020). Auxin guides roots to avoid obstacles during gravitropic growth. The New Phytologist, 225(3), 1049.

Zhou, P.M., Liang, Y., Mei, J., Liao, H.Z., Wang, P., Hu, K., Chen, L.Q., Zhang, X.Q. & Ye, D. (2021). The Arabidopsis AGC kinases NDR2/4/5 interact with MOB1A/1B and play important roles in pollen development and germination. The Plant Journal, 105(4), 1035-1052.

Zhu, X., Yang, K., Wei, X., Zhang, Q., Rong, W., Du, L., Ye, X., Qi, L. & Zhang, Z. (2015). The wheat AGC kinase TaAGC1 is a positive contributor to host resistance to the necrotrophic pathogen Rhizoctonia cerealis. Journal of Experimental Botany, 66(21), 6591-6603.



20. 10. 2022



Original Scientific Article

How to Cite

HAJIBARAT, Z., & SAIDI, A. (2022). Genome wide identification of AGC kinase genes and their expression in response to heat and cold stresses in barley. Acta Agriculturae Slovenica, 118(3), 1–11.

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