Identification of Genes and inducible regulatory elements in response to heat and cold stresses in barley (Hordeum vulgare L.)

Document Type : Original Article

Author

Agricultural Biotechnology Department, Faculty of Agriculture, Tarbiat Modares University, Tehran, Iran

Abstract

Introduction: Barley (Hordeum vulgare), a member of the Poaceae family, is an important cereal grown in temperate climates worldwide. It was one of the first cultivated grains, especially in Eurasia 10,000 years ago. Globally, 70% of barley production is used for animal feed. This plant is reasonably tolerant of abiotic stresses. Environmental or abiotic stresses such as heat and cold can significantly affect crop production. Plants respond to these abiotic stresses by altering the expression of many genes involved in different biological and physiological processes.
Materials and methods: The microarray data of two experiments were analyzed to identify responsive genes related to cold and heat stresses in barley (Hordeum vulgare L.). This research was analyzed and investigated using the raw data in the ArrayExpress database, which is related to two separate experiments in heat and cold stress in 2 and 3 replications, respectively, in the barley plant. The desired analysis was performed using FlexArray software, and the differential genes present in the stresses were identified. The examined genes were normalized using the Robust Multiarray Average (RMA) method, and the genes with a P-value equal to and less than 5% were selected, and the fold change of genes above two was also selected. Gene ontology analysis was done using the AgriGo website, and their functional groups were categorized into three parts: biological processes, cellular components and molecular function. The sequence of 1500 nucleotides upstream of the effective genes in response to heat and cold stress was extracted from the Ensembl Plants site. Regulatory elements of effective functional genes in response to heat and cold stresses were identified and presented using the PlantCare site.
Results: The results demonstrated that 338 and 291 genes were differentially expressed in response to cold and heat stresses, respectively. The gene ontology analysis revealed that differential expressed genes (DEG) were mainly involved in cellular compounds, biological processes, and different molecular functions. Transcription regulator activity has a critical role in the regulation of genes against stresses. Moreover, 1500 bp upstream of the DEGs were identified to find the most represented regulatory elements.
Conclusion: Consequently, light and hormonal-related cis-regulatory elements, especially those related to methyl jasmonate, play an important role in controlling the gene expression against the studied abiotic stresses. This high-throughput comparative analysis provided insight into genes and cis-regulatory elements involved in response to heat and cold stresses in barley.

Keywords

References

Almutairi, Z. M. 2023. Expression profiling and characterization of a G-Box binding protein, B12Dg, from pearl millet. Journal of King Saud University-Science, 35(1):102448.
Alshareef, N. O., Otterbach, S. L., Allu, A. D., Woo, Y. H., de Werk, T., Kamranfar, I., Mueller-Roeber, B., Tester, M., Balazadeh, S., & Schmöckel, S. M. 2022. NAC transcription factors ATAF1 and ANAC055 affect the heat stress response in Arabidopsis. Scientific Reports, 12(1):1-15.
Ceylan, H. 2022. Integrated bioinformatics analysis to identify alternative therapeutic targets for alzheimer’s disease: insights from a synaptic machinery perspective. Journal of Molecular Neuroscience.Feb;72(2):273-86.
Deng, P., Yan, T., Ji, W., Zhang, G., Wu, L., & Wu, D. 2022. Population‐level transcriptomes reveal gene expression and splicing underlying cadmium accumulation in barley. The Plant Journal, 112(3):847-859.
Derbyshire, M. C., Batley, J., & Edwards, D. 2022. Use of multiple ‘omics techniques to accelerate the breeding of abiotic stress tolerant crops. Current Plant Biology, 100262.
Ebeed, H. T. 2022. Genome-wide analysis of polyamine biosynthesis genes in wheat reveals gene expression specificity and involvement of STRE and MYB-elements in regulating polyamines under drought. BMC genomics, 23(1):1-21.
Feng, L., Wei, L., Liu, Y., Hu, D., Gong, W., Liao, W.. 2023. Hydrogen peroxide is involved in methyl jasmonate-induced adventitious rooting in cucumber under cadmium stress. Scientia Horticulturae, 309:111666.
Ghorbani, A., Pishkar, L., Roodbari, N., Tavakoli, S. A., Jahromi, E. M., & Wu, C. 2022. Nitrate reductase is needed for methyl jasmonate-mediated arsenic toxicity tolerance of rice by modulating the antioxidant defense system, glyoxalase system and arsenic sequestration mechanism. Journal of Plant Growth Regulation,1-13.
Jin, Y., Ding, X., Li, J., & Guo, Z. 2022. Isolation and characterization of wheat ice recrystallisation inhibition gene promoter involved in low temperature and methyl jasmonate responses. Physiology and Molecular Biology of Plants,1-11.
Qi, X., Di, Z., Li, Y., Zhang, Z., Guo, M., Tong, B., Lu, Y., Zhang, Y., & Zheng, J. 2022. Genome-wide identification and expression profiling of heat shock protein 20 gene family in sorbus pohuashanensis (Hance) Hedl under abiotic stress. Genes, 13(12):2241.
Qiu, X., Zhao, H., Abubakar, A.S., Shao, D., Chen, J., Chen:, Yu, C., Wang, X., Chen, K., & Zhu, A. 2022. Genome-wide analysis of AP2/ERF fene superfamily in ramie (Boehmeria nivea L.) revealed their synergistic roles in regulating abiotic stress resistance and ramet development. International Journal of Molecular Sciences, 23(23):15117.
Ren, C., Kuang, Y., Lin, Y., Guo, Y., Li, H., Fan:, Li, S., & Liang, Z. 2022. Overexpression of grape ABA receptor gene VaPYL4 enhances tolerance to multiple abiotic stresses in Arabidopsis. BMC Plant Biology, 22(1):1-14.
Saharan, B. S., Brar, B., Duhan, J. S., Kumar, R., Marwaha, S., Rajput, V. D., & Minkina, T. 2022. Molecular and physiological mechanisms to mitigate abiotic stress conditions in plants. Life, 12(10):1634.
She, K., Pan, W., Yan, Y., Shi, T., Chu, Y., Cheng, Y., Ma, B., & Song, W. 2022. Genome-wide identification, evolution and expressional analysis of OSCA gene family in barley (Hordeum vulgare L.). International Journal of Molecular Sciences, 23(21):13027.
Shen, W., Song, Z., Zhong, X., Huang, M., Shen, D., Gao, P., Qian, X., Wang, M., He, X., Wang, T., & Li, S. 2022. Sangerbox: A comprehensive, interaction‐friendly clinical bioinformatics analysis platform. Imeta,1(3):e36.
Soliman, S., Wang, Y., Han, Z., Pervaiz, T. and El-Kereamy, A. 2022. Strigolactones in plants and their interaction with the ecological nicrobiome in response to abiotic stress. Plants, 11(24): 3499.
Tariq, R., Hussain, A., Tariq, A., Khalid, M. H. B., Khan, I., Basim, H., & Ingvarsson, K. 2022. Genome-wide analyses of the mung bean NAC gene family reveals orthologs, co-expression networking and expression profiling under abiotic and biotic stresses. BMC Plant Biology, 22(1):1-18.
Verslues, P. E., Bailey-Serres, J., Brodersen, C., Buckley, T. N., Conti, L., Christmann, A., Dinneny, J. R., Grill, E., Hayes, S., Heckman, R. W., & Hsu, P. K. 2023. Burning questions for a warming and changing world: 15 unknowns in plant abiotic stress. The Plant Cell. 35(1):67-108.
Cereal Biotechnology and Biochemistry
Volume 1, Issue 4 - Serial Number 4
December 2022
Pages 510-521

Files

Share

How to cite

Statistics