Bioinformatics analysis of differentially gene expression profiles related to heat stress in brain, liver, and leg muscle of broiler chickens based on microarray technique

Document Type : Research Paper

Authors

1 Department of Basic Science, Faculty of Veterinary Medicine, University of Tabriz, Tabriz, Iran

2 Department of Animal Sciences, Faculty of Agriculture, University of Tabriz, Tabriz, Iran

3 Department of Animal Science, College of Agriculture and Natural Resources, University of Tehran, Karaj, Iran

4 Iranian Fisheries Science Research Institute, Agricultural Research Education and Extension Organization (AREEO), Ahvaz, Iran

5 Agri-Food and Biosciences Institute, Hillsborough, UK and Assistant professor, School of Biological Sciences, Queen’s University Belfast, Belfast, UK

Abstract

In the poultry industry, the heat stress caused by high environmental temperature has a negative influence on broiler chicken performance and has become a major challenge. Transcriptome profile analysis of the data and identification of patterns of differential gene expression in related tissues can be involved in the discovery of molecular mechanisms resistant to heat stress. The main purpose of this study was to use transcriptome profiles of three tissues brain, liver, and leg muscle of two groups of the control and heat stress broiler chickens to identify candidate genes associated with heat stress. By the analysis of microarray data to express the gene differences, 657 significant genes (P<0.05) were extracted, which a total of 94 genes showed significant expression differences (FDR < 0.05, Fold change > ± 2). Then, by studying the ontology of the relevant genes resulting from data analysis and literature mining as well as the reconstructed protein-protein interaction network, hub genes including NSDHL, DHCR24, LSS, FDPS, PCK1, ACTA1, HSP90AA1, HSPA2, HSPB1, HSF1, CRYAB, APOB, and IL6 were identified. Annotation results of these genes indicated that they have a role in the main process of metabolic and signaling pathways related to the ion transport system, steroid, antibodies, cholesterol biosynthesis, lipid metabolism, immune system function, and various signaling pathways such as MAP kinase, RET, and ERK. Overall, the present study can provide new insights into evidence of the pathways activated by these genes to identify effective genes and a better understanding of biological processes related to heat stress.

Keywords

Main Subjects

Extended Abstract

Introduction

Transcriptome analysis is an important and valuable tool for identifying genes and their function in the mechanism of action of heat stress and for identifying the inherent genetic mechanisms to deal with it. Transcriptome analysis is actually a method of determining and identifying gene activity and expression. Using the resulting gene expression pattern, it is possible to uncover how biological systems are regulated at the transcriptional level. Therefore, the main objective of the current research is to identify candidate genes, using the analysis of samples based on microarray technology, in relation to the three tissues brain, liver and thigh muscles in two groups of broilers under control and under heat stress, to verify their expression levels as significant expression in the control group compared to those under heat stress.

 

Materials and Methods

This dataset contains the expression information of three tissues of brain, liver and thigh muscles belonging to the research of China in 2012. For each tissue, a total of 6 specimens (three specimens as control (at a temperature of 281 °C in the growth hall) and three specimens under heat stress (at a temperature of 401 °C in the growth hall), totaling 18 specimens, were used. Analysis of microarray data on expression of gene differences extracted 657 significant genes (P<0.05). with a total of 94 genes that show significant differences in expression (FDR < 0.05, fold change > 2). Subsequently, the ontology of the relevant genes emerging from the data analysis and literature review as well as the reconstructed protein-protein interaction network is examined.

 

Results and discussion

Interestingly, the results of this work highlighted different hub genes NSDHL, DHCR24, LSS, FDPS, PCK1, ACTA1, HSP90AA1, HSPA2, HSPB1, HSF1, CRYAB, APOB and IL6. Annotation results of these genes indicate that they play a role in the main process of metabolic and signaling pathways related to ion transport system, steroids, antibodies, cholesterol biosynthesis, lipid metabolism, immune system function and various signaling pathways such as MAP kinase. RET and ERK.

 

Conclusion

In general, identified genes (particularly hub genes) from data analysis and resource review in various metabolic and signaling pathways related to the ion transport system, steroid, antibody and cholesterol biosynthesis, lipid metabolism, immune system function, and various signaling pathways. Like MAP kinase, RET, and ERK play a role that may help improve our understanding of the important role of the three tissues brain, liver, and thigh muscles in performance and resilience to thermal stress in poultry and provide important molecular evidence for this association The level of gene expression in these tissues, along with other layers of omics, may lead to genetic enhancement of this trait in broilers and breeding strategies in the poultry industry.

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Iranian Journal of animal Science
Volume 54, Issue 3
October 2023
Pages 203-223

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History

  • Receive Date: 30 November 2021
  • Revise Date: 02 August 2022
  • Accept Date: 05 August 2022

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