Department of Animal Science, Faculty of Agriculture, Tabriz University & and Animal Breeding, Department of Animal Science, Faculty of Agriculture, Tabriz University
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Extended Abstract
Introduction and Objective: To date, one of the main areas of research is the creation of breeds with inherent resistance to digestive nematodes in sheep. In this context, resistance to digestive nematodes has been found to exhibit significant phenotypic differences both within and between sheep breeds, suggesting a genetic basis for these differences. According to the list of effective candidate genes and the identified gene network for parasite resistance in sheep, there are genes involved in the immune system, such as the interferon-γ gene (IFN-γ). Cytokinin is involved in biochemical immune system signaling pathways, parasite resistance, and immunological responses. In addition, certain mutations in this gene impair the ability of specialized cells of the immune system to fight off parasite invasion. One of the most popular approaches to generating gene expression data for genome function studies is DNA microarray technology, which allows the simultaneous expression of thousands of genes. Proteomics and genomics are two application areas of microarray technology. This research aims to identify and categorize some of the genes involved in the relative genetic resistance of sheep to nematode infection using microarray data.
Material and Methods: In this context, the GEO-Bank, part of the NCBI, was searched for access to open-access databases and downloaded microarray data corresponding to the infection with parasitic nematodes with the best replication (e.g. data in two resistant and sensitive groups) and using R -based appropriate software packages (Biobase، GEOquery، limma، affy، Genfilter، Pheatmap، Plyr، Reshape2، Ggplot2) and identified the set of genes with differential expression. The raw data were measured in a logarithmic scale and also the P-value fit statistics were used for expression comparisons between gene groups.
Results: The main analysis was performed after precorrection and processing of the raw data because the data have high intragroup variance, as evidenced by the observed quality control results of the raw data and the quality control-related results of the integrated data. After pre-processing the raw data, correlation analysis revealed a strong relationship between genes in the pre-Inf group (Pre-Inf) and the infected group (Inf) compared to the control group. Three heatmap reference charts, a PCA chart, and a volcano plot were used to verify data quality, and by verifying these charts, samples of unfavorable quality were removed from the next stages of analysis. Finally, the results of this finding, after performing a bioinformatic analysis, showed a significantly different expression (NACA, RPL4, NAGS, CTCF, GBP1, BHLHE, YTHDF3, PDHA1, MXI1) and increased expression patterns and genes (PDHA1, MXI1). a diminished expression pattern. According to the results of this study, these genes play a role in the process of cellular metabolism, molecular function, the formation of genetic connections, and cell life. Therefore, they were significant (p-value < 0.05) according to the magnitude of the change. The NAGS gene is the N-acryl glutamate synthetase gene, which is the cofactor of the first enzyme involved in the urea cycle in mammals. The functional role of this gene has been identified in many neurological diseases. The CTCF gene has a positive effect on the cells of the immune system and plays a special role in defending against viruses and pathogens that invade the host body. The guanylate Bidenig protein GBP1 gene plays a role in the body's defense against many infectious pathogens. This gene causes oxidative reactions and autophagy of the host immune system becomes a barrier to invading pathogens. The methyl adenosine RNA Babding 3 gene is more effective in antiviral immunity and is also closely linked to the guanylate Bidnig protein gene, which plays a role in the body's resistance to many infectious agents. This gene causes oxidative responses and autophagy of the host immune system against invading pathogens. The PDHA1 pyruvate dehydrogenase gene is involved in immune system metabolism. This gene plays a role in allosteric factor-induced regulation, repair of covalent bonds, and relatively rapid changes in the level of expressed proteins, either through altered gene expression or proteolytic degradation. The MXI1 gene helps control the entry of invading pathogens into the host's body and promotes recovery and healing from infections. Several reasons can be given for the results, including the use of different sample breeds and laboratory techniques, the level of parasite contamination, the age of the test material, the variety of nematodes used, techniques and tools of the current study not being consistent with those of previous studies. On the other hand, he was aware of the climatic differences between the test region and its physical location as well as the use of different RNA and microarray methods. However, the results of the study may be helpful under the circumstances.
Conclusion: On this basis, the results of microarrays and differential expression patterns can be of great help to molecularly modify livestock to resist internal parasites. Using more advanced tools like next-gen sequencing will provide more accurate and relevant information.
Introduction and Objective: To date, one of the main areas of research is the creation of breeds with inherent resistance to digestive nematodes in sheep. In this context, resistance to digestive nematodes has been found to exhibit significant phenotypic differences both within and between sheep breeds, suggesting a genetic basis for these differences. According to the list of effective candidate genes and the identified gene network for parasite resistance in sheep, there are genes involved in the immune system, such as the interferon-γ gene (IFN-γ). Cytokinin is involved in biochemical immune system signaling pathways, parasite resistance, and immunological responses. In addition, certain mutations in this gene impair the ability of specialized cells of the immune system to fight off parasite invasion. One of the most popular approaches to generating gene expression data for genome function studies is DNA microarray technology, which allows the simultaneous expression of thousands of genes. Proteomics and genomics are two application areas of microarray technology. This research aims to identify and categorize some of the genes involved in the relative genetic resistance of sheep to nematode infection using microarray data.
Material and Methods: In this context, the GEO-Bank, part of the NCBI, was searched for access to open-access databases and downloaded microarray data corresponding to the infection with parasitic nematodes with the best replication (e.g. data in two resistant and sensitive groups) and using R -based appropriate software packages (Biobase، GEOquery، limma، affy، Genfilter، Pheatmap، Plyr، Reshape2، Ggplot2) and identified the set of genes with differential expression. The raw data were measured in a logarithmic scale and also the P-value fit statistics were used for expression comparisons between gene groups.
Results: The main analysis was performed after precorrection and processing of the raw data because the data have high intragroup variance, as evidenced by the observed quality control results of the raw data and the quality control-related results of the integrated data. After pre-processing the raw data, correlation analysis revealed a strong relationship between genes in the pre-Inf group (Pre-Inf) and the infected group (Inf) compared to the control group. Three heatmap reference charts, a PCA chart, and a volcano plot were used to verify data quality, and by verifying these charts, samples of unfavorable quality were removed from the next stages of analysis. Finally, the results of this finding, after performing a bioinformatic analysis, showed a significantly different expression (NACA, RPL4, NAGS, CTCF, GBP1, BHLHE, YTHDF3, PDHA1, MXI1) and increased expression patterns and genes (PDHA1, MXI1). a diminished expression pattern. According to the results of this study, these genes play a role in the process of cellular metabolism, molecular function, the formation of genetic connections, and cell life. Therefore, they were significant (p-value < 0.05) according to the magnitude of the change. The NAGS gene is the N-acryl glutamate synthetase gene, which is the cofactor of the first enzyme involved in the urea cycle in mammals. The functional role of this gene has been identified in many neurological diseases. The CTCF gene has a positive effect on the cells of the immune system and plays a special role in defending against viruses and pathogens that invade the host body. The guanylate Bidenig protein GBP1 gene plays a role in the body's defense against many infectious pathogens. This gene causes oxidative reactions and autophagy of the host immune system becomes a barrier to invading pathogens. The methyl adenosine RNA Babding 3 gene is more effective in antiviral immunity and is also closely linked to the guanylate Bidnig protein gene, which plays a role in the body's resistance to many infectious agents. This gene causes oxidative responses and autophagy of the host immune system against invading pathogens. The PDHA1 pyruvate dehydrogenase gene is involved in immune system metabolism. This gene plays a role in allosteric factor-induced regulation, repair of covalent bonds, and relatively rapid changes in the level of expressed proteins, either through altered gene expression or proteolytic degradation. The MXI1 gene helps control the entry of invading pathogens into the host's body and promotes recovery and healing from infections. Several reasons can be given for the results, including the use of different sample breeds and laboratory techniques, the level of parasite contamination, the age of the test material, the variety of nematodes used, techniques and tools of the current study not being consistent with those of previous studies. On the other hand, he was aware of the climatic differences between the test region and its physical location as well as the use of different RNA and microarray methods. However, the results of the study may be helpful under the circumstances.
Conclusion: On this basis, the results of microarrays and differential expression patterns can be of great help to molecularly modify livestock to resist internal parasites. Using more advanced tools like next-gen sequencing will provide more accurate and relevant information.
Type of Study: Research |
Subject:
ژنتیک و اصلاح نژاد دام
Received: 2023/04/24 | Revised: 2023/10/29 | Accepted: 2023/10/30
Received: 2023/04/24 | Revised: 2023/10/29 | Accepted: 2023/10/30
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