Volume 15, Issue 4 (12-2024)
Res Anim Prod 2024, 15(4): 93-106 |
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Fazeli Moghadam N, Rahimi Miyanji G, Farhadi A, Nejati Jawarami A, Younesi Melardi E. (2024). Identification of Genetic Variants Based on Single Nucleotide Polymorphisms and Insertion-Deletion Events in TLR8, IRF10b, and GAPDH Genes Related to the Immune System in Rainbow Trout Using Transcriptomic Data
.. Res Anim Prod. 15(4), 93-106. doi:10.61186/rap.15.4.93
URL: http://rap.sanru.ac.ir/article-1-1444-en.html
URL: http://rap.sanru.ac.ir/article-1-1444-en.html
Najmeh Fazeli Moghadam *1 
, Ghodrat Rahimi Miyanji1, Ayoub Farhadi1, Ardeshir Nejati Jawarami2, Elham Younesi Melardi3
, Ghodrat Rahimi Miyanji1, Ayoub Farhadi1, Ardeshir Nejati Jawarami2, Elham Younesi Melardi3
1- Department of Animal Sciences, Sari University of Agricultural Sciences and Natural Resources, Sari, Iran
2- Department of Animal Sciences, Faculty of Agriculture, University of Tehran, Karaj, Iran
3- Sari University of Agricultural Sciences and Natural Resources, Sari, Iran
2- Department of Animal Sciences, Faculty of Agriculture, University of Tehran, Karaj, Iran
3- Sari University of Agricultural Sciences and Natural Resources, Sari, Iran
Abstract: (634 Views)
Extended Abstract
Background: Viral hemorrhagic septicemia (VHS) is one of the most common viral diseases in the rainbow salmon farming industry, which causes heavy economic losses. Rainbow trout’s importance in the Iranian aquaculture industry, on the one hand, and the increase in deaths due to the spread of infectious diseases, on the other hand, highlight the need for further understanding of the fish immune system and obtaining a tool to accurately diagnose the causes of diseases in this fish species. The control and prevention of disease outbreaks in farmed fish requires the implementation of a regular diagnosis and treatment program, for which molecular markers can be useful as a monitoring and diagnostic tool. Recent studies have shown that computational approaches to identify sequenced RNA variants are very efficient and cost-effective methods for tracking genomic diversity. Some variants based on single nucleotide polymorphisms (SNPs), including synonymous, non-synonymous, and non-coding, as well as insertion-deletion (InDel) events resulting in RNA sequencing data, can be used as a desirable genetic marker in genetic differentiation analysis, especially in investigating allele-specific expression. The present study aimed to identify genetic variants based on SNP and InDel occurrence using transcriptomic data in some genes expressed in rainbow trout treated with the VHS virus.
Methods: RNA sequencing data from the spleen tissue of rainbow trout treated with the VHS virus was used in this research. Quality control and alignment of readings were done using FastQC and STAR software, respectively. A set of bioinformatics tools (GATK) was used to identify SNPs and InDels. Variants were identified in the first step using GTAK HaplotypeCaller, and the GTAK Variant Filtration tool was used in the next step to increase the accuracy and filtering of the initially identified SNPs. After filtering, the detected variants were annotated and identified using SnpEff software. In the final step, the genes related to the three main genes (TLR8, IRF10, and GAPDH) were identified using STRING software, and the gene network was drawn based on these three genes. The GAPDH gene was considered the main gene.
Results: In this research, genomic variants of SNPs and InDel events in three TLR8, IRF10b, and GAPDH genes, which are related to the immune system, were identified and reported in rainbow trout for the first time. In total, 72 SNPs and 15 InDels in the TLR8 gene, 20 SNPs and 3 InDels in the IRF10 gene, and 21 SNPs and 8 InDels in the GAPDH gene were identified in this study. In the TLR8 gene locus, 9.7 and 2.8% of SNP variants were detected upstream and downstream of this gene, respectively, and the occurrence of InDel was equal to 26.7%, which was detected in both upstream and downstream of this gene. In the IRF10 gene locus, 10 and 65% of SNP variants were detected upstream and downstream, respectively, and only 33.3% of InDel events were detected downstream of this gene. In the GAPDH downstream gene position, each of the SNP and InsDel variants was detected with frequencies equal to 47.6% and 12.5%, respectively, only in the downstream site of this gene. None of these types of variants were identified in the upstream site of the GAPDH gene.
Conclusion: One of the essential research works in deciphering phenotypic and genotypic maps in domestic animals is to identify specific alleles in gene regulation. In this regard, the first step is to track the genomic variants in the expressed genes. The analysis of the results in this research showed that the location, type, and frequency of genetic variants were different in each of the studied marker sites. According to the identification of variants based on SNP and the occurrence of InDel in the three TLR8, IRF10b, and GAPDH genes, the results can be used in breeding programs using the MAS technique against viral infections, such as VHS, and in the design of SNP chips in fish species. Since the different variants identified in each of the studied marker sites have a regulatory role, it is very important to investigate the effect of each of them on allele-specific expression. Furthermore, acquiring information on genes involved in the immune system, identifying molecular markers associated with these loci, and studying the correlation between these loci and quantitative traits can be used in designing breeding programs in the fish farming industry to produce disease-resistant strains.
Background: Viral hemorrhagic septicemia (VHS) is one of the most common viral diseases in the rainbow salmon farming industry, which causes heavy economic losses. Rainbow trout’s importance in the Iranian aquaculture industry, on the one hand, and the increase in deaths due to the spread of infectious diseases, on the other hand, highlight the need for further understanding of the fish immune system and obtaining a tool to accurately diagnose the causes of diseases in this fish species. The control and prevention of disease outbreaks in farmed fish requires the implementation of a regular diagnosis and treatment program, for which molecular markers can be useful as a monitoring and diagnostic tool. Recent studies have shown that computational approaches to identify sequenced RNA variants are very efficient and cost-effective methods for tracking genomic diversity. Some variants based on single nucleotide polymorphisms (SNPs), including synonymous, non-synonymous, and non-coding, as well as insertion-deletion (InDel) events resulting in RNA sequencing data, can be used as a desirable genetic marker in genetic differentiation analysis, especially in investigating allele-specific expression. The present study aimed to identify genetic variants based on SNP and InDel occurrence using transcriptomic data in some genes expressed in rainbow trout treated with the VHS virus.
Methods: RNA sequencing data from the spleen tissue of rainbow trout treated with the VHS virus was used in this research. Quality control and alignment of readings were done using FastQC and STAR software, respectively. A set of bioinformatics tools (GATK) was used to identify SNPs and InDels. Variants were identified in the first step using GTAK HaplotypeCaller, and the GTAK Variant Filtration tool was used in the next step to increase the accuracy and filtering of the initially identified SNPs. After filtering, the detected variants were annotated and identified using SnpEff software. In the final step, the genes related to the three main genes (TLR8, IRF10, and GAPDH) were identified using STRING software, and the gene network was drawn based on these three genes. The GAPDH gene was considered the main gene.
Results: In this research, genomic variants of SNPs and InDel events in three TLR8, IRF10b, and GAPDH genes, which are related to the immune system, were identified and reported in rainbow trout for the first time. In total, 72 SNPs and 15 InDels in the TLR8 gene, 20 SNPs and 3 InDels in the IRF10 gene, and 21 SNPs and 8 InDels in the GAPDH gene were identified in this study. In the TLR8 gene locus, 9.7 and 2.8% of SNP variants were detected upstream and downstream of this gene, respectively, and the occurrence of InDel was equal to 26.7%, which was detected in both upstream and downstream of this gene. In the IRF10 gene locus, 10 and 65% of SNP variants were detected upstream and downstream, respectively, and only 33.3% of InDel events were detected downstream of this gene. In the GAPDH downstream gene position, each of the SNP and InsDel variants was detected with frequencies equal to 47.6% and 12.5%, respectively, only in the downstream site of this gene. None of these types of variants were identified in the upstream site of the GAPDH gene.
Keywords: Genetic Markers, InDel, Rainbow Trout, RNA-sequencing, SNP, Viral Hemorrhagic septicemia (VHS)
Type of Study: Research |
Subject:
ژنتیک و اصلاح نژاد دام
Received: 2024/02/22 | Accepted: 2024/06/15
Received: 2024/02/22 | Accepted: 2024/06/15
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