A comprehensive study of long noncoding genes associated with ascites syndrome in poultry

Document Type : Research Paper

Authors

1 Department of Animal Science, Faculty of Agriculture, University of Tabriz

2 Tabriz

Abstract

Objectives Objectives: Ascites syndrome occurs in growing broilers in all parts of the world and is a major cause of losses in many flocks. In addition to genetic and non-genetic factors, differential expression of genes in susceptible chickens compared to resistant chickens during or before onset of the disease is likely involved. This difference in gene expression can be influenced by long non-coding RNAs. Therefore, the aim of this research was to identify and discover long non-coding genes effective in ascites syndrome in four tissues of broilers.Ascites.
Materials and methods: Six data sets in four tissues (liver, kidney, heart and pulmonary artery) were used for this research. Hisat2 software was used to align the reads with chicken reference genome and Sting Tie software package was used to assemble the transcripts. To identify long non-coding genes, we used various software (CPC2, CNIT PLEK, FEELNC, PLIT) and BLAST methods. meta-RNAseq software and Fisher's method were used to perform meta-analysis.
Results: Examination of the results of this research revealed that 188 lncRNAs were detected in the examined tissues and identified as new long non-coding RNAs. Of these, 160 lncRNAs were located within 50,000 contiguous 689 genes. Coexpression analysis showed that there was a correlation of 0.9 between 13 lncRNAs and 17 neighboring genes. Of these 17 neighboring genes, 6 coding genes were known. Examination of the level of significance between the healthy group and the ascites group in the examined tissues showed that in the pulmonary artery tissue the expression of 4 genes was significantly different and these 4 adjacent coding genes with 3 lncRNAs, i.e. H. an lncRNA that controls two adjacent genes. In the meta-analysis, 9 lncRNA genes were differentially expressed between healthy chickens and ascites chickens.
Conclusion: The results of this research showed that lncRNAs play an important role in the
occurrence of ascites disease and that genetic management can reduce the occurrence of this
complication in poultry farms and control economic losses.
Key words: Ascites, Fisher, Long non-coding RNAs, Meta-analysis

Objectives Objectives: Ascites syndrome occurs in growing broilers in all parts of the world and is a major cause of losses in many flocks. In addition to genetic and non-genetic factors, differential expression of genes in susceptible chickens compared to resistant chickens during or before onset of the disease is likely involved. This difference in gene expression can be influenced by long non-coding RNAs. Therefore, the aim of this research was to identify and discover long non-coding genes effective in ascites syndrome in four tissues of broilers.Ascites.
Materials and methods: Six data sets in four tissues (liver, kidney, heart and pulmonary artery) were used for this research. Hisat2 software was used to align the reads with chicken reference genome and Sting Tie software package was used to assemble the transcripts. To identify long non-coding genes, we used various software (CPC2, CNIT PLEK, FEELNC, PLIT) and BLAST methods. meta-RNAseq software and Fisher's method were used to perform meta-analysis.
Results: Examination of the results of this research revealed that 188 lncRNAs were detected in the examined tissues and identified as new long non-coding RNAs. Of these, 160 lncRNAs were located within 50,000 contiguous 689 genes. Coexpression analysis showed that there was a correlation of 0.9 between 13 lncRNAs and 17 neighboring genes. Of these 17 neighboring genes, 6 coding genes were known. Examination of the level of significance between the healthy group and the ascites group in the examined tissues showed that in the pulmonary artery tissue the expression of 4 genes was significantly different and these 4 adjacent coding genes with 3 lncRNAs, i.e. H. an lncRNA that controls two adjacent genes. In the meta-analysis, 9 lncRNA genes were differentially expressed between healthy chickens and ascites chickens.
Conclusion: The results of this research showed that lncRNAs play an important role in the
occurrence of ascites disease and that genetic management can reduce the occurrence of this
complication in poultry farms and control economic losses.
Key words: Ascites, Fisher, Long non-coding RNAs, Meta-analysis

Objectives Objectives: Ascites syndrome occurs in growing broilers in all parts of the world and is a major cause of losses in many flocks. In addition to genetic and non-genetic factors, differential expression of genes in susceptible chickens compared to resistant chickens during or before onset of the disease is likely involved. This difference in gene expression can be influenced by long non-coding RNAs. Therefore, the aim of this research was to identify and discover long non-coding genes effective in ascites syndrome in four tissues of broilers.Ascites.
Materials and methods: Six data sets in four tissues (liver, kidney, heart and pulmonary artery) were used for this research. Hisat2 software was used to align the reads with chicken reference genome and Sting Tie software package was used to assemble the transcripts. To identify long non-coding genes, we used various software (CPC2, CNIT PLEK, FEELNC, PLIT) and BLAST methods. meta-RNAseq software and Fisher's method were used to perform meta-analysis.
Results: Examination of the results of this research revealed that 188 lncRNAs were detected in the examined tissues and identified as new long non-coding RNAs. Of these, 160 lncRNAs were located within 50,000 contiguous 689 genes. Coexpression analysis showed that there was a correlation of 0.9 between 13 lncRNAs and 17 neighboring genes. Of these 17 neighboring genes, 6 coding genes were known. Examination of the level of significance between the healthy group and the ascites group in the examined tissues showed that in the pulmonary artery tissue the expression of 4 genes was significantly different and these 4 adjacent coding genes with 3 lncRNAs, i.e. H. an lncRNA that controls two adjacent genes. In the meta-analysis, 9 lncRNA genes were differentially expressed between healthy chickens and ascites chickens.
Conclusion: The results of this research showed that lncRNAs play an important role in the
occurrence of ascites disease and that genetic management can reduce the occurrence of this
complication in poultry farms and control economic losses.
Key words: Ascites, Fisher, Long non-coding RNAs, Meta-analysis

Keywords

Main Subjects

References

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Animal Science Research
Volume 34, Issue 2
October 2024
Pages 31-44

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History

  • Receive Date: 26 June 2023
  • Revise Date: 30 January 2024
  • Accept Date: 30 January 2024

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