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The comparative analysis of phenotypic and whole transcriptome gene expression data of ascites susceptible versus ascites resistant chickens

  • Karim Hasanpur
  • Mohammadreza Nassiri
  • Ghasem Hosseini Salekdeh
Original Article

Abstract

Ascites syndrome (AS) is a metabolic disorder that mainly occurs at later ages of meat-type chickens. Despite many research, there is no consensus about the origin of this syndrome. Our main purpose were to investigate the syndrome using both phenotypic and RNA-Seq data to elucidate the most causative factors predisposing the birds to AS. Phenotypic data analysis showed that AS indicator traits (AITs) were moderate to high heritable. Inexistence of consistent direct genetic correlation between AITs and growth related traits, indicated that neither faster growth rate nor heavier body weight is the most causative factor affecting the susceptibility of broilers to AS. However, respiratory capacity was revealed to be the most probable factor predisposing the birds to AS, as both lung weight and lung percentage were negatively correlated with AITs. Transcriptomic data analysis revealed 125 differentially expressed genes (DEGs) between the ascitic and healthy groups. Up-regulated genes in ascitic group enriched mainly in gas transport biological process, while down-regulated genes involved in defense response to bacteria, biological adhesion, cell adhesion, killing of cells of another organism and cell division. Genetic association of the DEGs with human cardiovascular diseases suggested excessive heart problems of the ascitic chicks. Heart is, probably, the first tissue suffering from the incompetence of small respiratory system of the AS-susceptible chickens. In other word, tissue hypoxia, that causes free radicals to concentrate in heart cells, may be the commencement of events that finally result to heart failure, suffocation and death of chicks due to the AS.

Keywords

Gene expression profile Ascites RNA-seq Ascites indicator traits 

Notes

Acknowledgements

We cordially acknowledge Dr. Hamid Varnaseri, director of NDJ Co, Tehran, Iran, and staffs of the Pure Broiler Breeder Lines Co., Babolkenar, Iran for their technical assistance and for providing the pedigreed chickens for the current study.

Author contributions

KH drafted the manuscript and carried out the field work. GHS advised the laboratory work. KH and GHS designed the work and did the statistical and bioinformatics analysis. MN supervised the work and proof read the final manuscript. All authors read and approved the final manuscript.

Compliance with ethical standards

Conflict of interest

The authors declare that there is no conflict of interest.

Supplementary material

11033_2018_4534_MOESM1_ESM.png (56 kb)
Supplementary material 1 (PNG 55 KB). Supplementary Figure 1. Distribution of reads over genome DNA strands
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Supplementary material 2 (PNG 63 KB). Supplementary Figure 2. Distribution of reads over different gene feature positions
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Supplementary material 3 (PNG 11 KB). Supplementary Figure 3. IGV snapshot figure 1 from some of the un-annotated genes
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Supplementary material 4 (PNG 16 KB). Supplementary Figure 4. IGV snapshot figure 2 from some of the un-annotated genes
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Supplementary material 5 (PNG 22 KB). Supplementary Figure 5. IGV snapshot figure 3 from some of the un-annotated genes
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Supplementary material 6 (PNG 20 KB). Supplementary Figure 6. IGV snapshot figure 4 from some of the un-annotated genes
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Supplementary material 7 (PNG 21 KB). Supplementary Figure 7. IGV snapshot figure 5 from some of the un-annotated genes
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Supplementary material 8 (PNG 25 KB). Supplementary Figure 8. Significantly enriched pathway 1
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Supplementary material 9 (PNG 34 KB). Supplementary Figure 9. Significantly enriched pathway 2
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Supplementary material 10 (PNG 34 KB). Supplementary Figure 10. Significantly enriched pathway 3
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Supplementary material 11 (PNG 29 KB). Supplementary Figure 11. Significantly enriched pathway 4
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Supplementary material 12 (DOCX 13 KB). Supplementary Table 1. Ingredients of diets used during the rearing period
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Supplementary material 13 (DOCX 21 KB). Supplementary Table 2. The list of differentially expressed genes between the ascitic and non-ascitic healthy groups
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Supplementary material 14 (DOCX 16 KB). Supplementary Table 3. The list of differentially expressed isoforms between the ascitic and non-ascitic healthy groups
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Supplementary material 15 (DOCX 20 KB). Supplementary Table 4. The list of differentially expressed transcription start site (TSS) between the ascitic and non-ascitic healthy groups
11033_2018_4534_MOESM16_ESM.docx (15 kb)
Supplementary material 16 (DOCX 15 KB). Supplementary Table 5. The list of differentially expressed coding sequence (CDS) between the ascitic and non-ascitic healthy groups

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Copyright information

© Springer Nature B.V. 2018

Authors and Affiliations

  • Karim Hasanpur
    • 1
  • Mohammadreza Nassiri
    • 2
  • Ghasem Hosseini Salekdeh
    • 3
  1. 1.Department of Animal Science, Faculty of AgricultureUniversity of TabrizTabrizIran
  2. 2.Department of Animal ScienceFerdowsi University of MashhadMashhadIran
  3. 3.Agricultural Biotechnology Research Institute of Iran (ABRII)Agricultural Research, Education and Extension Organization (AREEO)KarajIran

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