Gene Expression Network Analysis on Angiogenesis Pathway in Low Temperature-Induced Ascites Susceptible Chickens in B-line Pedigree of Iranian Meat-Type Strain, Arian

پژوهشهای علوم دامی ایران

Article 6, Volume 10, Issue 2 - Serial Number 34, June 2018, Pages 249-262   

Document Type: Genetics & breeding

DOI: 10.22067/ijasr.v10i2.65215

Authors

vahid taghizadeh^{* 1}; Mohammad Reza Nassiry²; Mojtaba Tahmoorespur³; Mohammad Reza Bakhtiarizadeh⁴; Ali Javadmanesh⁵

¹Department of Animal Science, Ferdowsi University of Mashhad, Mashhad, Iran

²Department of Animal Science, Faculty of Agriculture, Ferdowsi University of Mashhad, Mashhad, Iran

³Department of Animal Sciences, Faculty of Agriculture, Ferdowsi University of Mashhad, Mashhad, Iran

⁴Department of Animal Science, Aburaihan Campus, University of Tehran, Iran

⁵Department Animal Science, Faculty of agriculture, Ferdowsi University of Mashhad, Mashhad, Iran.

Abstract

Introduction
Ascites syndrome is a metabolic disorder in late ages of meat-type chickens. The only commercial broiler strain of Iran, Arian, has been incurred by this syndrome during a couple of decades ago. Due to susceptibility to ascites and some poor performance issues this strain are wiping out from indigenous market. Prevalence of ascites syndrome in commercial broiler of Arian is nearly 10% in average and in paternal lines it gets more fatality. Role of genetic factors in arising ascites has been proven by former researchers. Fighting against this syndrome through old methods are expensive and time consuming. Since presence of hypertrophy in a tissue needs to make facilities such as blood vessels to providing oxygen and nutrients so studying on angiogenesis pathway and its key important genes was directed. Whereas numerous organs engage the disease and among them heart has key role for initiating and developing the disease, so genomic study dealing with next generation sequencing (NGS) technology has been conducted to identify genes relating to angiogenesis and hypertrophy in right ventricle of ascites susceptible birds.
Materials and methods:
464 one-day-old chicks from B-line pedigree of Arian strain have been reared up to 21 days at the same rearing and nutritional conditions. At the age of 21 the rearing house was divided to 3 sections. Normal and cold sections at the ends of the house and buffer section at the middle. 464 chickens were transferred from normal to the cold section and kept the ambient temperature lower than 16 degrees for inducing ascites. 120 birds from cold section were selected randomly and slaughtered at the age of 42. Those of birds having ascites symptoms classified to ascites susceptible (As) and the other assigned to healthy (He). Samples of right ventricle was picked up and stored with RNAase-Later in liquid N tank. Then 12 As samples and 12 He samples were chosen for extracting total RNA by Biozol kit. After that every 6 samples in each groups pooled together and finally 2 As and 2 He samples prepared to make cDNA libraries for high throughput sequencer machine, Ilumina Hiseq 2000. RNA integrity score (RIN) were more than 7 for all samples. All small RNAs such as microRNAs, rRNAs and tRNAs were eliminated by oligo dt beads and finally all mRNAs was used for preparing library. cDNAs as long as 200 bp were selected for library. Sequencing has been done by BGI Company. For mapping, aligning, and DE analyzing several softwares were used such as: Tophat, cufflinks, cuffmerge and cuffdiff. Then significant DEGs imported to String for creating gene expression network and use DAVID 6.8 for investigation gene annotation and pathway analysis and finally Cytoscape v. 3.5.1 was used for network and cluster analysis.
Results and Discussion:
Nearly 90% of reads mapped on genome reference. In ascites group among 125 DEGs 79 genes was up-regulated and 46 loci was down-regulated. Among 125 significant differentially expressed genes (FDR

Keywords

Angiogenesis; Ascites; Gene Network; Gene Ontology; Pathway Analysis; RNA-seq

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