فهرست مطالب a.a. masoudi

Fatty Liver Hemorrhagic Syndrome (FLHS) is common in poultry. Long non-coding RNAs (lncRNAs) regulate gene expression in a variety of ways at epigenetic, chromatin remodeling, transcriptional, and translational levels. Chicken liver produces lipoproteins and most of the precursors to egg yolk with the help of RNA such as MicroRNAs (miRNAs) and lncRNAs. In order to analyze lncRNAs in liver, RNA-seq data of six samples were downloaded from National Center for Biotechnology Information (NCBI) (3 birds with fatty livers from the paternal group and 3 control birds).Then, using the DESeq2 package, the difference in expression of lncRNAs in the samples was analyzed. Functional enrichment analysis was established by STRING and the PPI network visualized by Cytoscape. Annotation of the data was carried out by DAVID 6.8. The biological pathways were searched in Kyoto Encyclopedia of Genes and Genomes (KEGG). The results of the analysis of Differentially Expressed Genes (DEGs) showed that there were 24356 annotated genes. Also, 101 lncRNAs were found. Gene Ontology (GO) term enrichment analysis suggested that DEGs significantly enriched in metallocarboxypeptidase activity, protein ubiquitination, etc. KEGG pathway analysis showed that DEGs related with biosynthesis of antibiotics and biosynthesis of amino acids (P< 0.05). Examination of gene loci revealed that the expression process of GCGR, PDK3 and PCK1 genes was in line with the expression of neighboring lncRNAs. Examination of this number of lncRNAs along with their target genes can help in selecting laying hen lines with less chance of developing fatty livers.

Mating in honeybees causes dramatic changes not only in its behavior and physiology but in genes’ transcriptional level. To determine the molecular mechanisms regulating post-mating behavioral changes, we examined gene expression modification and exon-specific expression of the virgin queen versus the queen injected with semen in hemocoel. The DESeq2 package of R was used to identify the Differentially Expressed Genes (DEGs). The DEGs were selected for functional enrichment analysis and Protein-Protein Interaction (PPI) network construction. We also performed differential exon usage analysis using the DEXseq R package. Results identified a significant expression (FDR< 0.05) of a total of 971 genes between two groups of insects. The mating process produced significant changes in the expression of cell surface receptor signaling pathway, innate immune response, extracellular region, proteinaceous extracellular matrix, nucleous, G-protein coupled receptor activity, heme binding, and transmembrane transporter activity genes. Protein-Protein Interaction (PPI) network shows that LOC552504 (titin-like) could be considered as a super-hub gene in the mating process of queens. In addition, we identified exons that were differentially expressed in two groups of honeybee queens. At 10% FDR, we found significant differential exon usage in 79 genes. Among them, GB55396 gene had the most differences in exon usage and could be the best candidate gene for mating and reproductive activation in queens.

Alternative splicing, alternative transcript start site, and alternative transcript polyadenylation site are the main factors resulting in diversity of the transcripts of a gene. The main objectives of this study were to analyze the alternation process in breeds of sheep and goat, and to identify its role in differentiation of breeds of a species. RNA-seq data were prepared from ovarian tissue of two breeds of Shal and Sangsari sheep and two breeds of Tibetan and Jintang black goats. Reads were aligned to the reference genome and significant genes with respect to differential exon usage were identified. The statistical comparison revealed that 8,104 genes were significantly different in exon usage between the sheep breeds and 173 genes differed between the goat breeds. Out of the 121,861 studied exons, only 22.7% were preserved during future generations between the breeds, of which 99.3% did not display any alternatives. The high protection was probably due to the lack of involvement of the exons in alternative process. The genes with differential exon usage in goat had a higher percentage of alternatives than those in sheep. The interracial analysis showed that alternative splicing was the most influential type of alternatives in the breeds of sheep and goats. It seems that the conservation process of the exons is related to the contribution of these exons in alterative process in both sheep and goat breeds. The significant PI3K-Akt and alternative splicing pathways play a role in cell growth, development of ovaries, and mRNAs splicing.

Pedigree information of Iranian Holstein dairy cattle، collected via Animal Breeding Centre of Iran from 1971 to 2007، were utilized to describe the reasons for the increasing inbreed coefficient. Inbreeding coefficient (F) and Pedigree Completeness (PCI) of all the available cattle were found out using a pedigree structure of 883713 animals. The herds with PCI of above 0. 85 were picked out and divided into two groups، one group (G1) with high F (and PCI=0. 97) and the other (G2) with low F (and PCI=0. 95). For each group، a reference population (animals born within years 2002 to 2007) was defined and the pedigree traced back. The number of individuals picked out from the pedigree were 35638 and 41850، for G1 and G2 respectively. The probability of gene origin (effective number of founders، founder genome equivalent and non-founders) were estimated for both groups. The number of founders، effective number of founders، founder genome equivalent، non-founders، and the number of founders، contributing to 50% of the gene pool of reference population were recorded as 5226، 296. 84، 9. 31، 9. 61، and 134 in G1 and while 7562، 331. 46، 16. 78، 17. 67، and 153 in G2، respectively. The results finally indicated that the higher inbreeding coefficient in Iranian Holstein may be attributed to a small number of effective founders.