The purpose of the current study was to examine transcriptomic-based profiling of differentially expressed innate immune genes between indigenous and commercial chickens. In order to compare the transcriptome profiles of the different chicken breeds, we extracted RNA from blood samples of the Isfahan indigenous chicken (as indigenous) and Ross broiler chicken (as commercial) breeds. RNA-Seq yielded totals of 36,763,939 and 31,545,002 reads for the indigenous and commercial breeds, respectively, with clean reads then aligned to the chicken reference genome (Galgal5). Overall, 1327 genes were significantly differentially expressed, of which 1013 genes were upregulated in the commercial versus the indigenous breed, while 314 were more highly expressed in the indigenous birds. Furthermore, our results demonstrated that the SPARC, ATP6V0D2, IL4I1, SMPDL3A, ADAM7, TMCC3, ULK2, MYO6, THG1L and IRG1 genes were the most significantly expressed genes in the commercial birds and the PAPPA, DUSP1, PSMD12, LHX8, IL8, TRPM2, GDAP1L1, FAM161A, ABCC2 and ASAH2 genes were the most significant in the indigenous chickens. Of notable finding in this study was that the high-level gene expressions of heat-shock proteins (HSPs) in the indigenous breeds could serve as a guideline for future genetic improvement. This study identified genes with breed-specific expression, and comparative transcriptome analysis helped understanding of the differences in underlying genetic mechanisms between commercial and local breeds. Therefore, the current results can be used to identify candidate genes for further breed improvement.

The present study was aimed at identifying causative hub genes within modules formed by co-expression and protein–protein interaction (PPI) networks, followed by Bayesian network (BN) construction in the liver transcriptome of starved zebrafish. To this end, the GSE11107 and GSE112272 datasets from the GEO databases were downloaded and meta-analyzed using the MetaDE package, an add-on R package. Differentially expressed genes (DEGs) were identified based upon expression intensity N(µ = 0.2, σ² = 0.4). Reconstruction of BNs was performed by the bnlearn R package on genes within modules using STRINGdb and CEMiTool. ndufs5 (shared among PPI, BN and COEX), rps26, rpl10, sdhc (shared between PPI and BN), ndufa6, ndufa10, ndufb8 (shared between PPI and COEX), skp1, atp5h, ndufb10, rpl5b, zgc:193613, zgc:123327, zgc:123178, wu:fc58f10, zgc:111986, wu:fc37b12, taldo1, wu:fb62f08, zgc:64133 and acp5a (shared between COEX and BN) were identified as causative hub genes affecting gene expression in the liver of starving zebrafish. Future work will shed light on using integrative analyses of miRNA and DNA microarrays simultaneously, and performing in silico and experimental validation of these hub-causative (CST) genes affecting starvation in zebrafish.

Background: Interleukie-8 is a proinflammatory cytokine and a potent chemotactic and activation factor for neutrophils. It has been reported to be expressed in high levels by various cell types after immune stimulation and mediates neutrophil recruitment in host. Objectives: The aim of this study was to analysis of the relationship between single nucleotide polymorphisms (SNPs) at position -180 G/A in the promoter region of bovine IL8 gene with milk production traits and somatic cell score (SCS). Materials and Methods: The part of promoter region in the bovine IL8 gene containing -180 G/A SNP was screened by single strand conformation polymorphism (SSCP) and DNA sequencing in Holstein cattle of Iran. The association analysis between different genotypes of IL8-180 SNP and performance traits of Holstein cattle was carried out by Mixed procedure of SAS 9.1 program. Results: A total of 3 distinct SSCP patterns were observed. Sequence analysis indicated a reported polymorphism at position -180 G/A relative to the start codon. This SNP created a putative binding site for Oct-1 transcription factor which associated with lower SCS. The association of IL8-180 genotypes was studied with milk production traits and SCS. The IL8-180 associated (P

Background: Tumor necrosis factor- a (TNF-α) is a cytokine that was identified as a factor with a wide range of proinflammatory activities. The expression of bovine TNF-α in mammary tissue during pregnancy seems to have a role in development of the corresponding glands.Objective: Single nucleotide polymorphisms (SNPs) were defined in 3′-flanking region of bovine TNF-α in cattle. Moreover, its association with performance traits in Holstein dairy cattle was evaluated.Materials and Methods: The 3′-flanking region of TNF-α was screened by single strand conformation polymorphism (SSCP) and DNA sequencing in Holstein cattle breed. SAS statistical software was used to analyze the relationship between different genotypes of amplified fragment with milk production traits (daily milk yield, fat and protein percentage) and somatic cell score (SCS).Results: A total of 6 distinct SSCP patterns were observed. It was further revealed to be 3 novel SNPs. Statistical analysis revealed that different haplotypes of amplified fragment in the TNF-α 3′-region had a significant effect on average daily milk production (p < 0.05), but no such correlation was established with fat percentage, protein percentage and SCS.Conclusion: The association identified in the 3′-flanking region of TNF-α may have potential to serve as candidate genetic marker for genomic selection in dairy cattle.