Genomic Landscape of Copy Number Variations and Their Associations with Climatic Variables in the World's Sheep.

Sheep show characteristics of phenotypic diversity and adaptation to diverse climatic regions. Previous studies indicated associations between copy number variations (CNVs) and climate-driven adaptive evolution in humans and other domestic animals. Here, we constructed a genomic landscape of CNVs (n = 39,145) in 47 old autochthonous populations genotyped at a set of high-density (600 K) SNPs to detect environment-driven signatures of CNVs using a multivariate regression model. We found 136 deletions and 52 duplications that were significantly (Padj. < 0.05) associated with climatic variables. These climate-mediated selective CNVs are involved in functional candidate genes for heat stress and cold climate adaptation (e.g., B3GNTL1, UBE2L3, and TRAF2), coat and wool-related traits (e.g., TMEM9, STRA6, RASGRP2, and PLA2G3), repairing damaged DNA (e.g., HTT), GTPase activity (e.g., COPG), fast metabolism (e.g., LMF2 and LPIN3), fertility and reproduction (e.g., SLC19A1 and CCDC155), growth-related traits (e.g., ADRM1 and IGFALS), and immune response (e.g., BEGAIN and RNF121) in sheep. In particular, we identified significant (Padj. < 0.05) associations between probes in deleted/duplicated CNVs and solar radiation. Enrichment analysis of the gene sets among all the CNVs revealed significant (Padj. < 0.05) enriched gene ontology terms and pathways related to functions such as nucleotide, protein complex, and GTPase activity. Additionally, we observed overlapping between the CNVs and 140 known sheep QTLs. Our findings imply that CNVs can serve as genomic markers for the selection of sheep adapted to specific climatic conditions.

Effect of dietary inclusion of atorvastatin, garlic, and dill on growth performance, antioxidant defense, gut, and cardio-pulmonary function, and lipogenesis in broiler chickens.

In the present study, we evaluated the antihyperlipidemic and antioxidant effects of garlic and dill in comparison with atorvastatin to combat lipogenesis in broiler chickens. A total of 400 1-day-old chicks (Ross 308 strain) were randomly distributed into four experimental diets. Dietary treatments included a control diet, the control diet plus atorvastatin at 20 mg/kg, the control diet plus garlic dry powder (GDP) at 7.5 g/kg, and the control diet plus dill dry powder (DDP) at 7.5 g/kg. Chicks were maintained on experimental diets for 42 days under the recommended environmental conditions set out by the strain management manual. The results showed that weight gain, feed conversion ratio (FCR), and duodenal, jejunal, and ileal dimensions of villi (height, width, and the surface absorptive area) were improved by in-feed atorvastatin, GDP, or DDP when compared to the control (P < 0.05). The inclusion of atorvastatin or phytobiotic products increased circulatory levels of nitric oxide (NO) but decreased circulatory levels of malondialdehyde (MDA), triacylglycerol (TAG), and low-density lipoproteins cholesterol (LDL), with concomitant reductions in the T, R, and S waves amplitudes in the Lead 2 electrocardiogram (ECG) (P < 0.05). Dietary supplements caused an up-regulation of inducible nitric oxide synthase (iNOS), superoxide dismutase 1 (SOD1), and glutathione peroxidase (GPX) but reduced the expression of key hepatic lipogenic enzymes (fatty acid synthase (FAS) and hydroxy-methylglutaryl-CoA reductase (HMGCR) (P < 0.05). In conclusion, feed supplementation with atorvastatin, GDP, or DDP suppressed lipogenesis, enhanced antioxidant response, and improved gut and cardio-pulmonary function in broiler chicks subjected to hypobaric hypoxia.

Multi-Omics Integration and Network Analysis Reveal Potential Hub Genes and Genetic Mechanisms Regulating Bovine Mastitis.

Mastitis, inflammation of the mammary gland, is the most prevalent disease in dairy cattle that has a potential impact on profitability and animal welfare. Specifically designed multi-omics studies can be used to prioritize candidate genes and identify biomarkers and the molecular mechanisms underlying mastitis in dairy cattle. Hence, the present study aimed to explore the genetic basis of bovine mastitis by integrating microarray and RNA-Seq data containing healthy and mastitic samples in comparative transcriptome analysis with the results of published genome-wide association studies (GWAS) using a literature mining approach. The integration of different information sources resulted in the identification of 33 common and relevant genes associated with bovine mastitis. Among these, seven genes-CXCR1, HCK, IL1RN, MMP9, S100A9, GRO1, and SOCS3-were identified as the hub genes (highly connected genes) for mastitis susceptibility and resistance, and were subjected to protein-protein interaction (PPI) network and gene regulatory network construction. Gene ontology annotation and enrichment analysis revealed 23, 7, and 4 GO terms related to mastitis in the biological process, molecular function, and cellular component categories, respectively. Moreover, the main metabolic-signalling pathways responsible for the regulation of immune or inflammatory responses were significantly enriched in cytokine-cytokine-receptor interaction, the IL-17 signaling pathway, viral protein interaction with cytokines and cytokine receptors, and the chemokine signaling pathway. Consequently, the identification of these genes, pathways, and their respective functions could contribute to a better understanding of the genetics and mechanisms regulating mastitis and can be considered a starting point for future studies on bovine mastitis.

Comparison of performance and feed digestibility of the non-antibiotic feed supplement (Novacid) and an antibiotic growth promoter in broiler chickens.

Antibiotic growth promoters have been widely used in poultry to improve overall performance. The emergence of antibiotic resistance has resulted in sanctions imposed on the use of antibiotics in poultry diets, and alternatives such as herbal extracts are being considered to improve growth performance. The aim of this study was to compare the performance and feed digestibility of the feed supplement Novacid, which contains organic acids, glucomannan, and phytochemicals, with that of the antibiotic growth promoter bacitracin methylene disalicylate (BMD) in commercial broiler chickens. Six hundred 1-d-old Ross × Ross 308 male broiler chicks were randomly and equally assigned to six treatment groups with five replicates each (20 chicks per replicate). The chicks were fed a corn-soybean meal basal diet, and divided into two groups: unchallenged and challenged with E. coli (400 mg/kg Escherichia coli inoculation). Each of these groups was divided into three study groups: untreated, treated with 0.05% Novacid, and treated with 400 mg/kg BMD. At day 42, inclusion of Novacid or BMD significantly (P < 0.05) improved the performance in the unchallenged groups relative to the control group. However, in E. coli-challenged groups, Novacid and BMD did not improve performance. Ileal digestibility of crude fat, crude protein, and gross energy were reduced in the Novacid group (P < 0.05). BMD and Novacid were equally effective in controlling ileal nutrient digestibility and feed coliform count (P < 0.05). Novacid reduced cecal E. coli and Salmonella count compared to BMD and control. Thus, a phytochemical feed supplement with organic acids and glucomannan could be an effective substitute for antibiotic growth promoters in broiler diets, but cannot replace antibiotics to counter potent infectious agents such as E. coli.