Template-Type: ReDIF-Article 1.0 Author-Name: A. Barazandeh Author-Workplace-Name: Department of Animal Science, Shahid Bahonar University of Kerman, Kerman, Iran Author-Workplace-Name: Department of Animal Science, University of Jiroft, Jiroft, Iran Author-Name: M.R. Mohammadabadi Author-Workplace-Name: Department of Animal Science, Shahid Bahonar University of Kerman, Kerman, Iran Author-Name: M. Ghaderi-Zefrehei Author-Workplace-Name: Department of Animal Science, University of Yasouj, Yasouj, Iran Author-Name: H. Nezamabadi-pour Author-Workplace-Name: Department of Electrical Engineering, Shahid Bahonar University of Kerman, Kerman, Iran Title: Genome-wide analysis of CpG islands in some livestock genomes and their relationship with genomic features Abstract: CpG islands (CGIs) are an important group of CpG dinucleotides in the guanine- and cytosine-rich regions as they harbour functionally relevant epigenetic loci for whole genome studies. As a matter of fact, since there has not been a formal comparative analysis of CGIs in domestic even-toed ungulate genomes, this study was performed to serve this comparison. The Hidden Markov Model was used to detect CGIs in the genomes. The results indicated that the CGIs number and CGI densities had scant variations across genomes. The goat genome had the highest number of CGIs (99 070), whereas the alpaca genome had the highest CGI density (43.39 CGIs/Mb). Significant positive correlations were observed among CGI densities with chromosome pair number, observed CpG/expected CpG, recombination rate, and gene density. When the size of chromosomes increased, the CGI densities decreased and a trend of higher CGI densities in the telomeric regions was observed. Only 10.96% of CGIs were methylated underscoring this postulation that the majority of CGIs remains to be unmethylated. The highest amount of the methylated CGIs was observed in the introns, intergenic, and coding (CDS) regions and the lowest amount of the methylated CGIs was observed in the promoter regions, implying that the DNA methylation of CGIs may control gene expression at the genome level. Detected differences between even-toed ungulate and other vertebrate genomes showed that CGI densities varied greatly among the genomes. These findings would contribute to better understanding the even-toed ungulate (epi) genomes, the role of CGIs in epigenomic functions and molecular evolution. Keywords: even-toed ungulate, (epi) genomic, Hidden Markov Model, DNA methylation Journal: Czech Journal of Animal Science Pages: 487-495 Volume: 61 Issue: 11 Year: 2016 DOI: 10.17221/78/2015-CJAS File-URL: http://cjas.agriculturejournals.cz/doi/10.17221/78/2015-CJAS.html File-Format: text/html X-File-Ref: http://agriculturejournals.cz/RePEc/caa/references/cjs-201611-0001.txt Handle: RePEc:caa:jnlcjs:v:61:y:2016:i:11:id:78-2015-CJAS Template-Type: ReDIF-Article 1.0 Author-Name: A. Myška Author-Workplace-Name: Faculty of Agrobiology, Food and Natural Resources, Czech University of Life Sciences Prague, Prague, Czech Republic Author-Name: J. Száková Author-Workplace-Name: Faculty of Agrobiology, Food and Natural Resources, Czech University of Life Sciences Prague, Prague, Czech Republic Author-Name: A. Fučíková Author-Workplace-Name: Faculty of Agrobiology, Food and Natural Resources, Czech University of Life Sciences Prague, Prague, Czech Republic Author-Name: P. Mlejnek Author-Workplace-Name: Institute of Physiology, Czech Academy of Sciences, Prague, Czech Republic Author-Name: V. Zídek Author-Workplace-Name: Institute of Physiology, Czech Academy of Sciences, Prague, Czech Republic Author-Name: J. Tremlová Author-Workplace-Name: Faculty of Agrobiology, Food and Natural Resources, Czech University of Life Sciences Prague, Prague, Czech Republic Author-Name: O. Mestek Author-Workplace-Name: Faculty of Chemical Engineering, University of Chemistry and Technology Prague, Prague, Czech Republic Author-Name: R. Koplík Author-Workplace-Name: Faculty of Food and Biochemical Technology, University of Chemistry and Technology Prague, Prague, Czech Republic Author-Name: J. Zídková Author-Workplace-Name: Faculty of Food and Biochemical Technology, University of Chemistry and Technology Prague, Prague, Czech Republic Author-Name: M. Melčová Author-Workplace-Name: Faculty of Food and Biochemical Technology, University of Chemistry and Technology Prague, Prague, Czech Republic Author-Name: P. Tlustoš Author-Workplace-Name: Faculty of Agrobiology, Food and Natural Resources, Czech University of Life Sciences Prague, Prague, Czech Republic Title: Effect of selenium-enriched defatted rape seeds on tissue cadmium and essential elements utilization in rats Abstract: The effect of selenium-enriched defatted rapeseeds (DRS) added to the diet on Se uptake by rat organisms (whole blood, liver, kidney) was investigated in model conditions. Additionally, the response of other essential trace and major mineral elements (Cu, Ca, Fe, K, Mg, Mn, P, S, and Zn) in rat organisms on selenium and/or DRS addition was assessed. The experimental diets for the individual experimental groups were prepared as follows: group DRS 0 (control diet), group DRS 30 (30% of soybean meal in the diet replaced with DRS), group DRS60 (60% of soybean meal in the diet replaced with DRS), and group DRS100 (100% of soybean meal in the diet replaced with DRS), either unenriched or naturally fortified with Se. Whereas Se content in the blood and liver of the animals remained unchanged, increased Se levels were observed in kidney of the selenized DRS100 group compared to the others. Moreover, the results showed decreasing Cd content in the rat liver with increasing Se content in the diet, confirming antagonism of these elements. Concerning the essential elements, the application of the selenized DRS did not result in any serious imbalance in the utilization of these elements. In contrast, Se addition seems to be helpful for the improved utilization of essential elements such as P, S, and Zn, compared to the DRS-containing diet without Se fortification. Keywords: Se, Brassica napus, fortification, Rattus norvegicus, trace and major minerals Journal: Czech Journal of Animal Science Pages: 496-505 Volume: 61 Issue: 11 Year: 2016 DOI: 10.17221/88/2015-CJAS File-URL: http://cjas.agriculturejournals.cz/doi/10.17221/88/2015-CJAS.html File-Format: text/html X-File-Ref: http://agriculturejournals.cz/RePEc/caa/references/cjs-201611-0002.txt Handle: RePEc:caa:jnlcjs:v:61:y:2016:i:11:id:88-2015-CJAS Template-Type: ReDIF-Article 1.0 Author-Name: D. Miśta Author-Workplace-Name: Department of Animal Physiology and Biostructure, Wroclaw University of Environmental and Life Sciences, Wrocław, Poland Author-Name: B. Króliczewska Author-Workplace-Name: Department of Animal Physiology and Biostructure, Wroclaw University of Environmental and Life Sciences, Wrocław, Poland Author-Name: E. Pecka-Kiełb Author-Workplace-Name: Department of Animal Physiology and Biostructure, Wroclaw University of Environmental and Life Sciences, Wrocław, Poland Author-Name: J. Bujok Author-Workplace-Name: Department of Animal Physiology and Biostructure, Wroclaw University of Environmental and Life Sciences, Wrocław, Poland Author-Name: W. Zawadzki Author-Workplace-Name: Department of Animal Physiology and Biostructure, Wroclaw University of Environmental and Life Sciences, Wrocław, Poland Author-Name: J. Górecka Author-Workplace-Name: Department of Animal Products Technology and Quality Management, Wroclaw University of Environmental and Life Sciences, Wrocław, Poland Author-Name: J. Piekarska Author-Workplace-Name: Department of Internal Medicine and Clinic of Diseases of Horses, Dogs and Cats, Wroclaw University of Environmental and Life Sciences, Wrocław, Poland Title: In vitro fermentation pattern in the large intestine of hybrids between wild boars and domestic pigs - a preliminary study Abstract: Breeding of hybrids between wild boars and domestic pigs is in the consumer interest because of the need to ensure food security and diversification via widening the genetic basis of animals reared for meat. To expand the knowledge about their nutritional requirements, this study aimed to investigate hindgut fermentation in these animals. Caecal and colon cultures were incubated for 12 h in vitro with or without wheat bran as a supplementary substrate. Short-chain fatty acids, ammonia, methane, and total gas production were determined. The total concentrations of short-chain fatty acids in unincubated caecal and colon samples were 93.1 and 115 mmol/kg, respectively. The short-chain fatty acid profile in fresh hindgut contents was characterized by a high molar proportion of acetate (74.8-75.0 mol%), followed by propionate (18.2-18.5 mol%) and butyrate (5.4-5.5 mol%). The presence of wheat bran lowered acetate and increased butyrate, propionate, and valerate molar proportions. The ammonia level remained low (1.3-2.43 mmol/kg) regardless of the addition of the substrate. The relatively low pH and ammonia concentration in wild boar/pig hybrids may be caused by the low level of crude protein in diet of these animals. The rate of methanogenesis increased during the fermentation simultaneously with an increase in the production of gases after wheat bran addition. Methane production in the caecal and colon samples incubated with the substrate reached 15.6 and 16.1 mmol/kg, respectively. The hindgut fermentation pattern in wild boar/pig hybrids generally resembled that described earlier in domestic pigs, although some observed dissimilarities may be caused by distinct microbial activity. Keywords: cross-breed, Sus scrofa, caecal fermentation, colon fermentation, short-chain fatty acids, methane Journal: Czech Journal of Animal Science Pages: 506-514 Volume: 61 Issue: 11 Year: 2016 DOI: 10.17221/7/2016-CJAS File-URL: http://cjas.agriculturejournals.cz/doi/10.17221/7/2016-CJAS.html File-Format: text/html X-File-Ref: http://agriculturejournals.cz/RePEc/caa/references/cjs-201611-0003.txt Handle: RePEc:caa:jnlcjs:v:61:y:2016:i:11:id:7-2016-CJAS Template-Type: ReDIF-Article 1.0 Author-Name: M. Doležalová Author-Workplace-Name: Czech University of Life Sciences Prague, Faculty of Agrobiology, Food and Natural Resources, Department of Animal Husbandry, Prague, Czech Republic Author-Name: L. Stádník Author-Workplace-Name: Czech University of Life Sciences Prague, Faculty of Agrobiology, Food and Natural Resources, Department of Animal Husbandry, Prague, Czech Republic Author-Name: Z. Biniová Author-Workplace-Name: Czech University of Life Sciences Prague, Faculty of Agrobiology, Food and Natural Resources, Department of Animal Husbandry, Prague, Czech Republic Author-Name: J. Ducháček Author-Workplace-Name: Czech University of Life Sciences Prague, Faculty of Agrobiology, Food and Natural Resources, Department of Animal Husbandry, Prague, Czech Republic Author-Name: R. Stupka Author-Workplace-Name: Czech University of Life Sciences Prague, Faculty of Agrobiology, Food and Natural Resources, Department of Animal Husbandry, Prague, Czech Republic Title: Equilibration and freezing interactions affecting bull sperm characteristics after thawing Abstract: The objective was to determine effects of equilibration length and freezing curve type as well as their interactions on motility and live spermatozoa proportion in bull sperm after thawing. The ejaculates of 6 sires were repeatedly collected. Fresh semen was diluted with one extender and divided into 3 groups equilibrated for 30, 120, and 240 min. Subsequently, half straws of each group were frozen using standard 3-phase or 2-phase freezing curve differing in the rate of temperature decrease. The spermatozoa motility (M) was evaluated immediately after thawing and at 30, 60, 90, and 120 min of thermodynamic test (TDT). Live spermatozoa proportion was evaluated after thawing and at the end of TDT. Average of spermatozoa motility (AM), decrease of spermatozoa motility (MD), average proportion of live spermatozoa (ALS), and decrease of live spermatozoa proportion (DLS) through the TDT were calculated. Significant inter-sire differences in AM (0.45-17.0%; P < 0.05-0.01), MD (0.76-12.57%; P < 0.05-0.01), and ALS (0.99-23.8%; P < 0.01) were detected. The longest equilibration ensured the highest M during TDT and AM (+2.72 and +4.58%; P < 0.05-0.01), however higher MD (+4.06%; P < 0.01) compared to standard length as well. Straws freezed using 2-phase curve achieved higher M through TDT, AM (+7.3%; P < 0.01) as well as ALS (+11.77%; P < 0.01). The 2-phase curve presented higher M compared to the 3-phase freezing curve within all equilibration lengths. Significant differences in AM, MD, and ALS (0.45-6.78%, 0.62-5.35%, and 20.79-21.11%; P < 0.05-0.01) between equilibration length vs freezing curve interactions were determined. Results document the importance of equilibration length, freezing curve, and their interaction effect on live spermatozoa proportion and sperm motility after thawing as well as necessity of individual conditions for bulls semen processing and insemination doses production. Keywords: sire, spermatozoa, cryopreservation, insemination dose, fertilization capability Journal: Czech Journal of Animal Science Pages: 515-525 Volume: 61 Issue: 11 Year: 2016 DOI: 10.17221/23/2016-CJAS File-URL: http://cjas.agriculturejournals.cz/doi/10.17221/23/2016-CJAS.html File-Format: text/html X-File-Ref: http://agriculturejournals.cz/RePEc/caa/references/cjs-201611-0004.txt Handle: RePEc:caa:jnlcjs:v:61:y:2016:i:11:id:23-2016-CJAS Template-Type: ReDIF-Article 1.0 Author-Name: T. Suchocki Author-Workplace-Name: Biostatistics Group, Department of Genetics, Wroclaw University of Environmental and Life Sciences, Wroclaw, Poland Author-Name: K. Wojdak-Maksymiec Author-Workplace-Name: Department of Animal Genetics and Breeding, West Pomeranian University of Technology in Szczecin, Szczecin, Poland Author-Name: J. Szyda Author-Workplace-Name: Biostatistics Group, Department of Genetics, Wroclaw University of Environmental and Life Sciences, Wroclaw, Poland Title: Using gene networks to identify genes and pathways involved in milk production traits in Polish Holstein dairy cattle Abstract: When analyzing phenotypes undergoing a complex mode of inheritance, it is of great interest to switch the scope from single genes to gene pathways, which form better defined functional units. We used gene networks to search for physiological processes and underlying genes responsible for complex traits recorded in dairy cattle. Major problems addressed included loss of information from multiple single nucleotide polymorphisms (SNPs) located within or close to the same gene, ignoring information on linkage disequilibrium and validation of the obtained gene network. 2601 bulls genotyped by the Illumina BovineSNP50 BeadChip were used. SNP effects were estimated using a mixed model, then underlying gene effects were estimated and tested for significance, subsequently a gene network was constructed and the functional information represented by the network was retrieved. The networks were validated by repeating the above-mentioned analyses after permutation of bulls' pseudophenotypes. Effects of 4345 genes were estimated, what makes 16.4% of all genes mapped to the UMD3.1 reference genome. Assuming the maximum 10% type I error rate, for milk yield 50 different gene ontology (GO) terms and three pathways defined by the Kyoto Encyclopedia of Genes and Genomes (KEGG) were significantly overrepresented in the real data as compared to the permuted data sets, while for fat yield nine of the GO terms were significantly overrepresented in the real data network, although none of the KEGG pathways reached the significance level. In turn, for protein yield 28 of the GO terms and six KEGG pathways were significantly overrepresented in the real data. Based on the physiological information we identified sets of loci involved in the determination of milk yield (224 genes), fat yield (72 genes), and protein yield (546 genes). Among the genes some have large effects and have already been reported in previous studies, whereas some others represent novel discoveries and thus most probably genes with medium or small effects on trait variation. Keywords: cattle, gene networks, GO, GWAS, KEGG, mixed model, SNP, validation Journal: Czech Journal of Animal Science Pages: 526-538 Volume: 61 Issue: 11 Year: 2016 DOI: 10.17221/43/2015-CJAS File-URL: http://cjas.agriculturejournals.cz/doi/10.17221/43/2015-CJAS.html File-Format: text/html X-File-Ref: http://agriculturejournals.cz/RePEc/caa/references/cjs-201611-0005.txt Handle: RePEc:caa:jnlcjs:v:61:y:2016:i:11:id:43-2015-CJAS