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Coordinated international action to accelerate genome-to-phenome with FAANG, the Functional Annotation of Animal Genomes project
Download2015
Tosser-Klopp, G., Zhou, H., Palti, Y., Nanduri, B., Tixier-Boichard, M., Silverstein, J., Plastow, G. S., Sarropoulou, E., Brauning, R., Zhao, S., Rohrer, G. A., Elsik, C. G., Cheng, H. H., Giuffra, E., Notredame, C., Khatib, H., Vilkki, J., Couldrey, C., Archibald, A. L., Tellam, R. L., Schmidt, C. J., Reecy, J. M., Clarke, L., Huang, L. S., Groenen, M. A., McEwan, J. C., Burt, D. W., Kim, H., Bottema, C. D., Kijas, J. W., Dalrymple, B. P., White, S. N., Burgess, S. C., Hayes, B. J., McCarthy, F. M., Moore, S., Foissac, S., Lunney, J. K., Andersson, L., Tuggle, C. K., Casas, E.
We describe the organization of a nascent international effort, the Functional Annotation of Animal Genomes (FAANG) project, whose aim is to produce comprehensive maps of functional elements in the genomes of domesticated animal species.
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Identification of a putative quantitative trait nucleotide in guanylate binding protein 5 for host response to PRRS virus infection
Download2015
Choi, I., Guan, L., Plastow, G. S., Liu, P., Koltes, J. E., Loyd, H., Boddicker, N. J., Eisley, C. J., Schroyen, M., Bao, H., Dekkers, J. C. M., Kommadath, A., Abrams, S. M., Reecy, J. M., Rowland, R. R. R., Serão, N. V. L., Lunney, J. K., Carpenter, S., Stothard, P., Fritz-Waters, E., Tuggle, C. K.
Background Previously, we identified a major quantitative trait locus (QTL) for host response to Porcine Respiratory and Reproductive Syndrome virus (PRRSV) infection in high linkage disequilibrium (LD) with SNP rs80800372 on Sus scrofa chromosome 4 (SSC4). Results Within this QTL,...
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Genome-wide association studies (GWAS) identify a QTL close to PRKAG3 affecting meat pH and colour in crossbred commercial pigs
Download2015
Miar, Y., Plastow, G. S., Charagu, P., Wang, Z., Kemp, R. A., Bruce, H., Zhang, Z., Yang, T.
Background Improving meat quality is a high priority for the pork industry to satisfy consumers’ preferences. GWAS have become a state-of-the-art approach to genetically improve economically important traits. However, GWAS focused on pork quality are still relatively rare. Results Six...
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2014
Aalhus, J. L., Basarab, J. A., Juárez, M., Larsen, I. L., Rymer, R. T.
Steaks from longissimus lumborum and semimembranosus muscles, aged 2 or 27 d, were obtained from a population of steers (n=112) managed to produce a range in tenderness (shear force range from 2.57 to 17.2 kg). All available carcass (live weight, hot commercial weight, pH, temperature, marbling,...
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MicroRNA Buffering and Altered Variance of Gene Expression in Response to Salmonella Infection
Download2014
Plastow, G. S., Bao, H., Kommadath, A., Guan, L. L., Tuggle, C. K., Stothard, P.
One potential role of miRNAs is to buffer variation in gene expression, although conflicting results have been reported. To investigate the buffering role of miRNAs in response to Salmonella infection in pigs, we sequenced miRNA and mRNA in whole blood from 15 pig samples before and after...
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Genetic and Phenotypic Correlations between Performance Traits with Meat Quality and Carcass Characteristics in Commercial Crossbred Pigs
Download2014
Wang, Z., Kemp, R., van Haandel, B., Charagu, P., Zhang, C., Bruce, H., Miar, Y., McKay, R., Huisman, A., Plastow, G., Manafiazar, G., Moore, S.
Genetic correlations between performance traits with meat quality and carcass traits were estimated on 6,408 commercial crossbred pigs with performance traits recorded in production systems with 2,100 of them having meat quality and carcass measurements. Significant fixed effects (company, sex...
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International genetic evaluations for feed intake in dairy cattle through the collation of data from multiple sources
Download2014
Coffey, M. P., Løvendahl, P., Wang, Z., de Haas, Y., Krattenmacher, N., Berry, D. P., Crowley, J. J., Pryce, J. E., Veerkamp, R. F., Weigel, K., Macdonald, K., Spurlock, D.
Feed represents a large proportion of the variable costs in dairy production systems. The omission of feed intake measures explicitly from national dairy cow breeding objectives is predominantly due to a lack of information from which to make selection decisions. However, individual cow feed...
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Increasing gene discovery and coverage using RNA-seq of globin RNA reduced porcine blood samples
Download2014
Stothard, P., Fritz-Waters, E., Choi, I., Abrams, S. M., Kommadath, A., Hosseini, A., Plastow, G. S., Guan, L. L., Tuggle, C. K., Bao, H., Meng, Y., Lunney, J. K., Reecy, J. M., Sun, X.
Background Transcriptome analysis of porcine whole blood has several applications, which include deciphering genetic mechanisms for host responses to viral infection and vaccination. The abundance of alpha- and beta-globin transcripts in blood, however, impedes the ability to cost-effectively...
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Gene co-expression network analysis identifies porcine genes associated with variation in Salmonella shedding
Download2014
Plastow, G. S., Bearson, S. M. D., Arantes, A. S., Bao, H., Kommadath, A., Stothard, P., Guan, L. L., Tuggle, C. K.
Background Salmonella enterica serovar Typhimurium is a gram-negative bacterium that can colonise the gut of humans and several species of food producing farm animals to cause enteric or septicaemic salmonellosis. While many studies have looked into the host genetic response to Salmonella...
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Effects of production system and growth promotants on the physiological maturity scores in steers
Download2014
Aalhus, J. L., Basarab, J. A., N. Prieto, I. L., López-Campos, Ó., Larsen, M.
Over a 2-yr period, 224 crossbred steers were allotted to a 2×2×2 factorial arrangement of treatments to determine the effect of the production system (calf-fed vs. yearling-fed), growth implant strategy (non-implanted vs. implanted) and β-agonist supplementation (no ractopamine vs. ractopamine)...