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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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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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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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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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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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Estimation of genetic and phenotypic parameters for ultrasound and carcass merit traits in crossbred beef cattle
Download2014
Bruce, H. L., Plastow, G. S., Moore, S. S., Wang, Z., Nkrumah, D., Miar, Y., Durunna, O.
Ultrasound measurements of 852 crossbred steers along with carcass merit measurements on 756 of them were used to examine their genetic and phenotypic parameters. Traits including ultrasound backfat thickness (UBF), ultrasound ribeye area (UREA), ultrasound marbling (UMAR), carcass weight (CWT),...
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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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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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Candidate genes and biological pathways associated with carcass quality traits in beef cattle
Download2013
Karisa, B. K., Bruce, H. L., Plastow, G. S., Moore, S. S., Thomson, J., Wang, Z.
The objective of this study was to use the candidate gene approach to identify the genes associated with carcass quality traits in beef cattle steers at the University of Alberta Ranch at Kinsella, Canada. This approach involved identifying positional candidate genes and prioritizing them...
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Expansion of ruminant-specific microRNAs shapes target gene expression divergence between ruminant and non-ruminant species
Download2013
Kommadath, A., Bao, H., Meng, Y., Plastow, G. S., Stothard, P., Sun, X., Arantes, A. S., Guan, L. L.
Background Understanding how species-specific microRNAs (miRNAs) contribute to species-specific phenotypes is a central topic in biology. This study aimed to elucidate the role of ruminant-specific miRNAs in shaping mRNA expression divergence between ruminant and non-ruminant species. ...