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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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Dominant Red Coat Color in Holstein Cattle Is Associated with a Missense Mutation in the Coatomer Protein Complex, Subunit Alpha (COPA) Gene
Download2015
Sällman Almén, M., Liao, X., Stothard, P., Henegar, C., Van Doormaal, B., Rubin, C. -J., Andersson, L., Barsh, G. S., Ito, S., Plastow, G., Wakamatsu, K., Dorshorst, B.
Coat color in Holstein dairy cattle is primarily controlled by the melanocortin 1 receptor (MC1R) gene, a central determinant of black (eumelanin) vs. red/brown pheomelanin synthesis across animal species. The major MC1R alleles in Holsteins are Dominant Black (MC1RD) and Recessive Red (MC1Re). A...
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Single nucleotide polymorphisms for feed efficiency and performance in crossbred beef cattle
Download2014
Squires, J. J., Moore, S., Stothard, P., Swanson, K. C., Miller, S. P., Abo-Ismail, M. K., Vander Voort, G., Liao, X., Plastow, G., Mandell, I. B.
Background This study was conducted to: (1) identify new SNPs for residual feed intake (RFI) and performance traits within candidate genes identified in a genome wide association study (GWAS); (2) estimate the proportion of variation in RFI explained by the detected SNPs; (3) estimate the...
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Birth Weight, Intrauterine Growth Retardation and Fetal Susceptibility to Porcine Reproductive and Respiratory Syndrome Virus
Download2014
Ashley, C., Foxcroft, G., Plastow, G., Harding, J. C. S., Lunney, J. K., Ladinig, A.
The severity of porcine reproductive and respiratory syndrome was compared in pregnant gilts originating from high and low birth weight litters. One-hundred and eleven pregnant gilts experimentally infected with porcine reproductive and respiratory syndrome virus on gestation day 85 (±1) were...
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2014
Plastow, G., Stothard, P., Moore, S., Bao, H., Meng, Y., Liao, X.
Gene duplication is a widespread phenomenon in genome evolution, and it has been proposed to serve as an engine of evolutionary innovation. In the present study, we performed the first comprehensive analysis of duplicate genes in the bovine genome. A total of 3131 putative duplicated gene pairs...
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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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Variation in Fetal Outcome, Viral Load and ORF5 Sequence Mutations in a Large Scale Study of Phenotypic Responses to Late Gestation Exposure to Type 2 Porcine Reproductive and Respiratory Syndrome Virus
Download2014
Plastow, G., Lunney, J. K., Ladinig, A., Ashley, C., Detmer, S. E., Wilkinson, A., Harding, J. C. S.
In spite of extensive research, the mechanisms of reproductive disease associated with Porcine Reproductive and Respiratory Syndrome virus (PRRSv) are still poorly understood. The objectives of this large scale study were to evaluate associations between viral load and fetal preservation,...
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Cytokine profiles in pregnant gilts experimentally infected with porcine reproductive and respiratory syndrome virus and relationships with viral load and fetal outcome
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Plastow, G., Souza, C. J. H., Lunney, J. K., Ashley, C., Ladinig, A., Harding, J. C. S.
In spite of extensive research, immunologic control mechanisms against Porcine Reproductive and Respiratory Syndrome virus (PRRSv) remain poorly understood. Cytokine responses have been exhaustively studied in nursery pigs and show contradictory results. Since no detailed reports on cytokine...
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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...