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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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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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2012
Xia, Y., Zhang, X., Mu, Z., Li, X., Wang, T., Qu, J., Chen, H., Li, K., Zhu, L., Wang, L., Liu, Y., Zhang, K., Guan, J., Wu, H., Jiang, A., Yin, G., Xi, D., Shuai, S., Lang, Q., Jiang, Y., Wang, Z., Luo, Z., Xiao, H., Li, Y., Huang, S., Gu, Y., Beck, S., Ma, J., Wang, H., Jing, L., Plastow, G. S., Jiang, Z., Gao, X., Chen, L., Tang, G., Wang, J., Li,R., Li, M., Mai, M., Wang, Y., Wang, X., Zhong, Z., Nie, J., Zhou, S., Yang, H., Yi, N., Li, N.
It is evident that epigenetic factors, especially DNA methylation, have essential roles in obesity development. Here, using pig as a model, we investigate the systematic association between DNA methylation and obesity. We sample eight variant adipose and two distinct skeletal muscle tissues from...
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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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2006
Geverink, N. A., Plastow, G. S., Foury, A., Gil, M., Gispert, M., Moisan, M. P., Hortós, M., Gort, G., Font i Furnols, M., Mormède, P.
The gene (Cbg) encoding cortisol-binding globulin (CBG) has been proposed as a candidate gene to explain genetic variation in cortisol secretion and carcass composition in pigs. The objective of this study was to evaluate the association between CBG and pork quality in 5 European breeding lines,...
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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. ...
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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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Allometric association between in vivo estimation of body composition during growth using deuterium dilution technique and chemical analysis of serial slaughtered pigs
Download2006
Looft, H., Landgraf, S., Kalm, E., Roehe, R., Plastow, G. S., Susenbeth, A., Knap, P. W.
The objective of this study was to develop accurate mathematical-statistical functions to estimate body composition of live pigs between 20 and 140 kg weight from total body water (TBWA) determined by the deuterium dilution technique. Chemical body compositions during the growth period are...
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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,...