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2011
Nalaila, S., Li, C., Moore, S. S., Stothard, P., Wang, Z.
Quantitative trait loci (QTL) mapped to large chromosomal regions have limited utility as DNA markers for marker-assisted selection (MAS) and are less informative as a reference for the identification of the underlying causative quantitative trait nucleotides (QTN). The objective of this study...
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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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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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2009
Xu, J., Goebel, R. A., Cai, Z., Sabaai, H., Lin, G., Wang, Z., Wang, Y., Stothard, P.
Background The \"common disease – common variant\" hypothesis and genome-wide association studies have achieved numerous successes in the last three years, particularly in genetic mapping in human diseases. Nevertheless, the power of the association study methods are still low, in particular on...
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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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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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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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High resolution radiation hybrid maps of bovine chromosome 19 and 29 and comparison with the bovine genome sequence assembly
Download2007
Murdoch, B., Wang, Z., Stothard, P., Womack, J. E., Mckay, S. D., Moore, S. S., Schiex, T., Prasad, A.
Background High resolution radiation hybrid (RH) maps can facilitate genome sequence assembly by correctly ordering genes and genetic markers along chromosomes. The objective of the present study was to generate high resolution RH maps of bovine chromosomes 19 (BTA19) and 29 (BTA29), and...
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2008
Kolbehdari, D., Stothard, P., Schnabel, R., Wang, Z., Marques, E., Taylor, J. F., Moore, S. S.
Background Linkage disequilibrium (LD) maps can provide a wealth of information on specific marker-phenotype relationships, especially in areas of the genome where positional candidate genes with similar functions are located. A recently published high resolution radiation hybrid map of bovine...
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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...