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Genotype imputation from various low-density SNP panels and its impact on accuracy of genomic breeding values in pigs
- D. A. Grossi, L. F. Brito, M. Jafarikia, F. S. Schenkel, Z. Feng
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The uptake of genomic selection (GS) by the swine industry is still limited by the costs of genotyping. A feasible alternative to overcome this challenge is to genotype animals using an affordable low-density (LD) single nucleotide polymorphism (SNP) chip panel followed by accurate imputation to a high-density panel. Therefore, the main objective of this study was to screen incremental densities of LD panels in order to systematically identify one that balances the tradeoffs among imputation accuracy, prediction accuracy of genomic estimated breeding values (GEBVs), and genotype density (directly associated with genotyping costs). Genotypes using the Illumina Porcine60K BeadChip were available for 1378 Duroc (DU), 2361 Landrace (LA) and 3192 Yorkshire (YO) pigs. In addition, pseudo-phenotypes (de-regressed estimated breeding values) for five economically important traits were provided for the analysis. The reference population for genotyping imputation consisted of 931 DU, 1631 LA and 2103 YO animals and the remainder individuals were included in the validation population of each breed. A LD panel of 3000 evenly spaced SNPs (LD3K) yielded high imputation accuracy rates: 93.78% (DU), 97.07% (LA) and 97.00% (YO) and high correlations (>0.97) between the predicted GEBVs using the actual 60 K SNP genotypes and the imputed 60 K SNP genotypes for all traits and breeds. The imputation accuracy was influenced by the reference population size as well as the amount of parental genotype information available in the reference population. However, parental genotype information became less important when the LD panel had at least 3000 SNPs. The correlation of the GEBVs directly increased with an increase in imputation accuracy. When genotype information for both parents was available, a panel of 300 SNPs (imputed to 60 K) yielded GEBV predictions highly correlated (⩾0.90) with genomic predictions obtained based on the true 60 K panel, for all traits and breeds. For a small reference population size with no parents on reference population, it is recommended the use of a panel at least as dense as the LD3K and, when there are two parents in the reference population, a panel as small as the LD300 might be a feasible option. These findings are of great importance for the development of LD panels for swine in order to reduce genotyping costs, increase the uptake of GS and, therefore, optimize the profitability of the swine industry.
Associations of rumen parameters with feed efficiency and sampling routine in beef cattle
- S. Lam, J. C. Munro, M. Zhou, L. L. Guan, F. S. Schenkel, M. A. Steele, S. P. Miller, Y. R. Montanholi
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Characterizing ruminal parameters in the context of sampling routine and feed efficiency is fundamental to understand the efficiency of feed utilization in the bovine. Therefore, we evaluated microbial and volatile fatty acid (VFA) profiles, rumen papillae epithelial and stratum corneum thickness and rumen pH (RpH) and temperature (RT) in feedlot cattle. In all, 48 cattle (32 steers plus 16 bulls), fed a high moisture corn and haylage-based ration, underwent a productive performance test to determine residual feed intake (RFI) using feed intake, growth, BW and composition traits. Rumen fluid was collected, then RpH and RT logger were inserted 5.5±1 days before slaughter. At slaughter, the logger was recovered and rumen fluid and rumen tissue were sampled. The relative daily time spent in specific RpH and RT ranges were determined. Polynomial regression analysis was used to characterize RpH and RT circadian patterns. Animals were divided into efficient and inefficient groups based on RFI to compare productive performance and ruminal parameters. Efficient animals consumed 1.8 kg/day less dry matter than inefficient cattle (P⩽0.05) while achieving the same productive performance (P⩾0.10). Ruminal bacteria population was higher (P⩽0.05) (7.6×1011v. 4.3×1011 copy number of 16S rRNA gene/ml rumen fluid) and methanogen population was lower (P⩽0.05) (2.3×109v. 4.9×109 copy number of 16S rRNA gene/ml rumen fluid) in efficient compared with inefficient cattle at slaughter with no differences (P⩾0.10) between samples collected on-farm. No differences (P⩾0.10) in rumen fluid VFA were also observed between feed efficiency groups either on-farm or at slaughter. However, increased (P⩽0.05) acetate, and decreased (P⩽0.05) propionate, butyrate, valerate and caproate concentrations were observed at slaughter compared with on-farm. Efficient had increased (P⩽0.05) rumen epithelium thickness (136 v. 126 µm) compared with inefficient cattle. Efficient animals also spent 318% and 93.2% more time (P⩽0.05) in acidotic (4.14% v. 1.30%) (pH⩽5.6) and optimal (5.6<pH<6.0) (8.53% v. 4.42%) RpH range compared with inefficient cattle. The circadian patterns revealed lower (P⩽0.05) RpH and no differences (P⩾0.10) in RT pre-, during, and post-prandial periods in efficient compared with inefficient cattle. In essence, superior feed efficiency in cattle seems linked to rumen features consistent with improved efficiency of feed utilization. Microbial abundance, rumen epithelial histomorphology, and RpH, may serve as indicators for feed efficiency in cattle. The divergences of assessments made on-farm and at slaughter should be considered in the development of proxies for feed efficiency.
Contributors
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- By Venkataraman Anantharaman, Philip D. Anderson, Christopher W. Baugh, J. Stephen Bohan, Kirsten Boyd, Matthias Brachmann, Peter R. Brown, Shelley Calder, David Callaway, Peter Cameron, Jody Crane, Meaghan Cussen, Christina Dempsey, Jonathan A. Edlow, Thomas Fleischmann, Robert L. Freitas, John D. Halamka, Manuel Hernandez, Cherri Hobgood, Jock Hoffman, Steven Horng, Kirk B. Jensen, Jennifer R. Johnson, Stephanie Kayden, Tasnim Khan, Daniel G. Kirkpatrick, James Lennon, Mary Leupold, Thom Mayer, J. Lawrence Mottley, Scott B. Murray, Deirdre Mylod, Larry A. Nathanson, Michael P. Pietrzak, Elke Platz, Nadeem Qureshi, Matthew M. Rice, Andrew Schenkel, Chet Schrader, Puneet Seth, Richard B. Siegrist, David Smith, Robert E. Suter, Carrie Tibbles, Sebastian N. Walker, Lee A. Wallis, Julie Welch, Leana S. Wen
- Edited by Stephanie Kayden, Philip D. Anderson, Robert Freitas, Elke Platz
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- Book:
- Emergency Department Leadership and Management
- Published online:
- 05 December 2014
- Print publication:
- 27 November 2014, pp ix-xii
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Negative emotion impairs working memory in pediatric patients with bipolar disorder type I
- L. S. Schenkel, A. M. Passarotti, J. A. Sweeney, M. N. Pavuluri
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- Journal:
- Psychological Medicine / Volume 42 / Issue 12 / December 2012
- Published online by Cambridge University Press:
- 08 May 2012, pp. 2567-2577
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Background
We investigated affect recognition and the impact of emotional valence on working memory (using happy, angry, and neutral faces) in pediatric patients with bipolar disorder (BD) and healthy control (HC) subjects.
MethodSubjects (N=70) consisted of unmedicated patients with BD type I (BD I, n=23) and type II (BD II, n=16) and matched HC subjects (n=31). All subjects completed tasks of emotion recognition (Chicago Pediatric Emotional Acuity Task; Chicago PEAT) and working memory for happy, angry, and neutral faces (Affective N-Back Memory Task; ANMT).
ResultsCompared to HC subjects, BD patients performed significantly more poorly when identifying the intensity of happy and angry expressions on the Chicago PEAT, and demonstrated working-memory impairments regardless of the type of facial emotional stimuli. Pediatric BD patients displayed the most impaired accuracy and reaction time performance with negative facial stimuli relative to neutral stimuli, but did not display this pattern with positive stimuli. Only BD I patients displayed working-memory deficits, while both BD I and BD II patients displayed emotion-identification impairments. Results remained significant after controlling for co-morbid ADHD and mood state.
ConclusionsBoth BD I and BD II youth demonstrate emotion-identification deficits. BD youth also demonstrate working-memory impairments for facial stimuli irrespective of emotional valence; however, working-memory deficits were the most pronounced with negative emotional stimuli. These deficits appear to be specific to BD I patients, and suggest therefore that a more severe form of illness is characterized by more severe social-cognitive impairment.
Theory of mind and social inference in children and adolescents with bipolar disorder
- L. S. Schenkel, M. Marlow-O'Connor, M. Moss, J. A. Sweeney, M. N. Pavuluri
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- Journal:
- Psychological Medicine / Volume 38 / Issue 6 / June 2008
- Published online by Cambridge University Press:
- 14 January 2008, pp. 791-800
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Background
Deficits in theory of mind (ToM), or the ability to infer what another person is thinking or feeling, have been reported in manic and euthymic adults with bipolar disorder. To date, there have been no investigations of ToM in pediatric bipolar disorder (PBD). The aim of the current study was to investigate this ability in PBD patients and healthy controls.
MethodPBD patients (n=26) and intellectually and demographically similar healthy comparison subjects (n=20) were administered two ToM tasks. In the Affective Story Task, subjects were read positive-, negative- and neutral-valenced stories, and were assessed on their ability to recognize that a misleading series of events could lead one character to develop a false belief about another character. On the Hinting Task, subjects were required to infer the real intentions behind subtle hints.
ResultsThe PBD group performed significantly more poorly than controls on the Hinting Task and the positive and negative conditions of the Affective Story Task. In the PBD group only, younger age, earlier illness onset and manic symptoms were associated with poorer ToM performance.
ConclusionsConsistent with past findings in adult bipolar disorder (BD), PBD youth performed more poorly than controls on ToM tasks. Data suggest that ToM ability may be more impaired in affectively charged contexts. Additionally, an earlier onset of illness among PBD youth may interfere with the development of social-cognitive skills. ToM disturbances may be a useful treatment target in PBD, with the aim of facilitating more accurate assessment of social cues and better interpersonal functioning.