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Hulsegge I.,Animal Breeding and Genomics Center | Woelders H.,Animal Breeding and Genomics Center | Smits M.,Animal Breeding and Genomics Center | Schokker D.,Animal Breeding and Genomics Center | And 2 more authors.
Physiological Genomics | Year: 2013

Reproduction is of significant economic importance in dairy cattle. Improved understanding of mechanisms that control estrous behavior and other reproduction traits could help in developing strategies to improve and/or monitor these traits. The objective of this study was to predict and rank genes and processes in brain areas and pituitary involved in reproductive traits in cattle using information derived from three different data sources: gene expression, protein-protein interactions, and literature. We identified 59, 89, 53, 23, and 71 genes in bovine amygdala, dorsal hypothalamus, hippocampus, pituitary, and ventral hypothalamus, respectively, potentially involved in processes underlying estrus and estrous behavior. Functional annotation of the candidate genes points to a number of tissue-specific processes of which the "neurotransmitter/ion channel/synapse" process in the amygdala, "steroid hormone receptor activity/ion binding" in the pituitary, "extracellular region" in the ventral hypothalamus, and "positive regulation of transcription/metabolic process" in the dorsal hypothalamus are most prominent. The regulation of the functional processes in the various tissues operate at different biological levels, including transcriptional, posttranscriptional, extracellular, and intercellular signaling levels. © 2013 the American Physiological Society.

Sorensen L.P.,Center for Quantitative Genetics and Genomics | Bjerring M.,University of Aarhus | Lovendahl P.,Center for Quantitative Genetics and Genomics
Journal of Dairy Science | Year: 2016

This study presents and validates a detection and monitoring model for mastitis based on automated frequent sampling of online cell count (OCC). Initially, data were filtered and adjusted for sensor drift and skewed distribution using ln-transformation. Acceptable data were passed on to a time-series model using double exponential smoothing to estimate level and trends at cow level. The OCC levels and trends were converted to a continuous (0-1) scale, termed elevated mastitis risk (EMR), where values close to zero indicate healthy cow status and values close to 1 indicate high risk of mastitis. Finally, a feedback loop was included to dynamically request a time to next sample, based on latest EMR values or errors in the raw data stream. The estimated EMR values were used to issue 2 types of alerts, new and (on-going) intramammary infection (IMI) alerts. The new alerts were issued when the EMR values exceeded a threshold, and the IMI alerts were issued for subsequent alerts. New alerts were only issued after the EMR had been below the threshold for at least 8. d. The detection model was evaluated using time-window analysis and commercial herd data (6 herds, 595,927 milkings) at different sampling intensities. Recorded treatments of mastitis were used as gold standard. Significantly higher EMR values were detected in treated than in contemporary untreated cows. The proportion of detected mastitis cases using new alerts was between 28.0 and 43.1% and highest for a fixed sampling scheme aiming at 24. h between measurements. This was higher for IMI alerts, between 54.6 and 89.0%, and highest when all available measurements were used. The lowest false alert rate of 6.5 per 1,000 milkings was observed when all measurements were used. The results showed that a dynamic sampling scheme with a default value of 24. h between measurements gave only a small reduction in proportion of detected mastitis treatments and remained at 88.5%. It was concluded that filtering of raw data combined with a time-series model was effective in detecting and monitoring mastitis status in dairy cows when based on IMI alerts, and by using a dynamically adjusting sampling scheme almost full performance was still obtainable. However, results were less desirable when based on new alerts most likely because of the used gold standard for mastitis, which may not necessarily reflect the onset of and IMI case in contrast to a new alert. © 2016 American Dairy Science Association.

Edwards D.,Center for Quantitative Genetics and Genomics
BMC Bioinformatics | Year: 2013

Background: Detailed study of genetic variation at the population level in humans and other species is now possible due to the availability of large sets of single nucleotide polymorphism data. Alleles at two or more loci are said to be in linkage disequilibrium (LD) when they are correlated or statistically dependent. Current efforts to understand the genetic basis of complex phenotypes are based on the existence of such associations, making study of the extent and distribution of linkage disequilibrium central to this endeavour. The objective of this paper is to develop methods to study fine-scale patterns of allelic association using probabilistic graphical models.Results: An efficient, linear-time forward-backward algorithm is developed to estimate chromosome-wide LD models by optimizing a penalized likelihood criterion, and a convenient way to display these models is described. To illustrate the methods they are applied to data obtained by genotyping 8341 pigs. It is found that roughly 20% of the porcine genome exhibits complex LD patterns, forming islands of relatively high genetic diversity.Conclusions: The proposed algorithm is efficient and makes it feasible to estimate and visualize chromosome-wide LD models on a routine basis. © 2013 Edwards; licensee BioMed Central Ltd.

Gebreyesus G.,Wageningen University | Lund M.S.,Center for Quantitative Genetics and Genomics | Janss L.,Center for Quantitative Genetics and Genomics | Poulsen N.A.,University of Aarhus | And 3 more authors.
Journal of Dairy Science | Year: 2016

Genetic parameters were estimated for the major milk proteins using bivariate and multi-trait models based on genomic relationships between animals. The analyses included, apart from total protein percentage, αS1-casein (CN), αS2-CN, β-CN, κ-CN, α-lactalbumin, and β-lactoglobulin, as well as the posttranslational sub-forms of glycosylated κ-CN and αS1-CN-8P (phosphorylated). Standard errors of the estimates were used to compare the models. In total, 650 Danish Holstein cows across 4 parities and days in milk ranging from 9 to 481 d were selected from 21 herds. The multi-trait model generally resulted in lower standard errors of heritability estimates, suggesting that genetic parameters can be estimated with high accuracy using multi-trait analyses with genomic relationships for scarcely recorded traits. The heritability estimates from the multi-trait model ranged from low (0.05 for β-CN) to high (0.78 for κ-CN). Genetic correlations between the milk proteins and the total milk protein percentage were generally low, suggesting the possibility to alter protein composition through selective breeding with little effect on total milk protein percentage. © 2016 American Dairy Science Association.

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