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      Genomics and disease resistance studies in livestock

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          Abstract

          This paper considers the application of genetic and genomic techniques to disease resistance, the interpretation of data arising from such studies and the utilisation of the research outcomes to breed animals for enhanced resistance. Resistance and tolerance are defined and contrasted, factors affecting the analysis and interpretation of field data presented, and appropriate experimental designs discussed. These general principles are then applied to two detailed case studies, infectious pancreatic necrosis in Atlantic salmon and bovine tuberculosis in dairy cattle, and the lessons learnt are considered in detail. It is concluded that the rate limiting step in disease genetic studies will generally be provision of adequate phenotypic data, and its interpretation, rather than the genomic resources. Lastly, the importance of cross-disciplinary dialogue between the animal health and animal genetics communities is stressed.

          Highlights

          • Factors influencing disease genetics studies are reviewed.
          • Results are presented in detail for a viral disease and a bacterial disease.
          • Breeding for resistance is often possible, but not always appropriate or necessary.
          • Effective studies combine disease biology, epidemiology and genetics.
          • Rate limiting step is likely to be provision of phenotypes rather than genotypes.

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          Most cited references 38

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          Accuracy of Predicting the Genetic Risk of Disease Using a Genome-Wide Approach

          Background The prediction of the genetic disease risk of an individual is a powerful public health tool. While predicting risk has been successful in diseases which follow simple Mendelian inheritance, it has proven challenging in complex diseases for which a large number of loci contribute to the genetic variance. The large numbers of single nucleotide polymorphisms now available provide new opportunities for predicting genetic risk of complex diseases with high accuracy. Methodology/Principal Findings We have derived simple deterministic formulae to predict the accuracy of predicted genetic risk from population or case control studies using a genome-wide approach and assuming a dichotomous disease phenotype with an underlying continuous liability. We show that the prediction equations are special cases of the more general problem of predicting the accuracy of estimates of genetic values of a continuous phenotype. Our predictive equations are responsive to all parameters that affect accuracy and they are independent of allele frequency and effect distributions. Deterministic prediction errors when tested by simulation were generally small. The common link among the expressions for accuracy is that they are best summarized as the product of the ratio of number of phenotypic records per number of risk loci and the observed heritability. Conclusions/Significance This study advances the understanding of the relative power of case control and population studies of disease. The predictions represent an upper bound of accuracy which may be achievable with improved effect estimation methods. The formulae derived will help researchers determine an appropriate sample size to attain a certain accuracy when predicting genetic risk.
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            Mycobacterium bovis at the animal-human interface: a problem, or not?

            Mycobacterium bovis is a pathogen of significant importance in livestock and a wide range of wild animal species worldwide. It is also known to cause tuberculosis disease in humans, a fact which has raised renewed concerns regarding the zoonotic risk for humans, especially those living at the animal-human interface. This review consolidates recent reports in the literature mainly on animal and zoonotic tuberculosis with an emphasis on evolution, epidemiology, treatment and diagnosis. The information presented reveals the fundamental differences in the complexity and level at which the disease affects the economy, ecosystem and human population of regions where animal tuberculosis control is achieved and regions where little or no control is implemented. In conclusion the review suggests that bovine tuberculosis has essentially been reduced to a disease of economic importance in the developed world, while low-income countries are facing a multifaceted impact which potentially affects the health of livestock, humans and ecosystems and which is likely to increase in the presence of debilitating diseases such as HIV/AIDS and other factors which negatively affect human livelihoods. Copyright 2009 Elsevier B.V. All rights reserved.
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              Major quantitative trait loci affect resistance to infectious pancreatic necrosis in Atlantic salmon (Salmo salar).

              Infectious pancreatic necrosis (IPN) is a viral disease currently presenting a major problem in the production of Atlantic salmon (Salmon salar). IPN can cause significant mortality to salmon fry within freshwater hatcheries and to smolts following transfer to seawater, although challenged populations show clear genetic variation in resistance. To determine whether this genetic variation includes loci of major effect, a genomewide quantitative trait loci (QTL) scan was performed within 10 full-sib families that had received a natural seawater IPN challenge. To utilize the large difference between Atlantic salmon male and female recombination rates, a two-stage mapping strategy was employed. Initially, a sire-based QTL analysis was used to detect linkage groups with significant effects on IPN resistance, using two to three microsatellite markers per linkage group. A dam-based analysis with additional markers was then used to confirm and position any detected QTL. Two genomewide significant QTL and one suggestive QTL were detected in the genome scan. The most significant QTL was mapped to linkage group 21 and was significant at the genomewide level in both the sire and the dam-based analyses. The identified QTL can be applied in marker-assisted selection programs to improve the resistance of salmon to IPN and reduce disease-related mortality.
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                Author and article information

                Contributors
                Journal
                Livest Sci
                Livest Sci
                Livestock Science
                Elsevier
                1871-1413
                1 August 2014
                August 2014
                : 166
                : 190-198
                Affiliations
                The Roslin Institute & Royal (Dick) School of Veterinary Studies, University of Edinburgh, Midlothian EH25 9RG, UK
                Author notes
                [* ]Corresponding author. Tel.: +44 131 651 9100. Stephen.Bishop@ 123456roslin.ed.ac.uk
                Article
                S1871-1413(14)00235-2
                10.1016/j.livsci.2014.04.034
                4547482
                © 2014 Elsevier B.V. All rights reserved.
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