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      A Point Mutation in Suppressor of Cytokine Signalling 2 ( Socs2) Increases the Susceptibility to Inflammation of the Mammary Gland while Associated with Higher Body Weight and Size and Higher Milk Production in a Sheep Model

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          Abstract

          Mastitis is an infectious disease mainly caused by bacteria invading the mammary gland. Genetic control of susceptibility to mastitis has been widely evidenced in dairy ruminants, but the genetic basis and underlying mechanisms are still largely unknown. We describe the discovery, fine mapping and functional characterization of a genetic variant associated with elevated milk leukocytes count, or SCC, as a proxy for mastitis. After implementing genome-wide association studies, we identified a major QTL associated with SCC on ovine chromosome 3. Fine mapping of the region, using full sequencing with 12X coverage in three animals, provided one strong candidate SNP that mapped to the coding sequence of a highly conserved gene, suppressor of cytokine signalling 2 ( Socs2). The frequency of the SNP associated with increased SCC was 21.7% and the Socs2 genotype explained 12% of the variance of the trait. The point mutation induces the p.R96C substitution in the SH2 functional domain of SOCS2 i.e. the binding site of the protein to various ligands, as well-established for the growth hormone receptor GHR. Using surface plasmon resonance we showed that the p.R96C point mutation completely abrogates SOCS2 binding affinity for the phosphopeptide of GHR. Additionally, the size, weight and milk production in p.R96C homozygote sheep, were significantly increased by 24%, 18%, and 4.4%, respectively, when compared to wild type sheep, supporting the view that the point mutation causes a loss of SOCS2 functional activity. Altogether these results provide strong evidence for a causal mutation controlling SCC in sheep and highlight the major role of SOCS2 as a tradeoff between the host’s inflammatory response to mammary infections, and body growth and milk production, which are all mediated by the JAK/STAT signaling pathway.

          Author Summary

          Mastitis is an inflammation of the mammary gland mainly caused by invading bacteria. Ruminants show natural variability in their predisposition to mastitis, and therefore provide unique models for study of the genetics and physiology of host response to bacterial infection. A genome-wide association study was conducted in a dairy sheep population for milk somatic cell counts as a proxy for mastitis. Fine mapping, using whole genome sequencing, led to the identification of a mutation in the Suppressor of Cytokine Signaling 2 gene (socs2). This mutation was shown to cause a loss of functional activity of the SOCS2 protein, which suggested impairment of feedback control of the JAK/STAT signaling pathways in susceptible animals. Additionally, size, weight and milk production were increased in animals carrying the susceptible variant suggesting a pleiotropic effect of the gene on production versus health traits. Results gave strong evidence of the role of SOCS2 in the host’s inflammation of the udder and provided new insights into the key mechanisms underlying the genetic control of mastitis.

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          Most cited references34

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          The genome sequence of taurine cattle: a window to ruminant biology and evolution.

          To understand the biology and evolution of ruminants, the cattle genome was sequenced to about sevenfold coverage. The cattle genome contains a minimum of 22,000 genes, with a core set of 14,345 orthologs shared among seven mammalian species of which 1217 are absent or undetected in noneutherian (marsupial or monotreme) genomes. Cattle-specific evolutionary breakpoint regions in chromosomes have a higher density of segmental duplications, enrichment of repetitive elements, and species-specific variations in genes associated with lactation and immune responsiveness. Genes involved in metabolism are generally highly conserved, although five metabolic genes are deleted or extensively diverged from their human orthologs. The cattle genome sequence thus provides a resource for understanding mammalian evolution and accelerating livestock genetic improvement for milk and meat production.
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            Mapping mendelian factors underlying quantitative traits using RFLP linkage maps.

            The advent of complete genetic linkage maps consisting of codominant DNA markers [typically restriction fragment length polymorphisms (RFLPs)] has stimulated interest in the systematic genetic dissection of discrete Mendelian factors underlying quantitative traits in experimental organisms. We describe here a set of analytical methods that modify and extend the classical theory for mapping such quantitative trait loci (QTLs). These include: (i) a method of identifying promising crosses for QTL mapping by exploiting a classical formula of SEWALL WRIGHT; (ii) a method (interval mapping) for exploiting the full power of RFLP linkage maps by adapting the approach of LOD score analysis used in human genetics, to obtain accurate estimates of the genetic location and phenotypic effect of QTLs; and (iii) a method (selective genotyping) that allows a substantial reduction in the number of progeny that need to be scored with the DNA markers. In addition to the exposition of the methods, explicit graphs are provided that allow experimental geneticists to estimate, in any particular case, the number of progeny required to map QTLs underlying a quantitative trait.
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              Molecular dissection of a quantitative trait locus: a phenylalanine-to-tyrosine substitution in the transmembrane domain of the bovine growth hormone receptor is associated with a major effect on milk yield and composition.

              We herein report on our efforts to improve the mapping resolution of a QTL with major effect on milk yield and composition that was previously mapped to bovine chromosome 20. By using a denser chromosome 20 marker map and by exploiting linkage disequilibrium using two distinct approaches, we provide strong evidence that a chromosome segment including the gene coding for the growth hormone receptor accounts for at least part of the chromosome 20 QTL effect. By sequencing individuals with known QTL genotype, we identify an F to Y substitution in the transmembrane domain of the growth hormone receptor gene that is associated with a strong effect on milk yield and composition in the general population.
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                Author and article information

                Contributors
                Role: Editor
                Journal
                PLoS Genet
                PLoS Genet
                plos
                plosgen
                PLoS Genetics
                Public Library of Science (San Francisco, CA USA )
                1553-7390
                1553-7404
                11 December 2015
                December 2015
                : 11
                : 12
                : e1005629
                Affiliations
                [1 ]INRA, UMR 1388 Génétique, Physiologie et Systèmes d’Elevage, Castanet-Tolosan, France
                [2 ]Université de Toulouse INPT ENSAT, UMR 1388 Génétique, Physiologie et Systèmes d’Elevage, Castanet-Tolosan, France
                [3 ]Université de Toulouse INPT ENVT, UMR 1388 Génétique, Physiologie et Systèmes d’Elevage, Toulouse, France
                [4 ]INRA, Sigenae, Castanet-Tolosan, France
                [5 ]INRA, UR 0875, Mathématiques et Intelligence Artificielle Toulouse, Castanet-Tolosan, France
                [6 ]Université de Toulouse, Institut National Polytechnique (INP), École Nationale Vétérinaire de Toulouse (ENVT), Unité Mixte de Recherche (UMR) 1225, Interactions Hôtes—Agents Pathogènes (IHAP), Toulouse, France
                [7 ]INRA, UMR1225, Interactions Hôtes—Agents Pathogènes (IHAP), Toulouse, France
                [8 ]INSERM UMR1037, Centre Recherches en Cancérologie de Toulouse, Toulouse, France
                [9 ]Université Toulouse III Paul-Sabatier, Toulouse, France
                [10 ]INRA, UE0321 Domaine de La Fage, Saint Jean et Saint Paul, France
                [11 ]INRA, GeT-PlaGe, Genotoul, Castanet-Tolosan, France
                CSIRO, AUSTRALIA
                Author notes

                The authors have declared that no competing interests exist.

                Conceived and designed the experiments: RR GF GTK. Performed the experiments: JS CA CT LL FW OB DP CC GT ML. Analyzed the data: RR PS GF GTK. Wrote the paper: RR GF GTK. Raised the experimental animals: DP.

                Article
                PGENETICS-D-15-01538
                10.1371/journal.pgen.1005629
                4676722
                26658352
                c3490ecf-061f-400c-a060-d3a1c70fe69f
                © 2015 Rupp et al

                This is an open access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited

                History
                : 22 June 2015
                : 6 October 2015
                Page count
                Figures: 6, Tables: 0, Pages: 19
                Funding
                This work was funded by ANR and APISGENE (“SheepSNPQTL” Project, Toulouse, France) and an EU grant (Seventh framework program, “Sustainable Solutions for Small Ruminants” project; http://www.3srbreeding.eu/). The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript.
                Categories
                Research Article
                Custom metadata
                Interested researchers can use the following contact information to request access to the genotypes of the GWAS animals and also to their phenotypes and pedigree data which are included in the genetic national data base, (Centre de Traitement de l’Information Génétique, CTIG, Jouy en Josas, France) as part of the official data system for livestock (ministerial order NOR: AGRT1431011A for ruminants, 24th March 2015, Ministry of Agriculture, France): didier.bouchel@ 123456agriculture.gouv.fr (Ministry of Agriculture, CNAG, Commission Nationale d’Amélioration Génétique, MAAF/DGPE/SDFE/SDFA/BLSA, 3 rue Barbet de Jouy—75349 PARIS 07 SP); laurent.journaux@ 123456idele.fr : (FGE, France Génetique Elevage, Interprofession de l’Amélioration Génétique de Ruminants, 149 rue de Bercy, Paris, France) and rachel.rupp@ 123456toulouse.inra.fr (corresponding author of this publication). The 207 variations identified in the QTL region are available from the public NCBI databases (dbSNP Build143; http://www.ncbi.nlm.nih.gov/projects/SNP/snp_ss.cgi?subsnp_id=1553223136; ss references in S2 Table). The sequence data is fully available on the public SRA database ( http://www.ebi.ac.uk/ena/data/view/PRJEB9911). All other relevant data are within the paper and its Supporting Information files.

                Genetics
                Genetics

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