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OBJECTIF DU TRAVAIL
La Thônes et Marthod est une race ovine française originaire de la région savoyarde. L’insémination artificielle est peu répandue dans cette race rustique et locale. Plusieurs béliers sont habituellement laissés en permanence dans le troupeau. Ce management de la reproduction rend impossible le calcul de la consanguinité au sein de la race par la méthode des pedigrees. L’objectif de ce travail est donc d’estimer le coefficient de consanguinité au sein de la race par étude génomique. 

RÉSUMÉ
48 individus originaires de 4 départements différents ont été génotypés à l’aide de la puce Illumina – ISGC_sheepLD2015_15K. 9856 marqueurs ont pu être localisés au sein du génome et ainsi 776 Runs of Homozygosity (ROH) ont été identifiés avec le logiciel PLINK v.1.07. Le coefficient de consanguinité calculé est de 0,058. Ce coefficient est égal à celui calculé dans les races ovines françaises originaires des Pyrénées. En plus de ses origines communes avec les races alpines suisses et italiennes, la Thônes et Marthod a été, tout comme ces races, menacée d’extinction à cause du confinement entre vallées et l’important essor des races très productives. La Thônes et Marthod présente un coefficient de consanguinité proche de celui des races Fabrianese, Appenica, Sardinian, Sambucana et Mouton des Grisons. Ces races sont parmi les races transalpines celles qui ont la plus grande variabilité génétique. Cette étude génomique a permis de mettre en évidence deux ROHs partagés par plus de 25% des individus. Le premier sur le chromosome 22 entre les paires de bases 30 et 40Mb correspond au locus de caractères quantitatifs (QTL) de la résistance à la tremblante du mouton. Le second situé entre les paires de base 17 et 20Mb correspondant au QTL « nombre d’agneaux ». La prolificité est l’un des principaux critères de sélection pour la lignée maternelle tandis que les mâles reproducteurs sont tous testés contre la tremblante du mouton avant leur entrée dans le centre à bélier. Enfin, parmi les 1% des Single Nucleotide Polymorphism (SNPs) les plus fréquents dans les ROHs, une majorité d’entre eux se situent au niveau du chromosome 22 dans la région correspondant au gène ADRA2A. La littérature recense que ce gène est impliqué dans les qualités maternelles chez les bovins et que beaucoup de ROHs apparaissent dans cette région du génome chez les brebis de spéculation laine. AIM OF THE WORK
The Thônes et Marthod is a french breed of sheep native from the region of Savoie. Artificial insemination is a little bit developed in this hardy and local breed. Normally several rams always remain in the herd. This reproductive management makes it impossible to calculate the coefficient of inbreeding with pedigree-based information. The aim of this work is therefore to estimate the inbreeding coefficient within the breed through a genomic study.

SUMMARY
48 natives sheeps for four departments were genotyped thanks to Illumina – ISGC_sheepLD2015_15K chip. 9856 genetic markers could be localized in the genome and 776 Runs of Homozygosity (ROH) have been identified with the software PLINK v.1.07. The inbreeding coefficient calculated is 0,058. This coefficient is equal to that of the Pyrenean sheep breeds. In addition to her common origins with the alpine Swiss and Italian breeds, The Thônes et Marthod, like these breeds, faced extinction through the partitioning between the valleys and the growing importance of the more productive breeds. The inbreeding coefficient for the Thônes et Marthod is closed to that of the Fabrianese, Appenica, Sardinian, Sambucana and Bündner Oberländerschaf breeds. These breeds are among the transalpine breeds which have the higher genetic variability. This genomic study allowed to detect two ROHs shared by more than 25% of the sheep. The first is on chromosome 22 between the 30 and 40Mb base pairs and matches the scrapie resistance quantitative trait locus (QTL). The second detected between the 17 and 20Mb corresponds to the QTL named « Total Lambs born ». The prolificity is one of the main selection criteria in the maternal lines whereas breeding rams are all genotyped against scrapie before they enter breeding centre. Lastly, amongst the 1% Single Nucleotide Polymorphism (SNPs) which are the most common in the ROHs, a majority are localized on chromosome 22 in the region encoding the ADRA2A gene. The literature documents that this gene is involved in maternal behavior of beef cows and lots of ROHs are detected in this genomic region in ewes which are intended to produce whool.

Inbreeding coefficient, Genetic diversity, Runs of homozygosity, Loci quantitative traits, Single nucleotide polymorphism, Thônes et Marthod sheep breed --- Sciences du vivant > Médecine vétérinaire & santé animale

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The Identification of the Genetic Components of Autism Spectrum Disorders 2019 will serve as a resource for laboratory and clinical scientists as well as translational-based researchers, primary healthcare providers or physicians, psychologists/psychiatrists, neurologists, developmental pediatricians, clinical geneticists, and other healthcare providers, teachers, caregivers and students involved in autism spectrum disorders (ASD) with the goal to translate information directly to the clinic, education and home setting. Other professionals, students and families might find this textbook of value based on better awareness, causes and understanding of genetic components leading to autism and open avenues for treatment. Genetics play a role with up to 90% of autism, with over 800 currently recognized genes contributing to causes, clinical presentation, treatment, and counseling of family members. This textbook includes 13 chapters divided into three sections (clinical, genetics, other) written by experts in the field dedicated to research and clinical care, description, treatment and generating relevant reviews for ASD and related disorders impacting gene expression, profiling, and pathways. Identification of potential risk factors will be discussed, including obesity, microbiota, malignancy, and the immune system, as well as their direct or indirect contribution to ASD treatment and causation.

Research & information: general --- Biology, life sciences --- Genetics (non-medical) --- autism spectrum disorders (ASD) --- cancer --- overlapping genes and gene profiling --- super-pathways --- phenotypes and diseases --- molecular functions and processes --- 15q11.2 BP1-BP2 microdeletion (Burnside-Butler) syndrome --- imprinting --- parent-of-origin effects --- phenotype-genotype correlation --- autism --- developmental delays --- motor delays --- microbiome --- gut --- ProSAP2 --- Phelan McDermid Syndrome --- gut–brain interaction --- leaky gut --- IL-6 --- SHANK --- collapsin response mediator protein 4 --- autism spectrum disorder --- neurodevelopmental disorder --- whole-exome sequencing --- animal model --- sex different phenotypes --- 15q11.2 BP1–BP2 microdeletion (Burnside–Butler syndrome) --- NIPA1 --- NIPA2 --- CYFIP1 --- TUBGCP5 genes --- Prader–Willi and Angelman syndromes --- magnesium transporters and supplementation --- potential treatment options --- intellectual disability --- AMPA receptors --- NMDA receptors --- guanine nucleotide exchange factor --- synaptic plasticity --- Autism spectrum disorder --- ASD --- Obesity --- Overweight --- Body mass index --- BMI --- autism candidate genes --- synaptotagmin-like protein 4 (SYTL4) --- transmembrane protein 187 (TMEM187) --- SYTL4-protein structure --- STRING-protein-protein interaction --- expression profile --- microRNA- interactions --- autism spectrum disorders --- biological networks --- genomics --- multi-omics --- network diffusion --- data integration --- genetics --- quantitative traits --- stratification by trait severity --- heterogeneity reduction --- case-control association analysis --- fragile X syndrome --- RNA toxicity --- DNA methylation --- mosaicism --- pediatrics --- MS-QMA --- AmplideX --- cytokine --- monocyte --- β-glucan --- T cell cytokine --- trained immunity --- maternal immune activation --- epigenetics --- mice --- postnatal VPA injection --- SAM --- gene expression --- nanostring --- autism spectrum disorders (ASD) --- cancer --- overlapping genes and gene profiling --- super-pathways --- phenotypes and diseases --- molecular functions and processes --- 15q11.2 BP1-BP2 microdeletion (Burnside-Butler) syndrome --- imprinting --- parent-of-origin effects --- phenotype-genotype correlation --- autism --- developmental delays --- motor delays --- microbiome --- gut --- ProSAP2 --- Phelan McDermid Syndrome --- gut–brain interaction --- leaky gut --- IL-6 --- SHANK --- collapsin response mediator protein 4 --- autism spectrum disorder --- neurodevelopmental disorder --- whole-exome sequencing --- animal model --- sex different phenotypes --- 15q11.2 BP1–BP2 microdeletion (Burnside–Butler syndrome) --- NIPA1 --- NIPA2 --- CYFIP1 --- TUBGCP5 genes --- Prader–Willi and Angelman syndromes --- magnesium transporters and supplementation --- potential treatment options --- intellectual disability --- AMPA receptors --- NMDA receptors --- guanine nucleotide exchange factor --- synaptic plasticity --- Autism spectrum disorder --- ASD --- Obesity --- Overweight --- Body mass index --- BMI --- autism candidate genes --- synaptotagmin-like protein 4 (SYTL4) --- transmembrane protein 187 (TMEM187) --- SYTL4-protein structure --- STRING-protein-protein interaction --- expression profile --- microRNA- interactions --- autism spectrum disorders --- biological networks --- genomics --- multi-omics --- network diffusion --- data integration --- genetics --- quantitative traits --- stratification by trait severity --- heterogeneity reduction --- case-control association analysis --- fragile X syndrome --- RNA toxicity --- DNA methylation --- mosaicism --- pediatrics --- MS-QMA --- AmplideX --- cytokine --- monocyte --- β-glucan --- T cell cytokine --- trained immunity --- maternal immune activation --- epigenetics --- mice --- postnatal VPA injection --- SAM --- gene expression --- nanostring