A genome scan for milk production traits in dairy goats reveals two new mutations in <i>Dgat1</i> reducing milk fat content

The quantity of milk and milk fat and proteins are particularly important traits in dairy livestock. However, little is known about the regions of the genome that influence these traits in goats. We conducted a genome wide association study in French goats and identified 109 regions associated with dairy traits. For a major region on chromosome 14 closely associated with fat content, the Diacylglycerol O-Acyltransferase 1 (DGAT1) gene turned out to be a functional and positional candidate gene. The caprine reference sequence of this gene was completed and 29 polymorphisms were found in the gene sequence, including two novel exonic mutations: R251L and R396W, leading to substitutions in the protein sequence. The R251L mutation was found in the Saanen breed at a frequency of 3.5% and the R396W mutation both in the Saanen and Alpine breeds at a frequencies of 13% and 7% respectively. The R396W mutation explained 46% of the genetic variance of the trait, and the R251L mutation 6%. Both mutations were associated with a notable decrease in milk fat content. Their causality was then demonstrated by a functional test. These results provide new knowledge on the genetic basis of milk synthesis and will help improve the management of the French dairy goat breeding program

Optimized diffusion of buck semen for saving genetic variability in selected dairy goat populations

BACKGROUND: Current research on quantitative genetics has provided efficient guidelines for the sustainable management of selected populations: genetic gain is maximized while the loss of genetic diversity is maintained at a reasonable rate. However, actual selection schemes are complex, especially for large domestic species, and they have to take into account many operational constraints. This paper deals with the actual selection of dairy goats where the challenge is to optimize diffusion of buck semen on the field. Three objectives are considered simultaneously: i) natural service buck replacement (NSR); ii) goat replacement (GR); iii) semen distribution of young bucks to be progeny-tested. An appropriate optimization method is developed, which involves five analytical steps. Solutions are obtained by simulated annealing and the corresponding algorithms are presented in detail. RESULTS: The whole procedure was tested on two French goat populations (Alpine and Saanen breeds) and the results presented in the abstract were based on the average of the two breeds. The procedure induced an immediate acceleration of genetic gain in comparison with the current annual genetic gain (0.15 genetic standard deviation unit), as shown by two facts. First, the genetic level of replacement natural service (NS) bucks was predicted, 1.5 years ahead at the moment of reproduction, to be equivalent to that of the progeny-tested bucks in service, born from the current breeding scheme. Second, the genetic level of replacement goats was much higher than that of their dams (0.86 unit), which represented 6 years of selection, although dams were only 3 years older than their replacement daughters. This improved genetic gain could be achieved while decreasing inbreeding coefficients substantially. Inbreeding coefficients (%) of NS bucks was lower than that of the progeny-tested bucks (-0.17). Goats were also less inbred than their dams (-0.67). CONCLUSIONS: It was possible to account for complex operational constraints while developing goat selection schemes, both efficient and sustainable. Therefore, the recommended selection and mating decisions might receive attention from goat breeders using both AI and NS

Биофизика зрительной сенсорной системы человека

Зрительная сенсорная система – это система, которая воспринимает излучение видимого спектра, после чего формируется изображение предметов окружающей среды в виде определенных ощущений (сенсорных чувств)

Author Correction:A genome scan for milk production traits in dairy goats reveals two new mutations in Dgat1 reducing milk fat content (Scientific Reports DOI: 10.1038/s41598-017-02052-0)

A correction to this article has been published and is linked from the HTML and PDF versions of this paper. The error has not been fixed in the pape

VarGoats project : a dataset of 1159 whole-genome sequences to dissect Capra hircus global diversity

Since their domestication 10,500 years ago, goat populations with distinctive genetic backgrounds have adapted to a broad variety of environments and breeding conditions. The VarGoats project is an international 1000-genome resequencing program designed to understand the consequences of domestication and breeding on the genetic diversity of domestic goats and to elucidate how speciation and hybridization have modeled the genomes of a set of species representative of the genus Capra. A dataset comprising 652 sequenced goats and 507 public goat sequences, including 35 animals representing eight wild species, has been collected worldwide. We identified 74,274,427 single nucleotide polymorphisms (SNPs) and 13,607,850 insertion-deletions (InDels) by aligning these sequences to the latest version of the goat reference genome (ARS1). A Neighbor-joining tree based on Reynolds genetic distances showed that goats from Africa, Asia and Europe tend to group into independent clusters. Because goat breeds from Oceania and Caribbean (Creole) all derive from imported animals, they are distributed along the tree according to their ancestral geographic origin. We report on an unprecedented international effort to characterize the genome-wide diversity of domestic goats. This large range of sequenced individuals represents a unique opportunity to ascertain how the demographic and selection processes associated with post-domestication history have shaped the diversity of this species. Data generated for the project will also be extremely useful to identify deleterious mutations and polymorphisms with causal effects on complex traits, and thus will contribute to new knowledge that could be used in genomic prediction and genome-wide association studies

AdaptMap: exploring goat diversity and adaptation

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Dispositif Génétique Français – les filières petits ruminants (présentation transversalité petits ruminants GenPhySE)

National audienc

La Sélection à Parenté Minimum Génomique : principes et résultats pour les deux races caprines laitières principales françaises

International audienceLa Sélection à Parenté Minimum (SPM) est une stratégie de sélection performante d’optimisation combinée du progrès génétique et de la variabilité génétique des reproducteurs, développée en France au début des années 2000. Elle utilise la méthode dite du « recuit simulé ». Son application dans les schémas de sélection caprins a démarré en 2006 pour la procréation des mâles d’Insémination Artificielle (IA) par l’Organisme de Sélection (OS) français des deux races principales françaises, Alpine et Saanen. En 2018, alors que la sélection génomique est mise en place par l’OS dans les deux races, une version « génomique » de la SPM a été développée, tenant compte des informations génomiques pour évaluer les relations de parenté entre reproducteurs, et des différences de fiabilité des valeurs génétiques des boucs d’IA selon s’ils sont testés ou non sur descendance. Son efficacité est présentée pour les accouplements entre « pères à boucs » et « mères à boucs », réellement réalisés en 2021 par l’OS. Les animaux issus des accouplements présentent un niveau génétique global élevé), une consanguinité modérée (3,0 à 3,6 %) et peu de défauts sur les valeurs génétiques de chacun des caractères élémentaires en sélection. Le pourcentage de « pères à boucs » non testés sur descendance, critère clé nouvellement optimisé dans la SPM, est de 35 %. Il est atteint à la fois à l’échelle de tous les accouplements, et à l’échelle des troupeaux. L’étude des mâles d’IA nés entre 2000 et 2020 permet de mesurer l’impact réel de la SPM sur le long terme et d’estimer les premiers effets de la version génomique. Le progrès génétique annuel sur l’index de synthèse correspondant à l’objectif de sélection est conséquent avec 0,17 écart-type génétique dans chacune des races. En parallèle, le taux d’augmentation de la consanguinité par génération est très modéré : 0,26 % en race Alpine et 0,21 % en race Saanen