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Avant-Propos : Anomalies génétiques Les anomalies génétiques sont observées depuis toujours par les éleveurs et ont été décrites depuis longtemps par les chercheurs. Toutefois, elles ont toujours eu une situation à part dans la sélection des espèces d’élevage. Si la sélection s’est structurée, organisée, raffinée, elle n’a le plus souvent concerné que des caractères économiquement importants mais dits « quantitatifs », c’est-à-dire des caractères au déterminisme génétique complexe soumis à la fois à des effets du milieu et un nombre important de gènes. Parfois, des gènes à effet majeur ont également été pris en compte (gène culard, gène « sans cornes », coloration, absence de plumes…). Mais les anomalies ont toujours été considérées comme un problème inévitable, éventuellement à cacher. Elles ont été peu prises en compte en sélection, elles ne font pas l’objet de déclarations dans le cadre du contrôle de performances usuel et, au contraire, jusqu’à récemment, faisaient plutôt l’objet d’éliminations, volontairement ou non, sans déclaration. Considérées comme rares, elles ont été intégrées dans les incompressibles pertes d’élevage. La situation se complique en général lorsqu’un reproducteur largement diffusé s’avère porteur d’une anomalie. L’anomalie change alors de statut : d’inconvénient inéluctable mais peu important, elle apparaît comme un problème majeur pour les éleveurs, source de contentieux, porteur d’une mauvaise image. Son éradication rapide devient prioritaire, et l’élimination des reproducteurs porteurs est généralement préconisée. Au cours des années 1990 et 2000, quelques cas dans l’espèce bovine, finalement peu nombreux, ont marqué les esprits par l’impact qu’ils ont eu dans les populations concernées quand les meilleurs taureaux du moment se sont révélés porteurs. De plus, aucun réseau « du déclarant au généticien » n’étant mis en place, il a fallu du temps entre la déclaration des premiers cas et la disponibilité d’un test moléculaire permettant une éradication réellement efficace. Les anomalies génétiques sont inéluctables. Elles résultent de mutations de l’ADN qui sont un phénomène normal source de la diversité génétique. Souvent neutres, parfois fonctionnelles, les mutations peuvent dans des cas rares être responsables d’anomalies. Les populations d’élevage étant des populations génétiquement petites (malgré des effectifs physiques parfois très élevés), elles présentent des conditions favorables pour la diffusion et l’expression de ces anomalies, du fait de la dérive génétique et de la consanguinité. Contrairement à ce qui est parfois supposé, la sélection ne crée pas les anomalies, mais elle peut favoriser leur diffusion (l’augmentation de leur fréquence allélique et l’apparition de cas), de façon analogue aux antibiotiques qui ne créent pas de résistance, mais sélectionnent les populations bactériennes résistantes. On pense également à tort que les populations génétiquement petites présentent plus d’anomalies. Il est plus exact de dire qu’à effectif d’animaux identique, les populations génétiquement petites présentent un nombre d’anomalies différentes plus faible, mais un nombre de cas par anomalie plus élevé. Alors que la sélection est un modèle de rationalité, les anomalies sont longtemps restées hors de ce cadre. Une des raisons était sans doute le manque d’outils pour les éliminer. Une mise en place progressive depuis quinze ans et une accélération certaine des techniques de dépistage depuis le début des années 2010 a permis de définir un nouveau cadre pour intégrer les anomalies dans le processus de sélection. Tout d’abord, il est essentiel de disposer d’un système d’observation des anomalies. Les cas étant souvent rares et dispersés, il est essentiel que ce système soit largement implanté sur le terrain et que les informations soient centralisées, de façon à détecter les émergences le plus tôt possible, à partir de cas considérés éventuellement à tort comme sporadiques. Différents observatoires dédiés, souvent distincts du contrôle de performances classique, ont été mis en place à travers le monde et dans différentes espèces d’élevage ou de compagnie. Nous présentons dans ce dossier l’Observatoire National des Anomalies Bovines – ONAB ; https://www.onab.fr/ – (Grohs et al 2016) et la situation chez le porc (Riquet et al 2016). Ces dispositifs ont réellement montré toute leur efficacité lorsque les outils moléculaires les plus récents, de génotypage et séquençage, ont été disponibles, permettant de caractériser rapidement une anomalie à partir de quelques cas (Duchesne et al 2016). Ces outils génomiques peuvent même être utilisés pour orienter la recherche des anomalies avant leur observation (Fritz et al 2016). Enfin, il convient d’insister sur le fait que l’analyse de cas mais aussi de leurs ancêtres n’est possible que si d’excellentes collections d’échantillons sont stockées, comme c’est le cas pour l’ONAB ou pour le Centre de Ressources Biologiques pour les animaux domestiques (CRB-Anim ; https://www.crb-anim.fr/). La situation est bien sûr très variable selon les espèces. L’impact d’une anomalie, et donc la prise de conscience des sélectionneurs, est plus élevé dans les espèces conduites en race pure et quand l’individu a une forte valeur. L’espèce bovine est caractérisée par un double réseau de phénotypage associé au conseil en élevage et au travers des vétérinaires, par une conduite en race pure quasi-exclusive, par une sélection puissante, devenue génomique. Elle connaît une évolution récente favorisant la détection des anomalies. La situation est également très avancée chez le chien, une espèce bénéficiant d’une bonne supervision vétérinaire et organisée en de nombreuses races pures d’effectifs génétiques très petits et souvent sujettes à des anomalies spécifiques. Aujourd’hui, la situation a beaucoup évolué, de sorte qu’un nombre croissant d’anomalies est mis en évidence, dans toutes les races, quel que soit le mode de reproduction prédominant (monte naturelle ou insémination artificielle). En revanche, leur prise en compte reste encore partielle, et rarement à la hauteur (c’est-à-dire parfois trop, parfois trop peu) de leur importance réelle. Nous proposons dans Boichard et al (2016) différentes approches pour inclure les anomalies de façon objective dans la sélection. Pour le chercheur, les anomalies sont des objets d’étude hors du commun. L’anomalie, en provoquant une perturbation sévère en dehors de la gamme physiologique normale, permet parfois de comprendre un mécanisme habituellement peu variable et donc peu étudiable autrement. On comprend ainsi mieux le rôle des gènes au travers de leurs effets lorsqu’ils sont mutés. Les mécanismes mis en jeu touchent souvent des voies fondamentales du vivant et, à ce titre, sont souvent transposables entre espèces. Les connaissances sont bien sûr bien plus avancées chez l’Homme ou les espèces modèles comme la souris et nous bénéficions de ces informations pour caractériser rapidement les mutations découvertes dans les espèces d’élevage. Mais parfois, une anomalie observée dans une espèce d’élevage peut aussi contribuer à résoudre des questions chez l’Homme, par exemple pour des maladies très rares alors que la structure des populations d’élevage avec de grandes familles permet l’étude de cas familiaux. Il arrive alors que l’espèce d’élevage, de même que le chien, prenne le rôle d’espèce modèle de pathologies humaines.

Cet article rappelle les notions et principes relatifs aux anomalies génétiques dont on observe régulièrement des émergences dans les populations animales d’élevage. Ces anomalies proviennent de mutations naturelles et certaines d’entre elles voient leur fréquence augmenter du fait principalement de la dérive génétique, parfois de la sélection. Lorsqu’elles sont dominantes, elles sont généralement rapidement contre-sélectionnées et tendent à disparaître. Mais lorsqu’elles sont récessives, les cas observables ne représentent qu’une toute petite fraction des individus porteurs. On définit généralement les anomalies génétiques comme des syndromes monogéniques. Toutefois, cette règle a beaucoup d’exceptions, soit parce que l’anomalie se révèle plus complexe qu’initialement supposé, soit parce que le syndrome présente une variabilité phénotypique due à des gènes modulateurs. Les anomalies récessives sont principalement dues à des mutations de type perte de fonction, tandis que les mutations dominantes résultent souvent d’interactions entre gènes ou entre protéines, ou de l’altération d’un gène répresseur. Les anomalies cytogénétiques conduisent à des phénotypes anormaux généralement différents entre types de caryotypes déséquilibrés. Enfin, les anomalies présentent parfois des déterminismes particuliers, par exemple dans le cas de gènes portés par les chromosomes sexuels ou soumis à empreinte parentale.

Through the Horizon 2020 project ’GenRes Bridge’ the new journal Genetic Resources was conceived to serve as a new cross-cutting platform for stakeholders and practitioners in genetic resources. Its ambition is to provide access to relevant information and tools for the monitoring, conservation, management, characterization and use of genetic resources, and thus to contribute to the FAO global plans of action on genetic resources. Conceived to fill the gaps left by the discontinuation of the journals Plant Genetic Resources Newsletter and Animal Genetic Resources, it aims at serving the genetic resources community worldwide and across sectors.

Different methods and formulae have been suggested to estimate effective population size based on pedigree data. These methods vary in their sensitivity to various sources of bias related to heterogenous pedigree knowledge or pedigree structure. We propose here to adapt a pre-existing method estimating coancestry rate for the specific purpose of monitoring genetic variability within livestock and captive populations. Coancestry rate is computed by averaging coancestries between pairs of individuals corrected by their equivalent numbers of generations, while restricting pedigree information to a maximum number of generations. Simulation demonstrated that restricting the number of generations allows a much clearer observation of the impact of recent events on genetic variability. Restricting the number of generations for the calculation of coancestry also has less bias related to incomplete pedigree, although it may overestimate effective population size due to non-independence in family sizes across generations. This strategy was tested on the Norwegian Nordland Lyngen horse, the Colblood Trotter horse, the French Avranchin sheep, and Bresse chicken, illustrating the applications of the approach for the monitoring of genetic variability.

In the course of evolution, pecorans (i.e., higher ruminants) developed a remarkable diversity of osseous cranial appendages, collectively referred to as “headgear,” which likely share the same origin and genetic basis. However, the nature and function of the genetic determinants underlying their number and position remain elusive. Jacob and other rare populations of sheep and goats are characterized by polyceraty, the presence of more than two horns. Here, we characterize distinct POLYCERATE alleles in each species, both associated with defective HOXD1 function. We show that haploinsufficiency at this locus results in the splitting of horn bud primordia, likely following the abnormal extension of an initial morphogenetic field. These results highlight the key role played by this gene in headgear patterning and illustrate the evolutionary co-option of a gene involved in the early development of bilateria to properly fix the position and number of these distinctive organs of Bovidae.

International audience; The negative effects of inbreeding (higher occurrence of genetic defects, inbreeding depression…) are well knownby breeds’ managers. However we still have a poor insight of how the genome is impacted by inbreeding. Forover a 200 years period, a French sheep breed called the Rambouillet has been kept in a single flock without anyintrogression. Pedigree information was fully recorded since the 1870s. For the last fifty years, minimizing thebreed’s inbreeding level has been the only goal of its management plan. It reached 52% for nowadays animalsaccording to simulation data based on pedigrees. Despite this level, the breed’s weight, prolificacy and fertility havenot changed over the last forty years. Altogether this breed gives a unique opportunity to explore the consequencesof inbreeding at the genome level. To do so, we used a high density chip (600 K SNP) on a panel of 46 individuals.Among these animals, 38 were born between 2006 and 2012, and eight are older males born in the 1980s whosesamples come from the French National Cryobank. First results showed that the genome of the breed was highlystructured with a very low level of diversity. However the genomic inbreeding level based on run of homozygosity(ROH) was about half the estimation based on pedigree information, and a very weak inbreeding depression wasdetected. Therefore, we investigated more precisely at the chromosome level for ‘cold spots’ of diversity basedon ROH. When compared with two related breeds, the Mourerous and the Arles, the Rambouillet showed muchmore ROH segments, but the total length of ROH is actually lower than expected. Linkage disequilibrium (LD)was also calculated at chromosome level and the genome structure appeared to differ between each chromosome.This information suggests a mutational load purge that occurred throughout the years. Ongoing research seems toconfirm this hypothesis since hot spots of diversity are found in regions with genes involved in major developmentpatterns (such as cells division). Finally, the Rambouillet sheep proves to be a valuable source of investigation inthe understanding the genome aspects of inbreeding.

In the course of evolution, pecorans (i.e. higher ruminants) developed a remarkable diversity of osseous cranial appendages, collectively referred to as ‘headgear’, which likely share the same origin and genetic basis. However, the nature and function of the genetic determinants underlying their number and position remain elusive. Jacob and other rare populations of sheep and goats, are characterized by polyceraty, the presence of more than two horns. Here, we characterize distinct POLYCERATE alleles in each species, both associated with defective HOXD1 function. We show that haploinsufficiency at this locus results in the splitting of horn bud primordia, likely following the abnormal extension of an initial morphogenetic field. These results highlight the key role played by this gene in headgear patterning and illustrate the evolutionary co-option of a gene involved in the early development of bilateria to properly fix the position and number of these distinctive organs of Bovidae.

Cryoconservation is one of the main strategies to conserve farm animal genetic resources, providing opportunities for genetic improvement and adaptation to changes in production environments and consumer demands. In this study, we combine livestock breed-related data from the Domesticated Animal Diversity Information System (DAD-IS) and information provided by gene banks from 15 European and 2 non-European countries on material stored for livestock breeds to analyze the gaps in cryomaterial collections according to species, countries and various breed categories. Out of the 2949 breeds registered in DAD-IS for these countries, 15.9% have been reported to have material stored in gene banks, but only 4.3% have material sufficient to allow breed reconstitution. The proportion of breeds with stored cryomaterial was greater than 20% for ruminants and pigs, between 10% and 20% for equids, and below 10% for rabbit and avian species. According to the results of two logistic regressions, countries show significant differences in the proportion of populations collected for cryostorage, while breeds not-at-risk are more likely to have cryomaterial preserved than are other breeds. Also, a relatively larger proportion of transboundary breeds have cryomaterial in gene banks than do local breeds, likely due in part to the fact that multiple countries have the opportunity to collect this material. These results highlight the need for increased efforts in material collection for at-risk local breeds and regional coordination on cryoconservation of material from transboundary breeds.

Threatened populations that have undergone a strong reduction of their size are subsequently more likely to reproduce under inbred conditions. The adverse effects of such matings on the fitness of the progeny have long been known. Unlike natural populations for which detailed records of genealogy are scarce, domestic and captive populations can benefit from available pedigree data. In this regard, the Merino population from Rambouillet, which has been maintained at small size since its arrival at the Bergerie Nationale de Rambouillet, is a valuable model to study the effects of a small population size associated with a closed registry system on genome structure and genetic diversity. This study showed that, despite a low genetic diversity and a strong structure of the genome, the population management, aiming to minimize matings between the most closely related animals was an adequate breeding policy: the population is not structured into family groups. Furthermore inbreeding depression is low. This project should help to assess the evolutionary potential of the flock. In the long term, it should contribute to the development of recommendations on the management of endangered populations where inbreeding and genetic drift are inevitable, due to their small size.

The limiting factor of genetic defect identification in farm animal populations is the outbreak detection and clinical characterization. Indeed these events are rare and poorly recorded in animal breeding databases. After several experiences in the past showing that outbreaks can be missed, a National Observatory for Bovine Abnormalities was implemented in 2002, jointly by INRA, the main actors in animal breeding, and veterinarian organizations. The goal of this observatory is primarily to collect cases in a central database as well as their corresponding epidemiologic context and biological samples. Another goal is to ensure a scientific watch, to provide information, and to coordinate actions between partners (www.onab.fr). Records are by far not exhaustive with several hundred files per year but are probably sufficient, through a good geographical and breed coverage, to detect most new outbreaks. This article presents an overview of ONAB’s activities, focusing on different defects encountered as well as on the identification of the corresponding causative mutations, paving the way for their management in selection.; Le facteur limitant de l’identification des anomalies génétiques dans les populations animales d’élevage est la phase de détection des émergences et de caractérisation clinique. En effet, ces évènements sont rares et mal répertoriés dans les bases nationales d’information génétique. Après différentes expériences passées montrant que des anomalies n’avaient pas été détectées, un Observatoire National des Anomalies Bovines a été mis en place en 2002, rassemblant l’INRA, les acteurs de la sélection animale et les acteurs du monde vétérinaire. L’objectif de cet observatoire est avant tout de collecter les déclarations de cas sur une base normalisée, ainsi que les échantillons biologiques associés, mais aussi d’assurer une veille et une information scientifique et une coordination des actions (www.onab.fr). Les déclarations sont loin d’être exhaustives avec quelques centaines de dossiers par an. Mais par la bonne couverture géographique, raciale et partenariale de l’ONAB, elles sont sans doute suffisantes pour détecter la plupart des nouvelles émergences. Cet article présente un bilan des activités, en mettant l’accent sur les différentes anomalies rencontrées ainsi que les succès en termes d’identification des mutations causales correspondantes, ouvrant la voie à leur gestion en sélection.

For years, genetic defects were discovered sporadically and this led breeders to eradicate drastically all the carriers in combination with the procreation of non carrier future reproducing animals. However there is a new paradigm with the setting up of genomic selection since genetic defects are now detected much faster and, consequently, in larger numbers. Therefore it is necessary to adapt the way genetic defects are taken into account in selection. A good overview of the genetic situation must be obtained by estimating the allelic frequency in the population and by assessing the status of most major reproducing animals with the available diagnosis tests, now often included in SNP chips. Noteworthy, this status may also be assessed indirectly through haplotypic prediction for older animals and does not always require to genotype them again. Then the selection plan must be set up in the light of the economic weight of the defects, which depends on the cost of affected cases and allelic frequency. The optimal method to gradually eradicate genetic defects relies on the use of a breeding objective combining genetic defects with the other traits, with their economic weights. The transition phase between the discovery of a genetic defect and its complete eradication is always delicate and is usually coped by orienting the matings to avoid cases. Finally, it is recalled that using a large number of breeding animals while restricting their number of offspring is a simple measure that efficiently limits the outbreaks of new genetic defects.; Pendant plusieurs dizaines d’années après la mise en place des programmes de sélection génétique, la découverte de nouvelles anomalies est restée sporadique. Cela a incité jusqu’à présent les gestionnaires de ces programmes à appliquer une politique d’éradication drastique des reproducteurs porteurs, combinée à la procréation de futurs reproducteurs non porteurs. Mais la situation est en train de changer avec l’avènement de la sélection génomique et des technologies associées, qui permettent de détecter les anomalies plus rapidement et donc en plus grand nombre. Il est donc indispensable de faire évoluer la façon de les prendre en compte dans les programmes de sélection. Un état de la situation dans la population doit d’abord être établi en estimant la fréquence allélique de l’anomalie et en caractérisant le statut des reproducteurs les plus importants avec les tests moléculaires disponibles, en particulier avec les puces à « Single Nucleotide Polymorphism » (SNP). Dans certains cas, une prédiction indirecte, à partir d’haplotypes ou d’imputation, permet de connaître le statut à la mutation des reproducteurs plus anciens avec une forte probabilité sans nécessité de ré-analyser leur ADN. Une fois ce bilan établi, les mesures à prendre dépendent du poids économique des anomalies qui est fonction de deux paramètres, le coût par individu atteint et la fréquence allélique dans la population. La méthode optimale permettant une éradication progressive des anomalies repose sur l’utilisation d’un objectif de sélection combinant les anomalies aux autres caractères. Une phase délicate à gérer, principalement au travers des accouplements, est celle de l’utilisation de reproducteurs porteurs durant la période de transition entre la découverte de l’anomalie et l’éradication complète. Enfin, il est rappelé qu’une mesure simple permettant de limiter l’émergence de nouvelles anomalies est d’utiliser un nombre élevé de reproducteurs tout en restreignant leur taille de descendance.

Summary A pedigree analysis was performed on eight French dairy cattle breeds to assess their change in genetic variability since a first analysis com- pleted in 1996. The Holstein, Normande and Montbeliarde breeds are selected internationally with over hundreds of thousands cows regis- tered in the performance recording system. Three breeds are interna- tionally selected but with limited numbers of cows in France (Brown Swiss, French Simmental and French Red Pied). The last two remaining breeds (Abondance and Tarentaise) are raised at regional level. The effective numbers of ancestors of cows born between 2004 and 2007 varied between 15 (Abondance and Tarentaise) and 51 (French Red Pied). The effective population sizes (classical approach) varied between 53 (Abondance) and 197 (French Red Pied). This article also compares the genetic variability of the ex situ (collections of the French National Cryobank) and in situ populations. The results were commented in regard to the recent history of gene flows in the different breeds as well as the existence of more or less stringent bottlenecks. Our results showed that whatever the size of the breeds, their genetic diversity impoverished quite rapidly since 1996 and they all could be considered as quite poor from a genetic diversity point of view. It shows the need for setting up cryobanks as gene reservoirs as well as sustainable breed- ing programmes that include loss of genetic diversity as an integrated control parameter.

On the basis of correlations between pairwise individual genealogical kinship coefficients and allele sharing distances computed from genotyping data, we propose an approximate Bayesian computation (ABC) approach to assess pedigree file reliability through genedropping simulations. We explore the features of the method using simulated data sets and show precision increases with the number of markers. An application is further made with five dog breeds, four sheep breeds and one cattle breed raised in France and displaying various characteristics and population sizes, using microsatellite or SNP markers. Depending on the breeds, pedigree error estimations range between 1% and 9% in dog breeds, 1% and 10% in sheep breeds and 4% in cattle breeds.

Pedigree information was analyzed in 7 small populations of sheep raised in France (Bleu du Maine, Charmoise, Cotentin, on-farm Romanov, Romanov ex situ in vivo, Roussin de la Hague, Solognote) to estimate their genetic variability. The pedigree information for each breed, estimated by the number of equivalent generations traced, ranged from rather poor (4.6) to very good (10.5) when compared with other studies. On the basis of probabilities of gene origin, the effective number of ancestors ranged from 17 (on-farm Romanov breed) to 59 (Bleu du Maine). On the basis of the rate of inbreeding, the realized effective size was found to range from 65 (Romanov breed ex situ) to 231 (Bleu du Maine). The average kinship coefficients between rams from which semen doses are available in the French National Cryobank and the active ram and ewe populations were also computed. Results found in each breed were analyzed by taking into consideration the demographic evolution of the breeds, their management practices, and the use of cryopreservation as a way to preserve genetic variability. It appeared quite clear that, in populations in which AI with frozen semen is seldom used, factors that mainly affect the genetic variability are the female-to-male ratio, which should be as small as possible, and the number of reproducing female offspring by males, which should be as balanced as possible. Finally, our work showed that all populations under study have fairly good genetic variability in comparison with other species, despite their scarce numbers.

L’amélioration génétique des animaux : une action collective au service des éleveurs et des filières. Carrefour International Ovin-Caprin

espanolLa clasificacion de las razas animales segun su nivel de peligro en cuanto a su desaparicion es un elemento de base para un sistema nacional de alerta y de monitoreo de los recursos geneticos. Un enfoque multicriterio ha sido desarrollado para establecer el nivel de peligro de una poblacion animal domestica. En total, se mantuvieron seis criterios: (i) el numero total de hembras reproductoras, (ii) la evolucion de este numero en los cincos ultimos anos, o las cincos generaciones, segun la especie; (iii) la proporcion de cruzamientos; (iv) el tamano efectivo de la poblacion, (v) la organizacion de los criadores y el apoyo tecnico; (vi) el contexto socio-economico. Con el proposito de facilitar la combinacion de estos criterios de tipo diferente, los valores observados fueron convertidos en una escala de 0 (ausencia de amenaza) a 5 (amenaza maxima), la correspondencia entre valores observados y notas siendo especifica por cada criterio. Para cada raza, las notas estan presentadas de forma grafica y una nota de sintesis esta calculada como la media de las seis notas. Este metodo ha sido aplicado a 178 razas locales francesas perteneciendo a diez diferentes especies: ganado, ovino, caprino, cerdo, caballo, asno, gallina, pavo, oca, pato comun. Asi se demostro que la mayoria de las razas locales francesas se pueden considerar como en peligro: todas las razas locales de equido y de cerdo, casi la totalidad de las razas locales de aves de corral, alrededor de 80% de las razas locales de ganado o caprinos y la mitad de razas locales de ovinos. Se discute el interes de este metodo para la definicion de estrategias de conservacion et la elaboracion de politicas publicas. EnglishBreed risk status assessment methods are key components of country-based early warning and response systems. In this study, a multiindicator method was developed to assess the risk status of livestock populations. Six indicators were used: (i) the current number of breeding females; (ii) the change in the number of breeding females over the last 5 years or generations (depending on the species); (iii) percentage of cross-breeding; (iv) effective population size; (v) breeders organization and technical support; and (vi) socio-economic context. To make these indicators comparable, observed values were converted into scores on a six-point scale (from 0 = no threat to 5 = maximum threat); a specific conversion method was used for each indicator. For each breed, the different scores were analysed graphically and an overall score was calculated by averaging the six separate indicator scores. This approach was applied to 178 French local breeds, belonging to ten different species: horse, donkey, goat, pig, chicken, turkey, goose and Pekin duck. A large percentage of local breeds were found to be at risk to be lost for farming, although the results were species dependent. All local equine and pig breeds, as well as almost all local poultry breeds appeared to be endangered. About 80 percent of local goat and cattle breeds, and half local sheep breeds were also found to be at risk. The usefulness of this method with regards to conservation strategies and public policy is discussed francaisLa classification des races animales selon leur statut vis-a-vis d’un risque de disparition est un element-clef d’un systeme national d’alerte et de suivi des ressources genetiques. Une approche multi-indicateurs a ete developpee pour etablir le degre de menace d’une population animale domestique. Au total, six indicateurs ont ete retenus : (i) le nombre total de femelles reproductrices, (ii) l’evolution de ce nombre dans les cinq dernieres annees, ou generations, selon l’espece ; (iii) la proportion de croisement ; (iv) la taille efficace de la population ; (v) l’organisation des eleveurs et l’appui technique ; (vi) le contexte socio-economique. Afin de faciliter la combinaison de ces indicateurs de nature differente, les valeurs observees sont converties sur une echelle de 0 (absence de menace) a 5 (menace maximale), la correspondance entre valeurs observees et notes etant specifique de chaque indicateur. Pour chaque race, les notes sont representees de facon graphique et une note de synthese est attribuee en calculant la simple moyenne des six notes. Cette methode a ete appliquee a 178 races locales francaises appartenant a dix especes differentes : cheval, âne, bovins, ovins, caprins, porc, poule, dinde, oie, canard commun. Il a ete ainsi montre que la plupart des races locales francaises peuvent etre considerees comme menacees : toutes les races locales d’equides et de porc, la quasi-totalite des races locales de volailles, environ 80% des races locales bovines ou caprines, et la moitie des races locales ovines. L’interet de cette methode pour la definition de strategies de conservation et l’elaboration de politiques publiques est discute.

Background From domestication to the current pattern of differentiation, domestic species have been influenced by reticulate evolution with multiple events of migration, introgression, and isolation; this has resulted in a very large number of breeds. In order to manage these breeds and their genetic diversity, one must know the current genetic structure of the populations and the relationships among these. This paper presents the results of a genetic diversity analysis on an almost exhaustive sample of the sheep breeds reared in France. Molecular characterization was performed with a set of 21 microsatellite markers on a collection of 49 breeds that include five breed types: meat, hardy meat, dairy, high prolificacy and patrimonial breeds. Results Values of expected heterozygosity ranged from 0.48 to 0.76 depending on the breed, with specialized meat breeds exhibiting the lowest values. Neighbor-Net, multidimensional analysis or clustering approaches revealed a clear differentiation of the meat breeds compared to the other breed types. Moreover, the group that clustered meat breeds included all the breeds that originated from the United Kingdom (UK) and those that originated from crossbreeding between UK breeds and French local breeds. We also highlighted old genetic introgression events that were related to the diffusion of Merino rams to improve wool production. As a result of these introgression events, especially that regarding the UK breeds, the breeds that were clustered in the ‘meat type cluster’ exhibited the lowest contribution to total diversity. That means that similar allelic combinations could be observed in different breeds of this group. Conclusions The genetic differentiation pattern of the sheep breeds reared in France results from a combination of factors, i.e. geographical origin, historic gene flow, and breed use. The Merino influence is weaker than that of UK breeds, which is consistent with how sheep use changed radically at the end of 19th century when wool-producing animals (Merino-like) were replaced by meat-producing breeds. These results are highly relevant to monitor and manage the genetic diversity of sheep and can be used to set priorities in conservation programs when needed. Electronic supplementary material The online version of this article (doi:10.1186/s12711-015-0131-7) contains supplementary material, which is available to authorized users.

Background Since 2010, four Charolais calves with a congenital mechanobullous skin disorder that were born in the same herd from consanguineous matings were reported to us. Clinical and histopathological examination revealed lesions that are compatible with junctional epidermolysis bullosa (JEB). Results Fifty-four extended regions of homozygosity (>1 Mb) were identified after analysing the whole-genome sequencing (WGS) data from the only case available for DNA sampling at the beginning of the study. Filtering of variants located in these regions for (i) homozygous polymorphisms observed in the WGS data from eight healthy Charolais animals and (ii) homozygous or heterozygous polymorphisms found in the genomes of 234 animals from different breeds did not reveal any deleterious candidate SNPs (single nucleotide polymorphisms) or small indels. Subsequent screening for structural variants in candidate genes located in the same regions identified a homozygous deletion that includes exons 17 to 23 of the integrin beta 4 (ITGB4), a gene that was previously associated with the same defect in humans. Genotyping of a second case and of six parents of affected calves (two sires and four dams) revealed a perfect association between this mutation and the assumed genotypes of the individuals. Mining of Illumina BovineSNP50 Beadchip genotyping data from 6870 Charolais cattle detected only 44 heterozygous animals for a 5.6-Mb haplotype around ITGB4 that was shared with the carriers of the mutation. Interestingly, none of the 16 animals genotyped for the deletion carried the mutation, which suggests a rather recent origin for the mutation. Conclusions In conclusion, we successfully identified the causative mutation for a very rare autosomal recessive mutation with only one case by exploiting the most recent DNA sequencing technologies. Electronic supplementary material The online version of this article (doi:10.1186/s12711-015-0110-z) contains supplementary material, which is available to authorized users.

In livestock species, selection programs are getting more and more efficient. Meanwhile, the development of new tools such as genomic selection will probably fasten how breeds are evolving. However, preserving the breeds’ genetic variability is a necessity. First of all, genetic progress is correlated with this factor. Also, a sharp increase in inbreeding in a breed might have a very negative impact on production and functional traits. Therefore, in order to achieve the sustainability of our selection choices for the future, the breeds’ genetic variability requires an accurate management. To do so, two type or data can be used to calculate variability genetic indicators: pedigrees and genotype data. These indicators can be used to monitor the impact of a main ancestor in a breed for instance. The VARUME (Genetic VARiability of Ruminants and Equids) project goal is to set up a genetic variability observatory for the Ruminants and Equids species. It will generate indicators that can assess breed genetic variability on a regular basis, by using a common method that will be acknowledged and used by all breed managers.

Chantier qualité GA; Background: Effective population sizes of 140 populations (including 60 dog breeds, 40 sheep breeds, 20 cattle breeds and 20 horse breeds) were computed using pedigree information and six different computation methods. Simple demographical information (number of breeding males and females), variance of progeny size, or evolution of identity by descent probabilities based on coancestry or inbreeding were used as well as identity by descent rate between two successive generations or individual identity by descent rate.[br/] Results: Depending on breed and method, effective population sizes ranged from 15 to 133 056, computation method and interaction between computation method and species showing a significant effect on effective population size (P < 0.0001). On average, methods based on number of breeding males and females and variance of progeny size produced larger values (4425 and 356, respectively), than those based on identity by descent probabilities (average values between 93 and 203). Since breeding practices and genetic substructure within dog breeds increased inbreeding, methods taking into account the evolution of inbreeding produced lower effective population sizes than those taking into account evolution of coancestry. The correlation level between the simplest method (number of breeding males and females, requiring no genealogical information) and the most sophisticated one ranged from 0.44 to 0.60 according to species.[br/] Conclusions: When choosing a method to compute effective population size, particular attention should be paid to the species and the specific genetic structure of the population studied.

Pedigree analyses have been widely used to assess the genetic variability of livestock species, however, limited number of examples can be found for the goat species. France is one of the only countries in the world where collective goat selection is well implemented with successful breeding programs. This paper will briefly describe the French dairy goat and fiber goat selection schemes. It will present the results of a pedigree analysis, by using the PEDIG software, of two dairy goat breeds, the Alpine and Saanen, and a fiber goat breed, the Angora, in order to assess their genetic variability. The populations under study are large for the Saanen and Alpine (125,797 and 183,611 goats, respectively) and small (1271) for the Angora. The pedigree depth can be considered to be good (from 5.5 equivalent generations for the Angora to 7.8 for the Alpine). The effective number of ancestors is equal to 34, 46 and 51 for the Angora, Alpine and Saanen breeds respectively, while the effective population size varies between 76, 129 and 149 for the Angora, Saanen and Alpine breeds respectively. In the light of these results, in the case of the dairy breeds, there are reasons to believe that despite the fact that genetic variability has narrowed as an effect of 30 years of efficient selection, the specific management program implemented 10 years ago to maintain genetic diversity was successful. Meanwhile, for the Angora breed, the narrower genetic basis of the breed appears to be caused by its thin population basis as well as the small number of founders used at the start of the selection scheme. These results give us a good insight on the genetic variability of intensively selected populations as well as a direction on the programs that are efficient to keep a sustainable level of genetic variability.

Background High selection pressure on domestic cattle has led to an undesirable increase in inbreeding, as well as to the deterioration of some functional traits which are indirectly selected. Semen stored in a cryobank may be a useful way to redirect selection or limit the loss of genetic diversity in a selected breed. The purpose of this study was to analyse the efficiency of current cryobank sampling methods, by investigating the benefits of using cryopreserved semen in a selection scheme several generations after the semen was collected. Methods The theoretical impact of using cryopreserved semen in a selection scheme of a dairy cattle breed was investigated by simulating various scenarios involving two negatively correlated traits and a change in genetic variability of the breed. Results Our results indicate that using cryopreserved semen to redirect selection will have an impact on negatively selected traits only if it is combined with major changes in selection objectives or practices. If the purpose is to increase genetic diversity in the breed, it can be a viable option. Conclusions Using cryopreserved semen to redirect selection or to improve genetic diversity should be carried out with caution, by considering the pros and cons of prospective changes in genetic diversity and the value of the selected traits. However, the use of genomic information should lead to more interesting perspectives to choose which animals to store in a cryobank and to increase the value of cryobank collections for selected breeds.

Holstein-Friesian (HF) gene bank collections were established in France, the Netherlands, and the United States to conserve genetic diversity for this breed. Genetic diversity of HF collections within and between countries was assessed and compared with active male HF populations in each country by using pedigree data. Measures of genetic diversity such as probability of gene origin inbreeding and kinship were calculated. The cryobanks have captured substantial amounts of genetic diversity for the HF compared with the current populations. A substantial part of the US, French, and Dutch collections seems to be genetically similar. On the other hand, the US collection in particular represents an interesting reservoir of HF genes of the past. Gene banks can play an important role in conserving genetic diversity within livestock breeds over time, and may support industry in the future when needed.

The aim of this paper was to understand the complexity of a conservation programme of a local breed by linking genetic and social data. This approach is illustrated by the case of the Flemish Red cattle breed, which has been crossbred since the 1950s, mainly with the Danish Red breed. Farmers and other people involved in the management of this breed were interviewed about breeding goals and practices. The genetic variability of the breed and the genetic impact of crossbreeding were assessed via pedigree data. The opportunity to use crossbreeding was found to be the main controversy, if not the only one, among the different institutional stakeholders involved in the management of the breed. However, the farmers said that they attributed little importance to the proportion of Danish Red genes in the AI bull genome. From the pedigree analysis, the proportion of Danish Red genes in the Flemish Red breed was found to increase from the early 1970s to the early 1980s and to then stabilise around an average value of 28%. The proportion of Flemish Red cows with no Danish Red genes in their genome decreased regularly and became null in the early 2000s. More than 90% of the Flemish Red cows born at that time had a proportion of Danish Red genes ranging from 1/8 to 1/2. The Danish Red genes were found to mainly originate from crossbred bulls and not from pure Danish Red bulls. This paper focuses on the nature of the gene pool preserved in such a case, and the need to clearly define the goals of conservation programmes is highlighted.

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