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International audience; The objective of the study was to estimate the efficiency of genotypes imputation of the Affymetrix Axiom Equine genotyping array (670 806 SNPs), from genotypes of the Illumina Equine SNP50 BeadChip (54 602 SNPs) and the Illumina Equine SNP-74k-chip (65 157 SNPs). Genotypes from 5 populations: Arabs (AR, 1 207 horses), Trotteurs Français (TF, 979 horses), Selle Français (SF, 1 979 horses), Anglo-Arabs (AA, 229 horses), and various foreign sport horses (FH, 209 horses) were available. In AR, 15% of horses were genotyped with the high density chip, in SF 57%, in TF 30%, in AA 10% and FH 15%. A validation set equal to the third of the sample was drawn in horses genotyped with high density chip and their genotypes suppressed. Two strategies were compared, one with a reference population with only the horses of the same breed as the validation set and another one with horses from multi-breeds. The software FImpute was used. For the first strategy, the mean error rates were 0.97% in TF, 1.29% in SF and 2.16% in AR populations. For the second strategy, the mean error rates ranged from 1.11% (TF) to 2.63% (AR). SF, FH and AA populations had intermediate error rates: 1.35%, 1.55% and 1.87% respectively. For each population and each strategy, the mean error rates were inferior to 3% which indicates that imputation of high density genotypes from medium density genotypes is feasible and accurate. The imputation accuracy depended on the size of the reference population, the genetic diversity of the breed, the importance of relationship between validation and reference populations and the linkage disequilibrium (LD). The comparison between the two imputation strategies showed that the addition of horses from different populations in the reference population did not improve the imputation accuracy.

Dans les espèces d’élevage, les programmes de sélection sont de plus en plus performants, et l’essor de nouveaux outils tels que l’utilisation de données de génotypages pour réaliser la sélection génomique est de nature à accélérer nettement l’évolution de ces populations. Or, il est indispensable de préserver la variabilité génétique de ces populations, d’une part parce que le progrès génétique y est corrélé, et d’autre part parce que l’augmentation brutale de la consanguinité dans les populations peut les impacter très défavorablement. Il est donc nécessaire d’assurer un suivi régulier de la variabilité génétique, pour garantir la durabilité des choix de sélection de demain, et ce aussi bien pour les populations à faible effectif que celles en sélection. Pour cela, deux types de données permettent le calcul d’indicateurs de variabilité génétique : les généalogies et les données de génotypages. Ces indicateurs permettent, par exemple, d’évaluer l’impact d’un ancêtre majeur sur la population actuelle. L’objectif du projet VARUME (VAriabilité génétique des RUMinants et des Equidés) est la mise en place d’un observatoire de la variabilité génétique des ruminants et équidés, afin de produire de façon régulière des indicateurs permettant d’apprécier la « santé génétique » des races, sur des bases communes reconnues par l’ensemble des gestionnaires., Selection programs in livestock species are becoming more and more efficient. New tools, such as molecular data used for genomic selection is accelerating how livestock breeds are evolving. Yet it is necessary to preserve the breeds’ genetic variability firstly because genetic progress is correlated to it, and any sudden increase of the inbreeding level can impact these populations in a negative way. Therefore it is necessary to regularly assess the genetic variability of both rare breeds and selected breeds in order to maintain their sustainability. Two types of data make it possible to calculate genetic variability indicators: pedigrees and genotyped data. For instance, thanks to these indicators, we can evaluate the impact of a major ancestor on the current population. The main goal of the VARUME project was to set up a genetic variability observatory for ruminant and equid breeds, in order to provide, on a regular basis, indicators that can assess the “genetic health” of the breeds, and that are agreed on by all the breed managers.

National audience

National audience

International audience; The French genetic resources are very diverse and are a real wealth that must be maintained. However, given the significant changes in breeding farms and the use of horses in recent decades, the potential risk of disappearance of these genetic resources has become real. To help the preservation of this diversity, a major research project (CRB-anim) was built in 2010, for 11 species, aiming to develop, consolidate and enrich the already existing biological resources centres for domestic animals in France. This project is funded by the National Research Agency (‘Investissements d’Avenir’, ANR-11-INBS-0003); it has started in 2013 and will finish in 2020. A close collaboration between INRA and IFCE has started and two main axes will be conducted: (1) A research axis to remove technical locks to the conservation of biological samples: (a) to improve the fertility using donkey frozen semen; the new freezing extenders recently finalized for stallion sperm will be tested, (b) to develop a reliable technique for equine embryo freezing; the first approach will be to evaluate the effect of a deposit of prostaglandin E2 to the uterus-tubal junction on the arrival of the embryo in the uterus. The objective is to get small embryos (morula stage), more readily freezable by slow freezing technique. (2) A second axis encompasses a further collections of biological material in our National Cryobank; so the most endangered breeds in terms of number or genetic variability are properly represented. A genetic analysis of French horse breeds is conducted to determine which populations were given priority for preservation. Sperm collections for donkey breeds will be processed as soon as the research will have removed the lock on semen freezing in this species.

National audience

International audience

L'échantillon génotypé comporte 910 chevaux dont 71% de Selle Français, 13% d' Anglo-Arabe et 16% de selle étranger. Les pères de 37% des chevaux sont génotypés. La moyenne des indices génétiques pour le CSO est 10.9 et l'écart type est 10.2. Sur les 54602 SNP (Single Nucleotide Polymorphism) initiaux, 44444 sont conservés selon des normes de qualité. Pour calculer les valeurs génomiques (à partir des SNP) et génétiques (à partir des parentés généalogiques), un modèle équivalent basé sur une pseudo-performance qui regroupe la performance propre et les performances des produits non génotypés corrigées pour les effets environnementaux est utilisé. L'échantillon est divisé en un échantillon d'apprentissage, pour estimer les effets des SNP et les valeurs génétiques classiques, et un échantillon de validation, pour calculer les valeurs génomiques et génétiques à partir de ces estimations sans inclure les performances. Un test préliminaire sur un échantillon de validation de 200 chevaux montre que les corrélations entre les deux types d'estimations et la performance équivalente sont proches mais en faveur de l'évaluation génomique (0.46 contre 0.44). D'autres analyses permettront de conclure.

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International audience

National audience