SNPMace – A meta-analysis to estimate SNP effects by combining results from multiple countries

Selection of bulls and cows is increasingly made on genomic estimated breeding values (GEBVs) calculated from their SNP genotypes and the estimated effects of each SNP. To obtain the most accurate GEBVs a large training population of animals with phenotypes and genotypes is needed. For some traits, some breeds and some countries such a large training population is not available. In these cases it would increase the accuracy of GEBVs if information from multiple countries and breeds were combined. This paper describes a meta-analysis to combine SNP effects from multiple countries. A project to test this procedure is under way and, if successful, may result in a new Interbull service

MetaGS: an accurate method to impute and combine SNP effects across populations using summary statistics

Background Meta-analysis describes a category of statistical methods that aim at combining the results of multiple studies to increase statistical power by exploiting summary statistics. Different industries that use genomic prediction do not share their raw data due to logistic or privacy restrictions, which can limit the size of their reference populations and creates a need for a practical meta-analysis method. Results We developed a meta-analysis, named MetaGS, that duplicates the results of multi-trait best linear unbiased prediction (mBLUP) analysis without accessing raw data. MetaGS exploits the correlations among different populations to produce more accurate population-specific single nucleotide polymorphism (SNP) effects. The method improves SNP effect estimations for a given population depending on its relations to other populations. MetaGS was tested on milk, fat and protein yield data of Australian Holstein and Jersey cattle and it generated very similar genomic estimated breeding values to those produced using the mBLUP method for all traits in both breeds. One of the major difficulties when combining SNP effects across populations is the use of different variants for the populations, which limits the applications of meta-analysis in practice. We solved this issue by developing a method to impute missing summary statistics without using raw data. Our results showed that imputing summary statistics can be done with high accuracy (r > 0.9) even when more than 70% of the SNPs were missing with a minimal effect on prediction accuracy. Conclusions We demonstrated that MetaGS can replace the mBLUP model when raw data cannot be shared, which can lead to more flexible collaborations compared to the single-trait BLUP model

Reproduction and welfare in the domestic horse (behavioural approach)

This study aimed to identify factors, particularly behavioural, involved in the problems of infertility observed in the domestic horse. In the first part of this work, we examined the effect of some individual factors (age, reproduction status and sire of the mare and the bredding stallion) on mares reproductive success. Results confirmed the effects of age, reproductive status and the stallion observed in other studies and showed for the first time an effect of the sire of the mare on its fertility. A preliminary study of breeding mares kept in barren paddocks with a high density revealed unusual behavioural repertoires and time-budgets compared to those observed in more natural conditions. In order to evaluate theses behavioural troubles and identify their origins, we proceeded to experimentation. The aim of the experiment was to test the effect of giving the animals the opportunity to forage, on their behaviour, welfare and reproduction performances. Results showed that increasing foraging opportunities influenced the behavioural repertoires and time budgets of the mares but also enhaced their fertility by increasing conception rates and reducing estrous problems. In a third part of this work, we studied the link between stereotypies, considered as poor welfare indicators, and mares reproductive success. Our results revealed for the first time, a lower reproductive success in mares that showed stereotypic behaviour.Le but de ce travail était d identifier les facteurs mis en jeu, en particulier comportementaux, dans les problèmes de fertilité constatés chez la jument domestique. Dans une première partie, nous nous sommes intéressés à l effet de certains facteurs liés à l individu tels que l âge, statut de reproduction et père de la jument ains que l étalon de saillie. Les résultats de cette analyse ont confirmé les effets âge, statut de reproduction et étalon de saillie observés chez d autres races de chevaux mais ont aussi permis de mettre en évidence pour la première fois l effet de l origine paternelle de la jument sur sa fertilité. Une étude préliminaire du comportement de poulinières maintenues en forte densité dans des paddocks dénudés a révélé des répertoires comportementaux et des budgets temps inhabituels par rapport à ceux observés à l état naturel. Afin d évaluer ces perturbations comportementales et de rechercher leurs causes possibles, nous avons procédé à l expérimentation. Nous avons donc testé l effet de promouvoir un comportement alimentaire naturel sur le bien-être et la reproduction des juments. Cette expérience a montré des effets significatifs du traitement sur le comportement social, le répertoire comportemental et le budget temps des juments mais aussi sur leurs performances de reproduction (des taux de conception meilleurs et une faible fréquence de troubles du cycle ovarien). Dans une troisième étape de ce travail, nous nous sommes intéressés au lien entre les stéréotypies, considérées comme étant des indicateurs de stress chronique, en réponse à des conditions environnementales défavorables et les performances de reproduction des juments. Nos résultats ont révélé, pour la première fois, un succès reproducteur plus faible chez les juments montrant une activité stéréotypique.RENNES1-BU Sciences Philo (352382102) / SudocSudocFranceF

Modifying MACE to accommodate genomic preselection effects

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Age and type of mating of the experimental (<i>N</i> = 32) and the standard feeding pattern (<i>N</i> = 38) groups.

1<p>Natural mating.</p>2<p>Artificial insemination with fresh semen.</p

First-service and overall fertility (%) of CF (<i>N</i> = 32) and RF (<i>N</i> = 38) mares. significant differences (<i>p</i><0.05) are indicated by the symbol *.

<p>First-service and overall fertility (%) of CF (<i>N</i> = 32) and RF (<i>N</i> = 38) mares. significant differences (<i>p</i><0.05) are indicated by the symbol *.</p