Foreword to the international workshop on major genes and QTL in sheep and goats

This is the third international meeting dealing with major genes in small ruminants. The first was held in Armidale (NSW, Australia) in 1980, just after the discovery of the Booroola gene by B. Bindon and L. Piper. The discovery of a gene having such a large effect on ovulation rate and prolificacy in sheep was totally unsuspected at this time and a number of research teams all over the world concentrated their efforts to study its effects and identify the causal mutation. About 20 years were finally needed to obtain this information, which opened a new approach to the physiological regulation of reproduction

On the relevance of three genetic models for the description of genetic variance in small populations undergoing selection

International audienc

Using haplotypes for the prediction of allelic identity to fine-map QTL: characterization and properties

Numerous methods have been developed over the last decade to predict allelic identity at unobserved loci between pairs of chromosome segments along the genome. These loci are often unobserved positions tested for the presence of quantitative trait loci (QTL). The main objective of this study was to understand from a theoretical standpoint the relation between linkage disequilibrium (LD) and allelic identity prediction when using haplotypes for fine mapping of QTL. In addition, six allelic identity predictors (AIP) were also compared in this study to determine which one performed best in theory and application. A criterion based on a simple measure of matrix distance was used to study the relation between LD and allelic identity prediction when using haplotypes. The consistency of this criterion with the accuracy of QTL localization, another criterion commonly used to compare AIP, was evaluated on a set of real chromosomes. For this set of chromosomes, the criterion was consistent with the mapping accuracy of a simulated QTL with either low or high effect. As measured by the matrix distance, the best AIP for QTL mapping were those that best captured LD between a tested position and a QTL. Moreover the matrix distance between a tested position and a QTL was shown to decrease for some AIP when LD increased. However, the matrix distance for AIP with continuous predictions in the [0,1] interval was algebraically proven to decrease less rapidly up to a lower bound with increasing LD in the simplest situations, than the discrete predictor based on identity by state between haplotypes (IBS hap), for which there was no lower bound. The expected LD between haplotypes at a tested position and alleles at a QTL is a quantity that increases naturally when the tested position gets closer to the QTL. This behavior was demonstrated with pig and unrelated human chromosomes. When the density of markers is high, and therefore LD between adjacent loci can be assumed to be high, the discrete predictor IBS hap is recommended since it predicts allele identity correctly when taking LD into account

Threshold and power for Quantitative Trait Locus detection

We propose several new methods to calculate threshold and power for Quantitative Trait Locus (QTL) detection. They are based on asymptotic theoretical results presented in Rabier et al. (2009) . The asymptotic validity is checked by simulations. The methods proposed are fast and easy to implement. A comparison of power between a multiple testing procedure and a global test has been realized, showing far better performances of the global test for the detection of a QTL

A dynamic deterministic model to evaluate breeding strategies under mixed inheritance

A dynamic deterministic model is proposed to study the combined use of an identified major gene and performance information for selection of traits expressed in one sex. The model considers simultaneously combined adult selection via within genotype thresholds, mating structures according to major genotypes and preselection of young males. The application given indicates that an optimum combination between performances and genotypic information yields better results, in terms of polygenic means, genotype frequencies and cumulated discounted genetic progress, than classical selection ignoring the genotype information. The greatest advantage of combined selection occurs for rare recessive alleles of large effect on phenotypes (up to +49 % for polygenic gains; +26 % for total genetic gain). Optimum within genotype proportions of selected individuals and mating structures vary with generations thus highlighting the value of a dynamic approach.Un modèle déterministe et dynamique est proposé pour étudier l’utilisation conjointe des performances et des génotypes à un locus majeur pour la sélection des caractères exprimés dans un sexe. Le modèle prévoit la sélection des adultes au-delà de seuils de performances intra-génotype, des accouplements en fonction des génotypes et la présélection de jeunes mâles sur leur génotype. L’application présentée indique que la combinaison optimale des performances et des génotypes permet d’obtenir des meilleurs résultats, en terme de moyennes polygéniques, de fréquences génotypiques et du progrès génétique actualisé et cumulé, que la sélection classique ignorant l’informationgénotypique. Les avantages de la sélection combinée sont plus importants quand l’allèle favorable est rare et récessif, les différences avec la sélection classique pouvant atteindre +49 % en gains polygéniques et +26 % en gain génétique total. Les taux optimaux de sélection intra-génotype et les structures d’accouplement optimales varient au cours des générations, confirmant l’intérêt de l’approche dynamique

Comparison of analyses of the XVth QTLMAS common dataset III: Genomic Estimations of Breeding Values

<p>Abstract</p> <p>Background</p> <p>The QTLMAS XV^thdataset consisted of pedigree, marker genotypes and quantitative trait performances of animals with a sib family structure. Pedigree and genotypes concerned 3,000 progenies among those 2,000 were phenotyped. The trait was regulated by 8 QTLs which displayed additive, imprinting or epistatic effects. The 1,000 unphenotyped progenies were considered as candidates to selection and their Genomic Estimated Breeding Values (GEBV) were evaluated by participants of the XV^thQTLMAS workshop. This paper aims at comparing the GEBV estimation results obtained by seven participants to the workshop.</p> <p>Methods</p> <p>From the known QTL genotypes of each candidate, two "true" genomic values (TV) were estimated by organizers: the genotypic value of the candidate (TGV) and the expectation of its progeny genotypic values (TBV). GEBV were computed by the participants following different statistical methods: random linear models (including BLUP and Ridge Regression), selection variable techniques (LASSO, Elastic Net) and Bayesian methods. Accuracy was evaluated by the correlation between TV (TGV or TBV) and GEBV presented by participants. Rank correlation of the best 10% of individuals and error in predictions were also evaluated. Bias was tested by regression of TV on GEBV.</p> <p>Results</p> <p>Large differences between methods were found for all criteria and type of genetic values (TGV, TBV). In general, the criteria ranked consistently methods belonging to the same family.</p> <p>Conclusions</p> <p>Bayesian methods - A<B<C<Cπ - were the most efficient whatever the criteria and the True Value considered (with the notable exception of the MSEP of the TBV). The selection variable procedures (LASSO, Elastic Net and some adaptations) performed similarly, probably at a much lower computing cost. The TABLUP, which combines BayesB and GBLUP, generally did well. The simplest methods, GBLUP or Ridge Regression, and even worst, the fixed linear model, were much less efficient.</p

Genetic components of litter size variability in sheep

Classical selection for increasing prolificacy in sheep leads to a concomitant increase in its variability, even though the objective of the breeder is to maximise the frequency of an intermediate litter size rather than the frequency of high litter sizes. For instance, in the Lacaune sheep breed raised in semi-intensive conditions, ewes lambing twins represent the economic optimum. Data for this breed, obtained from the national recording scheme, were analysed. Variance components were estimated in an infinitesimal model involving genes controlling the mean level as well as its environmental variability. Large heritability was found for the mean prolificacy, but a high potential for increasing the percentage of twins at lambing while reducing the environmental variability of prolificacy is also suspected. Quantification of the response to such a canalising selection was achieved

Prediction of the response to a selection for canalisation of a continuous trait in animal breeding

International audienc

Alternative models for QTL detection in livestock. III. Heteroskedastic model and models corresponding to several distributions of the QTL effect

This paper describes two kinds of alternative models for QTL detection in livestock: an heteroskedastic model, and models corresponding to several hypotheses concerning the distribution of the QTL substitution effect among the sires: a fixed and limited number of alleles or an infinite number of alleles. The power of different tests built with these hypotheses were computed under different situations. The genetic variance associated with the QTL was shown in some situations. The results showed small power differences between the different models, but important differences in the quality of the estimations. In addition, a model was built in a simplified situation to investigate the gain in using possible linkage disequilibrium.Ce papier décrit deux types de modèles alternatifs pour la détection de QTL dans les populations animales : un modèle hétéroscédastique d’une part, et des modèles correspondants à différentes hypothèses sur la distribution de l’effet de substitution du QTL pour chaque mâle : un nombre fixe et limité d’allèles ou au contraire un nombre infini d’allèles. Les puissances des différents tests construits avec ces hypothèses sont calculées dans différentes situations. L’estimation de la variance génétique liée au QTL est donnée dans certaines situations. Les résultats montrent de faibles différences de puissance entre les différents modèles, mais des différences importantes dans la qualité des estimations. De plus, on construit un modèle dans une situation simplifiée pour étudier le gain que l’on peut obtenir en utilisant un éventuel déséquilibre de liaison