Should genetic groups be fitted in BLUP evaluation? Practical answer for the French AI beef sire evaluation

Some analytical and simulated criteria were used to determine whether a priori genetic differences among groups, which are not accounted for by the relationship matrix, ought to be fitted in models for genetic evaluation, depending on the data structure and the accuracy of the evaluation. These criteria were the mean square error of some extreme contrasts between animals, the true genetic superiority of animals selected across groups, i.e. the selection response, and the magnitude of selection bias (difference between true and predicted selection responses). The different statistical models studied considered either fixed or random genetic groups (based on six different years of birth) versus ignoring the genetic group effects in a sire model. Including fixed genetic groups led to an overestimation of selection response under BLUP selection across groups despite the unbiasedness of the estimation, i.e. despite the correct estimation of differences between genetic groups. This overestimation was extremely important in numerical applications which considered two kinds of within-station progeny test designs for French purebred beef cattle AI sire evaluation across years: the reference sire design and the repeater sire design. When assuming a priori genetic differences due to the existence of a genetic trend of around 20% of genetic standard deviation for a trait with h2 = 0.4, in a repeater sire design, the overestimation of the genetic superiority of bulls selected across groups varied from about 10% for an across-year selection rate p = 1/6 and an accurate selection index (100 progeny records per sire) to 75% for p = 1/2 and a less accurate selection index (20 progeny records per sire). This overestimation decreased when the genetic trend, the heritability of the trait, the accuracy of the evaluation or the connectedness of the design increased. Whatever the data design, a model of genetic evaluation without groups was preferred to a model with genetic groups when the genetic trend was in the range of likely values in cattle breeding programs (0 to 20% of genetic standard deviation). In such a case, including random groups was pointless and including fixed groups led to a large overestimation of selection response, smaller true selection response across groups and larger variance of estimation of the differences between groups. Although the genetic trend was correctly predicted by a model fitting fixed genetic groups, important errors in predicting individual breeding values led to incorrect ranking of animals across groups and, consequently, led to lower selection response

Construction of a large collection of small genome variations in French dairy and beef breeds using whole-genome sequences

Background: In recent years, several bovine genome sequencing projects were carried out with the aim of developing genomic tools to improve dairy and beef production efficiency and sustainability.[br/] Results: In this study, we describe the first French cattle genome variation dataset obtained by sequencing 274 whole genomes representing several major dairy and beef breeds. This dataset contains over 28 million single nucleotide polymorphisms (SNPs) and small insertions and deletions. Comparisons between sequencing results and SNP array genotypes revealed a very high genotype concordance rate, which indicates the good quality of our data.[br/] Conclusions: To our knowledge, this is the first large-scale catalog of small genomic variations in French dairy and beef cattle. This resource will contribute to the study of gene functions and population structure and also help to improve traits through genotype-guided selection

Genetic determinism of spontaneous masculinisation in XX female rainbow trout: new insights using medium throughput genotyping and whole-genome sequencing

International audienceRainbow trout has a male heterogametic (XY) sex determination system controlled by a major sex-determining gene, sdY. Unexpectedly, a few phenotypically masculinised fish are regularly observed in all-female farmed trout stocks. To better understand the genetic determinism underlying spontaneous maleness in XX-rainbow trout, we recorded the phenotypic sex of 20,210 XX-rainbow trout from a French farm population at 10 and 15 months post-hatching. The overall masculinisation rate was 1.45%. We performed two genome-wide association studies (GWAS) on a subsample of 1139 individuals classified as females, intersex or males using either medium-throughput genotyping (31,811 SNPs) or whole-genome sequencing (WGS, 8.7 million SNPs). The genomic heritability of maleness ranged between 0.48 and 0.62 depending on the method and the number of SNPs used for the estimation. At the 31K SNPs level, we detected four QTL on three chromosomes (Omy1, Omy12 and Omy20). Using WGS information, we narrowed down the positions of the two QTL detected on Omy1 to 96 kb and 347 kb respectively, with the second QTL explaining up to 14% of the total genetic variance of maleness. Within this QTL, we detected three putative candidate genes, fgfa8, cyp17a1 and an uncharacterised protein (LOC110527930), which might be involved in spontaneous maleness of XX-female rainbow trout

Novel Insights into the Bovine Polled Phenotype and Horn Ontogenesis in Bovidae

Despite massive research efforts, the molecular etiology of bovine polledness and the developmental pathways involved in horn ontogenesis are still poorly understood. In a recent article, we provided evidence for the existence of at least two different alleles at the Polled locus and identified candidate mutations for each of them. None of these mutations was located in known coding or regulatory regions, thus adding to the complexity of understanding the molecular basis of polledness. We confirm previous results here and exhaustively identify the causative mutation for the Celtic allele (PC) and four candidate mutations for the Friesian allele (PF). We describe a previously unreported eyelash-and-eyelid phenotype associated with regular polledness, and present unique histological and gene expression data on bovine horn bud differentiation in fetuses affected by three different horn defect syndromes, as well as in wild-type controls. We propose the ectopic expression of a lincRNA in PC/p horn buds as a probable cause of horn bud agenesis. In addition, we provide evidence for an involvement of OLIG2, FOXL2 and RXFP2 in horn bud differentiation, and draw a first link between bovine, ovine and caprine Polled loci. Our results represent a first and important step in understanding the genetic pathways and key process involved in horn bud differentiation in Bovidae

Modélisation et Optimisation de programmes de sélection sur la croissance en races bovines allaitantes

French beef cattle breeding schemes have been established throughsuccessive phases (1960-1990) and have become extremely complex due to thediversity of aims they are to fulfil : (1) the choice of artificial insemination bulls andnatural service bulls ; (2) the purebred use and/or crossing use of breeding animals(males and females) ; (3) the wide variety of consumer needs (beef calves, youngbulls, culling cows).To optimize and to, eventually, simplify these breeding schemes, theirefficiency needs to be evaluated by the prediction of expected genetic gains andeconomic gains. It is actually difficult to take into account all the possible traits ofeconomic interest, due to a lack of knowledge concerning their economic values inFrench production conditions and the many possible genetic correlations betweenthem. Limiting itself to the consideration of growth traits only, this thesis aimed tostudy deterministic modelling and the optimization of breeding schemes includingthe two main objectives of beef cattle breeding schemes : the improvement of beeftraits for beef production (for purebred or for terminal crossing) and theimprovement of maternal abilities in purebred breeding. Thus, the selectionefficiency was predicted for an existing purebred breeding scheme and for aproposed breeding scheme with terminal crossing. In terms of methodology, thesestudies led to proposals, on one hand, of a simple analytical method to calculateasymptotic genetic gains for any large-sized population structure and, on the otherhand, of an empirical approximation of selection differentials in homogeneouspopulations of small size.The purebred breeding scheme that was modelled, because of its potentialefficiency, was the scheme currently implemented in the Limousine breed. Abreeding objective was defined for growth traits integrating the post-weaninggrowth (final fattening weight) and both components of pre-weaning growth : beeftrait (direct effects on weaning weight) and maternal ability (maternal effects onweaning weight, mainly due to the dam’s milk production). The results have shownthat the breeding scheme conception was correct (positive expected responsesrecorded for all traits), but its implementation could be improved.Currently, the bulls selected for beef traits in the selection nucleus are used forpurebred beef production and for terminal cross-breeding. A initial study wascarried out to evaluate the opportunity to create a small selection nucleus inspecialized beef breeds, where the selection effort was concentrated towards aterminal crossing. The breeding objective considered was the maximization of preweaninggrowth, without a genetic evolution on birth weight. Such a constraint wasset to avoid a long term increase in calving difficulties, a result that would beunpopular with dairy breeders. The initial results seemed to support theimplementation of such a selection nucleus, at least from a technical point of view.However, they will need to be confirmed by further studies, addressing feasabilityand cost.Les programmes de sélection français mis en place par étapes successives(1960- 1990) en races bovines allaitantes sont devenus extrêmement complexes enraison de la diversité des finalités qu’ils doivent assurer : (1) le choix des taureauxd’insémination artificielle et de monte naturelle ; (2) l’utilisation en race pure et/ou encroisement des reproducteurs mâles ou femelles ; (3) la multiplicité des besoins dela consommation (veaux de boucherie, jeunes bovins, vaches de réforme).Afin d’optimiser voire de simplifier ces programmes de sélection, il estnécessaire d’évaluer leur efficacité par la prédiction des progrès génétiques et desgains économiques espérés. La prise en compte dans de telles études del’ensemble des caractères d’inté rêt est actuellement difficile en raison d’unemauvaise connaissance, d’une part, de leur poids économique dans les conditionsfrançaises de production, d’autre part, des corrélations génétiques entre nombrede ces caractères. En se limitant aux caractères de croissance, cette thèse a pourobjet la modélisation déterministe et l’optimisation de plans de sélection incluantles deux principaux objectifs des programmes de sélection des races bovinesallaitantes spécialisées : l’amélioration des aptitudes bouchères pour la productionde viande (en race pure et en croisement) et l’amélioration des qualitésmaternelles pour l’élevage en race pure. Ainsi, l’efficacité d’un programme desélection en race pure existant, et celle d’un programme de sélection envisageablepour le croisement sont prédites. Sur le plan méthodologique, ces études amènentà proposer, d’une part, une méthode analytique simple de prédiction du progrèsgénétique asymptotique dans des populations de grande taille et de structurecomplexe et , d’autre part, une approximation empirique des différentielles desélection dans des populations homogènes de petite taille.Le plan de sélection en race pure modélisé a pour base le programmeactuellement mis en oeuvre en race Limousine , en raison de son efficacitépotentielle. Un objectif de sélection racial est dé fini et intègre la croissance aprèssevrage (poids final d’engraissement) et les deux composantes de la croissancejusqu’au sevrage : aptitude bouchère (effet direct sur le poids au sevrage) et qualitématernelle (effet maternel sur le poids au sevrage, principalement dû à laproduction laitière de la mère). Les résultats montrent que la conception duprogramme de sélection est correcte (réponses potentielles favorables sur tous lescaractères), mais que sa mise en oeuvre pratique est à améliorer.Actuellement, les taureaux sélectionnés sur les aptitudes bouchères en baseraciale sont utilisés à la fois pour la production de viande en race pure et pour lecroisement terminal. Une première étude est menée pour évaluer l'opportunité dela création, dans les races allaitantes spécialisées, de noyaux de sélection oùl’effort de sélection est concentré à des fins de croisement terminal. L’objectif desélection envisagé est la maximisation de la croissance avant sevrage des veaux,sans évolution génétique de leur poids à la naissance. Cette contrainte est posé eparce qu’à long terme, les éleveurs laitiers n’accepteront sans doute pas unaccroissement de la fréquence des naissances difficiles dans leurs troupeaux. Lespremiers résultats semblent favorables à la création de tels noyaux de sélection, dumoins d’un point de vue technique. Mais ils restent à confirmer par des études pluscomplètes, intégrant notamment les aspects de faisabilité et de coût

Un modele mecaniste pour simuler la regulation a long terme de la nutrition de la vache laitiere

Supplement 1 Abstr.International audienc

Un modele mecaniste pour simuler la regulation a long terme de la nutrition de la vache laitiere

International audienc