Holstein (HH), Jersey (JJ), and crosses of these breeds were mated to HH or JJ bulls to form purebreds, reciprocal crosses, backcrosses, and other crosses in a rotational mating system. The herd was located at the Center for Environmental Farming Systems in Goldsboro, North Carolina. Data for calf birth weight (CBW), calving ease (0 for unassisted, n=1,135, and 1 for assisted, n=96), and neonatal calf mortality (0 for alive, n=1,150, and 1 for abortions recorded after mid-gestation, stillborn, and dead within 48 h, n=81) of calves (n=1,231) were recorded over 9 calving seasons from 2003 through 2011. Gestation length (GL) was calculated as the number of days from last insemination to calving. Linear mixed models for CBW and GL included fixed effects of sex, parity (first vs. later parities), twin status, and 6 genetic groups: HH, JJ, reciprocal F(1) crosses (HJ, JH), crosses >50% Holsteins (HX) and crosses >50% Jerseys (JX), where sire breed is listed first. The CBW model also included GL as a covariate. Logistic regression for calving ease and neonatal calf mortality included fixed effects of sex, parity, and genetic group. Genetic groups were replaced by linear regression using percentage of HH genes as coefficients on the above models and included as covariates to determine various genetic effects. Year and dam were included as random effects in all models. Female calves (27.57±0.54 kg), twins (26.39±1.0 kg), and calves born to first-parity cows (27.67±0.56 kg) had lower CBW than respective male calves (29.53±0.53 kg), single births (30.71±0.19 kg), or calves born to multiparous cows (29.43±0.52 kg). Differences in genetic groups were observed for CBW and GL. Increased HH percentage in the calf increased CBW (+9.3±0.57 kg for HH vs. JJ calves), and increased HH percentage in the dams increased CBW (+1.71±0.53 kg for calves from HH dams vs. JJ dams); JH calves weighed 1.33 kg more than reciprocal HJ calves. Shorter GL was observed for twin births (272.6±1.1 d), female calves (273.9±0.6 d), and for first-parity dams (273.8±0.6 d). Direct genetic effects of HH alleles shortened GL (-3.5±0.7 d), whereas maternal HH alleles increased GL (2.7±0.6 d). Female calves had lower odds ratio (0.32, confidence interval=0.10-0.99) for neonatal calf mortality in second and later parities than did male calves. Maternal heterosis in crossbred primiparous dams was associated with reduced calf mortality.

Genomic selection in Lacaune dairy sheep was investigated based on genotypes from the OvineSNP50 BeadChip (Illumina Inc., San Diego, CA). Historical artificial insemination progeny-tested rams formed a population of 2,892 genotyped rams. Additional ungenotyped rams and females were included by single-step genomic BLUP (ssGBLUP). Three prediction strategies were tried: pseudo-BLUP (using all rams and daughter yield deviations), pseudo-ssGBLUP (using all rams and daughter yield deviations), and regular ssGBLUP (using all phenotypes and pedigree in an animal model). The population linkage disequilibrium was determined, with an average squared correlation coefficient of 0.11 for markers closer than 0.1cM (lower than in dairy cattle). The estimated effective population is 370 individuals. Gain in accuracy of genomic selection over parent averages ranged from 0.10 to 0.20. Highest accuracies and lowest bias were found using regular ssGBLUP. Transition to a genomic breeding scheme is possible but costs need to be carefully evaluated.

Genotypes, phenotypes and pedigrees of 6 breeds of dairy sheep (including subdivisions of Latxa, Manech, and Basco-Béarnaise) from the Spain and France Western Pyrenees were used to estimate genetic relationships across breeds (together with genotypes from the Lacaune dairy sheep) and to verify by forward cross-validation single-breed or multiple-breed genetic evaluations. The number of rams genotyped fluctuated between 100 and 1,300 but generally represented the 10 last cohorts of progeny-tested rams within each breed. Genetic relationships were assessed by principal components analysis of the genomic relationship matrices and also by the conservation of linkage disequilibrium patterns at given physical distances in the genome. Genomic and pedigree-based evaluations used daughter yield performances of all rams, although some of them were not genotyped. A pseudo-single step method was used in this case for genomic predictions. Results showed a clear structure in blond and black breeds for Manech and Latxa, reflecting historical exchanges, and isolation of Basco-Béarnaise and Lacaune. Relatedness between any 2 breeds was, however, lower than expected. Single-breed genomic predictions had accuracies comparable with other breeds of dairy sheep or small breeds of dairy cattle. They were more accurate than pedigree predictions for 5 out of 6 breeds, with absolute increases in accuracy ranging from 0.05 to 0.30 points. They were significantly better, as assessed by bootstrapping of candidates, for 2 of the breeds. Predictions using multiple populations only marginally increased the accuracy for a couple of breeds. Pooling populations does not increase the accuracy of genomic evaluations in dairy sheep; however, single-breed genomic predictions are more accurate, even for small breeds, and make the consideration of genomic schemes in dairy sheep interesting.

Genomic selection aims to increase accuracy and to decrease generation intervals, thus increasing genetic gains in animal breeding. Using real data of the French Lacaune dairy sheep breed, the purpose of this study was to compare the observed accuracies of genomic estimated breeding values using different models (infinitesimal only, markers only, and joint estimation of infinitesimal and marker effects) and methods [BLUP, Bayes Cπ, partial least squares (PLS), and sparse PLS]. The training data set included results of progeny tests of 1,886 rams born from 1998 to 2006, whereas the validation set had results of 681 rams born in 2007 and 2008. The 3 lactation traits studied (milk yield, fat content, and somatic cell scores) had heritabilities varying from 0.14 to 0.41. The inclusion of molecular information, as compared with traditional schemes, increased accuracies of estimated breeding values of young males at birth from 18 up to 25%, according to the trait. Accuracies of genomic methods varied from 0.4 to 0.6, according to the traits, with minor differences among genomic approaches. In Bayes Cπ, the joint estimation of marker and infinitesimal effects had a slightly favorable effect on the accuracies of genomic estimated breeding values, and were especially beneficial for somatic cell counts, the less heritable trait. Inclusion of infinitesimal effects also improved slopes of predictive regression equations. Methods that select markers implicitly (Bayes Cπ and sparse PLS) were advantageous for some models and traits, and are of interest for further quantitative trait loci studies.

In 2010, a routine genetic evaluation on occurrence of clinical mastitis in three main dairy cattle breeds -Montbéliarde (MO), Normande (NO) and Holstein (HO) -was implemented in France. Records were clinical mastitis events reported by farmers to milk recording technicians and the analyzed trait was the binary variable describing the occurrence of a mastitis case within the first 150 days of the first three lactations. Genetic parameters of clinical mastitis were estimated for the three breeds. Low heritability estimates were found: between 2% and 4% depending on the breed. Despite its low heritability, the trait exhibits genetic variation so efficient genetic improvement is possible. Genetic correlations with other traits were estimated, showing large correlations (often > 0.50, in absolute value) between clinical mastitis and somatic cell score (SCS), longevity and some udder traits. Correlation with milk yield was moderate and unfavorable (ρ = 0.26 to 0.30). High milking speed was genetically associated with less mastitis in MO (ρ = − 0.14) but with more mastitis in HO (ρ = 0.18). A two-step approach was implemented for routine evaluation: first, a univariate evaluation based on a linear animal model with permanent environment effect led to pre-adjusted records (defined as records corrected for all non-genetic effects) and associated weights. These data were then combined with similar pre-adjusted records for others traits in a multiple trait BLUP animal model. The combined breeding values for clinical mastitis obtained are the official (published) ones. Mastitis estimated breeding values (EBV) were then combined with SCSs EBV into an udder health index, which receives a weight of 14.5% to 18.5% in the French total merit index (ISU) of the three breeds. Interbull genetic correlations for mastitis occurrence were very high (ρ = 0.94) with Nordic countries, where much stricter recording systems exist reflecting a satisfactory quality of phenotypes as reported by the farmers. They were lower (around 0.80) with countries supplying SCS as a proxy for the international evaluation on clinical mastitis.

Après une présentation du contexte de la sélection ovine laitière française et de la stratégie de sélection génomique qui en découle, cet article retrace l’ensemble des travaux de recherche et développement entrepris depuis 2009 pour mettre en oeuvre cette stratégie et qui débouchent sur le déploiement de la sélection génomique en 2015. Sont abordés successivement la constitution des populations de référence, les investissements en méthodes et stratégies de calcul d’index génomique, les résultats de précision des index génomiques en ovins laitiers, l’expérimentation génomique originale mise en oeuvre en race Lacaune, la conception, la modélisation et l’optimisation de schémas de sélection génomique adaptés aux spécificités des races ovines laitières, les choix opérés par les entreprises et organismes de sélection et leurs conséquences organisationnelles et contractuelles. Les perspectives ouvertes par la sélection génomique sont évoquées : inclusion de nouveaux caractères, plus grande flexibilité, meilleure gestion de la variabilité génétique. La sélection génomique est effective depuis 2015 en race Lacaune et devrait être déployée en 2017 dans les races Pyrénéennes.