Tuberculosis (TB) caused by Mycobacterium bovis is a re-emerging disease of livestock that is of major economic importance worldwide, as well as being a zoonotic risk. There is significant heritability for host resistance to bovine TB (bTB) in dairy cattle. To identify resistance loci for bTB, we undertook a genome-wide association study in female Holstein–Friesian cattle with 592 cases and 559 age-matched controls from case herds. Cases and controls were categorised into distinct phenotypes: skin test and lesion positive vs skin test negative on multiple occasions, respectively. These animals were genotyped with the Illumina BovineHD 700K BeadChip. Genome-wide rapid association using linear and logistic mixed models and regression (GRAMMAR), regional heritability mapping (RHM) and haplotype-sharing analysis identified two novel resistance loci that attained chromosome-wise significance, protein tyrosine phosphatase receptor T (PTPRT; P=4.8 × 10−7) and myosin IIIB (MYO3B; P=5.4 × 10−6). We estimated that 21% of the phenotypic variance in TB resistance could be explained by all of the informative single-nucleotide polymorphisms, of which the region encompassing the PTPRT gene accounted for 6.2% of the variance and a further 3.6% was associated with a putative copy number variant in MYO3B. The results from this study add to our understanding of variation in host control of infection and suggest that genetic marker-based selection for resistance to bTB has the potential to make a significant contribution to bTB control.

For populations undergoing mass selection, previous studies have shown that the rate of inbreeding is directly related to the mean and variance of long-term contributions from ancestors to descendants, and thus prediction of the rate of inbreeding can be achieved via the prediction of long-term contributions. In this paper, it is shown that the same relationship between the rate of inbreeding and long-term contributions is found when selection is based on an index of individual and sib records (index selection) and where sib records may be influenced by a common environment. In these situations, rates of inbreeding may be considerably higher than under mass selection. An expression for the rate of inbreeding is derived for populations undergoing index selection based on variances of (one-generation) family size and incorporating the concept of long-term selective advantage. When the mating structure is hierarchical, and when half-sib records are included in the index, the correlation between parental breeding values and the index values of their offspring is higher for male parents than female parents. This introduces an important asymmetry between the contributions of male and female ancestors to the evolution of inbreeding which is not present when selection is based on individual and/or full-sib records alone. The prediction equation for index selection accounts for this asymmetry. The prediction is compared to rates of inbreeding calculated from simulation. The prediction is good when family size is small relative to the number selected. The reasons for overprediction in other situations are discussed.

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The effect of improved reproductive techniques on genetic progress and inbreeding was investigated in MOET (multiple ovulation and embryo transfer) schemes for beef cattle. Stochastic simulation was used to model a closed scheme with overlapping generations. Selection was on a trait measured in both sexes, with heritability 0.35, and was carried out for 25 years. The number of breeding animals was 9 sires and 18 donors. Embryo production was modelled using a Poisson distribution with the parameter distributed according to a gamma distribution. The mean number of transferable embryos per flush and per donor was 5.0, with a coefficient of variation of 1.28 and repeatability between flushes of 0.22. This model was compared with models used in previous studies (fixed number of embryos per flush or variable number of embryos but with zero repeatability between flushes). The coefficient of variation and the repeatability of embryo yield influenced inbreeding rates. The rate of inbreeding was underestimated by up to 17% when variability of embryo production was ignored. Without a constraint on the number of calves born per year, improved success rates for embryo collection and embryo transfer technologies led to notable increases in genetic progress. However, the rate of inbreeding was also increased with improved techniques. When the number of calves born per year was fixed, genetic progress was maintained but inbreeding rates were substantially reduced (by up to 11%) with improved techniques due to the opportunity of equalizing family sizes.There was no benefit from sexed semen with constrained number of calves per year. beef cattle / MOET / embryo / genetic gain / inbreeding Résumé -Effet de l'amélioration des techniques de reproduction sur le progrès génétique et sur la consanguinité dans des schémas MOET pour bovins à viande.Notre investigation avait pour but d'étudier l'effet de techniques de reproduction améliorées sur le progrès génétique et sur la consanguinité, dans le cadre de schémas MOET (ovulation multiple et transfert d'embryon) pour les bovins à viande. Grâce à une simulation stochastique, un schéma fermé a été modélisé avec générations chevauchantes. La sélection a été effectuée pendant une période de 25 ans, sur un caractère mesurable dans les sexes, dont l'héritabilité était de 0,35. Les nombres de reproducteurs mâles et de donneuses étaient de 9 et 18 respectivement. La production d'embryons a été modélisée en utilisant une distribution de Poisson dont le paramètre avait une distribution gamma. Le nombre moyen d'embryons transférables recueillis par collecte et par donneuse était de 5,0 avec un coefficient de variation de 1,28 et avec une répétabilité de 0,22 entre collectes. Ce modèle a été comparé avec d'autres modèles utilisés dans des études antérieures (qui utilisaient un nombre déterminé d'embryons par collecte, ou un nombre variable d'embryons mais avec une répétabilité nulle entre collectes). Le coefficient de variation et la répétabilité de la production d'embryons infLuencent le taux de con...