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This study investigated the potential application of genomic selection under a multi-breed scheme in the Spanish autochthonous beef cattle populations using a simulation study that replicates the structure of linkage disequilibrium obtained from a sample of 25 triplets of sire/dam/offspring per population and using the BovineHD Beadchip. Purebred and combined reference sets were used for the genomic evaluation and several scenarios of different genetic architecture of the trait were investigated. The single-breed evaluations yielded the highest within-breed accuracies. Across breed accuracies were found low but positive on average confirming the genetic connectedness between the populations. If the same genotyping effort is split in several populations, the accuracies were lower when compared with single-breed evaluation, but showed a small advantage over small-sized purebred reference sets over the accuracies of subsequent generations. Besides, the genetic architecture of the trait did not show any relevant effect on the accuracy with the exception of rare variants, which yielded slightly lower results and higher loss of predictive ability over the generations. [ABSTRACT FROM AUTHOR]

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The aim of this study was to compare the goodness of fit of the threshold models with homoscedasticity or heteroscedasticity and the grouped data model for the analysis of calving ease in beef cattle by using a parametric bootstrap procedure. Field data included 8,205 records of the Bruna dels Pirineus beef cattle breed in the Pyrenean mountain areas of Catalonia (Spain). The actual distribution was 81.81% of calvings without assistance, 11.02% slightly assisted by the farmer, 5.12% strongly assisted by the farmer, 0.89% assisted by the veterinarian, and 1.16% cesarean, but these percentages were very different in the different herds. This can be explained partially by the different subjective way of scoring of each farmer. Primiparous cows had a greater (P < 0.001) difficulty calving than cows with 5 or more parities (11.74 vs. 4.49% of calvings strongly assisted by the farmer or the veterinarian and 2.8 vs. 0.65% cesarean). Male calves caused greater (P < 0.001) calving difficulty than females (7.71% of male calvings strongly assisted by the farmer or the veterinarian vs. 4.25% of females and 1.83% cesarean in males vs. 0.47% in females). The month and year of calving also had a strong influence on calving ease. These data were analyzed using 3 different models: the threshold models with homoscedasticity or heteroscedasticity and the grouped data model. The bootstrap comparison among models suggested that the threshold models, even allowing for heteroscedasticity, did not fit the herd effects well. In contrast, fitting deficiencies were not observed for the grouped data model in any factor. The variance of direct effect of the calf was estimated using the 3 models, and the heritability estimate ranged from 0.165 for the grouped data model to 0.185 for the hereroscedastic threshold model. This heritability was moderate, but it would justify the inclusion of direct effects of the calf on calving ease in the breeding objective. Overall, results highlighted the flexibility of the grouped data model for the analysis of discrete traits, like calving ease of beef calves. [ABSTRACT FROM AUTHOR]

Copyright of Journal of Animal Breeding & Genetics is the property of Wiley-Blackwell and its content may not be copied or emailed to multiple sites or posted to a listserv without the copyright holder's express written permission. However, users may print, download, or email articles for individual use. This abstract may be abridged. No warranty is given about the accuracy of the copy. Users should refer to the original published version of the material for the full abstract. (Copyright applies to all Abstracts.)

An analysis of the length of productive life in the Bruna dels Pirineus beef breed was performed with a non-parametric approach giving an average value of 9 years of productive life, and a corresponding replacement rate of 11%. Using a proportional hazards model stratified by herd, the influence of calf birth weight and weight gain until weaning, calving difficulty, calving interval and age at first calving on length of productive life were studied. Two models were explored : the first one included time-dependent variables taking the current value of the covariate at each calving date, while the second one also comprised time-dependent interactions between the value of the covariate of the current calving and its mean value during the last (up to) three previous calvings. Results from the first model showed that the risk of culling increases with very high ages at first calving, increasing calving difficulties, very large calf birth weights, very small weight gains until weaning and very long calving intervals. Furthermore, results from the second model showed that these increases also depend upon a sequence of values for the same covariate in previous calvings. Finally, these higher risks of culling implied lower survival functions that increased replacement rates but only slightly decreased average performances. [ABSTRACT FROM AUTHOR]

Abstract The implementation of genetic groups in BLUP evaluations accounts for different expectations of breeding values in base animals. Notwithstanding, many feasible structures of genetic groups exist and there are no analytical tools described to compare them easily. In this sense, the recent development of a simple and stable procedure to calculate the Bayes factor between nested competing models allowed us to develop a new approach of that method focused on compared models with different structures of random genetic groups. The procedure is based on a reparameterization of the model in terms of intraclass correlation of genetic groups. The Bayes factor can be easily calculated from the output of a Markov chain Monte Carlo sampling by averaging conditional densities at the null intraclass correlation. It compares two nested models, a model with a given structure of genetic groups against a model without genetic groups. The calculation of the Bayes factor between different structures of genetic groups can be quickly and easily obtained from the Bayes factor between the nested models. We applied this approach to a weaning weight data set of the Bruna dels Pirineus beef cattle, comparing several structures of genetic groups, and the final results showed that the preferable structure was an only group for unknown dams and different groups for unknown sires for each year of calving.

This study analyzed the haplotype diversity along the genome of seven Spanish Beef Cattle populations within regions of 500 kb using the information provided by the BovineHD Beadchip. The results of the analysis pointed out a strong variability of the haplotype diversity across the genome, which is greatly conserved across populations. This strong concordance between populations suggests that the reasons behind it are intrinsic to the structure of the bovine genome and caused probably by the mutation or recombination rate. Nevertheless, some of the genomic regions with very large haplotype diversity are also due of genome assembly errors. [ABSTRACT FROM AUTHOR]