Assessment of the value of international genetic evaluations for yield in predicting domestic breeding values for foreign Holstein bulls.

International genetic evaluations are a valuable source of information for decisions about the importation of (the semen of) foreign bulls. This study analyzed data from 6 countries (Australia, Canada, Italy, France, the Netherlands, and the United States) and compared international evaluations for production traits of foreign bulls (i.e., when no national daughter information was available) to their national breeding values in August 2009, which were based only on domestic daughters' data. A total of 821 bulls with highly reliable estimated breeding values (EBV) for milk, fat, and protein yield were analyzed. No evidence of systematic over- or underestimation was found in most of the countries analyzed. Observed correlations between national and international evaluations were close to 0.9 and, for most countries, generally close to their expected values (calculated from national and international EBV reliabilities). In Italy, however, higher differences between observed and expected correlations and significant mean differences between EBV for more than one trait were observed in bulls progeny-tested in the United States and in other European countries (with differences up to 33.1% of the genetic standard deviation). These results were probably induced by a relatively recent change in the model for national evaluation. The findings in this study reflect a conservative estimate of the real value of international evaluations, as changes in methodologies in either the national or the international evaluations decreased the ability of past international evaluations to predict current national evaluations. Nevertheless, our results indicate that international evaluations based on foreign information for Holstein bulls were reasonably accurate predictors of the future national breeding values based only upon domestic daughters

Bayesian Analysis of Heterogeneous Residual Variance in Canine Behaviour

Non-additive effects like for instance genotype-environment interactions and genetically structured heterogeneity of residual variance are notoriously dependent on scale: many statistical non-additive phenomena disappear after a careful choice of transformation of the phenotypic values. Particularly for behavioural measures, scale is a delicate matter. We present a novel Bayesian approach that assesses heterogeneity in environmental variance as a function of genetic effects, where the scale is defined by a psychometric model based on item-response theory. This makes analysis results independent of what items are in a particular test version. We apply the method to fearful behaviour in dogs and compare results with the more usual sum score approac

Mating allocations in Holstein combining genomic information and linear programming optimization at the herd level

In this study, we explored mating allocation in Hol-stein using genomic information for 24,333 Holstein fe-males born in Denmark, Finland, and Sweden. We used 2 data sets of bulls: the top 50 genotyped bulls and the top 25 polled genotyped bulls on the Nordic total merit scale. We used linear programming to optimize economic scores within each herd, considering genetic level, genetic relationship, semen cost, the economic impact of genetic defects, polledness, and 0-casein. We found that it was possible to reduce genetic relation-ships and eliminate expression of genetic defects with minimal effect on the genetic level in total merit index. Compared with maximizing only Nordic total merit in-dex, the relative frequency of polled offspring increased from 13.5 to 22.5%, and that of offspring homozygous for 0-casein (A2A2) from 66.7 to 75.0% in one genera-tion, without any substantial negative impact on other comparison criteria. Using only semen from polled bulls, which might become necessary if dehorning is banned, considerably reduced the genetic level. We also found that animals carrying the polled allele were less likely to be homozygous for 0-casein (A2A2) and more likely to be carriers of the genetic defect HH1. Hence, adding economic value to a monogenic trait in the economic score used for mating allocation sometimes negatively affected another monogenetic trait. We rec-ommend that the comparison criteria used in this study be monitored in a modern genomic mating program

Breeding Value Estimation for Environmental Sensitivity on a Large Dairy Cattle Data Set

Animal robustness, or environmental sensitivity, may be studied through individual differences in re-sidual variance. These differences appear to be heritable, and there is therefore a need to fit models having breeding values explaining differences in residual variance. The aim of this report is to study whether breeding value estimation for environmental sensitivity (vEBV) can be performed on a large dairy cattle data set having around 1.6 million records. Two traits were analyzed separately, somatic cell score and milk yield. Estimation of variance components, ordinary breeding values and vEBVs was performed using standard variance component estimation software (ASReml), applying the me-thodology for double hierarchical generalized linear models. Converged estimates were obtained by running ASReml iteratively 20 times, which took less than 10 days on a Linux server. The genetic co-efficients of variation for environmental variance were 0.45 and 0.52, for somatic cell score and milk yield, respectively, which indicate a substantial genetic variance for environmental variance. This study shows that estimation of variance components, EBVs and vEBVs, is feasible for large dairy cat-tle data sets using standard variance component estimation software

Reliabilities of genomic prediction using combined reference data of the Nordic Red dairy cattle populations

AbstractThis study investigated the possibility of increasing the reliability of direct genomic values (DGV) by combining reference populations. The data were from 3,735 bulls from Danish, Swedish, and Finnish Red dairy cattle populations. Single nucleotide polymorphism markers were fitted as random variables in a Bayesian model, using published estimated breeding values as response variables. In total, 17 index traits were analyzed. Reliabilities were estimated using a 5-fold cross validation, and calculated as the within-year squared correlation between estimated breeding values and DGV. Marker effects were estimated using reference populations from individual countries, as well as using a combined reference population from all 3 countries. Single-country reference populations gave mean reliabilities across 17 traits of 0.19 to 0.23, whereas the combined reference gave mean reliabilities of 0.26 for all populations. Using marker effects from 1 population to predict the other 2 gave a loss in mean reliability of 0.14 to 0.21 when predicting Swedish or Finnish animals with Danish marker effects, or vice versa. Using Swedish or Finnish marker effects to predict each other only showed a loss in mean reliability of 0.03 to 0.05. A combined Swedish-Finnish reference population led to an average reliability as high as that from the 3-country reference population, but somewhat different for individual traits. The results from this study show that it is possible to increase the reliability of DGV by combining reference populations from related populations

Variance component and breeding value estimation for genetic heterogeneity of residual variance in Swedish Holstein dairy cattle

Trait uniformity, or micro-environmental sensitivity, may be studied through individual differences in residual variance. These differences appear to be heritable, and the need exists, therefore, to fit models to predict breeding values explaining differences in residual variance. The aim of this paper is to estimate breeding values for micro-environmental sensitivity (vEBV) in milk yield and somatic cell score, and their associated variance components, on a large dairy cattle data set having more than 1.6 million records. Estimation of variance components, ordinary breeding values, and vEBV was performed using standard variance component estimation software (ASReml), applying the methodology for double hierarchical generalized linear models. Estimation using ASReml took less than 7 d on a Linux server. The genetic standard deviations for residual variance were 0.21 and 0.22 for somatic cell score and milk yield, respectively, which indicate moderate genetic variance for residual variance and imply that a standard deviation change in vEBV for one of these traits would alter the residual variance by 20%. This study shows that estimation of variance components, estimated breeding values and vEBV, is feasible for large dairy cattle data sets using standard variance component estimation software. The possibility to select for uniformity in Holstein dairy cattle based on these estimates is discussed

Genetic consequences of terminal crossbreeding, genomic test, sexed semen, and beef semen in dairy herds

The development of breeding tools, such as genomic selection and sexed semen, has progressed rapidly in dairy cattle breeding during the past decades. In combination with beef semen, these tools are adopted increasingly at herd level. Dairy crossbreeding is emerging, but the economic and genetic consequences of combining it with the other breeding tools are relatively unknown. We investigated 5 different sexed semen schemes where 0, 50, and 90% of the heifers; 50% of the heifers + 25% of the first-parity cows; and 90% of the heifers + 45% of the first-parity cows were bred to sexed semen. The 5 schemes were combined in scenarios managing pure-breeding or terminal crossbreeding, including genomic testing of all newborn heifers or no testing, and keeping Swedish Red or Swedish Holstein as an initial breed. Thus, 40 scenarios were simulated, combining 2 stochastic simulation models: SimHerd Crossbred (operational returns) and ADAM (genetic returns). The sum of operational and genetic returns equaled the total economic return. Beef semen was used in all scenarios to limit the surplus of replacement heifers. Terminal crossbreeding implied having a nucleus of purebred females, where some were inseminated with semen of the opposite breed. The F-1 crossbred females were inseminated with beef semen. The reproductive performance played a role in improving the benefit of any of the tools. The most considerable total economic returns were achieved when all 4 breeding tools were combined. For Swedish Holstein, the highest total economic return compared with a pure-breeding scenario, without sexed semen and genomic test, was achieved when 90% sexed semen was used in heifers and 45% sexed semen was used for first-parity cows combined with genomic test and crossbreeding (+(sic)58, 33% crossbreds in the herd). The highest total economic return for Swedish Red compared with a pure-breeding scenario, without sexed semen and genomic test, was achieved when 90% sexed semen was used in heifers combined with genomic test and crossbreeding (+(sic)94, 46% crossbreds in the herd). Terminal crossbreeding resulted in lower genetic returns across the herd compared with the corresponding pure-breeding scenarios but was compensated by a higher operational return