How pedigree errors affect genetic evaluations and validation statistics.

Pedigrees used in genetic evaluations contain errors. Because of such errors, assumptions regarding the relatedness among individuals in genetic evaluation models are wrong. Consequences of that have been investigated in earlier studies focusing on models that did not account for genomic information yet. The objective of this work was to investigate the effects of pedigree errors on the results from genetic evaluations using the single-step model, and the effect of such effects on results from validation studies with forward prediction. We used a real pedigree (n = 361,980) and real genotypes (n = 25,950) of Fleckvieh cattle, sampled in a way to provide a good consistency between pedigree and genomic relationships. Given the real pedigree and genotypes, true breeding values (TBV) were simulated to have a covariance structure equal to the matrix H assumed in a single-step model. Based on TBV, phenotypes were simulated with a heritability of 0.25. Genetic evaluations were conducted with a conventional animal model (i.e., without genomic information) and a single-step animal model under scenarios using either the correct pedigree or a pedigree containing 5%, 10%, or 20% of wrong records. Wrong records were simulated by randomly assigning wrong sires to nongenotyped females. The increasing rates of pedigree errors led to decreasing correlations between TBV and EBV and lower standard deviations of predictions. Less variation was observed because pedigree errors operate actually as a random exchange of daughters among bulls, making them look more similar to each other than they actually are. This occurs of course only when animals have progeny. Therefore, this decreased variation was more pronounced for progeny tested bulls than for young selection candidates. In a forward prediction validation scenario, the stronger decrease in variation when animals get progeny caused an apparent inflation of early predictions. This phenomenon may contribute to the usually observed problem of inflation of early predictions observed in validation studies.

Technical note: Methods for interim prediction of single-step breeding values for young animals.

Single-step genomic evaluations have the advantage of simultaneously combining all pedigree, phenotypic, and genotypic information available. However, systems with a large number of genotyped animals have some computational challenges. In many genomic breeding programs, genomic predictions of young animals should become available for selection decisions in the shortest time possible, which requires either a very effective estimation or an approximation with negligible loss in accuracy. We investigated different procedures for predicting breeding values of young genotyped animals without setting up the full single-step system augmented for the additional genotypes. Methods were based on transmitting the information from single-step breeding values of genotyped animals that took part in the previous full run to young animals, either through genomic relationships or through a marker-based model. The different procedures were tested on real data from the April 2017 run of the German-Austrian official genomic evaluation for Fleckvieh. The data set included 62,559 genotyped animals and was used to run single-step evaluations for 23 conformation traits. A further data set comprising 1,768 young animals was used for interim prediction and we called it the validation set. The reference values for validation were the predicted breeding values of the young animals from a full single-step run containing the genotypes of all 64,327 animals. Correlations between the approximated predictions and those from the full single-step run also containing genotypes from young animals averaged 0.9932 for the best method (from 0.990 to 0.995 across traits). In conclusion, prediction of single-step breeding values for young animals can be well approximated using systems of size equal to the number of markers.

Short communication: Calculating analytical reliabilities for single-step predictions.

It has been shown that single-step genomic BLUP (ssGBLUP) can be reformulated, resulting in an equivalent SNP model that includes the explicit imputation of gene contents of all ungenotyped animals in the pedigree. This reformulation reveals the underlying mechanism enabling ungenotyped animals to contribute information to genotyped animals via estimates of marker effects and consequently to the reliability of genomic predictions, a key feature generally associated with the single-step approach. Irrespective of which BLUP formulation is used for genomic prediction, with increasing numbers of genotyped animals, the marker-oriented model is recommended when calculating the reliabilities of genomic predictions. This approach has the advantage of a manageable and stable size of the model matrix that needs to be inverted to calculate analytical prediction error variances of marker effects, an advantage that also holds for prediction with the single-step model. However, when including imputed genotypes in the design matrix of marker effects, an additional imputation residual term has to be considered to account for the prediction error of imputation. We summarize some of the theoretical aspects associated with the calculation of analytical reliabilities of single-step predictions. Derivations are based on the equivalent reformulation of ssGBLUP as a marker-oriented model and the calculation of prediction error variances of marker effects. We propose 2 approximations that allow for a substantial reduction of the complexity of the matrix operations involved, while retaining most of the relevant information required for reliability calculations. We additionally provide a general framework for an implementation of single-step reliability approximation using standard animal model reliabilities as a starting point. Finally, we demonstrate the effectiveness of the proposed approach using a small example extracted from data of the routine evaluation on dual-purpose Fleckvieh (Simmental) cattle.

Considering dominance in reduced single-step genomic evaluations.

Single-step models including dominance can be an enormous computational task and can even be prohibitive for practical application. In this study, we try to answer the question whether a reduced single-step model is able to estimate breeding values of bulls and breeding values, dominance deviations and total genetic values of cows with acceptable quality. Genetic values and phenotypes were simulated (500 repetitions) for a small Fleckvieh pedigree consisting of 371 bulls (180 thereof genotyped) and 553 cows (40 thereof genotyped). This pedigree was virtually extended for 2,407 non-genotyped daughters. Genetic values were estimated with the single-step model and with different reduced single-step models. Including more relatives of genotyped cows in the reduced single-step model resulted in a better agreement of results with the single-step model. Accuracies of genetic values were largest with single-step and smallest with reduced single-step when only the cows genotyped were modelled. The results indicate that a reduced single-step model is suitable to estimate breeding values of bulls and breeding values, dominance deviations and total genetic values of cows with acceptable quality.

[Hemodynamic interplay between tricuspid valve and right ventricle]. / Hämodynamik im Wechselspiel zwischen Trikuspidalklappe und rechtem Ventrikel.

The tricuspid valve and the right ventricle are hemodynamically closely related. Pathological changes of the valve or of the ventricle itself and also various diseases beyond that can result in a downward spiral of mutual interference, which is of prognostic importance for the patient. The development of a functional tricuspid regurgitation is of great importance. Especially with the help of 3D-echocardiography, more and more changes and mechanisms have been identified that are crucial in this process. This article provides a review of the relationship between the tricuspid valve and the right ventricle emphasizing the current knowledge of the causes, the pathophysiological concepts, the underlying structural changes and the therapeutic approaches based on this.

Short communication: The role of genotypes from animals without phenotypes in single-step genomic evaluations.

In a 2-step genomic system, genotypes of animals without phenotypes do not influence genomic prediction of other animals, but that might not be the case in single-step systems. We investigated the effects of including genotypes from culled bulls on the reliability of genomic predictions from single-step evaluations. Four scenarios with a constant amount of phenotypic information and increasing numbers of genotypes from culled bulls were simulated and compared with respect to prediction reliability. With increasing numbers of genotyped culled bulls, there was a corresponding increase in prediction reliability. For instance, in our simulation scenario the reliability for selection candidates was twice as large when all culled bulls from the last 4 generations were included in the analysis. Single-step evaluations imply the imputation of all nongenotyped animals in the pedigree. We showed that this imputation was increasingly more accurate as increasingly more genotypic information from the culled bulls was taken into account. This resulted in higher prediction reliabilities. The extent of the benefit from including genotypes from culled bulls might be more relevant for small populations with low levels of reliabilities.

Genomic selection in the German Landrace population of the Bavarian herdbook.

The aim of our study was to compare different validation methods with respect to their impact on validation results and to evaluate the feasibility of genomic selection in the German Landrace population of the Bavarian herdbook. For this purpose, a sample of 337 boars and 1,676 sows was genotyped with the Illumina PorcineSNP60 BeadChip. Conventional BLUP breeding values for fertility, growth, carcass, and quality traits were deregressed and used as phenotypes in genomic BLUP. The resulting genomic breeding values were also blended with information from the full conventional breeding value estimation to include information from nongenotyped parents. Subsequent validation used forward prediction, realized reliabilities, and theoretical reliabilities. The results indicate that the validation methods showed a relatively large effect on in the displayed reliability levels in our study: forward prediction reliabilities were found to be much lower than the conventional parent-average reliabilities whereas corresponding realized and theoretical reliabilities were found substantially greater. Theoretical reliabilities appear to be the most consistent validation approach tested in our study, because they avoid the use of proxy variables. Generally, our results suggest a substantial potential for a genomic selection implementation for the Bavarian herdbook by using both sows and boars. Theoretical genomic reliabilities of direct genomic values of selection candidates were, on average, 31 to 36% greater than the conventional parent average reliabilities. However, the inclusion of residual information from conventional breeding values had only a marginal effect on reliabilities.

Short communication: The effect of genotyping cows to improve the reliability of genomic predictions for selection candidates.

In this study we investigate the potential of enlarging the reference population for genomic prediction in dairy cattle by routinely genotyping a random sample of the first-crop daughters of every AI bull in the breeding program. We analyzed small nuclear pedigrees, each consisting of a genotyped selection candidate and 3 generations of genotyped male ancestors. Genotypes were taken from the genomic routine evaluation of Fleckvieh cattle in Germany and Austria. The phenotypic information of a daughter of any one male in each of these pedigrees was either considered to be part of the daughter yield deviation of the corresponding sire, or was assumed to be an individually observed genotyped daughter of this sire. Daughter genotypes in this case were simulated from phased haplotypes of their sires and random maternal gametes drawn from a haplotype library. We measured the gain from genotyping daughters as the increase in model-based theoretical reliability of the genomic prediction for a putative selection candidate. We expressed the improvements as a marginal increase, corresponding to an increase in reliability at a reliability baseline level of zero, to simplify comparisons. Results were encouraging with 2 to 40% of marginal reliability increase for selection candidates depending on the assumed heritability of the trait and the number of daughters modeled to be genotyped in the design.

How imputation errors bias genomic predictions.

The objective of this study was to investigate in detail the biasing effects of imputation errors on genomic predictions. Direct genomic values (DGV) of 3,494 Brown Swiss selection candidates for 37 production and conformation traits were predicted using either their observed 50K genotypes or their 50K genotypes imputed from a mimicked 6K chip. Changes in DGV caused by imputation errors were shown to be systematic. The DGV of top animals were, on average, underestimated and that of bottom animals were, on average, overestimated when imputed genotypes were used instead of observed genotypes. This pattern might be explained by the fact that imputation algorithms will usually suggest the most frequent haplotype from the sample whenever a haplotype cannot be determined unambiguously. That was empirically shown to cause an advantage for the bottom animals and a disadvantage for the top animals.

On the limited increase in validation reliability using high-density genotypes in genomic best linear unbiased prediction: observations from Fleckvieh cattle.

This study investigated reliability of genomic predictions using medium-density (40,089; 50K) or high-density (HD; 388,951) marker sets. We developed an approximate method to test differences in validation reliability for significance. Model-based reliability and the effect of HD genotypes on inflation of predictions were analyzed additionally. Genomic breeding values were predicted for at least 1,321 validation bulls based on phenotypes and genotypes of at least 5,324 calibration bulls by means of a linear model in milk, fat, and protein yield; somatic cell score; milkability; muscling; udder, feet, and legs score as well as stature. In total, 1,485 bulls were actually HD genotyped and HD genotypes of the other animals were imputed from 50K genotypes using FImpute software. Validation reliability was measured as the coefficient of determination of the weighted regression of daughter yield deviations on predicted breeding values divided by the reliability of daughter yield deviations and inflation was evaluated by the slope of this regression. Model-based reliability was calculated from the model. Distributions for validation reliability of 50K markers were derived by repeated sampling of 50,000-marker samples from HD to test differences in validation reliability statistically. Additionally, the benefit of HD genotypes in validation reliability was tested by repeated sampling of validation groups and calculation of the difference in validation reliability between HD and 50K genotypes for the sampled groups of bulls. The mean benefit in validation reliability of HD genotypes was 0.015 compared with real 50K genotypes and 0.028 compared with 50K samples from HD affected by imputation error and was significant for all traits. The model-based reliability was, on average, 0.036 lower and the regression coefficient was 0.036 closer to the expected value with HD genotypes. The observed gain in validation reliability with HD genotypes was similar to expectations based on the number of markers and the effective number of segregating chromosome segments. Sampling error in the marker-based relationship coefficients causing overestimation of the model-based reliability was smaller with HD genotypes. Inflation of the genomic predictions was reduced with HD genotypes, accordingly. Similar effects on model-based reliability and inflation, but not on the validation reliability, were obtained by shrinkage estimation of the realized relationship matrix from 50K genotypes.

Gastroenteritis outbreaks in elderly homes in the east of France during winter 2009/10: aetiology research for a series of 37 outbreaks.

Although acute gastroenteritis is a common cause of morbi-mortality in care homes, there is no national surveillance system in France except for food-borne gastroenteritis. Since 2008, a specific surveillance system has been operating in nursing homes in Alsace, a region in eastern French. In the winter season 2009/10 we had the opportunity to study 37 outbreaks, collecting data on attack rate, duration and aetiology as well as epidemic management in nursing homes. We noticed the responsiveness of the institutions, with a mean period of 1.6 days between the onset of first symptoms and the implementation of management measures (95% confidence interval (CI): 1.0­2.2). One or several stool samples were taken in 27 of the 37 described outbreaks. The only pathogen detected was norovirus, and the positive samples were from outbreaks with a very typical pattern: vomiting in 36 of the outbreaks, a high average attack rate of 36.8% (95% CI: 31.5­42.2) and a short average duration of 8.9 days (95% CI: 5.8­7.0). No severe cases, hospitalisations or deaths were reported. The high frequency of norovirus isolation indicated that systematic bacteriological analysis in local laboratories is not cost-effective. Consequently, Cire Est recommends to test for bacteria and viruses only in cases presenting with fever or atypical symptoms. Nevertheless, Cire Est also recommends to continue sending stool samples to the French National Centre for enteric viruses, more for the benefit of the virological surveillance programme than for diagnostic purposes.

Population structure of the Trakehner Horse breed.

The objective of this study was to examine the population structure of the Trakehner Horse breed. A total of 13 793 pedigree records were used for analysing the active breeding population and their ancestors dating back to 1950. Ancestors that were born before 1950 were called as base animals. The average generation interval was calculated as 10.2 years. The effective population size (Ne) was estimated by the increase in average year-wise inbreeding coefficient and average coancestry, respectively. Two methods were applied to estimate the effective population size: 1. Numerator-relationship-matrix (NRM), which did not consider missing ancestries. 2. Uncertain-parentage-matrix (UPM), which considered a probabilistic correction for unknown ancestors. There were no major differences between these two methods with respect to the rate of increase in inbreeding although the global levels using the UPM method were observed to be higher. Estimates for the inbreeding coefficients and the average coancestries varied little between both methods. The estimates of the effective population size per generation based on the rate of inbreeding ranged from 169 (NRM) to 150 (UPM) and 158 (NRM) to 144 (UPM) calculated by the average coancestry. From the early 1990s onwards, a strong increase in the rate of inbreeding was observed. This may be due to an increasing variance of the family size of sires and may be interpreted as a consequence of the growing use of artificial insemination. Analysing coancestries within and between the centrally managed regional breeding societies in Germany further revealed the Trakehner horse breed to be a genetically fragmented population with a main partition corresponding to formerly divided East and West Germany. The average rate of gene contributions (Thoroughbred (xx), Arab Horse breed (ox)) to the defined actual breeding population was calculated to be 22.3% xx-genes and 11.7% ox-genes.

Circulating markers of inflammation and their link to indices of adiposity.

BACKGROUND: Adipose tissue produces a number of inflammatory mediators. Circulating concentrations of these inflammatory markers are increasingly used as markers of local or systemic inflammation. This study compares results for 3 inflammatory adipokines measured using 2 techniques, (multiplex and ELISA), and determines the relationships with C-reactive protein (CRP), obesity, and the impact of moderate weight loss. SUBJECTS AND METHODS: Fasting blood samples were collected at baseline and after a 24-week weight loss intervention. Interleukin 6 (IL-6), tumour necrosis factor alpha(TNF-alpha), and monocyte chemoattractant protein 1 (MCP-1) were measured using a standard ELISA technique or a new multiplex technique. A total of 54 women with complete data were included in this analysis. RESULTS: Multiplex showed poor correlation with ELISA results, and were not significantly correlated with CRP. Using ELISA data, IL-6 and CRP were significantly correlated with body mass index (BMI) (r = 0.42 and r = 0.55), but MCP-1 and TNF-alpha were not (r = - 0.07 and r = 0.06). Changes in MCP-1, TNF-alpha, and IL-6 were not significantly different between control and weight loss groups. CRP was significantly reduced in weight loss vs. control group (p < 0.05), and change in CRP correlated with change in BMI (r = 0.31). CONCLUSION: Circulating IL-6 and CRP, but not MCP-1 and TNF-alpha, are significantly associated with indices of adiposity in obese women. This study suggests that circulating IL-6 and CRP, but not MCP-1 and TNF-alpha, are useful markers of obesity-related inflammation.

FSBA modifies both alpha- and beta-subunits of F1 specifically and can be bound together with AXP at the same alpha-subunit.

Binding of 1 mole 5'-fluorosulfonylbenzoyladenosine (FSBA) per mol F1 induces about 50% inhibition of ATPase activity and 80% inhibition of ITPase activity. The binding of additional ligand results in a further inhibition of both activities. Maximally 5 mol/mol F1, causing complete inhibition of activity, can be bound. Using radioactive FSBA more label is found on alpha-subunits than on beta-subunits under the usual buffer conditions. The modified amino acids are alpha-Tyr300, alpha-Tyr244 and beta-Tyr368. Binding of FSBA, at least up to 3 mol/mol F1, does not result in loss of bound ADP, whether the starting enzyme contains 2, 3 or 4 bound nucleotides. Added adenine nucleotides compete with FSBA only for binding that results in modification of beta-subunits, shifting the alpha/beta ratio of bound label to higher values. It is concluded that the alpha-subunits contain two hydrophobic pockets for the binding of nucleoside moieties, with a different orientation relative to the P-loop. One pocket contains alpha-Tyr244 and alpha-Tyr300, the other beta-Tyr368. Since, however, in the binding of adenine nucleotide di- or triphosphates the P-loop is involved, only one of these ligands can bind per subunit. The previously not understood binding characteristics of several substrate analogues have now become interpretable on the assumption that also the structurally homologous beta-subunits contain 2 pockets where nucleoside moieties can bind. The kinetic effects of FSBA binding indicate that the first FSBA binds at the regulatory site that has a high affinity for ADP and pyrophosphate. Binding of pyrophosphate at this high-affinity regulatory site increases the Vmax of the enzyme, while binding at a second regulatory site, a low-affinity site, increases the rate of binding of FSBA with a factor of about 3. Binding of bicarbonate at this latter site is responsible for the disappearance of the apparent negative cooperativity of the ATPase activity.

Identification of an exchangeable non-catalytic site on mitochondrial F1-ATPase which is involved in the negative cooperativity of ATP hydrolysis.

Labeling of mitochondrial F1-ATPase with 8-azido-ATP or 8-azido-ADP under turnover conditions with Mg(2+)-ATP resulted in the identification of one exchangeable non-catalytic site whose occupation with a ligand does not influence the ATPase activity of F1 when measured at Vmax. With 8-azido-ADP two exchangeable non-catalytic sites could be labeled, but at one of them the bound ligand exchanges, at least partly, during the illumination under turnover conditions. After labeling an exchangeable non-catalytic site under turnover conditions with 8-azido-ATP or with 8-azido-ADP, F1-ATPase kept the ability to bind NAP3-2N3ADP at the slowly exchangeable noncatalytic site, thereby inhibiting the ATPase activity by 45%, as recently described (Edel et al. (1992) Biochim. Biophys. Acta 1101, 329-338). Covalent modification of the low-affinity non-catalytic site with 8-nitreno-AT(D)P increased the Km of ATP and abolished the negative cooperativity of ATP hydrolysis. This site can therefore be marked as a regulatory site, whose occupation with a nucleotide decreases the affinity of the catalytic sites for ATP.

Inhibition of mitochondrial F1-ATPase activity by binding of (2-azido-) ADP to a slowly exchangeable non-catalytic nucleotide binding site.

F1-ATPase was treated so that it contained three tightly bound nucleotides per molecule. One of these was bound at a catalytic site and was rapidly exchangeable, the two remaining nucleotides were nonexchangeable. Incubation of this preparation with ADP in the presence of Mg2+ results in 40-45% inhibition of the ATPase activity. With 2-azido-ADP instead of ADP, the ligand was covalently bound to F1 by illumination, in the presence or absence of turnover of the enzyme, and the site of binding was determined. In this way, one site could be identified, which induces the inhibition. The attachment of the covalently bound 2-nitreno-ADP is at Tyr-368 of a beta-subunit, characterized in the literature as a non-catalytic site. A second, non-catalytic site also binds 2-azido-ADP, but this binding is partially reversed by the addition of ATP and does not cause further inhibition of the ATPase activity. It is concluded that the slowly exchangeable non-catalytic site is the site of inhibition by ADP.

Characteristics of the non-exchangeable nucleotide binding sites of mitochondrial F1 revealed by dissociation and reconstitution with 2-azido-ATP.

The dissociation of mitochondrial F1-ATPase with 3 M LiCl at 0 degrees C, followed by reconstitution, has been analysed. FPLC over a gel filtration column in the dissociation buffer revealed the presence of two protein moieties, an alpha 3 gamma delta epsilon complex and single beta-subunits. When the dissociation and chromatography is performed at pH 6.2, the former protein moiety still contains some adenine nucleotides. Reconstitution of the dissociated complex is not possible any more after FPLC, probably due to the loss of residual adenine nucleotides. After a single column centrifugation step one nucleotide per F1 still remains bound. For reconstitution, additional ATP, or a suitable analog, is required. 2-Azido-ATP, but not 8-azido-ATP or ITP, can replace ATP during the reconstitution. F1, reconstituted in the presence of 2-azido-ATP, contains three tightly bound nucleotides, similar to freshly isolated F1, of which in this case one is an adenine nucleotide and two are azido-adenine nucleotides. One of the latter can be rapidly exchanged and is bound to a catalytic site. Covalent binding (at a beta-subunit) of the other tightly bound 2-azido-ATP by ultraviolet illumination does not result in inhibition of the enzyme. Digestion of F1 with trypsin, followed by HPLC, showed that the label is not bound to the fragment containing Tyr-368, nor to the fragment containing Tyr-345. This result was confirmed by CNBr digestion, followed by SDS-urea PAGE. We conclude that during dissociation of F1 one tightly bound nucleotide (ADP) remains bound at an alpha/beta interface site and that for reconstitution binding of ATP to a (non-catalytic) beta-site is required. The conformation of this site differs from that of the two catalytic beta-sites.