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Beef cattle international evaluations, led by Interbeef, combine data from different countries to compute international estimated breeding values (EBVINT) which are expressed on the same country scale as national ones, allowing participating countries to compare national and foreign sires. These two EBV might be in disagreement due to differences in the information used in national and international evaluations. This can be overcome by integrating the EBVINT into the national evaluations to obtain a ‘blended’ EBV. Here we tested and validated a general procedure to integrate publishable sires EBVINT at the national level. Using evaluations for Limousin weaning weight and the integration for Italy as a case study, we show that the integration procedure accurately blends international information at the national level while avoiding double-counting of national information which are used as input to compute EBVINT in Interbeef evaluations. This procedure can also be used with other traits and breeds.

Many traits of economical relevance in beef cattle are influenced in their phenotypic expression by the dam. Genetic evaluations of maternally affected traits require to model direct, maternal and direct-maternal genetic (co)variances next to non-genetic effects. In Interbeef beef cattle international evaluations, direct-maternal genetic correlations (rdm) may be different both within countries (rdm_WC) and between countries (rdm_BC). rdm_WC for growth traits up to weaning are often reported to be negative and significantly different from zero. As rdm_BC are difficult to estimate, these are currently assumed to be equal to zero in Interbeef evaluations. The objective of this study was to evaluate the impact of using estimated values for rdm_BC instead of assuming them to be zero, on international estimated breeding values (IEBV). We implemented two scenarios that differed only in the modelling of rdm_BC: A) the current Interbeef evaluation with assumes rdm_BC to be 0 and fits estimated rdm_WC, and B) an Interbeef evaluation in which both estimated rdm_WC and rdm_BC were fitted. Weaning weight phenotypes and pedigree information were available for more than 3 million Limousin beef cattle males and females, born between 1972 and 2017, and distributed across ten European countries. We evaluated the impact of ignoring rdm_BC on different groups of animals by comparing animals’ direct and maternal IEBV between scenarios A and B. Ignoring rdm_BC resulted in no re-ranking for direct IEBV, and limited re-ranking for maternal IEBV. Less re-ranking in maternal IEBV was observed with increasing reliability. Moreover, ignoring rdm_BC resulted in no re-ranking for publishable sires, i.e. of sires with IEBV that can be exchanged across countries. Our study suggests that the current practice of ignoring rdm_BC has limited impact on Interbeef evaluations when rdm_BC are close to 0 on average (ranging from +0.14 to -0.14) as is the case for weaning weight.

Computing time and memory requirements increase with single-step methods to estimate genomic breeding values when the number of genotyped animals increases. Computational costs can be reduced by omitting genotypes of animals without phenotype and progeny, often the candidate animals for selection. Indirect prediction of a candidate animal GEBV can be based on the animal’s genotype and SNP marker solutions (DGV). Alternatively, the sum of DGV and residual polygenic (RPG) effect can be computed, denoted GRV (Genomic and Residual polygenic Value). We applied indirect genomic prediction for a 6 trait calving difficulty evaluation. There were 1.50 million genotyped animals of which 36% were considered candidate animals. Based on our results, DGV showed high accuracy but also bias due to omitting the RPG effect. The GRV prediction had high accuracy and low bias. Computing time was reduced by 33%.

Defining multiple base populations for a genetic evaluation is subjective and there is generally no feedback on the suitability of the defined base populations prior to model validation. We present a number of statistics that can be used to evaluate defined base populations. Application of these statistics to one simulated and two practical datasets showed that in practical datasets the number of base animals per base population was in one case very low. In many cases the available genotype information for different base populations was coming from exactly the same genotyped animals. Both issues are likely to complicate genomic evaluation. A tool to estimate these statistics is available in the MiXBLUP software suite.

Precision livestock farming tools, such as sensor and automation techniques, enable animal breeders to define novel traits. New challenges are data storage and handling and the development of genetic evaluation. Traditionally, the development of genetic evaluation for novel traits requires several steps, i.e. data curation, trait definition, variance component estimation (ASReml), genetic evaluation (MiXBLUP), and validation of the estimated breeding values (EBVs), requiring many iterations to optimize the genetic evaluations. We combined these steps in a cloud solution to make this entire process more efficient. An experiment was run with 1,782,373,113 daily milk yield records of 1,120,550 cows, all the way from data curation to trait definition and validation of the EBV. The resulting wall-time, i.e. elapsed actual time from start to finish ofthe entire process, was ~23 hours. The flexible cloud solution can be easily modified or adapted to develop novel traits.

The software package MiXBLUP 3.0 allows to efficiently estimate (genomic enhanced) breeding values in livestock using various linear mixed effect models. MiXBLUP aims to be user-friendly while supporting efficient algorithms for solving large genomic evaluations. Originally developed for pedigree-based models, MiXBLUP has been extended to four different approaches for single-step genomic evaluations, allowing simultaneous analyses of all information for both genotyped and ungenotyped individuals. For all approaches, shared-memory parallelism is supported using tailor-made procedures and parallel libraries. It has been tested on some of the largest genomic datasets in the world. The software is developed by Wageningen University and Research in collaboration with the Natural Resources Institute Finland (Luke).

Genomic prediction of feed intake using predictor traits A total of 77,640 weekly records on dry matter intake (DMI), 64,443 on fat and protein corrected milk (FPCM) and 73,415 on live weight (LW) were analysed from 3,188 Dutch dairy cows in 6,820 lactations (first to third lactation) from 1980 to 2015. The objective of this study was to compare the accuracies of the genomic estimated breeding values (GEBV) for DMI, with or without predictor traits included (FPCM and LW) with a single step method (SS-GBLUP). Accuracies of GEBV for DMI was0.36 when FPCM and LW were included as reference traits, 0.37 when DMI was the only reference trait, and 0.38 when all 3 traits (DMI, FPCM and LW) were included as reference traits. When only using predictor traits in the reference population, the accuracies of estimated GEBV for DMI, were lower than in the scenarios using DMI as LW and FPCM can only explain 53% of the variation in DMI. Moreover, there was very little benefit of adding information on predictor traits to the reference population when DMI was already included on the same animals. However, in the absence of DMI records, having records on FPCM and LW from different lactations is a good way to obtain GEBV with a relatively good accuracy.

A method was developed and tested to estimate challenge load due to disease outbreaks and other challenges in sows using reproduction records. The method was based on reproduction records from a farm with known disease outbreaks. It was assumed that the reduction in weekly reproductive output within a farm is proportional to the magnitude of the challenge. As the challenge increases beyond certain threshold, it is manifested as an outbreak. The reproduction records were divided into 3 datasets. The first dataset called the Training dataset consisted of 57,135 reproduction records from 10,901 sows from 1 farm in Canada with several outbreaks of porcine reproductive and respiratory syndrome (PRRS). The known disease status of sows was regressed on the traits number born alive, number of losses as a combination of still birth and mummified piglets, and number of weaned piglets. The regression coefficients from this analysis were then used as weighting factors for derivation of an index measure called challenge load indicator. These weighting factors were derived with i) a two-step approach using residuals or year-week solutions estimated from a previous step, and ii) a single-step approach using the trait values directly. Two types of models were used for each approach: a logistic regression model and a general additive model. The estimates of challenge load indicator were then compared based on their ability to detect PRRS outbreaks in a Test dataset consisting of records from 65,826 sows from 15 farms in the Netherlands. These farms differed from the Canadian farm with respect to PRRS virus strains, severity and frequency of outbreaks. The single-step approach using a general additive model was best and detected 14 out of the 15 outbreaks. This approach was then further validated using the third dataset consisting of reproduction records of 831,855 sows in 431 farms located in different countries in Europe and America. A total of 41 out of 48 outbreaks detected using data analysis were confirmed based on diagnostic information received from the farms. Among these, 30 outbreaks were due to PRRS while 11 were due to other diseases and challenging conditions. The results suggest that proposed method could be useful for estimation of challenge load and detection of challenge phases such as disease outbreaks.

Genomic prediction holds the promise to use information of other populations to improve prediction accuracy. Thus far, empirical evaluations showed limited benefit of multi-breed compared to single reed genomic prediction. We compared prediction accuracy of different models based on two losely related and one unrelated line of layer chickens. Multi-breed genomic prediction may be successful when lines are closely related, and when the number of training animals of the additional line is large compared to the line itself. Multi-breed genomic prediction requires models that are lexible enough to use beneficial and ignore detrimental sources of information in the training data. Combining linear and non-linear models may lead to small increases in accuracy of multibreed genomic prediction. Multitrait models, modelling a separate trait for each breed, appear especially beneficial when elationships between breeds are very low, or when the genetic correlation between breeds is negative.

A reduction in boar taint, an unpleasant odor arising in pork from some intact males, is desirable if routine castration of piglets needs to be stopped. Commercial slaughter pigs are typically crosses between sire lines mainly selected for finishing traits and dam lines mainly selected for reproduction traits. Previous studies suggest the possibility of reducing boar taint in sire lines due to favorable genetic correlations between boar taint and finishing traits. However, there are indications of unfavorable genetic associations between boar taint and female reproduction traits, but a lack of genetic correlation estimates remain a major roadblock in reducing boar taint in dam lines. This study was conducted to estimate genetic correlations between boar taint traits and female reproduction traits, investigate differences in these genetic relationships among sire and dam lines, and evaluate possible consequences of selection against boar taint in dam lines. The data consisted of 32,549 reproduction records from a Landrace dam line, 23,874 records from a Yorkshire dam line, and 3,745 records from a Pietrain sire line. Androstenone, skatole, and indole were measured on 1,896 carcasses, and human nose scores were recorded on 7,742 carcass samples. In general, the level of boar taint was significantly greater (P

Utilising monitoring for sustainability in breeding of farm animals. Verkenning om monitoring voor duurzaamheid te benutten voor de veefokkerij.

A measuring and breeding programme has been developed for easy calving doublemuscled beef cattle. Samen met fokkers van dikbilkoeien is een meet- en fokprogramma ontwikkeld gericht op natuurlijke geboorte.

The purpose of this study was to evaluate measures of boar (Sus scrofa) taint as potential selection criteria to reduce boar taint so that castration of piglets will become unnecessary. Therefore, genetic parameters of boar taint measures and their genetic correlations with finishing traits were estimated. In particular, the usefulness of a human panel assessing boar taint (human nose score) was compared with chemical assessment of boar taint compounds, androstenone, skatole, and indole. Heritability estimates for androstenone, skatole, and indole were 0.54, 0.41, and 0.33, respectively. The heritability for the human nose score using multiple panelists was 0.12, and ranged from 0.12 to 0.19 for individual panelists. Genetic correlations between scores of panelists were generally high up to unity. The genetic correlations between human nose scores and the boar taint compounds ranged from 0.64 to 0.999. The boar taint compounds and human nose scores had low or favorable genetic correlations with finishing traits. Selection index estimates indicated that the effectiveness of a breeding program based on human nose scores can be comparable to a breeding program based on the boar taint compounds themselves. Human nose scores can thus be used as a cheap and fast alternative for the costly determination of boar taint compounds, needed in breeding pigs without boar taint.

Three sheep breeds exempted from the ban on tail docking have set up breeding value estimation for shorter tails. Their breeding policy needs to be extended further in order to realise shorter tails in practice. Bij drie schapenrassen met een ontheffing op het coupeerverbod is een fokwaarden schatting voor kortere staarten opgezet. Een verdere aanscherping van het beleid is nodig om daadwerkelijk kortere staarten te realiseren.

Dikbilkoeien die probleemloos natuurlijk afkalven is geen utopie. Na drie jaar voorbereidend onderzoek en vier jaar onderzoek in de praktijk binnen het project Natuurlijke Luxe is duidelijk hoe dat moet. Het belangrijkste is om met fokkerij de ruimte in het geboortekanaal te vergroten. Of dat ook gebeurt, is nu een kwestie van willen en doen.

A concept and method are developed and applied to improve robustness in animal production.

Biologische varkenshouders kiezen bij het fokken van hun varkens voor een biologisch fokprogramma met rotatiekruising. Dit komt zowel de gezondheid van de dieren als de afzet van biologisch varkensvlees ten goede. Jaarlijks vervangen de varkenshouders gemiddeld 40 procent van hun vermeerderingszeugen

European and Dutch legislation allow applications for patenting animals, provided that certain criteria are met. In practice, the precise interpretation of these criteria is not clear en it takes relatively long before an application is granted or rejected. Analysis of patent applications concerning animal breeding in the last two decades shows that there is no imminent risk for the right to use animals in animal production. Europese en nationale regelgeving staan toe dat octrooi aangevraagd wordt op dieren, mits aan bepaalde voorwaarden wordt voldaan. In de praktijk blijkt de precieze interpretatie van die voorwaarden onduidelijk te zijn en duurt het relatief lang voor een aanvraag beoordeeld is. Analyse van fokkerijoctrooien van de laatste 20 jaar laten zien dat er geen direct gevaar is voor het gebruiksrecht van dieren in dierlijke productie.

De inwendige bekkenhoogte van een koe vertoont veel variatie, is sterk erfelijk en hangt nauw samen met de kans op een natuurlijke geboorte van het kalf. Dit maakt selectie voor een grotere inwendige bekkenhoogte een geschikt instrument om bij Verbeterd Roodbont en Belgisch Witblauw vleesvee te selecteren voor natuurlijke geboorten.

Vrijwel alle dikbilkoeien komen met een keizersnee ter wereld. Wageningen UR Livestock Research werkt in het project ‘Natuurlijke luxe’ met de Federatie van Vleesveestamboeken Nederland aan meer natuurlijke geboorten.

Om een optimale diergezondheid te kunnen realiseren, is het belangrijk dat een varken zo min mogelijk gevolgen ondervindt van dierziekten. De varkenshouder staat voor de uitdaging om een aanpak te kiezen die een robuuste gezondheid op het bedrijf mogelijk maakt. Dit kan helpen bij het reduceren van het gebruik van antibiotica. Maar welke aanpak is dat? WUR-onderzoek geeft enkele aanknopingspunten.

In dit essay benadrukken de auteurs het belang van genetische diversiteit in landbouwhuisdieren en het belang van verscheidenheid bij de ontwikkeling van veehouderijsystemen voor de toekomst. Dit in het licht van het streven naar mondiale voedselzekerheid en behoud van biodiversiteit in bredere zin.

Het streven naar meer natuurlijke geboorten bij Verbeterd Roodbont is in een nieuwe fase gekomen. Het stamboek heeft de trekkende rol overgenomen van Wageningen UR Livestock Research en stimuleert en ondersteunt zijn leden met concreet advies. Het doel wat het stamboek voor ogen heeft is 50 procent natuurlijke geboorten in 2020. Een portret van een cultuuromslag.

Kippengeluk wordt al bepaald in het ei. Een kuiken dat op de juiste temperatuur is uitgebroed is gezonder en waarschijnlijk ook minder angstig dan soortgenoten die het in het ei te heet of te koud hebben gehad. Ook de eerste levensweken van een kip blijken van grote invloed op de latere gezondheidstoestand van het dier

De biologische varkenshouders in Nederland maken voor de vervanging van hun zeugen gebruik van fokmateriaal uit de gangbare varkenshouderij. Dit via aankoop van fokgelten of via aankoop van sperma van gangbare zeugenlijnen voor de eigen aanfok van fokgelten. Echter, biologische bedrijven die alle fokgelten voor vervanging aankopen van niet-biologische bedrijven voldoen niet aan de SKAL richtlijn. Het doel van deze studie is om rassen, kruisingen en fokkerijstructuren te vergelijken om de meest geschikte werkwijze te vinden waarmee de biologische varkenshouderij zichzelf kan voorzien van fokgelten.