Staff Publications

Staff Publications

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    'Staff publications' is the digital repository of Wageningen University & Research

    'Staff publications' contains references to publications authored by Wageningen University staff from 1976 onward.

    Publications authored by the staff of the Research Institutes are available from 1995 onwards.

    Full text documents are added when available. The database is updated daily and currently holds about 240,000 items, of which 72,000 in open access.

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    Evaluation of the Discriminative Potential of a Novel Biomarker for Estradiol Treatments in Bovine Animals
    Regal, P. ; Blokland, M.H. ; Fente, C.A. ; Sterk, S.S. ; Cepeda, A. ; Ginkel, L.A. van - \ 2015
    Journal of Agricultural and Food Chemistry 63 (2015)1. - ISSN 0021-8561 - p. 370 - 378.
    tandem mass-spectrometry - timed artificial-insemination - beef-cattle - protein biomarkers - gene-expression - hormone abuse - plasma - 17-beta-estradiol - estrogen - detect
    The endogenous occurrence of natural hormones obstructs the application of classical targeted methods as confirmatory options. In the case of estradiol, the ultimate confirmation of its exogenous administration relies on gas chromatography coupled to combustion/isotope ratio mass spectrometry (GC-C/IRMS). A serum dipeptide composed of pyroglutamic acid and phenylalanine was identified as a potential biomarker of estradiol treatments in adult cows. To evaluate its potential to pinpoint suspicious samples, samples from prepubertal females under different estrogenic treatments have been analyzed. The results confirmed the up-regulation of the dipeptide in adult bovines. The 2-week-old females exhibited short-lasting responses only in a few animals. The 6-month-old female showed a delayed but clear increase on the biomarker level. The composition of the anabolic preparations, the dose, and/or the administration route are possible additional reasons for the reduced response in young animals. A comparison to previous results reported by various researchers is included.
    Accuracy of genomic prediction when combining two related crossbred populations
    Vallee, A.A.A. ; Arendonk, J.A.M. van; Bovenhuis, H. - \ 2014
    Journal of Animal Science 92 (2014)10. - ISSN 0021-8812 - p. 4342 - 4348.
    dairy-cattle breeds - beef-cattle - selection - performance - animals - values - uterine - traits - impact - gene
    Charolais bulls are selected for their crossbreed performance when mated to Montbéliard or Holstein dams. To implement genomic prediction, one could build a reference population for each crossbred population independently. An alternative could be to combine both crossbred populations into a single reference population to increase size and accuracy of prediction. The objective of this study was to investigate the accuracy of genomic prediction by combining different crossbred populations. Three scenarios were considered: 1) using 1 crossbred population as reference to predict phenotype of animals from the same crossbred population, 2) combining the 2 crossbred populations into 1 reference to predict phenotype of animals from 1 crossbred population, and 3) using 1 crossbred population as reference to predict phenotype of animals from the other crossbred population. Traits studied were bone thinness, height, and muscular development. Phenotypes and 45,117 SNP genotypes were available for 1,764 Montbéliard × Charolais calves and 447 Holstein × Charolais calves. The population was randomly spilt into 10 subgroups, which were assigned to the validation one by one. To allow fair comparison between scenarios, size of the reference population was kept constant for all scenarios. Breeding values were estimated with BLUP and genomic BLUP. Accuracy of prediction was calculated as the correlation between the EBV and the phenotypic values of the calves in the validation divided by the square root of the heritability. Genomic BLUP showed higher accuracies (between 0.281 and 0.473) than BLUP (between 0.197 and 0.452). Accuracies tended to be highest when prediction was within 1 crossbred population, intermediate when populations were combined into the reference population, and lowest when prediction was across populations. Decrease in accuracy from a prediction within 1 population to a prediction across populations was more pronounced for bone thinness (–27%) and height (–29%) than for muscular development (–14%). Genetic correlation between the 2 crossbred populations was estimated using pedigree relationships. It was 0.70 for bone thinness, 0.80 for height, and 0.99 for muscular development. Genetic correlation indicates the expected gain in accuracy of prediction when combining different populations into 1 reference population. The larger the genetic correlation is, the larger the benefit is to combine populations for genomic prediction.
    Evaluation of measures of correctness of genotype imputation in the context of genomic prediction: a review of livestock applications
    Calus, M.P.L. ; Bouwman, A.C. ; Hickey, J.M. ; Veerkamp, R.F. ; Mulder, H.A. - \ 2014
    Animal 8 (2014)11. - ISSN 1751-7311 - p. 1743 - 1753.
    density marker panels - nucleotide polymorphism genotypes - dutch holstein cattle - dairy-cattle - snp genotypes - jersey cattle - beef-cattle - accuracy - populations - selection
    In livestock, many studies have reported the results of imputation to 50k single nucleotide polymorphism (SNP) genotypes for animals that are genotyped with low-density SNP panels. The objective of this paper is to review different measures of correctness of imputation, and to evaluate their utility depending on the purpose of the imputed genotypes. Across studies, imputation accuracy, computed as the correlation between true and imputed genotypes, and imputation error rates, that counts the number of incorrectly imputed alleles, are commonly used measures of imputation correctness. Based on the nature of both measures and results reported in the literature, imputation accuracy appears to be a more useful measure of the correctness of imputation than imputation error rates, because imputation accuracy does not depend on minor allele frequency (MAF), whereas imputation error rate depends on MAF. Therefore imputation accuracy can be better compared across loci with different MAF. Imputation accuracy depends on the ability of identifying the correct haplotype of a SNP, but many other factors have been identified as well, including the number of genotyped immediate ancestors, the number of animals with genotypes at the high-density panel, the SNP density on the low- and high-density panel, the MAF of the imputed SNP and whether imputed SNP are located at the end of a chromosome or not. Some of these factors directly contribute to the linkage disequilibrium between imputed SNP and SNP on the low-density panel. When imputation accuracy is assessed as a predictor for the accuracy of subsequent genomic prediction, we recommend that: (1) individual-specific imputation accuracies should be used that are computed after centring and scaling both true and imputed genotypes; and (2) imputation of gene dosage is preferred over imputation of the most likely genotype, as this increases accuracy and reduces bias of the imputed genotypes and the subsequent genomic predictions.
    Fear responses to novelty in testing environments are related to day-to-day activity in the home environment in dairy cattle
    MacKay, J.R.D. ; Haskell, M.J. ; Deag, J.M. ; Reenen, C.G. van - \ 2014
    Applied Animal Behaviour Science 152 (2014). - ISSN 0168-1591 - p. 7 - 16.
    individual-differences - beef-cattle - behavior - cows - humans - personality - animals - consistency - situations - boldness
    Behavioural tests for cattle take time to perform and can be stressful for the animals but are currently the only way of assessing behavioural reactions to fear-causing stimuli in a standardised manner. It may be possible to use behavioural data collected remotely in the home pen environment through the use of activity monitors and robotic milkers to identify fearful cattle without testing. In this study eighty five dairy cows were given a novel arena novel object (NANO) test and 79 of these were also human approach (HAP) tested, both thought to reflect fear. All animals had their activity recorded for 40 days prior to the testing period using a tri-axial accelerometer activity monitor. High numbers of novel object contacts in the test was associated with younger animals with fewer lying bouts per day and were less variable in their lying bout duration (Radj2=0.13, F 3,75 = 4.65, P = 0.005). Cows with a higher tolerance for human approach had fewer lying bouts per day, a shorter average standing bout duration and presented themselves to the robot milker more often (Radj2=0.08, F 3,69 = 3.12, P = 0.032). Personality traits constructed from a principle components analysis of the observed NANO behaviours were also associated with home pen activity. Cows which scored highly on the first component termed ‘neophobia’ were older, had more lying bouts and a greater variation in the duration of their average lying bout (Radj2=0.15, F 3,75 = 5.32, P = 0.002) while cows which scored highly on the second component termed ‘boldness’ were older cows with less variation in their average lying bout duration (Radj2=0.11, F2,75 = 5.63, P = 0.005). To conclude, significant relationships exist between behaviours in short-term personality tests and home pen activity recorded over several weeks. As fearfulness is reflected in spontaneous home pen behaviours, activity databases could be incorporated into models predicting fearfulness and welfare assessment protocols.
    Genomic selection for feed efficiency in dairy cattle
    Pryce, J.E. ; Wales, W.J. ; Haas, Y. de; Veerkamp, R.F. ; Hayes, B.J. - \ 2014
    Animal 8 (2014)01. - ISSN 1751-7311 - p. 1 - 10.
    body condition score - dry-matter intake - 1st 3 lactations - genetic-parameters - beef-cattle - methane production - production traits - energy-balance - live weight - random regression
    Feed is a major component of variable costs associated with dairy systems and is therefore an important consideration for breeding objectives. As a result, measures of feed efficiency are becoming popular traits for genetic analyses. Already, several countries account for feed efficiency in their breeding objectives by approximating the amount of energy required for milk production, maintenance, etc. However, variation in actual feed intake is currently not captured in dairy selection objectives, although this could be possible by evaluating traits such as residual feed intake (RFI), defined as the difference between actual and predicted feed (or energy) intake. As feed intake is expensive to accurately measure on large numbers of cows, phenotypes derived from it are obvious candidates for genomic selection provided that: (1) the trait is heritable; (2) the reliability of genomic predictions are acceptable to those using the breeding values; and (3) if breeding values are estimated for heifers, rather than cows then the heifer and cow traits need to be correlated. The accuracy of genomic prediction of dry matter intake (DMI) and RFI has been estimated to be around 0.4 in beef and dairy cattle studies. There are opportunities to increase the accuracy of prediction, for example, pooling data from three research herds (in Australia and Europe) has been shown to increase the accuracy of genomic prediction of DMI from 0.33 within country to 0.35 using a three-country reference population. Before including RFI as a selection objective, genetic correlations with other traits need to be estimated. Weak unfavourable genetic correlations between RFI and fertility have been published. This could be because RFI is mathematically similar to the calculation of energy balance and failure to account for mobilisation of body reserves correctly may result in selection for a trait that is similar to selecting for reduced (or negative) energy balance. So, if RFI is to become a selection objective, then including it in an overall multi-trait selection index where the breeding objective is net profit is sensible, as this would allow genetic correlations with other traits to be properly accounted for. If genetic parameters are accurately estimated then RFI is a logical breeding objective. If there is uncertainty in these, then DMI may be preferable.
    Variation in phosphorus content of milk from dairy cattle as affected by differences in milk composition
    Klop, G. ; Ellis, J.L. ; Blok, M.C. ; Brandsma, G.G. ; Bannink, A. ; Dijkstra, J. - \ 2014
    The Journal of Agricultural Science 152 (2014)5. - ISSN 0021-8596 - p. 860 - 869.
    environmental-impact - methane production - blood-plasma - beef-cattle - cows - excretion - prediction - magnesium - calcium
    In view of environmental concerns with regard to phosphorus (P) pollution and the expected global P scarcity, there is increasing interest in improving P utilization in dairy cattle. In high-producing dairy cows, P requirements for milk production comprise a significant fraction of total dietary P requirements. Although variation in P content of milk can affect the efficiency of P utilization for milk production (i.e. the fraction of ingested P that is incorporated in milk), this variation is poorly understood. It was hypothesized that the P content of milk is related to both milk protein and milk lactose content, but not necessarily to milk fat content. Three existing experiments comprising individual animal data on milk yield and fat, protein, lactose and P content of milk (in total 278 observations from 121 cows) were analysed to evaluate this hypothesis using a mixed model analysis. The models including the effects of both protein and lactose content of milk yielded better prediction of milk P content in terms of root-mean-square prediction error (RMSPE) and concordance correlation coefficient (CCC) statistics than models with only protein included as prediction variable; however, estimates of effect sizes varied between studies. The inclusion of milk fat content in equations already including protein and lactose did not further improve prediction of milk P content. Equations developed to describe the relationship between milk protein and lactose contents (g/kg) and milk P content (g/kg) were: (Expt 1) P in milk=-0·44(±0·179)+0·0253(±0·00300)×milk protein+0·0133(±0·00382)×milk lactose (RMSPE: 5·2%; CCC: 0·71); (Expt 2) P in milk=-0·26 (±0·347)+0·0174(±0·00328)×milk protein+0·0143 (±0·00611)×milk lactose (RMSPE: 6·3%; CCC: 0·40); and (Expt 3) P in milk=-0·36(±0·255)+0·0131(±0·00230)×milk protein+0·0193(±0·00490)×milk lactose (RMSPE: 6·5%; CCC: 0·55). Analysis of the three experiments combined, treating study as a random effect, resulted in the following equation to describe the same relationship as in the individual study equations: P in milk=-0·64(±0·168)+0·0223(±0·00236)×milk protein+0·0191(±0·00316)×milk lactose (RMSPE: 6·2%; CCC: 0·61). Although significant relationships between milk protein, milk lactose and milk P were found, a considerable portion of the observed variation remained unexplained, implying that factors other than milk composition may affect the P content of milk. The equations developed may be used to replace current fixed milk P contents assumed in P requirement systems for cattle.
    Quantitative trait loci associated with pre-weaning growth in South African Angora goats
    Visser, C. ; Marle-Koster, E. van; Snyman, M.A. ; Bovenhuis, H. ; Crooijmans, R.P.M.A. - \ 2013
    Small Ruminant Research 112 (2013)1-3. - ISSN 0921-4488 - p. 15 - 20.
    genome-wide association - microsatellite markers - genetic-parameters - parentage verification - conformation traits - carcass composition - wool production - fleece traits - merino sheep - beef-cattle
    This study aimed to identify chromosomal regions associated with genetic variation in pre-weaning growth traits in Angora goats. A genome-wide scan was performed by genotyping 1042 offspring from 12 half-sib families using 88 microsatellite caprine markers covering 1368cM. Phenotypes were recorded at birth (BW) and weaning (WW) and analysed using GridQTL software. A total of six putative QTL were detected on six different chromosomes, all at chromosome-wide significance level. Four QTL were identified for BW on CHI 4, 8, 17 and 27 and two QTL for WW on CHI 16 and 19. QTL effects ranged from -0.32 to 0.25 in units of residual standard deviation in different families. Some of these QTL correspond to chromosomes where QTL associated with growth have been identified in other species. These chromosomal segments hold potential to influence weight gain in young goats.
    Genetic parameters for calving and conformation traits in Charolais x Montbéliard and Charolais x Holstein crossbred calves.
    Vallee, A.A.A. ; Arendonk, J.A.M. van; Bovenhuis, H. - \ 2013
    Journal of Animal Science 91 (2013)12. - ISSN 0021-8812 - p. 5582 - 5588.
    beef-cattle - livestock auctions - postnatal-growth - birth-weight - body-weight - model - difficulty - dairy - selection - parities
    Charolais sires can be mated to Montbéliard or Holstein dairy cows to produce crossbred calves sold for meat production. Heritabilities and correlations between traits can differ when they are calculated within Charolais × Montbéliard or within Charolais × Holstein population. Moreover, the genetic correlation between the same trait measured on Charolais × Montbéliard and on Charolais × Holstein crossbred calves is not necessarily unity. The first objective of this study was to estimate heritability and genetic correlation between traits within Charolais × Montbéliard and within Charolais × Holstein population. The second objective was to investigate if those traits are genetically identical between crossbred populations. Traits studied were calving difficulty, birth weight, height, bone thinness, and muscular development. Data included 22,852 Charolais × Montbéliard and 16,012 Charolais × Holstein crossbred calves from 391 Charolais sires. Heritabilities estimated separately within each crossbred population were similar. Stronger genetic correlations were observed in Charolais × Holstein population compared with Charolais × Montbéliard between calving difficulty and height (0.67 vs. 0.54), calving difficulty and bone thinness (0.42 vs. 0.27), birth weight and bone thinness (0.52 vs. 0.20), and birth weight and muscular development (0.41 vs. 0.18). Bivariate analysis considering observations on Charolais × Montbéliard and on Charolais × Holstein as different traits showed that genetic variances and heritabilities were similar for all traits except height. Birth weight and muscular development were genetically identical traits in each crossbred populations, with genetic correlations of 0.96 and 0.99. Genetic correlations were 0.91 for calving difficulty, 0.80 for height, and 0.70 for bone thinness and log-likelihood ratio tests indicated that they were significantly different from 1 (P = 0.01). Results show evidence for reranking of Charolais sires for calving difficulty, height, and bone thinness depending on whether they are mated to Montbéliard or Holstein cows.
    Factors affecting energy and nitrogen efficiency of dairy cows: A meta-analysis
    Phuong, H.N. ; Friggens, N.C. ; Boer, I.J.M. de; Schmidely, P. - \ 2013
    Journal of Dairy Science 96 (2013)11. - ISSN 0022-0302 - p. 7245 - 7259.
    residual feed-intake - milk protein yield - rumen-protected methionine - dry-matter intake - corn-silage - metabolizable protein - dietary-protein - alfalfa silage - beef-cattle - forage
    A meta-analysis was performed to explore the correlation between energy and nitrogen efficiency of dairy cows, and to study nutritional and animal factors that influence these efficiencies, as well as their relationship. Treatment mean values were extracted from 68 peer-reviewed studies, including 306 feeding trials. The main criterion for inclusion of a study in the meta-analysis was that it reported, or permitted calculation of, energy efficiency (Eeff; energy in milk/digestible energy intake) and nitrogen efficiency (Neff; nitrogen in milk/digestible nitrogen intake) at the digestible level (digestible energy or digestible protein). The effect of nutritional and animal variables, including neutral detergent fiber, acid detergent fiber (ADF), digestible energy, digestible protein, proportion of concentrate (PCO), dry matter intake, milk yield, days in milk, and body weight, on Eeff, Neff, and the Neff:Eeff ratio was analyzed using mixed models. The interstudy correlation between Eeff and Neff was 0.62, whereas the intrastudy correlation was 0.30. The higher interstudy correlation was partly due to milk yield and dry matter intake being present in both Eeff and Neff. We, therefore, also explored the Neff:Eeff ratio. Energy efficiency was negatively associated with ADF and PCO, whereas Neff was negatively associated with ADF and digestible energy. The Neff:Eeff ratio was affected by ADF and PCO only. In conclusion, the results indicate a possibility to maximize feed efficiency in terms of both energy and nitrogen at the same time. In other words, an improvement in Eeff would also mean an improvement in Neff. The current study also shows that these types of transverse data are not sufficient to study the effect of animal factors, such as days in milk, on feed efficiency. Longitudinal measurements per animal would probably be more appropriate
    Behavioural and physiological responses of heifer calves to acute stressors: Long-term consistency and relationship with adult reactivity to milking
    Reenen, C.G. van; Werf, J.T.N. van der; O'Connell, N.E. ; Heutinck, L.F.M. ; Spoolder, H.A.M. ; Jones, R.B. ; Koolhaas, J.M. ; Blokhuis, H.J. - \ 2013
    Applied Animal Behaviour Science 147 (2013)1-2. - ISSN 0168-1591 - p. 55 - 68.
    individual coping characteristics - t-maze behavior - open-field test - dairy-cows - feather pecking - japanese-quail - beef-cattle - laying hens - fear tests - pigs
    The present study investigated the long-term consistency of individual differences in dairy cattles’ responses in tests of behavioural and hypothalamo–pituitary–adrenocortical (HPA) axis reactivity, as well as the relationship between responsiveness in behavioural tests and the reaction to first milking. Two cohorts of heifer calves, Cohorts 1 (N = 25) and 2 (N = 16), respectively, were examined longitudinally from the rearing period until adulthood. Cohort 1 heifers were subjected to open field (OF), novel object (NO), restraint, and response to a human tests at 7 months of age, and were again observed in an OF test during first pregnancy between 22 and 24 months of age. Subsequently, inhibition of milk ejection and stepping and kicking behaviours were recorded in Cohort 1 heifers during their first machine milking. Cohort 2 heifers were individually subjected to OF and NO tests as well as two HPA axis reactivity tests (determining ACTH and/or cortisol response profiles after administration of exogenous CRH and ACTH, respectively) at 6 months of age and during first lactation at approximately 29 months of age. Principal component analysis (PCA) was used to condense correlated response measures (to behavioural tests and to milking) within ages into independent dimensions underlying heifers’ reactivity. Heifers demonstrated consistent individual differences in locomotion and vocalisation during an OF test from rearing to first pregnancy (Cohort 1) or first lactation (Cohort 2). Individual differences in struggling in a restraint test at 7 months of age reliably predicted those in OF locomotion during first pregnancy in Cohort 1 heifers. Cohort 2 animals with high cortisol responses to OF and NO tests and high avoidance of the novel object at 6 months of age also exhibited enhanced cortisol responses to OF and NO tests at 29 months of age. Measures of HPA axis reactivity, locomotion, vocalisation and adrenocortical and behavioural responses to novelty were largely uncorrelated, supporting the idea that stress responsiveness in dairy cows is mediated by multiple independent underlying traits. Inhibition of milk ejection and stepping and kicking behaviours during first machine milking were not related to earlier struggling during restraint, locomotor responses to OF and NO tests, or the behavioural interaction with a novel object. Heifers with high rates of OF and NO vocalisation and short latencies to first contact with the human at 7 months of age exhibited better milk ejection during first machine milking. This suggests that low underlying sociality might be implicated in the inhibition of milk ejection at the beginning of lactation in heifers.
    Whole-genome regression and prediction methods applied to plant and animal breeding
    Los Campos, G. De; Hickey, J.M. ; Pong-Wong, R. ; Daetwyler, H.D. ; Calus, M.P.L. - \ 2013
    Genetics 193 (2013)2. - ISSN 0016-6731 - p. 327 - 345.
    marker-assisted selection - quantitative trait locus - genetic-relationship information - single nucleotide polymorphisms - linear unbiased prediction - dense molecular markers - dairy-cattle - variable selection - reference population - beef-cattle
    Genomic-enabled prediction is becoming increasingly important in animal and plant breeding, and is also receiving attention in human genetics. Deriving accurate predictions of complex traits requires implementing whole-genome regression (WGR) models where phenotypes are regressed on thousands of markers concurrently. Following the groundbreaking contribution of MEUWISSEN et al. (2001) several methods have been proposed and evaluated, and genome-enabled selection (GS) is being implemented in several plant and animal breeding programs. The list of methods is long, and the relationships between the available methods have not been fully addressed. In this article we provide an overview of available methods for implementing parametric WGR models, discuss selected topics which emerge in the application of these methods and present a general discussion of lessons learnt from simulation and empirical data analysis in the last decade
    Feeding behavior and stress response explain individual differences in feed efficiency in juveniles of Nile tilapia Oreochromis niloticus
    Martins, C.I. ; Conceição, L.E.C. ; Schrama, J.W. - \ 2011
    Aquaculture 312 (2011)1-4. - ISSN 0044-8486 - p. 192 - 197.
    catfish clarias-gariepinus - salmon salmo-salar - beef-cattle - atlantic salmon - rainbow-trout - growth-performance - genetic-variation - metabolic differences - food-consumption - body-composition
    Feed efficiency is a trait of enormous importance in any animal production sector including aquaculture. Individuals that are more feed efficient need to use less feed to achieve similar growth rates as compared to less efficient individuals. Considering that feed represents the largest cost of production and one of the main causes for the ecological footprint of a farm, more knowledge on the extent of individual differences in feed efficiency and underlying physiological processes are needed. This study is the first to investigate individual differences in feed efficiency, measured as residual feed intake and its relationship with feeding behaviour and stress response in one of the most important farmed fish, the Nile tilapia. The individual feed intake of twenty-four juvenile of Nile tilapia was followed during 57 days. Fish were fed until apparent satiation with a commercial feed twice per day. Individual feed behavior was registered once per week and consisted on measuring the latency to start feeding (LAT, min), total feeding time (TFT, min) and the number of feeding acts (NFA, min). Blood samples for plasma cortisol was taken at the end of the experiment (control, indicative of undisturbed levels) and after a stress test (netting), 15 days after the previous sampling. Individual growth rates and residual feed intake were determined at the end of the experiment. Results show pronounced individual differences in residual feed intake as well as a significant correlation with both feeding behavior (feeding latency, total feeding time and number of feeding acts) and stress (cortisol) response. Cortisol levels obtained after the stress test and feeding behavior could explain differences in residual feed intake by 4%. These results show that individuals with higher feeding activity and higher cortisol response are less efficient fish. This suggests that individual differences in feeding activity and stress response explain part of the differences in feed efficiency by explaining variance in maintenance energy expenditure.
    Genetic parameters for predicted methane production and potential for reducing enteric emissions through genomic selection
    Haas, Y. de; Windig, J.J. ; Calus, M.P.L. ; Dijkstra, J. ; Haan, M.H.A. de; Bannink, A. ; Veerkamp, R.F. - \ 2011
    Journal of Dairy Science 94 (2011)12. - ISSN 0022-0302 - p. 6122 - 6134.
    residual feed-intake - dairy-cows - energy-balance - milk-yield - rumen fermentation - beef-cattle - efficiency - ruminants - information - mitigation
    Mitigation of enteric methane (CH4) emission in ruminants has become an important area of research because accumulation of CH4 is linked to global warming. Nutritional and microbial opportunities to reduce CH4 emissions have been extensively researched, but little is known about using natural variation to breed animals with lower CH4 yield. Measuring CH4 emission rates directly from animals is difficult and hinders direct selection on reduced CH4 emission. However, improvements can be made through selection on associated traits (e.g., residual feed intake, RFI) or through selection on CH4 predicted from feed intake and diet composition. The objective was to establish phenotypic and genetic variation in predicted CH4 output, and to determine the potential of genetics to reduce methane emissions in dairy cattle. Experimental data were used and records on daily feed intake, weekly body weights, and weekly milk production were available from 548 heifers. Residual feed intake (MJ/d) is the difference between net energy intake and calculated net energy requirements for maintenance as a function of body weight and for fat- and protein-corrected milk production. Predicted methane emission (PME; g/d) is 6% of gross energy intake (Intergovernmental Panel on Climate Change methodology) corrected for energy content of methane (55.65 kJ/g). The estimated heritabilities for PME and RFI were 0.35 and 0.40, respectively. The positive genetic correlation between RFI and PME indicated that cows with lower RFI have lower PME (estimates ranging from 0.18 to 0.84). Hence, it is possible to decrease the methane production of a cow by selecting more-efficient cows, and the genetic variation suggests that reductions in the order of 11 to 26% in 10 yr are theoretically possible, and could be even higher in a genomic selection program. However, several uncertainties are discussed; for example, the lack of true methane measurements (and the key assumption that methane produced per unit feed is not affected by RFI level), as well as the limitations of predicting the biological consequences of selection. To overcome these limitations, an international effort is required to bring together data on feed intake and methane emissions of dairy cows.
    Dietary inclusion of diallyl disulfide, yucca powder, calcium fumarate, an extruded linseed product, or medium-chain fatty acids does not affect methane production in lactating dairy cows
    Zijderveld, S.M. van; Dijkstra, J. ; Perdok, H.B. ; Newbold, J.R. ; Gerrits, W.J.J. - \ 2011
    Journal of Dairy Science 94 (2011)6. - ISSN 0022-0302 - p. 3094 - 3104.
    production in-vitro - rumen microbial fermentation - ruminal fermentation - linolenic acids - essential oils - beef-cattle - garlic oil - metaanalysis - metabolism - schidigera
    Two similar experiments were conducted to assess the effect of diallyl disulfide (DADS), yucca powder (YP), calcium fumarate (CAFU), an extruded linseed product (UNSAT), or a mixture of capric and caprylic acid (MCFA) on methane production, energy balance, and dairy cow performance. In experiment 1, a control diet (CON1) and diets supplemented with 56 mg of DADS/kg of dry matter (DM), 3g of YP/kg of DM, or 25 g of CAFU/kg of DM were evaluated. In experiment 2, an inert saturated fat source in the control diet (CON2) was exchanged isolipidically for an extruded linseed source (100g/kg of DM; UNSAT) or a mixture of C8:0 and C10:0 (MCFA; 20.3g/kg of DM). In experiment 2, a higher inclusion level of DADS (200mg/kg of DM) was also tested. Both experiments were conducted using 40 lactating Holstein-Friesian dairy cows. Cows were adapted to the diet for 12 d and were subsequently kept in respiration chambers for 5 d to evaluate methane production, diet digestibility, energy balance, and animal performance. Feed intake was restricted to avoid confounding effects of possible differences in ad libitum feed intake on methane production. Feed intake was, on average, 17.5 and 16.6 kg of DM/d in experiments 1 and 2, respectively. None of the additives reduced methane production in vivo. Methane production in experiment 1 was 450, 453, 446, and 423 g/d for CON1 and the diets supplemented with DADS, YP, and CAFU, respectively. In experiment 2, methane production was 371, 394, 388, and 386 g/d for CON2 and the diets supplemented with UNSAT, MCFA, and DADS, respectively. No effects of the additives on energy balance or neutral detergent fiber digestibility were observed. The addition of MCFA increased milk fat content (5.38% vs. 4.82% for control) and fat digestibility (78.5% vs. 59.8% for control), but did not affect milk yield or other milk components. The other products did not affect milk yield or composition. Results from these experiments emphasize the need to confirm methane reductions observed in vitro with in vivo data.
    SIMSDAIRY: A modelling framework to identify sustainable dairy farms in the UK. Framework description and test for organic systems and N fertiliser optimisation
    Prado, A. Del; Misselbrook, T. ; Chadwick, D. ; Hopkins, A. ; Dewhurst, R.J. ; Davison, P. ; Butler, A. ; Schroder, J.J. ; Scholefield, D. - \ 2011
    Science of the Total Environment 409 (2011)19. - ISSN 0048-9697 - p. 3993 - 4009.
    conjugated linoleic-acid - greenhouse-gas emissions - polyunsaturated fatty-acids - life-cycle assessment - ruminant livestock systems - dietary fish-oil - milk-fat - methane production - beef-cattle - agricultural catchments
    Multiple demands are placed on farming systems today. Society, national legislation and market forces seek what could be seen as conflicting outcomes from our agricultural systems, e.g. food quality, affordable prices, a healthy environmental, consideration of animal welfare, biodiversity etc., Many of these demands, or desirable outcomes, are interrelated, so reaching one goal may often compromise another and, importantly, pose a risk to the economic viability of the farm. SIMSDAIRY, a farm-scale model, was used to explore this complexity for dairy farm systems. SIMSDAIRY integrates existing approaches to simulate the effect of interactions between farm management, climate and soil characteristics on losses of nitrogen, phosphorus and carbon. The effects on farm profitability and attributes of biodiversity, milk quality, soil quality and animal welfare are also included. SIMSDAIRY can also be used to optimise fertiliser N. In this paper we discuss some limitations and strengths of using SIMSDAIRY compared to other modelling approaches and propose some potential improvements. Using the model we evaluated the sustainability of organic dairy systems compared with conventional dairy farms under non-optimised and optimised fertiliser N use. Model outputs showed for example, that organic dairy systems based on grass-clover swards and maize silage resulted in much smaller total GHG emissions per l of milk and slightly smaller losses of NO3 leaching and NOx emissions per l of milk compared with the grassland/maize-based conventional systems. These differences were essentially because the conventional systems rely on indirect energy use for ‘fixing’ N compared with biological N fixation for the organic systems. SIMSDAIRY runs also showed some other potential benefits from the organic systems compared with conventional systems in terms of financial performance and soil quality and biodiversity scores. Optimisation of fertiliser N timings and rates showed a considerable scope to reduce the (GHG emissions per l milk too).
    A single nucleotide polymorphism set for paternal identification to reduce the costs of trait recording in commercial pig breeding
    Harlizius, B. ; Lopes, M.S. ; Duijvesteijn, N. ; Goor, L.H.P.V. van der; Haeringen, W.A. van; Panneman, H. ; Guimaraes, S.E.F. ; Merks, J.W.M. ; Knol, E.F. - \ 2011
    Journal of Animal Science 89 (2011)6. - ISSN 0021-8812 - p. 1661 - 1668.
    parentage exclusion - beef-cattle - snp markers - traceability - probability - population - selection - pedigree - number - impact
    In animal breeding, recording of correct pedigrees is essential to achieve genetic progress. Markers on DNA are useful to verify the on-farm pedigree records (parental verification) but can also be used to assign parents retrospectively (parental identification). This approach could reduce the costs of recording for traits with low incidence, such as those related to diseases or mortality. In this study, SNP were used to assign the true sires of 368 purebred animals from a Duroc-based sire line and 140 crossbred offspring from a commercial pig population. Some of the sires were closely related. There were 3 full sibs and 17 half sibs among the true fathers and 4 full sibs and 35 half sibs among all putative fathers. To define the number of SNP necessary, 5 SNP panels (40, 60, 80, 100, and 120 SNP) were assembled from the Illumina PorcineSNP60 Beadchip (Illumina, San Diego, CA) based on minor allele frequency (>0.3), high genotyping call rate (=90%), and equal spacing across the genome. For paternal identification considering only the 66 true sires in the data set, 60 SNP resulted in 100% correct assignment of the sire. By including additional putative sires (n = 304), 80 SNP were sufficient for 100% correct assignment of the sire. The following criteria were derived to identify the correct sire for the current data set: the logarithm of odds (LOD) score for assigning the correct sire was =5, the number of mismatches was =1, and the difference in the LOD score between the first and the second most likely sire was >5. If the correct sire was not present among all putative sires, the mean LOD for the most likely sire was close to zero or negative when using 100 SNP. More SNP would be needed for paternal identification if the number of putative sires increased and the degree of relatedness was greater than in the data set used here. The threshold for the number of mismatches can be adjusted according to the practical situation to account for the trade-off between false negatives and false positives. The latter can be avoided efficiently, ensuring that the correct father is being sampled. Nevertheless, a restriction on the number of putative sires is advisable to reduce the risk of assigning close relatives.
    Effects of a combination of feed additives on methane production, diet digestibility, and animal performance in lactating dairy cows
    Zijderveld, S.M. van; Fonken, B.C.J. ; Dijkstra, J. ; Gerrits, W.J.J. ; Perdok, H.B. ; Fokkink, W.B. ; Newbold, J.R. - \ 2011
    Journal of Dairy Science 94 (2011)3. - ISSN 0022-0302 - p. 1445 - 1454.
    chain fatty-acids - ruminal methanogenesis - fumaric-acid - beef-cattle - coconut oil - linseed oil - extruded linseed - detergent fiber - myristic acid - crude linseed
    Two experiments were conducted to assess the effects of a mixture of dietary additives on enteric methane production, rumen fermentation, diet digestibility, energy balance, and animal performance in lactating dairy cows. Identical diets were fed in both experiments. The mixture of feed additives investigated contained lauric acid, myristic acid, linseed oil, and calcium fumarate. These additives were included at 0.4, 1.2, 1.5, and 0.7% of dietary dry matter, respectively (treatment ADD). Experimental fat sources were exchanged for a rumen inert source of fat in the control diet (treatment CON) to maintain isolipidic rations. Cows (experiment 1, n = 20; experiment 2, n = 12) were fed restricted amounts of feed to avoid confounding effects of dry matter intake on methane production. In experiment 1, methane production and energy balance were studied using open-circuit indirect calorimetry. In experiment 2, 10 rumen-fistulated animals were used to measure rumen fermentation characteristics. In both experiments animal performance was monitored. The inclusion of dietary additives decreased methane emissions (g/d) by 10%. Milk yield and milk fat content tended to be lower for ADD in experiment 1. In experiment 2, milk production was not affected by ADD, but milk fat content was lower. Fat- and protein-corrected milk was lower for ADD in both experiments. Milk urea nitrogen content was lowered by ADD in experiment 1 and tended to be lower in experiment 2. Apparent total tract digestibility of fat, but not that of starch or neutral detergent fiber, was higher for ADD. Energy retention did not differ between treatments. The decrease in methane production (g/d) was not evident when methane emission was expressed per kilogram of milk produced. Feeding ADD resulted in increases of C12:0 and C14:0 and the intermediates of linseed oil biohydrogenation in milk in both experiments. In experiment 2, ADD-fed cows tended to have a decreased number of protozoa in rumen fluid when compared with that in control cows. Total volatile fatty acid concentrations were lower for ADD, whereas molar proportions of propionate increased at the expense of acetate and butyrate
    Evaluation of enteric methane prediction equations for dairy cows used in whole farm models
    Ellis, J.L. ; Bannink, A. ; France, J. ; Kebreab, E. ; Dijkstra, J. - \ 2010
    Global Change Biology 16 (2010)12. - ISSN 1354-1013 - p. 3246 - 3256.
    ruminant livestock systems - greenhouse-gas emissions - energy value - lactation response - mechanistic model - physical form - holstein cows - beef-cattle - corn grain - rumen
    The importance of evaluating greenhouse gas (GHG) emissions from dairy cows within the whole farm setting is being realized as more important than evaluating these emissions in isolation. Current whole farm models aimed at evaluating GHG emissions make use of simple regression equations to predict enteric methane (CH4) production. The objective of the current paper is to evaluate the performance of nine CH4 prediction equations that are currently being used in whole farm GHG models. Data used to evaluate the prediction equations came from a collection of individual (IND) and treatment averaged (TRT) data. Equations were compared based on mean square prediction error (MSPE) and concordance correlation coefficient (CCC) analysis. In general, predictions were poor, with root MSPE (as a percentage of observed mean) values ranging from 20.2 to 52.5 for the IND database and from 24.0 to 38.2 for the TRT database and CCC values ranging from 0.009 to 0.493 for the IND database and from 0.000 to 0.271 for the TRT database. Overall, the equations of Moe & Tyrrell and IPCC Tier II performed best on the IND dataset, and the equations of Moe & Tyrrell and Kirchgeßner et al., performed best on the TRT dataset. Results show that the simple more generalized equations performed worse than those that attempted to represent important aspects of diet composition, but in general significant amounts of bias and deviation of the regression slope from unity existed for all equations. The low prediction accuracy of CH4 equations in whole farm models may introduce substantial error into inventories of GHG emissions and lead to incorrect mitigation recommendations.
    Prevalence and risk factors for bruises in Chilean bovine carcasses
    Strappini, A.C. ; Frankena, K. ; Metz, J.H.M. ; Kemp, B. - \ 2010
    Meat Science 86 (2010)3. - ISSN 0309-1740 - p. 859 - 864.
    pre-slaughter - meat quality - beef-cattle - behavior - transport - classification - welfare - bulls - time
    Records of cattle slaughtered at two Chilean slaughterhouses (SLH1 and SLH2) were used to determine prevalence and risk factors for carcasses with bruises. Bruise prevalence amounted to 12.3% but differed between slaughterhouses (20.8% for SLH1 and 8.6% for SLH2 respectively). Bruise severity grade 1 (mild) was most frequently recorded. The type of the animal, source of animal, the level of fat cover and lairage time were associated with the presence of bruises. Older categories of animals and animals that pass through a market before being moved to the slaughterhouse are more prone to show bruises. The results also indicate that under the reported Chilean circumstances animals that have longer lairage times (over 12h) have a significantly reduced risk for bruises, except for oxen. Presence of bruises is also significantly associated with increased carcass pH values
    On-farm welfare and estimated daily carcass gain of slaughtered bulls
    Herva, T. ; Virtala, A.M. ; Huuskonen, A. ; Saatkamp, H.W. ; Peltoniemi, O. - \ 2009
    Acta Agriculturae Scandinavica Section A-Animal Science 59 (2009)2. - ISSN 0906-4702 - p. 104 - 120.
    space allowance - grass-silage - beef-cattle - feed-intake - growing cattle - rumen fermentation - finishing steers - housing systems - diet digestion - meat quality
    Welfare of growing bulls was evaluated using on-farm scoring modified by well-described test theory methods. Production parameters of the bulls were collected at slaughter. A positive relationship was observed between on-farm welfare, using the full A-Index score, and daily carcass gain of bulls. This association was not observed with the more consistently defined welfare using the partial A-Index with selected items. Space allowance, feeding method, ration formulation and dehorning status at group level were the most important measured factors associated with daily carcass gain of the bulls. Given this association and the cohort design of the study, it is hypothesised that there is a causative relationship between the underlying welfare concept and daily carcass gain.
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