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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    Can greenhouse gases in breath be used to genetically improve feed efficiency of dairy cows?
    Difford, G.F. ; Løvendahl, P. ; Veerkamp, R.F. ; Bovenhuis, H. ; Visker, M.H.P.W. ; Lassen, J. ; Haas, Y. de - \ 2020
    Journal of Dairy Science 103 (2020)3. - ISSN 0022-0302 - p. 2442 - 2459.
    breath gas measurement - carbon dioxide - feed efficiency - methane - residual feed intake

    There is considerable interest in improving feed utilization of dairy cattle while limiting losses to the environment (i.e., greenhouse gases, GHG). To breed for feed-efficient or climate-friendly cattle, it is first necessary to obtain accurate estimates of genetic parameters and correlations of feed intake, greenhouse gases, and production traits. Reducing dry matter take (DMI) requirements while maintaining production has high economic value to farmers, but DMI is costly to record and thus limited to small research or nucleus herds. Conversely, enteric methane (CH4) currently has no economic value, is also costly to record, and is limited to small experimental trials. However, breath gas concentrations of methane (CH4c) and carbon dioxide (CO2c) are relatively cheap to measure at high throughput under commercial conditions by installing sniffers in automated milking stations. The objective of this study was to assess the genetic correlations between DMI, body weight (BW), fat- and protein-corrected milk yield (FPCM), and GHG-related traits: CH4c and CO2c from Denmark (DNK) and the Netherlands (NLD). A second objective was to assess the genetic potential for improving feed efficiency and the added benefits of using CH4c and CO2c as indicators. Feed intake data were available on 703 primiparous cows in DNK and 524 in NLD; CH4c and CO2c records were available on 434 primiparous cows in DNK and 656 in NLD. The GHG-related traits were heritable (e.g., CH4c h2: DNK = 0.26, NLD = 0.15) but were differentially genetically correlated with DMI and feed efficiency in both magnitude and sign, depending on the population and the definition of feed efficiency. Across feed efficiency traits and DMI, having bulls with 100 daughters with FPCM, BW, and GHG traits resulted in sufficiently high accuracy to almost negate the need for DMI records. Despite differences in genetic correlation structure, the relatively cheap GHG-related traits showed considerable potential for improving the accuracy of breeding values of highly valuable feed intake and feed efficiency traits.

    Multi-population GWAS and enrichment analyses reveal novel genomic regions and promising candidate genes underlying bovine milk fatty acid composition
    Gebreyesus, Grum ; Buitenhuis, A.J. ; Poulsen, Nina A. ; Visker, Marleen ; Zhang, Q. ; Valenberg, Hein van; Sun, Dengsheng ; Bovenhuis, Henk - \ 2019
    Wageningen University and Research
    Milk fatty acids - Multi-population GWAS - Candidate genes - Pathway analysis
    The power of genome-wide association studies (GWAS) is often limited by the sample size available for the analysis. Milk fatty acid (FA) traits are scarcely recorded due to expensive and time-consuming analytical techniques. Combining multi-population datasets can enhance the power of GWAS enabling detection of genomic region explaining medium to low proportions of the genetic variation. GWAS often detect broader genomic regions containing several positional candidate genes making it difficult to untangle the causative candidates. Post-GWAS analyses with data on pathways, ontology and tissue-specific gene expression status might allow prioritization among positional candidate genes. Results Multi-population GWAS for 16 FA traits quantified using gas chromatography (GC) in sample populations of the Chinese, Danish and Dutch Holstein with high-density (HD) genotypes detects 56 genomic regions significantly associated to at least one of the studied FAs; some of which have not been previously reported. Pathways and gene ontology (GO) analyses suggest promising candidate genes on the novel regions including OSBPL6 and AGPS on Bos taurus autosome (BTA) 2, PRLH on BTA 3, SLC51B on BTA 10, ABCG5/8 on BTA 11 and ALG5 on BTA 12. Novel genes in previously known regions, such as FABP4 on BTA 14, APOA1/5/7 on BTA 15 and MGST2 on BTA 17, are also linked to important FA metabolic processes. Conclusion Integration of multi-population GWAS and enrichment analyses enabled detection of several novel genomic regions, explaining relatively smaller fractions of the genetic variation, and revealed highly likely candidate genes underlying the effects. Detection of such regions and candidate genes will be crucial in understanding the complex genetic control of FA metabolism. The findings can also be used to augment genomic prediction models with regions collectively capturing most of the genetic variation in the milk FA traits.
    Comparison of methods to measure methane for use in genetic evaluation of dairy cattle
    Garnsworthy, Philip C. ; Difford, Gareth F. ; Bell, Matthew J. ; Bayat, Ali R. ; Huhtanen, Pekka ; Kuhla, Björn ; Lassen, Jan ; Peiren, Nico ; Pszczola, Marcin ; Sorg, Diana ; Visker, Marleen H.P.W. ; Yan, Tianhai - \ 2019
    Animals 9 (2019)10. - ISSN 2076-2615
    Dairy cows - Environment - Genetic evaluation - Greenhouse gases - Methane

    Partners in Expert Working Group WG2 of the COST Action METHAGENE have used several methods for measuring methane output by individual dairy cattle under various environmental conditions. Methods included respiration chambers, the sulphur hexafluoride (SF6) tracer technique, breath sampling during milking or feeding, the GreenFeed system, and the laser methane detector. The aim of the current study was to review and compare the suitability of methods for large-scale measurements of methane output by individual animals, which may be combined with other databases for genetic evaluations. Accuracy, precision and correlation between methods were assessed. Accuracy and precision are important, but data from different sources can be weighted or adjusted when combined if they are suitably correlated with the ‘true’ value. All methods showed high correlations with respiration chambers. Comparisons among alternative methods generally had lower correlations than comparisons with respiration chambers, despite higher numbers of animals and in most cases simultaneous repeated measures per cow per method. Lower correlations could be due to increased variability and imprecision of alternative methods, or maybe different aspects of methane emission are captured using different methods. Results confirm that there is sufficient correlation between methods for measurements from all methods to be combined for international genetic studies and provide a much-needed framework for comparing genetic correlations between methods should these become available.

    Improving disease resistance in chickens: divergent selection on natural antibodies
    Berghof, T.V.L. ; Poel, J.J. van der; Arts, J.A.J. ; Bovenhuis, H. ; Visker, M.H.P.W. ; Parmentier, H.K. - \ 2019
    - p. 507 - 507.
    Natural antibodies (NAb) are antibodies recognizing antigens without previous exposure to this antigen. Keyhole limpet hemocyanin (KLH)-binding NAb titers in chickens are heritable, and higher KLH-binding NAb titers have been associated with higher survival. This suggests that breeding for higher NAb titers might improve general disease resistance. A purebred White Leghorn chicken line was divergently selected and bred on total KLH-binding NAb titers at 16 weeks of age for 6 generations, and resulted in a High and Low line. The average estimated breeding value differences in KLH-binding NAb titers increased with 0.36 for total, 0.40 for IgM, and 0.32 for IgG per generation. Generations 4 and 6 of the selection lines were inoculated with an avian pathogenic Escherichia coli (APEC) at 8 days of age. Mortality and morbidity after 1 week were signicantly reduced in the High line compared to the Low line, which suggests a higher APEC resistance in the High line compared to the Low line. To investigate possible correlated responses on the immune system, several traits were measured at different ages in several generations: the High line showed higher different NAb titers at different ages, antibody concentrations, percentage of antibody-producing B cells, and bursa weight at young age compared to the Low line. This suggests that KLH-binding NAb selection has a favourable correlated response on the humoral adaptive immune system. No line differences were observed for T cells, γδ T cells, natural killer (NK) cells, and antigen-presenting cells (APC). This might indicate that the selection had no unfavourable correlated responses on other parts of the immune system. This selection experiment shows that selective breeding on total KLH-binding NAb titers at 16 weeks of age is possible, and that selection for higher NAb has a benecial effect on resistance to APEC infection. In addition, the selection experiment suggests a promising opportunity for improving general disease resistance without unfavourable correlated selection responses.
    Combining multi-population datasets for joint genome-wide association and meta-analyses: The case of bovine milk fat composition traits
    Gebreyesus, G. ; Buitenhuis, A.J. ; Poulsen, N.A. ; Visker, M.H.P.W. ; Zhang, Q. ; Valenberg, H.J.F. van; Sun, D. ; Bovenhuis, H. - \ 2019
    Journal of Dairy Science 102 (2019)12. - ISSN 0022-0302 - p. 11124 - 11141.
    mega-analysis - meta-analysis - multi-population GWAS

    In genome-wide association studies (GWAS), sample size is the most important factor affecting statistical power that is under control of the investigator, posing a major challenge in understanding the genetics underlying difficult-to-measure traits. Combining data sets available from different populations for joint or meta-analysis is a promising alternative to increasing sample sizes available for GWAS. Simulation studies indicate statistical advantages from combining raw data or GWAS summaries in enhancing quantitative trait loci (QTL) detection power. However, the complexity of genetics underlying most quantitative traits, which itself is not fully understood, is difficult to fully capture in simulated data sets. In this study, population-specific and combined-population GWAS as well as a meta-analysis of the population-specific GWAS summaries were carried out with the objective of assessing the advantages and challenges of different data-combining strategies in enhancing detection power of GWAS using milk fatty acid (FA) traits as examples. Gas chromatography (GC) quantified milk FA samples and high-density (HD) genotypes were available from 1,566 Dutch, 614 Danish, and 700 Chinese Holstein Friesian cows. Using the joint GWAS, 28 additional genomic regions were detected, with significant associations to at least 1 FA, compared with the population-specific analyses. Some of these additional regions were also detected using the implemented meta-analysis. Furthermore, using the frequently reported variants of the diacylglycerol acyltransferase 1 (DGAT1) and stearoyl-CoA desaturase (SCD1) genes, we show that significant associations were established with more FA traits in the joint GWAS than the remaining scenarios. However, there were few regions detected in the population-specific analyses that were not detected using the joint GWAS or the meta-analyses. Our results show that combining multi-population data set can be a powerful tool to enhance detection power in GWAS for seldom-recorded traits. Detection of a higher number of regions using the meta-analysis, compared with any of the population-specific analyses also emphasizes the utility of these methods in the absence of raw multi-population data sets to undertake joint GWAS.

    Investigation of a (putative) causal mutation in Toll-like receptor family member 1A in chickens
    Berghof, T.V.L. ; Voogdt, Carlos G.P. ; Arts, J.A.J. ; Bovenhuis, H. ; Parmentier, H.K. ; Poel, J.J. van der; Putten, Jos P.M. Van; Visker, M.H.P.W. - \ 2019
    Multi-population GWAS and enrichment analyses reveal novel genomic regions and promising candidate genes underlying bovine milk fatty acid composition
    Gebreyesus, G. ; Buitenhuis, A.J. ; Poulsen, N.A. ; Visker, M.H.P.W. ; Zhang, Q. ; Valenberg, H.J.F. Van; Sun, D. ; Bovenhuis, H. - \ 2019
    BMC Genomics 20 (2019)1. - ISSN 1471-2164
    Candidate genes - Milk fatty acids - Multi-population GWAS - Pathway analysis

    Background: The power of genome-wide association studies (GWAS) is often limited by the sample size available for the analysis. Milk fatty acid (FA) traits are scarcely recorded due to expensive and time-consuming analytical techniques. Combining multi-population datasets can enhance the power of GWAS enabling detection of genomic region explaining medium to low proportions of the genetic variation. GWAS often detect broader genomic regions containing several positional candidate genes making it difficult to untangle the causative candidates. Post-GWAS analyses with data on pathways, ontology and tissue-specific gene expression status might allow prioritization among positional candidate genes. Results: Multi-population GWAS for 16 FA traits quantified using gas chromatography (GC) in sample populations of the Chinese, Danish and Dutch Holstein with high-density (HD) genotypes detects 56 genomic regions significantly associated to at least one of the studied FAs; some of which have not been previously reported. Pathways and gene ontology (GO) analyses suggest promising candidate genes on the novel regions including OSBPL6 and AGPS on Bos taurus autosome (BTA) 2, PRLH on BTA 3, SLC51B on BTA 10, ABCG5/8 on BTA 11 and ALG5 on BTA 12. Novel genes in previously known regions, such as FABP4 on BTA 14, APOA1/5/7 on BTA 15 and MGST2 on BTA 17, are also linked to important FA metabolic processes. Conclusion: Integration of multi-population GWAS and enrichment analyses enabled detection of several novel genomic regions, explaining relatively smaller fractions of the genetic variation, and revealed highly likely candidate genes underlying the effects. Detection of such regions and candidate genes will be crucial in understanding the complex genetic control of FA metabolism. The findings can also be used to augment genomic prediction models with regions collectively capturing most of the genetic variation in the milk FA traits.

    Genome-wide association study for αS1- and αS2-casein phosphorylation in Dutch Holstein Friesian
    Fang, Z.H. ; Bovenhuis, H. ; Valenberg, H.J.F. van; Martin, P. ; Duchemin, S.I. ; Huppertz, T. ; Visker, M.H.P.W. - \ 2019
    Journal of Dairy Science 102 (2019)2. - ISSN 0022-0302 - p. 1374 - 1385.
    milk protein composition - post-translational modification - quantitative trait loci

    Phosphorylation of caseins (CN) is a crucial post-translational modification that allows caseins to form colloid particles known as casein micelles. Both αS1- and αS2-CN show varying degrees of phosphorylation (isoforms) in cow milk and were suggested to be more relevant for stabilizing internal micellar structure than β- and κ-CN. However, little is known about the genetic background of individual αS2-CN phosphorylation isoforms and the phosphorylation degrees of αS1- and αS2-CN (αS1-CN PD and αS2-CN PD), defined as the proportion of isoforms with higher degrees of phosphorylation in total αS1- and αS2-CN, respectively. We aimed to identify genomic regions associated with these traits using 50K single nucleotide polymorphisms for 1,857 Dutch Holstein Friesian cows. A total of 10 quantitative trait loci (QTL) regions were identified for all studied traits on 10 Bos taurus autosomes (BTA1, 2, 6, 9, 11, 14, 15, 18, 24, and 28). Regions associated with multiple traits were found on BTA1, 6, 11, and 14. We showed 2 QTL regions on BTA1, one affecting αS2-CN production and the other harboring the SLC37A1 gene, which encodes a phosphorus antiporter and affects αS1- and αS2-CN PD. The QTL on BTA6 harbors the casein gene cluster and affects individual αS2-CN phosphorylation isoforms. The QTL on BTA11 harbors the PAEP gene that encodes for β-lactoglobulin and affects relative concentrations of αS2-CN-10P and αS2-CN-11P as well as αS1-CN PD and αS2-CN PD. The QTL on BTA14 harbors the DGAT1 gene and affects relative concentrations of αS2-CN-10P and αS2-CN-11P as well as αS1-CN PD and αS2-CN PD. Our results suggest that effects of identified genomic regions on phosphorylation of αS1- and αS2-CN are related to changes in milk synthesis and phosphorus secretion in milk. The actual roles of SLC37A1, PAEP, and DGAT1 in αS1- and αS2-CN phosphorylation in Dutch Holstein Friesian require further investigation.

    Selective breeding for high natural antibody level increases resistance to avian pathogenic Escherichia coli (APEC) in chickens
    Berghof, T.V.L. ; Matthijs, M.G.R. ; Arts, J.A.J. ; Bovenhuis, H. ; Dwars, R.M. ; Poel, J.J. van der; Visker, M.H.P.W. ; Parmentier, H.K. - \ 2019
    Developmental and Comparative Immunology 93 (2019). - ISSN 0145-305X - p. 45 - 57.
    APEC - Breeding - Chicken - Disease resistance - Escherichia coli - Natural antibody

    Keyhole limpet hemocyanin (KLH)-binding natural antibody (NAb) titers in chickens are heritable, and higher levels have previously been associated with a higher survival. This suggests that selective breeding for higher NAb levels might increase survival by means of improved general disease resistance. Chickens were divergently selected and bred for total NAb levels binding KLH at 16 weeks of age for six generations, resulting in a High NAb selection line and a Low NAb selection line. To for test differences in disease resistance, chickens were challenged with avian pathogenic Escherichia coli (APEC) in two separate experiments. Chickens at 8 days of age received one of four intratracheal inoculations of 0.2 mL phosphate buffered saline (PBS): 1) mock inoculate, 2) with 0.2 mL PBS containing 108.20 colony-forming units (CFU)/mL APEC, 3) with 0.2 mL PBS containing 106.64 CFU/mL APEC, and 4) with 0.2 mL PBS containing 107.55 CFU/mL APEC. Mortality was recorded during 7 days post inoculation. Overall, 50–60% reduced mortality was observed in the High line compared to the Low line for all APEC doses. In addition, morbidity was determined of the surviving chickens at 15 days of age. The High line had lower morbidity scores compared to the Low line. We conclude that selective breeding for high KLH-binding NAb levels at 16 weeks of age increase APEC resistance in early life. This study and previous studies support the hypothesis that KLH-binding NAb might be used as an indicator trait for to selective breed for general disease resistance in an antigen non-specific fashion.

    The effect of linseed oil and DGAT1 K232A polymorphism on methane emission, energy and N metabolism, lactation performance ruminal fermentation, and rumen microbial composition of lactating Holstein-Friesian cows
    Gastelen, S. van; Visker, M.H.P.W. ; Edwards, J.E. ; Antunes Fernandes, E.C. ; Hettinga, K.A. ; Alferink, S.J.J. ; Hendriks, W.H. ; Bovenhuis, H. ; Smidt, H. ; Dijkstra, J. - \ 2018
    PRJEB17884 - ERP019788
    The effect of linseed oil, DGAT1 K232A polymorphism, and the interaction between linseed oil and DGAT1 K232A polymorphism on methane (CH4) emission, and on energy and nitrogen (N) metabolism, lactation performance, ruminal fermentation, and rumen microbial composition was investigated. The experiment involved 24 lactating Holstein-Friesian cows (i.e. 12 with DGAT1 KK genotype and 12 with DGAT1 AA genotype), and followed a cross-over design with two dietary treatments: control diet (CON), and linseed oil diet (LSO) with a difference of 22 g/kg dry matter (DM) in fat content between the two diets. Both diets consisted of 40% corn silage, 30% grass silage, and 30% concentrates, on DM basis. Apparent digestibility, lactation performance, N and energy balance, and CH4 emission were measured in climate respiration chambers. The DGAT1 K allele was associated with a lower milk yield, lactose yield, and proportion of poly-unsaturated fatty acids (FA) in milk fat, and a higher milk fat and protein content, and proportion of saturated FA in milk fat compared with the DGAT1 A allele. DGAT1 K232A polymorphism did not affect CH4 or H2 emission, ruminal fermentation or ruminal microbial concentrations. Rumen microbial composition was also unaffected in terms of the whole microbial population, however at the genus level the relative abundances of certain bacterial genera were found to be affected by the DGAT1 K232A polymorphism. The DGAT1 K allele was associated with a lower crude fat digestibility and metabolizability (i.e. ratio of metabolizable to gross energy intake), and with a tendency for a lower gross energy and NDF digestibility, and milk N efficiency compared with the DGAT1 A allele. Diet LSO decreased CH4 production (g/d) by 8%, CH4 yield (g/kg DM intake) by 6%, and CH4 intensity (g/kg fat- and protein-corrected milk) by 11%, but did not affect H2 emission. Diet LSO also decreased ruminal acetate molar proportion, the acetate to propionate ratio, and the archaea to bacteria ratio, whereas ruminal propionate molar proportion and milk N efficiency increased. Ruminal microbial composition tended to be affected by diet in terms of the whole microbial population, with certain bacterial genera found to be significantly affected by diet. These results indicate that the DGAT1 K232A polymorphism does not affect enteric CH4 production and production pathways, but that it does affect traits other than lactation characteristics, including nutrient digestibility, metabolizability, and the relative abundance of certain rumen bacterial genera. Additionally, linseed oil reduces CH4 emission independent of DGAT1 K232A polymorphism and affects the rumen microbiota and its fermentative activity.
    Selective breeding on natural antibodies in chickens: selection response, and correlated responses
    Berghof, T.V.L. ; Poel, J.J. van der; Arts, J.A.J. ; Bovenhuis, H. ; Visker, M.H.P.W. ; Parmentier, H.K. - \ 2018
    Breeding for high natural antibody levels reduces impact of E. coli (APEC) challenge in chickens
    Berghof, T.V.L. ; Matthijs, M.G.R. ; Arts, J.A.J. ; Bovenhuis, H. ; Dwars, R.M. ; Poel, J.J. van der; Parmentier, H.K. ; Visker, M.H.P.W. ; Parmentier, H.K. - \ 2018
    The genetics of phosphorylation of caseins in bovine milk
    Visker, M.H.P.W. ; Fang, F.H. ; Martin, P. ; Bovenhuis, H. - \ 2018
    In: 15th International Symposium Milk Genomics & Human Health. - - p. 23 - 24.
    Genome-wide association study of the de novo synthesized milk fatty acids based on Dutch, Danish and Chinese Holstein Friesians
    Gebreyesus, Grum ; Buitenhuis, Bart ; Poulsen, Nina A. ; Visker, M.H.P.W. ; Zhang, Qianqian ; Valenberg, H.J.F. van; Sun, D. ; Bovenhuis, H. - \ 2018
    In: Proceedings of the World Congress on Genetics Applied to Livestock Production. - WCGALP - 6 p.
    Data for the de novo synthesized milk fatty acids (FAs) were obtained from milk samples of 1736 Dutch, 675 Danish and 784 Chinese Holstein Friesian cows and combined for multipopulation genome-wide association study (GWAS) using a mixed linear model. Results were compared with population specific GWAS undertaken for each population. In the combined analysis, QTL regions spread across 16 chromosomes were found significantly associated with the de novo synthesized FAs. Compared to the population-specific analyses, our multipopulation GWAS resulted in more regions showing significant associations for the de novo synthesized FAs, some of which were not previously reported.
    Candidate gene for natural immune competence in chickens revealed through genome wide association study
    Visker, M.H.P.W. ; Berghof, T.V.L. ; Arts, J.A.J. ; Parmentier, H.K. ; Poel, J.J. van der; Vereijken, Addie ; Bovenhuis, H. - \ 2018
    In: Proceedings of the World Congress on Genetics Applied to Livestock Production. - WCGALP - 4 p.
    Natural antibodies (NAb) are antibodies that are present in individuals without prior exposure to the antigen that they bind. In chickens, NAb have been associated with survival. Furthermore, genetic variation between chickens in NAb levels has been demonstrated. To improve our understanding of the genetic variation for NAb levels in chickens we performed a genome wide association study. A population of 1,628 White Leghorn chickens was investigated. Animals were phenotyped for NAb levels using the antigen keyhole limpet hemocyanin (KLH) as model. Animals were genotyped for 15,579 single nucleotide polymorphisms (SNP). Highly significant association between SNP and NAb levels was observed on chicken chromosome 4. A single SNP was identified as the most likely candidate for this association. Identification of this candidate SNP was based on further analysis with full genome sequence genotypes and on predicted consequences of associated SNP. This candidate SNP causes a phenylalanine to leucine amino acid change in one of the leucine rich repeats in toll-like receptor 1 family member A (TLR1A). Our results suggest an important role for TLR1A in relation to NAb levels in chickens. Further study should confirm the effect of the SNP in TLR1A on NAb levels and on the (natural) immune competence of chickens. Keywords: natural antibodies, toll-like receptor, TLR1A
    Letter to the Editor : A response to Huhtanen and Hristov (2018)
    Bovenhuis, Henk ; Engelen, Sabine van; Visker, Marleen H.P.W. - \ 2018
    Journal of Dairy Science 101 (2018)11. - ISSN 0022-0302 - p. 9621 - 9622.
    Genetic parameters for αS1-casein and αS2-casein phosphorylation isoforms in Dutch Holstein Friesian
    Fang, Z.H. ; Bovenhuis, H. ; Valenberg, H.J.F. van; Martin, P. ; Huppertz, T. ; Visker, M.H.P.W. - \ 2018
    Journal of Dairy Science 101 (2018)2. - ISSN 0022-0302 - p. 1281 - 1291.
    capillary zone electrophoresis - genetic correlation - milk protein composition - posttranslational modification
    Relative concentrations of αS1-casein and αS2-casein (αS1-CN and αS2-CN) phosphorylation isoforms vary considerably among milk of individual cows. We estimated heritabilities for αS2-CN phosphorylation isoforms, determined by capillary zone electrophoresis from 1,857 morning milk samples, and genetic correlations among αS2-CN phosphorylation isoforms in Dutch Holstein Friesian. To investigate if phosphorylation of αS1-CN and αS2-CN are due to the same genetic mechanism, we also estimated genetic correlations between αS1-CN and αS2-CN phosphorylation isoforms as well as the genetic correlations between the phosphorylation degrees (PD) of αS1-CN and αS2-CN defined as the proportion of isoforms with higher degrees of phosphorylation in total αS1-CN and αS2-CN, respectively. The intra-herd heritabilities for the relative concentrations of αS2-CN phosphorylation isoforms were high and ranged from 0.54 for αS2-CN-10P to 0.89 for αS2-CN-12P. Furthermore, the high intra-herd heritabilities of αS1-CN PD and αS2-CN PD imply a strong genetic control of the phosphorylation process, which is independent of casein production. The genetic correlations between αS2-CN phosphorylation isoforms are positive and moderate to high (0.33–0.90). Furthermore, the strong positive genetic correlation (0.94) between αS1-CN PD and αS2-CN PD suggests that the phosphorylation processes of αS1-CN and αS2-CN are related. This study shows the possibility of breeding for specific αS1-CN and αS2-CN phosphorylation isoforms, and relations between the phosphorylation degrees of αS1-CN and αS2-CN and technological properties of milk need to be further investigated to identify potential benefits for the dairy industry.
    The genetic background of methane emission by dairy cows
    Engelen, Sabine van - \ 2018
    Wageningen University. Promotor(en): H. Bovenhuis, co-promotor(en): M.H.P. Visker. - Wageningen : Wageningen University - ISBN 9789463437325 - 144

    Dairy products are important food sources which contain nutrients that are essential for human development and healthy ageing. Greenhouse gasses are formed during the production of dairy of which methane (CH4) emission by dairy cows is the single largest source. A reduction in CH4 emission could be achieved via selective breeding, though this requires genetic variation in CH4 emission. In order to quantify the genetic variation in CH4 emission, 3 different indicators were used. The first indicator was CH4 emission predicted based on milk fatty acids (FA) which were measured using gas chromatography. Different FA based CH4 prediction equations were used and 12 to 44% of the variation was due to genetic differences between cows. The second indicator was CH4 emission measured with breath sensors. The breath of cows was analysed during milking in automatic milking systems. Genetics explained 3 to 12% of the total variation in this CH4 indicator. The third indicator was CH4 emission predicted based on milk mid-infrared (MIR) spectra. Of this indicator, between 17 and 21% of the total variation could be attributed to genetic factors. These results suggest that there is genetic variation in CH4 emission and selective breeding for lower CH4 emission is possible. The correlations between sensor measured CH4 emission and milk MIR predicted CH4 emission were low, indicating that both indicators explain a different part of the variation in true CH4 emission. The accuracy of the estimated breeding values (EBV) of these CH4 indicators confirms this suggestion. Combining information from sensor measured CH­4 emission with milk MIR predicted CH4 emission increases the accuracy of the EBV compared to using them separately. Correlations of sensor measured CH4 emission and milk MIR predicted CH4 emission with breeding goal traits (production and fertility traits) were low to medium. Genetic correlations between CH4 emission and production traits ranged between -0.61 and 0.65, and genetic correlations between CH4 emission and fertility traits ranged between -0.32 and 0.38. These results suggest that inclusion of CH4 emission in the breeding goal has a minor impact on the breeding goal traits studied. These correlations, however, are estimated on relatively small datasets. Increasing the amount of data by using EBV, correlations between the EBV of the CH4 indicators and the EBV of six breeding goal traits were also low to medium. In conclusion, there is a possibility to use selective breeding to reduce CH4 emission by dairy cows with an anticipated minor impact on other breeding goal traits.

    Genetic background of methane emission by Dutch Holstein Friesian cows measured with infrared sensors in automatic milking systems
    Engelen, S. van; Bovenhuis, H. ; Tol, P.P.J. van der; Visker, M.H.P.W. - \ 2018
    Journal of Dairy Science 101 (2018)3. - ISSN 0022-0302 - p. 2226 - 2234.
    AMS - Dairy cow - Methane emission - Nondispersive infrared sensor
    International environmental agreements have led to the need to reduce methane emission by dairy cows. Reduction could be achieved through selective breeding. The aim of this study was to quantify the genetic variation of methane emission by Dutch Holstein Friesian cows measured using infrared sensors installed in automatic milking systems (AMS). Measurements of CH4 and CO2 on 1508 Dutch Holstein Friesian cows located on 11 commercial dairy farms were available. Phenotypes per AMS visit were the mean of CH4, mean of CO2, mean of CH4 divided by mean of CO2, and their log10-transformations. The repeatabilities of the log10-transformated methane phenotypes were 0.27 for CH4, 0.31 for CO2, and 0.14 for the ratio. The log10-transformated heritabilities of these phenotypes were 0.11 for CH4, 0.12 for CO2, and 0.03 for the ratio. These results indicate that measurements taken using infrared sensors in AMS are repeatable and heritable and, thus, could be used for selection for lower CH4 emission. Furthermore, it is important to account for farm, AMS, day of measurement, time of day, and lactation stage when estimating genetic parameters for methane phenotypes. Selection based on log10-transformated CH4 instead of the ratio would be expected to give a greater reduction of CH4 emission by dairy cows.
    Genomic Region Containing Toll-Like Receptor Genes Has a Major Impact on Total IgM Antibodies Including KLH-Binding IgM Natural Antibodies in Chickens
    Berghof, T.V.L. ; Visker, M.H.P.W. ; Arts, J.A.J. ; Parmentier, H.K. ; Poel, J.J. van der; Vereijken, A.L.J. ; Bovenhuis, H. - \ 2018
    Frontiers in Immunology 8 (2018). - ISSN 1664-3224 - 14 p.
    Natural antibodies (NAb) are antigen binding antibodies present in individuals without a previous exposure to this antigen. Keyhole limpet hemocyanin (KLH)-binding NAb levels were previously associated with survival in chickens. This suggests that selective breeding for KLH-binding NAb may increase survival by means of improved general disease resistance. Genome-wide association studies (GWAS) were performed to identify genes underlying genetic variation in NAb levels. The studied population consisted of 1,628 adolescent layer chickens with observations for titers of KLH-binding NAb of the isotypes IgM, IgA, IgG, the total KLH-binding (IgT) NAb titers, total antibody concentrations of the isotypes IgM, IgA, IgG, and the total antibodies concentration in plasma. GWAS were performed using 57,636 single-nucleotide polymorphisms (SNP). One chromosomal region on chromosome 4 was associated with KLH-binding IgT NAb, and total IgM concentration, and especially with KLH-binding IgM NAb. The region of interest was fine mapped by imputing the region of the study population to whole genome sequence, and subsequently performing an association study using the imputed sequence variants. 16 candidate genes were identified, of which FAM114A1, Toll-like receptor 1 family member B (TLR1B), TLR1A, Krüppel-like factor 3 (KLF3) showed the strongest associations. SNP located in coding regions of the candidate genes were checked for predicted changes in protein functioning. One SNP (at 69,965,939 base pairs) received the maximum impact score from two independent prediction tools, which makes this SNP the most likely causal variant. This SNP is located in TLR1A, which suggests a fundamental role of TLR1A on regulation of IgM levels (i.e., KLH-binding IgM NAb, and total IgM concentration), or B cells biology, or both. This study contributes to increased understanding of (genetic) regulation of KLH-binding NAb levels, and total antibody concentrations.
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