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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Morphological and Molecular Characterization of Orchid Fruit Development
Dirks-Mulder, Anita ; Ahmed, I. ; Broek, Mark uit het; Krol, Louie ; Menger, Nino ; Snier, Jasmijn ; Winzum, Anne van; Wolf, Anneke de; Wout, Martijn van 't; Zeegers, Jamie J. ; Butôt, R. ; Heijungs, Reinout ; Heuven, B.J. Van; Kruizinga, Jaco ; Langelaan, Rob ; Smets, E.F. ; Star, W. ; Bemer, M. ; Gravendeel, B. - \ 2019
Frontiers in Plant Science 10 (2019). - ISSN 1664-462X - 18 p.
Efficient seed dispersal in flowering plants is enabled by the development of fruits, which can be either dehiscent or indehiscent. Dehiscent fruits open at maturity to shatter the seeds, while indehiscent fruits do not open and the seeds are dispersed in various ways. The diversity in fruit morphology and seed shattering mechanisms is enormous within the flowering plants. How these different fruit types develop and which molecular networks are driving fruit diversification is still largely unknown, despite progress in eudicot model species. The orchid family, known for its astonishing floral diversity, displays a huge variation in fruit dehiscence types, which have been poorly investigated. We undertook a combined approach to understand fruit morphology and dehiscence in different orchid species to get more insight into the molecular network that underlies orchid fruit development. We describe fruit development in detail for the epiphytic orchid species Erycina pusilla and compare it to two terrestrial orchid species: Cynorkis fastigiata and Epipactis helleborine. Our anatomical analysis provides further evidence for the split carpel model, which explains the presence of three fertile and three sterile valves in most orchid species. Interesting differences were observed in the lignification patterns of the dehiscence zones. While C. fastigiata and E. helleborine develop a lignified layer at the valve boundaries, E. pusilla fruits did not lignify at these boundaries, but formed a cuticle-like layer instead. We characterized orthologs of fruit-associated MADS-domain transcription factors and of the Arabidopsis dehiscence-related genes INDEHISCENT (IND)/HECATE 3 (HEC3), REPLUMLESS (RPL) and SPATULA (SPT)/ALCATRAZ (ALC) in E. pusilla, and found that the key players of the eudicot fruit regulatory network appear well-conserved in monocots. Protein-protein interaction studies revealed that MADS-domain complexes comprised of FRUITFULL (FUL), SEPALLATA (SEP) and AGAMOUS (AG) /SHATTERPROOF (SHP) orthologs can also be formed in E. pusilla, and that the expression of HEC3, RPL, and SPT can be associated with dehiscence zone development similar to Arabidopsis. Our expression analysis also indicates differences, however, which may underlie fruit divergence.
In-situ incubation of a coral patch for community-scale assessment of metabolic and chemical processes on a reef slope
Heuven, Steven M.A.C. van; Webb, Alice E. ; Bakker, Didier M. de; Meesters, Erik ; Duyl, Fleur C. van; Reichart, Gert-Jan ; Nooijer, Lennart J. de - \ 2018
PeerJ 6 (2018). - ISSN 2167-8359
Anthropogenic pressures threaten the health of coral reefs globally. Some of these pressures directly affect coral functioning, while others are indirect, for example by promoting the capacity of bioeroders to dissolve coral aragonite. To assess the Coral reef status, it is necessary to validate community-scale measurements of metabolic and geochemical processes in the field, by determining fluxes from enclosed coral reef patches. Here, we investigate diurnal trends of carbonate chemistry, dissolved organic carbon, oxygen, and nutrients on a 20 m deep coral reef patch offshore from the island of Saba, Dutch Caribbean by means of tent incubations. The obtained trends are related to benthic carbon fluxes by quantifying net community calcification (NCC) and net community production (NCP). The relatively strong currents and swell-induced near-bottom surge at this location caused minor seawater exchange between the incubated reef and ambient water. Employing a compensating
interpretive model, the exchange is used to our advantage as it maintains reasonably ventilated conditions, which conceivably prevents metabolic arrest during incubation periods of multiple hours. No diurnal trends in carbonate chemistry were detected and all net diurnal rates of production were strongly skewed towards respiration suggesting net heterotrophy in all incubations. The NCC inferred from our incubations ranges from -0.2 to 1.4 mmol CaCO3 m-2 h-1 (-0.2 to 1.2 kg CaCO3 m-2 year-1) and NCP varies from -9 to -21.7 mmol m-2 h-1 (net respiration). When comparing to the consensus-based ReefBudget approach, the estimated NCC rate for the incubated full planar area (0.36 kg CaCO3 m-2 year-1) was lower, but still within range of the different NCC inferred from our incubations. Field trials indicate that the tent-based incubation as presented here, coupled with an appropriate interpretive model, is an effective tool to investigate, in situ, the state of coral reef patches even when located in a relatively hydrodynamic environment.
Quantification of chemical and mechanical bioerosion rates of six Caribbean excavating sponge species found on the coral reefs of Curaçao
Bakker, Didier M. de; Webb, Alice E. ; Bogaart, Lisanne A. van den; Heuven, Steven M.A.C. van; Meesters, Erik H. ; Duyl, Fleur C. van - \ 2018
PLoS ONE 13 (2018)5. - ISSN 1932-6203

Excavating sponges are among the most important macro-eroders of carbonate substrates in marine systems. Their capacity to remove substantial amounts of limestone makes these animals significant players that can unbalance the reef carbonate budget of tropical coral reefs. Nevertheless, excavating sponges are currently rarely incorporated in standardized surveys and experimental work is often restricted to a few species. Here were provide chemical and mechanical bioerosion rates for the six excavating sponge species most commonly found on the shallow reef of Curaçao (southern Caribbean): Cliona caribbaea, C. aprica, C. delitrix, C. amplicavata, Siphonodictyon brevitubulatum and Suberea flavolivescens. Chemical, mechanical and total bioerosion rates were estimated based on various experimental approaches applied to sponge infested limestone cores. Conventional standing incubation techniques were shown to strongly influence the chemical dissolution signal. Final rates, based on the change in alkalinity of the incubation water, declined significantly as a function of incubation time. This effect was mitigated by the use of a flow-through incubation system. Additionally, we found that mechanically removed carbonate fragments collected in the flow-through chamber (1 h) as well as a long-term collection method (1 wk) generally yielded comparable estimates for the capacity of these sponges to mechanically remove substratum. Observed interspecific variation could evidently be linked to the adopted boring strategy (i.e. gallery-forming, cavity-forming or network-working) and presence or absence of symbiotic zooxanthellae. Notably, a clear diurnal pattern was found only in species that harbour a dense photosymbiotic community. In these species chemical erosion was substantially higher during the day. Overall, the sum of individually acquired chemical and mechanical erosion using flow-through incubations was comparable to rates obtained gravimetrically. Such consistency is a first in this field of research. These findings support the much needed confirmation that, depending on the scientific demand, the different approaches presented here can be implemented concurrently as standardized methods.

Global Carbon Budget 2017
Quéré, Corinne Le; Andrew, Robbie M. ; Friedlingstein, Pierre ; Sitch, Stephen ; Pongratz, Julia ; Manning, Andrew C. ; Ivar Korsbakken, Jan ; Peters, Glen P. ; Canadell, Josep G. ; Jackson, Robert B. ; Boden, Thomas A. ; Tans, Pieter P. ; Andrews, Oliver D. ; Arora, Vivek K. ; Bakker, Dorothee C.E. ; Barbero, Leticia ; Becker, Meike ; Betts, Richard A. ; Bopp, Laurent ; Chevallier, Frédéric ; Chini, Louise P. ; Ciais, Philippe ; Cosca, Catherine E. ; Cross, Jessica ; Currie, Kim ; Gasser, Thomas ; Harris, Ian ; Hauck, Judith ; Haverd, Vanessa ; Houghton, Richard A. ; Hunt, Christopher W. ; Hurtt, George ; Ilyina, Tatiana ; Jain, Atul K. ; Kato, Etsushi ; Kautz, Markus ; Keeling, Ralph F. ; Klein Goldewijk, Kees ; Körtzinger, Arne ; Landschützer, Peter ; Lefèvre, Nathalie ; Lenton, Andrew ; Lienert, Sebastian ; Lima, Ivan ; Lombardozzi, Danica ; Metzl, Nicolas ; Millero, Frank ; Monteiro, Pedro M.S. ; Munro, David R. ; Nabel, Julia E.M.S. ; Nakaoka, Shin Ichiro ; Nojiri, Yukihiro ; Padin, X.A. ; Peregon, Anna ; Pfeil, Benjamin ; Pierrot, Denis ; Poulter, Benjamin ; Rehder, Gregor ; Reimer, Janet ; Rödenbeck, Christian ; Schwinger, Jörg ; Séférian, Roland ; Skjelvan, Ingunn ; Stocker, Benjamin D. ; Tian, Hanqin ; Tilbrook, Bronte ; Tubiello, Francesco N. ; Laan-Luijkx, Ingrid T. van der; Werf, Guido R. van der; Heuven, Steven Van; Viovy, Nicolas ; Vuichard, Nicolas ; Walker, Anthony P. ; Watson, Andrew J. ; Wiltshire, Andrew J. ; Zaehle, Sönke ; Zhu, Dan - \ 2018
Earth System Science Data 10 (2018)1. - ISSN 1866-3508 - p. 405 - 448.
Accurate assessment of anthropogenic carbon dioxide (CO2) emissions and their redistribution among the atmosphere, ocean, and terrestrial biosphere-the "global carbon budget"-is important to better understand the global carbon cycle, support the development of climate policies, and project future climate change. Here we describe data sets and methodology to quantify the five major components of the global carbon budget and their uncertainties. CO2 emissions from fossil fuels and industry (EFF) are based on energy statistics and cement production data, respectively, while emissions from land-use change (ELUC), mainly deforestation, are based on land-cover change data and bookkeeping models. The global atmospheric CO2 concentration is measured directly and its rate of growth (GATM) is computed from the annual changes in concentration. The ocean CO2 sink (SOCEAN) and terrestrial CO2 sink (SLAND) are estimated with global process models constrained by observations. The resulting carbon budget imbalance (BIM), the difference between the estimated total emissions and the estimated changes in the atmosphere, ocean, and terrestrial biosphere, is a measure of imperfect data and understanding of the contemporary carbon cycle. All uncertainties are reported as ±1δ. For the last decade available (2007-2016), EFF was 9.4±0.5 GtC yr-1, ELUC 1.3±0.7 GtC yr-1, GATM 4.7±0.1 GtC yr-1, SOCEAN 2.4±0.5 GtC yr-1, and SLAND 3.0±0.8 GtC yr-1, with a budget imbalance BIM of 0.6 GtC yr-1 indicating overestimated emissions and/or underestimated sinks. For year 2016 alone, the growth in EFF was approximately zero and emissions remained at 9.9±0.5 GtC yr-1. Also for 2016, ELUC was 1.3±0.7 GtC yr-1, GATM was 6.1±0.2 GtC yr-1, SOCEAN was 2.6±0.5 GtC yr-1, and SLAND was 2.7±1.0 GtC yr-1, with a small BIM of-0.3 GtC. GATM continued to be higher in 2016 compared to the past decade (2007-2016), reflecting in part the high fossil emissions and the small SLAND consistent with El Ninõ conditions. The global atmospheric CO2 concentration reached 402.8±0.1 ppm averaged over 2016. For 2017, preliminary data for the first 6-9 months indicate a renewed growth in EFF of C2.0% (range of 0.8 to 3.0 %) based on national emissions projections for China, USA, and India, and projections of gross domestic product (GDP) corrected for recent changes in the carbon intensity of the economy for the rest of the world. This living data update documents changes in the methods and data sets used in this new global carbon budget compared with previous publications of this data set (Le Quéré et al., 2016, 2015b, a, 2014, 2013). All results presented here can be downloaded from https://doi.org/10.18160/GCP-2017 (GCP, 2017).
Population genetic analysis and genome-wide association study of patellar luxation in a Thai population of Pomeranian dogs
Wangdee, C. ; Leegwater, P.A.J. ; Heuven, H.C.M. ; Steenbeek, F.G. van; Techakumphu, M. ; Hazewinkel, H.A.W. - \ 2017
Research in Veterinary Science 111 (2017). - ISSN 0034-5288 - p. 9 - 13.
Canis lupus familiaris - Genome-wide association study - Heritability - Patellar luxation - Prevalence

The genetics of patellar luxation (PL) were investigated in Pomeranian dogs presented at the Small Animal Hospital, Faculty of Veterinary Science, Chulalongkorn University. A cohort of 339 Pomeranian dogs, part of a four-generation pedigree of 842 Pomeranians, was screened for PL from 2006 to 2013. PL was present in 77% of the screened dogs, with 84% having bilateral and 16% unilateral luxation. Medial PL was more common (95%) than lateral PL (2%) or bidirectional PL (3%). The risk of PL was similar in male and female dogs (female:male relative risk 1.11, 95% CI 0.98–1.25). The heritability of PL in the screened population was 0.44 ± 0.04 using a threshold model. A genome-wide association study of PL (48 cases and 48 controls) using a high-density SNP array indicated the possible involvement of 15 chromosomal regions, of which CFA05 and CFA32 remained associated in a larger study involving an additional 128 cases and 7 controls. Candidate genes in these regions may be involved in the pathogenesis of PL in Pomeranian dogs.

How to Ensure Access to Good Food for All in a Rapidly Urbanising World? : Seminar Report, December 8th 2016,Impulse Building, Wageningen, the Netherlands
Heuven, Ede ; Peters, B. ; Herens, M.C. ; Saavedra Gonzalez, Y.R. - \ 2016
Centre for Development Innovation - 5 p.
Advantages of continuous genotype values over genotype classes for GWAS in higher polyploids : A comparative study in hexaploid chrysanthemum
Grandke, Fabian ; Singh, Priyanka ; Heuven, Henri C.M. ; Haan, Jorn R. de; Metzler, Dirk - \ 2016
BMC Genomics 17 (2016). - ISSN 1471-2164 - 9 p.
Association study - Bayz - Continuous genotypes - Linear regression - Partial least squares - Polyploids

Background: Association studies are an essential part of modern plant breeding, but are limited for polyploid crops. The increased number of possible genotype classes complicates the differentiation between them. Available methods are limited with respect to the ploidy level or data producing technologies. While genotype classification is an established noise reduction step in diploids, it gains complexity with increasing ploidy levels. Eventually, the errors produced by misclassifications exceed the benefits of genotype classes. Alternatively, continuous genotype values can be used for association analysis in higher polyploids. We associated continuous genotypes to three different traits and compared the results to the output of the genotype caller SuperMASSA. Linear, Bayesian and partial least squares regression were applied, to determine if the use of continuous genotypes is limited to a specific method. A disease, a flowering and a growth trait with h 2 of 0.51, 0.78 and 0.91 were associated with a hexaploid chrysanthemum genotypes. The data set consisted of 55,825 probes and 228 samples. Results: We were able to detect associating probes using continuous genotypes for multiple traits, using different regression methods. The identified probe sets were overlapping, but not identical between the methods. Baysian regression was the most restrictive method, resulting in ten probes for one trait and none for the others. Linear and partial least squares regression led to numerous associating probes. Association based on genotype classes resulted in similar values, but missed several significant probes. A simulation study was used to successfully validate the number of associating markers. Conclusions: Association of various phenotypic traits with continuous genotypes is successful with both uni- and multivariate regression methods. Genotype calling does not improve the association and shows no advantages in this study. Instead, use of continuous genotypes simplifies the analysis, saves computational time and results more potential markers.

Epidemiology, presentation and population genetics of patent ductus arteriosus (PDA) in the Dutch Stabyhoun dog
Toom, Marjolein L. den; Meiling, Agnes E. ; Thomas, Rachel E. ; Leegwater, Peter A.J. ; Heuven, Henri C.M. - \ 2016
BMC Veterinary Research 12 (2016)1. - ISSN 1746-6148
Canine - Genetics - Heritability - Patent ductus arteriosus - PDA - Prevalence - Sex predisposition

Background: Patent ductus arteriosus (PDA) is one of the most common congenital heart defects in dogs and is considered to be a complex, polygenic threshold trait for which a female sex predisposition has been described. Histological studies in dogs suggest that smooth muscle hypoplasia and asymmetry of the ductus tissue is the major cause of PDA. The Stabyhoun population is small and a predisposition for PDA has been suggested. The aims of this study were to describe the incidence, presentation from a clinical and histopathological perspective, and the population genetics of PDA in the Dutch Stabyhoun population. Results: Forty-six cases were identified between 2000 and 2013. Between 2009 and 2012 the birth incidence of PDA in the Stabyhoun breed was 1.05 %. We estimated this to be 7-13 times higher than expected in the general dog population. Twelve of the 46 cases were part of a litter in which more than one sibling was affected. There was no sex predilection in our case cohort. Dogs diagnosed in adulthood showed severe cardiomegaly. The mean inbreeding coefficient of the reference population of Stabyhoun dogs was 31.4 % and the actual and effective numbers of founders were 14 and 6.5, respectively. The heritability of PDA was 0.51 (±0.09) for the reference population and 0.41 (±0.10) for the phenotyped population. Histopathology of sections of the PDA from two dogs showed findings similar to those described in other breeds although the smooth muscle of the ductus adjacent to the pulmonary artery appeared more hypoplastic than that in the ductus adjacent to the aorta. Conclusions: The Stabyhoun breed shows a strong predisposition for PDA. Apart from the absence of a higher incidence in females, no other significant features distinguish PDA in Stabyhouns from the condition in other dog breeds. Heritability and the mean inbreeding coefficient are both very high making the Dutch Stabyhoun breed particularly suited to the study of inherited risk factors for PDA.

Breeding implications resulting from classification of patellae luxation in dogs
Grevenhof, E.M. van; Hazewinkel, H.A.W. ; Heuven, H.C.M. - \ 2016
Journal of Animal Breeding and Genetics 133 (2016)4. - ISSN 0931-2668 - p. 316 - 322.
Patellar luxation (PL) is one of the major hereditary orthopaedic abnormalities observed in a variety of dog breeds. When the patellae move sideways out of the trochlear groove, this is called PL. The PL score varies between dogs from normal to very severe. Reducing the prevalence of PL by breeding could prevent surgery, thereby improve welfare. Orthopaedic specialists differentiate between normal and loose patellae, where the patellae can be moved to the edge of the trochlear groove, considering scoring loose patellae as normal in the future. Loose patellae are considered acceptable for breeding so far by the breeding organization. The aim of this study was to analyse the genetic background of PL to decide on the importance of loose patellae when breeding for healthy dogs. Data are available from two dog breeds, that is Flat-coated Retrievers (n = 3808) and Kooiker dogs (n = 794), with a total of 4602 dogs. Results show that loose patellae indicate that dogs are genetically more susceptible to develop PL because family members of the dogs with loose patellae showed more severe PL. In addition, the estimated breeding values for dogs with loose patellae indicate that breeding values of dogs with loose patellae were worse than breeding values obtained for dogs with a normal score. Given these results, it is advised to orthopaedic specialists to continue to score loose patellae as a separate class and to dog breeders to minimize the use of dogs in breeding with a genetically higher susceptibility for PL
Global Carbon Budget 2015
Quéré, C. Le; Moriarty, R. ; Andrew, R.M. ; Canadell, J.G. ; Sitch, S. ; Korsbakken, J.I. ; Friedlingstein, P. ; Peters, G.P. ; Andres, R.J. ; Houghton, R.A. ; House, J.I. ; Keeling, R.F. ; Tans, P.P. ; Arneth, A. ; Bakker, D. ; Barbero, L. ; Bopp, L. ; Chang, J. ; Chevallier, F. ; Chini, L.P. ; Ciais, P. ; Feely, R.A. ; Gkritzalis, T. ; Harris, I. ; Hauck, J. ; Ilyina, T. ; Jain, A.K. ; Kato, E. ; Kitidis, V. ; Klein-Goldewijk, K. ; Koven, C. ; Landschützer, Peter ; Lauvset, S.K. ; Lefèvre, N. ; Metzl, N. ; Millero, F. ; Munro, D.R. ; Murata, A. ; Nabel, Julia E.M.S. ; Nakaoka, S. ; Nojiri, Y. ; O'Brien, Kate ; Olson, A. ; Ono, T. ; Pérez, N. ; Pfeil, B. ; Pierrot, D. ; Poulter, B. ; Rehder, G. ; Rödenbeck, C. ; Saito, S. ; Schuster, U. ; Schwinger, J. ; Séférian, R. ; Steinhoff, T. ; Stocker, B.D. ; Sutton, A.J. ; Takahashi, T. ; Tilbrook, B. ; Laan-Luijkx, I.T. van der; Werf, G.R. van de; Heuven, S. Van; Vandemark, D. ; Viovy, N. ; Wiltshire, A. ; Zaehle, S. ; Zeng, N. - \ 2015
Global Carbon Budget 2015
Quéré, C. Le; Moriarty, R. ; Andrew, R.M. ; Canadell, J.G. ; Sitch, S. ; Korsbakken, J.I. ; Friedlingstein, P. ; Peters, G.P. ; Andres, R.J. ; Boden, T.A. ; Houghton, R.A. ; House, J.I. ; Keeling, R.F. ; Tans, P. ; Arneth, A. ; Bakker, D.C.E. ; Barbero, L. ; Bopp, L. ; Chang, J. ; Chevallier, F. ; Chini, L.P. ; Ciais, P. ; Fader, M. ; Feely, R.A. ; Gkritzalis, T. ; Harris, I. ; Hauck, J. ; Ilyina, T. ; Jain, A.K. ; Kato, E. ; Kitidis, V. ; Klein Goldewijk, K. ; Koven, C. ; Landschützer, P. ; Lauvset, S.K. ; Lefèvre, N. ; Lenton, A. ; Lima, I.D. ; Metzl, N. ; Millero, F. ; Munro, D.R. ; Murata, A. ; Nabel, J.E.M.S. ; Nakaoka, S. ; Nojiri, Y. ; O'Brien, K. ; Olsen, A. ; Ono, T. ; Pérez, F.F. ; Pfeil, B. ; Pierrot, D. ; Poulter, B. ; Rehder, G. ; Rödenbeck, C. ; Saito, S. ; Schuster, U. ; Schwinger, J. ; Séférian, R. ; Steinhoff, T. ; Stocker, B.D. ; Sutton, A.J. ; Takahashi, T. ; Tilbrook, B. ; Laan-Luijkx, I.T. Van Der; Werf, G.R. Van Der; Heuven, S. Van; Vandemark, D. ; Viovy, N. ; Wiltshire, A. ; Zaehle, S. ; Zeng, N. - \ 2015
Earth System Science Data 7 (2015)2. - ISSN 1866-3508 - p. 349 - 396.

Accurate assessment of anthropogenic carbon dioxide (CO2) emissions and their redistribution among the atmosphere, ocean, and terrestrial biosphere is important to better understand the global carbon cycle, support the development of climate policies, and project future climate change. Here we describe data sets and a methodology to quantify all major components of the global carbon budget, including their uncertainties, based on the combination of a range of data, algorithms, statistics, and model estimates and their interpretation by a broad scientific community. We discuss changes compared to previous estimates as well as consistency within and among components, alongside methodology and data limitations. CO2 emissions from fossil fuels and industry (EFF) are based on energy statistics and cement production data, while emissions from land-use change (ELUC), mainly deforestation, are based on combined evidence from land-cover-change data, fire activity associated with deforestation, and models. The global atmospheric CO2 concentration is measured directly and its rate of growth (GATM) is computed from the annual changes in concentration. The mean ocean CO2 sink (SOCEAN) is based on observations from the 1990s, while the annual anomalies and trends are estimated with ocean models. The variability in SOCEAN is evaluated with data products based on surveys of ocean CO2 measurements. The global residual terrestrial CO2 sink (SLAND) is estimated by the difference of the other terms of the global carbon budget and compared to results of independent dynamic global vegetation models forced by observed climate, CO2, and land-cover change (some including nitrogen-carbon interactions). We compare the mean land and ocean fluxes and their variability to estimates from three atmospheric inverse methods for three broad latitude bands. All uncertainties are reported as ±1σ, reflecting the current capacity to characterise the annual estimates of each component of the global carbon budget. For the last decade available (2005-2014), EFF was 9.0 ± 0.5 GtC yrg'1, ELUC was 0.9 ± 0.5 GtC yrg'1, GATM was 4.4 ± 0.1 GtC yrg'1, SOCEAN was 2.6 ± 0.5 GtC yrg'1, and SLAND was 3.0 ± 0.8 GtC yrg'1. For the year 2014 alone, EFF grew to 9.8 ± 0.5 GtC yrg'1, 0.6 % above 2013, continuing the growth trend in these emissions, albeit at a slower rate compared to the average growth of 2.2 % yrg'1 that took place during 2005-2014. Also, for 2014, ELUC was 1.1 ± 0.5 GtC yrg'1, GATM was 3.9 ± 0.2 GtC yrg'1, SOCEAN was 2.9 ± 0.5 GtC yrg'1, and SLAND was 4.1 ± 0.9 GtC yrg'1. GATM was lower in 2014 compared to the past decade (2005-2014), reflecting a larger SLAND for that year. The global atmospheric CO2 concentration reached 397.15 ± 0.10 ppm averaged over 2014. For 2015, preliminary data indicate that the growth in EFF will be near or slightly below zero, with a projection of g'0.6 [range of g'1.6 to +0.5] %, based on national emissions projections for China and the USA, and projections of gross domestic product corrected for recent changes in the carbon intensity of the global economy for the rest of the world. From this projection of EFF and assumed constant ELUC for 2015, cumulative emissions of CO2 will reach about 555 ± 55 GtC (2035 ± 205 GtCO2) for 1870-2015, about 75 % from EFF and 25 % from ELUC. This living data update documents changes in the methods and data sets used in this new carbon budget compared with previous publications of this data set (Le Quéré et al., 2015, 2014, 2013). All observations presented here can be downloaded from the Carbon Dioxide Information Analysis Center (doi:10.3334/CDIAC/GCP-2015).

Interval from last insemination to culling : I: The genetic background in crossbred sows
Grevenhof, E.M. van; Knol, E.F. ; Heuven, H.C.M. - \ 2015
Livestock Science 181 (2015). - ISSN 1871-1413 - p. 103 - 107.
Crossbred - Culling reason - Heritability - Interval last insemination to culling - Longevity - Sows

Improving longevity of sows is hampered by the lack of accurate and early recording of factors that contribute to reduced longevity. Besides, phenotypic data of parity number at culling or culling reason are potentially collected in purebred individuals, while these animals are not able to show full potential of their longevity due to EBVs, which makes the culling to take place earlier. In contrast to crossbred animals, of which usually very little information is collected, as phenotypes are expensive and difficult to obtain. Longevity is influenced by several culling reasons of which fertility and leg weakness are known to be the most important, although culling reason is unknown or unreliably recorded in crossbreds. To distinguish different reasons for (in)voluntary culling, interval from last insemination to culling (IL2C) might be able to function as an indicator, which could potentially enable us to breed for sow able to fulfil a complete production cycle. The aim is to quantify and understand the mechanism of parity number at culling by analysing the IL2C, in relation to parity number at culling. The results show that IL2C is a heritable trait that can be used in selection, in addition to parity number at culling. Parity number at culling and IL2C are not significantly correlated, which shows the potential to take both traits into account in breeding. By combining improvement of IL2C with improved longevity, economics and welfare of crossbred sows will even further be increased.

Interval from last insemination to culling : II: Culling reasons from practise and the correlation with longevity
Hollander, C.A. de; Knol, E.F. ; Heuven, H.C.M. ; Grevenhof, E.M. van - \ 2015
Livestock Science 181 (2015). - ISSN 1871-1413 - p. 25 - 30.
Culling reason - Genetic parameters - Interval from last insemination to culling - Longevity - Sow

This study studied the relation between longevity, the interval from last insemination to culling in days (IL2C) with 7 different cull classes; 1. Reproduction cull class, 2. Production cull class, 3. Locomotion cull class, 4. Accident cull class, 5. General disorder cull class, 6. Peri-partum cull class and 7. Unknown cull class. Overall, the most important cull classes were reproduction (19%) and production (50%). The IL2C for production (146.3±1.2) and reproduction (87.4±1.9) were significantly different from each other but also from locomotion (127.0±3.6), accident (120.1±7.3), general disorder (105.4±5.5), peri-partum (109.6±5.7) cull classes. Sows that were culled for production reasons had significantly the highest average parity number at culling (4.6±0.2) compared to all other culling reasons such as reproduction (3.1±0.2), locomotion (2.3±0.3), accident (2.9±0.5), general disorder (3.3±0.4) and peri-partum (3.3±0.4) cull classes. Furthermore, it was found that age in days, parity number at culling and IL2C showed to be heritable traits (0.13±0.05, 0.16±0.05 and 0.10±0.04 respectively). The genetic correlation between parity number at culling and IL2C was not significantly different from 0 (-0.04±0.28). Because IL2C is a heritable trait and sows that are culled within the production cull class obtain on average a higher parity and show the longest IL2C, this study showed the potential to select on longer IL2C and thereby select against sows to be culled within the reproduction, locomotion, accident, general disorder and peri-partum cull class and to be culled at the end of a parity.

Phenotypic and genetic relationships of bovine natural antibodies binding keyhole limpet hemocyanin in plasma and milk
Klerk, B. de; Ducro, B.J. ; Heuven, H.C.M. ; Uyl, I. den; Arendonk, J.A.M. van; Parmentier, H.K. ; Poel, J.J. van der - \ 2015
Journal of Dairy Science 98 (2015)4. - ISSN 0022-0302 - p. 2746 - 2752.
immune-responses - autoantibodies - cows - parameters - survival - titers
To improve the health status (resilience) of dairy cows, levels of natural antibodies (NAb) might be useful. The objective of the present study was to compare levels and to estimate genetic parameters for NAb measured in milk and plasma samples. Titers of NAb IgM and IgG isotype-binding keyhole limpet hemocyanin of 2,919 cows, in both plasma and milk, were measured using ELISA. Analysis revealed that NAb levels in milk significantly increased with parity, whereas they remained constant in plasma. Moderate positive phenotypic correlations were found between NAb levels in milk and in plasma: 0.18 for IgG and 0.40 for IgM. This indicates that NAb from milk and plasma might reflect different aspects of dairy cow health status. However, high genetic correlations were found for NAb in milk and plasma: 0.81 for IgG and 0.79 for IgM. Heritabilities (SE in parentheses) for NAb measured in plasma [0.15 (0.05) for IgG and 0.25 (0.06) for IgM] were higher than heritabilities of NAb measured in milk [0.08 (0.03) for IgG and 0.23 (0.05) for IgM]. Our results indicate that NAb measured in milk and plasma are heritable and likely have a common genetic background, suggesting that NAb levels measured in milk might be useful for genetic improvement of disease resistance.
Prevalence and co-occurrence of hip dysplasia and elbow dysplasia in Dutch pure-bred dogs
Lavrijsen, I.C.M. ; Heuven, H.C.M. ; Meij, B.P. ; Theyse, L.F.H. ; Nap, R.C. ; Leegwater, P.A.J. ; Hazewinkel, H.A.W. - \ 2014
Preventive Veterinary Medicine 114 (2014)2. - ISSN 0167-5877 - p. 114 - 122.
german-shepherd dogs - uk labrador retrievers - bernese mountain dog - canine hip - control program - cost-analysis - inheritance - osteochondrosis - heritability - breeds
Hip as well as elbow dysplasia (HD, ED) are developmental disorders leading to malformation of their respective joints. For a long time both disorders have been scored and targeted for improvement using selective breeding in several Dutch dog populations. In this paper all scores for both HD and ED, given to pure bred dogs in the Netherlands from 2002 to 2010, were analyzed. Heritabilities and correlations between HD and ED were calculated for the 4 most frequently scored breeds. Heritabilities ranged from 0.0 to 0.37 for HD related traits (FCI-score, osteoarthritis, congruity, shape and laxity (Norberg angle); FCI: Federation Cynologique Internationale) and from 0.0 to 0.39 for ED related traits (IEWG score, osteoarthritis, sclerosis and indentation; IEWG: International Elbow Working Group). HD related traits showed high genetic and residual correlations among each other but were only to a minor extent correlated with ED related traits, which also showed high correlations among each other. Genetic correlations were higher than residual correlations. Phenotypic and genetic trends since 2001 for the four most scored breeds were slightly positive but decreasing overtime, indicating that selection over the past decade has not been effective. (C) 2014 Published by Elsevier B.V.
Prevalence and genetics of patellar luxation in Kooiker dogs
Wangdee, C. ; Leegwater, P.A.J. ; Heuven, H.C.M. ; Steenbeek, F.G. van; Meutstege, F.J. ; Meij, B.P. ; Hazewinkel, H.A.W. - \ 2014
The Veterinary Journal 201 (2014)3. - ISSN 1090-0233 - p. 333 - 337.
breed - frequency - size
The prevalence of patellar luxation (PL) and genetic factors potentially involved in the disorder were investigated in Dutch Kooiker dogs. A cohort of 842 Kooiker dogs, the offspring of 195 sires and 318 dams, was screened for PL from 1994 to 2011. The cohort was included in a pedigree of 1737 Kooiker dogs comprising nine generations. PL was present in 24% of screened dogs, with unilateral and bilateral luxation being observed equally frequently. Medial PL was more common (61%) than lateral PL (32%) or bidirectional PL (7%). The frequency of PL was similar in male and female dogs, with a female:male relative risk of 1.15 (95% confidence interval, CI, 0.90-1.48). The heritability of PL in the screened population was 0.27 +/- 0.07. Since the start of the screening programme, the prevalence of PL decreased from 28% to 19%. A genome-wide association study of PL with 48 cases and 42 controls suggested the possible involvement of a region on chromosome 3 (P-raw = 1.32 x10(-5), P-genome = 0.142), but the involvement of this region could not be confirmed in a validation group. Breeding programmes for complex diseases, such as PL, would benefit from combining pedigrees, phenotypes and genotypes, i.e. from genomic selection, as is currently the method of choice for breeding of production animals. (C) 2014 Elsevier Ltd. All rights reserved.
Genome-wide survey indicates involvement of loci on canine chromosomes 7 and 31 in patellar luxation in flat-coated retrievers
Lavrijsen, I.C.M. ; Leegwater, P.A.J. ; Wangdee, C. ; Steenbeek, F.G. van; Schwencke, M. ; Breur, G.J. ; Meutstege, F.J. ; Nijman, I.J. ; Cuppen, E. ; Heuven, H.C.M. ; Hazewinkel, H.A.W. - \ 2014
BMC Genetics 15 (2014). - ISSN 1471-2156
dogs - breed - frequency - association - enrichment
Background: Patellar luxation is an orthopedic disorder in which the patella moves out of its normal location within the femoral trochlea of the knee and it can lead to osteoarthritis, lameness, and pain. In dogs it is a heritable trait, with both environmental and genetic factors contributing to the phenotype. The prevalence of patellar luxation in the Dutch Flat-Coated Retriever population is 24%. In this study, we investigated the molecular genetics of the disorder in this population. Results: Genome-wide association analysis of 15,823 single nucleotide polymorphisms (SNPs) in 45 cases and 40 controls revealed that patellar luxation was significantly associated with a region on chromosome CFA07, and possibly with regions on CFA03, CFA31, and CFA36. The exons of the genes in these regions, 0.5 Mb combined, were analyzed further. These exons from 15 cases and a pooled sample from 15 controls were enriched using custom genomic hybridization arrays and analyzed by massive parallel DNA sequencing. In total 7257 variations were detected. Subsequently, a selection of 144 of these SNPs were genotyped in 95 Flat-Coated Retrievers. Nine SNPs, in eight genes on CFA07 and CFA31, were associated with patellar luxation (P <10(-4)). Genotyping of these SNPs in samples from a variety of breeds revealed that the disease-associated allele of one synonymous SNP in a pseudogene of FMO6 was unique to Flat-Coated Retrievers. Conclusion: Genome-wide association analysis followed by targeted DNA sequencing identified loci on chromosomes 7 and 31 as being involved in patellar luxation in the Flat-Coated Retriever breed.
Bovine Neonatal Pancytopenia is a heritable trait of the dam rather than the calf and correlates with the magnitude of vaccine induced maternal alloantibodies not the MHC haplotype
Benedictus, L. ; Otten, H.G. ; Schaik, G. van; Ginkel, G.J. ; Heuven, H.C.M. ; Nielen, M. ; Rutten, V.P.M.G. ; Koets, A.P. - \ 2014
Veterinary Research 45 (2014). - ISSN 0928-4249 - 13 p.
class-i genes - hemorrhagic diathesis - cattle - antibody - calves - bnp - association - responses - sequence - beta-2-microglobulin
Bovine Neonatal Pancytopenia (BNP), a bleeding syndrome of neonatal calves, is caused by alloantibodies absorbed from the colostrum of particular cows. A commercial BVD vaccine is the likely source of alloantigens eliciting BNP associated alloantibodies. We hypothesized that the rare occurrence of BNP in calves born to vaccinated dams could be associated with genetic differences within dams and calves. We found that the development of BNP within calves was a heritable trait for dams, not for calves and had a high heritability of 19%. To elucidate which genes play a role in the development of BNP we sequenced candidate genes and characterized BNP alloantibodies. Alloantigens present in the vaccine have to be presented to the dam’s immune system via MHC class II, however sequencing of DRB3 showed no differences in MHC class II haplotype between BNP and non-BNP dams. MHC class I, a highly polymorphic alloantigen, is an important target of BNP alloantibodies. Using a novel sequence based MHC class I typing method, we found no association of BNP with MHC class I haplotype distribution in dams or calves. Alloantibodies were detected in both vaccinated BNP and non-BNP dams and we found no differences in alloantibody characteristics between these groups, but alloantibody levels were significantly higher in BNP dams. We concluded that the development of BNP in calves is a heritable trait of the dam rather than the calf and genetic differences between BNP and non-BNP dams are likely due to genes controlling the quantitative alloantibody response following vaccination.
The effect of genetic selection for Johne's disease resistance n dairy cattle: Results of a genetic-epidemiological model
Hulzen, K.J.E. van; Koets, A.P. ; Nielen, M. ; Heuven, H.C.M. ; Arendonk, J.A.M. van; Klinkenberg, D. - \ 2014
Journal of Dairy Science 97 (2014)3. - ISSN 0022-0302 - p. 1762 - 1773.
avium subspecies paratuberculosis - decision-analysis model - antibody-response - control program - fecal culture - holstein cows - mycobacterium - herd - infection - heritability
The objective of this study was to model genetic selection for Johne’s disease resistance and to study the effect of different selection strategies on the prevalence in the dairy cattle population. In the Netherlands, a certification-and-surveillance program is in use to reduce prevalence and presence of sources of infection in milk by culling ELISA-positive dairy cows in infected herds. To investigate the additional genetic effect of this program, a genetic-epidemiological model was developed to assess the effect of selection of cows that test negative for Johne’s disease (dam selection). The genetic effect of selection at the sire level was also considered (sire selection), assuming selection of 80% of sires producing the most resistant offspring based on their breeding values, as well as the combined effect. Parameters assumed to be affected by genetic selection were the length of the latent period, susceptibility (i.e., the number of infectious doses needed to become infected), or the length of susceptible period as a calf. The effect of selection was measured by the time in years required to eliminate infection. Sensitivity analysis was performed for heritability, accuracy of selection, and intensity of selection. For dam selection, responses to selection were small, requiring 379 to 702 yr for elimination. For sire selection, responses were much larger, although elimination still required 147 to 223 yr. The response to selection was largest if genetic selection affected the length of the susceptible period, followed by the susceptibility, and finally the length of the latent period. Genetic selection for Johne’s disease resistance by certification and surveillance is too slow for practical purpose, but that selection on the sire level is able to contribute to the control of Johne’s disease in the long run.
Design and Characterization of a 52K SNP Chip for Goats
Tosser-klopp, G. ; Bardou, P. ; Bouchez, O. ; Cabau, C. ; Crooijmans, R.P.M.A. ; Dong, Y. ; Donnadieu-Tonon, C. ; Eggen, A. ; Heuven, H.C.M. ; Jamli, S. ; Jiken, A.J. ; Klopp, C. ; Lawley, C.T. ; McEwen, J. ; Martin, P. ; Moreno, C.R. ; Mulsant, P. ; Nabihoudine, I. ; Pailhoux, E. ; Palhiere, I. ; Rupp, R. ; Sarry, J. ; Sayre, B.L. ; Tircazes, A. ; Wang, J. ; Wang, W. ; Zhang, W.G. - \ 2014
PLoS ONE 9 (2014)1. - ISSN 1932-6203
single-nucleotide polymorphisms - classical scrapie - genotyping assay - capra-hircus - prp gene - genome - association - polledness - generation - discovery
The success of Genome Wide Association Studies in the discovery of sequence variation linked to complex traits in humans has increased interest in high throughput SNP genotyping assays in livestock species. Primary goals are QTL detection and genomic selection. The purpose here was design of a 50–60,000 SNP chip for goats. The success of a moderate density SNP assay depends on reliable bioinformatic SNP detection procedures, the technological success rate of the SNP design, even spacing of SNPs on the genome and selection of Minor Allele Frequencies (MAF) suitable to use in diverse breeds. Through the federation of three SNP discovery projects consolidated as the International Goat Genome Consortium, we have identified approximately twelve million high quality SNP variants in the goat genome stored in a database together with their biological and technical characteristics. These SNPs were identified within and between six breeds (meat, milk and mixed): Alpine, Boer, Creole, Katjang, Saanen and Savanna, comprising a total of 97 animals. Whole genome and Reduced Representation Library sequences were aligned on >10 kb scaffolds of the de novo goat genome assembly. The 60,000 selected SNPs, evenly spaced on the goat genome, were submitted for oligo manufacturing (Illumina, Inc) and published in dbSNP along with flanking sequences and map position on goat assemblies (i.e. scaffolds and pseudo-chromosomes), sheep genome V2 and cattle UMD3.1 assembly. Ten breeds were then used to validate the SNP content and 52,295 loci could be successfully genotyped and used to generate a final cluster file. The combined strategy of using mainly whole genome Next Generation Sequencing and mapping on a contig genome assembly, complemented with Illumina design tools proved to be efficient in producing this GoatSNP50 chip. Advances in use of molecular markers are expected to accelerate goat genomic studies in coming years.
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