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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Improving accuracy of direct and maternal genetic effects in genomic evaluations using pooled boar semen: a simulation study
Maiorano, Amanda M. ; Assen, Alula ; Bijma, Piter ; Chen, Ching Yi ; Silva, Josineudson Augusto Ii Vasconcelos ; Herring, William O. ; Tsuruta, Shogo ; Misztal, Ignacy ; Lourenco, Daniela A.L. - \ 2019
Journal of Animal Science 97 (2019)8. - ISSN 0021-8812 - p. 3237 - 3245.
genomic prediction - maternal ability - multiple sire - prediction accuracy

Pooling semen of multiple boars is commonly used in swine production systems. Compared with single boar systems, this technique changes family structure creating maternal half-sib families. The aim of this simulation study was to investigate how pooling semen affects the accuracy of estimating direct and maternal effects for individual piglet birth weight, in purebred pigs. Different scenarios of pooling semen were simulated by allowing the same female to mate from 1 to 6 boars, per insemination, whereas litter size was kept constant (N = 12). In each pooled boar scenario, genomic information was used to construct either the genomic relationship matrix (G) or to reconstruct pedigree in addition to G. Genotypes were generated for 60,000 SNPs evenly distributed across 18 autosomes. From the 5 simulated generations, only animals from generations 3 to 5 were genotyped (N = 36,000). Direct and maternal true breeding values (TBV) were computed as the sum of the effects of the 1,080 QTLs. Phenotypes were constructed as the sum of direct TBV, maternal TBV, an overall mean of 1.25 kg, and a residual effect. The simulated heritabilities for direct and maternal effects were 0.056 and 0.19, respectively, and the genetic correlation between both effects was -0.25. All simulations were replicated 5 times. Variance components and direct and maternal heritability were estimated using average information REML. Predictions were computed via pedigree-based BLUP and single-step genomic BLUP (ssGBLUP). Genotyped littermates in the last generation were used for validation. Prediction accuracies were calculated as correlations between EBV and TBV for direct (accdirect) and maternal (accmat) effects. When boars were known, accdirect were 0.21 (1 boar) and 0.26 (6 boars) for BLUP, whereas for ssGBLUP, they were 0.38 (1 boar) and 0.43 (6 boars). When boars were unknown, accdirect was lower in BLUP but similar in ssGBLUP. For the scenario with known boars, accmat was 0.58 and 0.63 for 1 and 6 boars, respectively, under ssGBLUP. For unknown boars, accmat was 0.63 for 2 boars and 0.62 for 6 boars in ssGBLUP. In general, accdirect and accmat were lower in the single-boar scenario compared with pooled semen scenarios, indicating that a half-sib structure is more adequate to estimate direct and maternal effects. Using pooled semen from multiple boars can help us to improve accuracy of predicting maternal and direct effects when maternal half-sib families are larger than 2.

Methane budget estimates in Finland from the CarbonTracker Europe-CH4 data assimilation system
Tsuruta, Aki ; Aalto, Tuula ; Backman, Leif ; Krol, Maarten C. ; Peters, Wouter ; Lienert, Sebastian ; Joos, Fortunat ; Miller, Paul A. ; Zhang, Wenxin ; Laurila, Tuomas ; Hatakka, Juha ; Leskinen, Ari ; Lehtinen, Kari E.J. ; Peltola, Olli ; Vesala, Timo ; Levula, Janne ; Dlugokencky, Ed ; Heimann, Martin ; Kozlova, Elena ; Aurela, Mika ; Lohila, Annalea ; Kauhaniemi, Mari ; Gomez-Pelaez, Angel J. - \ 2019
Tellus Series B: Chemical and Physical Meteorology (2019). - ISSN 0280-6509 - 21 p.
atmospheric CH - CH flux - data assimilation - Finland - flux estimation

We estimated the CH4 budget in Finland for 2004–2014 using the CTE-CH4 data assimilation system with an extended atmospheric CH4 observation network of seven sites from Finland to surrounding regions (Hyytiälä, Kjølnes, Kumpula, Pallas, Puijo, Sodankylä, and Utö). The estimated average annual total emission for Finland is 0.6 ± 0.5 Tg CH4 yr−1. Sensitivity experiments show that the posterior biospheric emission estimates for Finland are between 0.3 and 0.9 Tg CH4 yr−1, which lies between the LPX-Bern-DYPTOP (0.2 Tg CH4 yr−1) and LPJG-WHyMe (2.2 Tg CH4 yr−1) process-based model estimates. For anthropogenic emissions, we found that the EDGAR v4.2 FT2010 inventory (0.4 Tg CH4 yr−1) is likely to overestimate emissions in southernmost Finland, but the extent of overestimation and possible relocation of emissions are difficult to derive from the current observation network. The posterior emission estimates were especially reliant on prior information in central Finland. However, based on analysis of posterior atmospheric CH4, we found that the anthropogenic emission distribution based on a national inventory is more reliable than the one based on EDGAR v4.2 FT2010. The contribution of total emissions in Finland to global total emissions is only about 0.13%, and the derived total emissions in Finland showed no trend during 2004–2014. The model using optimized emissions was able to reproduce observed atmospheric CH4 at the sites in Finland and surrounding regions fairly well (correlation > 0.75, bias < ± ppb), supporting adequacy of the observations to be used in atmospheric inversion studies. In addition to global budget estimates, we found that CTE-CH4 is also applicable for regional budget estimates, where small scale (1x1 in this case) optimization is possible with a dense observation network.

The CarbonTracker Data Assimilation Shell (CTDAS) v1.0 : Implementation and global carbon balance 2001-2015
Laan-Luijkx, Ingrid T. Van Der; Velde, Ivar R. Van Der; Veen, Emma Van Der; Tsuruta, Aki ; Stanislawska, Karolina ; Babenhauserheide, Arne ; Fang Zhang, Hui ; Liu, Yu ; He, Wei ; Chen, Huilin ; Masarie, Kenneth A. ; Krol, Maarten C. ; Peters, Wouter - \ 2017
Geoscientific Model Development 10 (2017)7. - ISSN 1991-959X - p. 2785 - 2800.
Data assimilation systems are used increasingly to constrain the budgets of reactive and long-lived gases measured in the atmosphere. Each trace gas has its own lifetime, dominant sources and sinks, and observational network (from flask sampling and in situ measurements to space-based remote sensing) and therefore comes with its own optimal configuration of the data assimilation. The CarbonTracker Europe data assimilation system for CO2 estimates global carbon sources and sinks, and updates are released annually and used in carbon cycle studies. CarbonTracker Europe simulations are performed using the new modular implementation of the data assimilation system: The CarbonTracker Data Assimilation Shell (CTDAS). Here, we present and document this redesign of the data assimilation code that forms the heart of CarbonTracker, specifically meant to enable easy extension and modification of the data assimilation system. This paper also presents the setup of the latest version of CarbonTracker Europe (CTE2016), including the use of the gridded state vector, and shows the resulting carbon flux estimates. We present the distribution of the carbon sinks over the hemispheres and between the land biosphere and the oceans. We show that with equal fossil fuel emissions, 2015 has a higher atmospheric CO2 growth rate compared to 2014, due to reduced net land carbon uptake in later year. The European carbon sink is especially present in the forests, and the average average net uptake over 2001-2015 was 0:17±0:11 PgCyr-1 with reductions to zero during drought years. Finally, we also demonstrate the versatility of CTDAS by presenting an overview of the wide range of applications for which it has been used so far.
Global methane emission estimates for 2000-2012 from CarbonTracker Europe-CH4 v1.0
Tsuruta, Aki ; Aalto, Tuula ; Backman, Leif ; Hakkarainen, Janne ; Laan-Luijkx, Ingrid T. Van Der; Krol, Maarten C. ; Spahni, Renato ; Houweling, Sander ; Laine, Marko ; Dlugokencky, Ed ; Gomez-Pelaez, Angel J. ; Schoot, Marcel Van Der; Langenfelds, Ray ; Ellul, Raymond ; Arduini, Jgor ; Apadula, Francesco ; Gerbig, Christoph ; Feist, D.G. ; Kivi, Rigel ; Yoshida, Yukio ; Peters, Wouter - \ 2017
Geoscientific Model Development 10 (2017)3. - ISSN 1991-959X - p. 1261 - 1289.

We present a global distribution of surface methane (CH4) emission estimates for 2000-2012 derived using the CarbonTracker Europe-CH4 (CTE-CH4) data assimilation system. In CTE-CH4, anthropogenic and biospheric CH4 emissions are simultaneously estimated based on constraints of global atmospheric in situ CH4 observations. The system was configured to either estimate only anthropogenic or biospheric sources per region, or to estimate both categories simultaneously. The latter increased the number of optimizable parameters from 62 to 78. In addition, the differences between two numerical schemes available to perform turbulent vertical mixing in the atmospheric transport model TM5 were examined. Together, the system configurations encompass important axes of uncertainty in inversions and allow us to examine the robustness of the flux estimates. The posterior emission estimates are further evaluated by comparing simulated atmospheric CH4 to surface in situ observations, vertical profiles of CH4 made by aircraft, remotely sensed dry-air total column-averaged mole fraction (XCH4) from the Total Carbon Column Observing Network (TCCON), and XCH4 from the Greenhouse gases Observing Satellite (GOSAT). The evaluation with non-assimilated observations shows that posterior XCH4 is better matched with the retrievals when the vertical mixing scheme with faster interhemispheric exchange is used. Estimated posterior mean total global emissions during 2000-2012 are 516 ± 51 Tg CH4 yr-1, with an increase of 18 Tg CH4 yr-1 from 2000-2006 to 2007-2012. The increase is mainly driven by an increase in emissions from South American temperate, Asian temperate and Asian tropical TransCom regions. In addition, the increase is hardly sensitive to different model configurations ( < 2 Tg CH4 yr-1 difference), and much smaller than suggested by EDGAR v4.2 FT2010 inventory (33 Tg CH4 yr-1), which was used for prior anthropogenic emission estimates. The result is in good agreement with other published estimates from inverse modelling studies (16-20 Tg CH4 yr-1). However, this study could not conclusively separate a small trend in biospheric emissions (-5 to +6.9 Tg CH4 yr-1) from the much larger trend in anthropogenic emissions (15-27 Tg CH4 yr-1). Finally, we find that the global and North American CH4 balance could be closed over this time period without the previously suggested need to strongly increase anthropogenic CH4 emissions in the United States. With further developments, especially on the treatment of the atmospheric CH4 sink, we expect the data assimilation system presented here will be able to contribute to the ongoing interpretation of changes in this important greenhouse gas budget.

Sexual dimorphism in livestock species selected for economically important traits
Heide, E.M.M. van der; Lourenco, D.A.L. ; Chen, C.Y. ; Herring, W.O. ; Sapp, R.L. ; Moser, D.W. ; Tsuruta, S. ; Masuda, Y. ; Ducro, B.J. ; Misztal, I. - \ 2016
Journal of Animal Science 94 (2016)9. - ISSN 0021-8812 - p. 3684 - 3692.
Beef cattle - Broiler chickens - Genetic correlation - Genomic selection - Purebred pigs - Sex difference

Most breeding companies evaluate economically important traits in males and females as a single trait, assuming genetic correlation of 1 between phenotypes measured in both sexes. This assumption may not be true because genes may be differently expressed in males and females. We estimated genetic correlations between males and females for growth and efficiency traits in broiler chickens, growth traits in American Angus beef cattle, and birth weight and preweaning mortality in purebred pigs; therefore, each trait was treated differently in males and females. Variance components were estimated in single- and multiple-trait models, jointly or separated into both sexes. Furthermore, we calculated traditional and genomic evaluations, and we correlated EBV or genomic EBV (GEBV) from joint and separate evaluations for males and females. For broiler chickens, genetic correlations ranged from 0.86 to 0.94. For Angus cattle, genetic correlations ranged from 0.86 to 0.98 for early growth traits and were less, ranging from 0.68 to 0.84, for postweaning gain. In pigs, genetic correlations ranged from 0.98 to 0.99 for birth weight and from 0.71 to 0.73 for preweaning mortality. For some models in all 3 animal species, the joint and separate analyses had different heritabilities. Despite differences in heritability, the correlations within the sex-specific trait EBV and between the sex-specific and the joint trait EBV were very strong, regardless of the model or inclusion of genomic information. Males and females differed for traits measured late in the animal’s life; however, strong traditional EBV correlations and also GEBV correlations indicate that considering the traits equal in males and females may have no negative impact on selection.

Evaluating atmospheric methane inversion model results for Pallas, northern Finland
Tsuruta, A. ; Aalto, T. ; Backman, L. ; Peters, W. ; Krol, M.C. ; Laan-Luijkx, I.T. van der; Hatakka, J. ; Heikkinen, P. ; Dlugokencky, E.J. ; Spahni, R. ; Paramonova, N.N. - \ 2015
Boreal environment research 20 (2015)4. - ISSN 1239-6095 - p. 506 - 525.
A state-of-the-art inverse model, CarbonTracker Data Assimilation Shell (CTDAS), was used to optimize estimates of methane (CH4) surface fluxes using atmospheric observations of CH4 as a constraint. The model consists of the latest version of the TM5 atmospheric chemistry-transport model and an ensemble Kalman filter based data assimilation system. The model was constrained by atmospheric methane surface concentrations, obtained from the World Data Centre for Greenhouse Gases (WDCGG). Prior methane emissions were specified for five sources: biosphere, anthropogenic, fire, termites and ocean, of which biosphere and anthropogenic emissions were optimized. Atmospheric CH4 mole fractions for 2007 from northern Finland calculated from prior and optimized emissions were compared with observations. It was found that the root mean squared errors of the posterior estimates were more than halved. Furthermore, inclusion of NOAA observations of CH4 from weekly discrete air samples collected at Pallas improved agreement between posterior CH4 mole fraction estimates and continuous observations, and resulted in reducing optimized biosphere emissions and their uncertainties in northern Finland.
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