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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    An investment order tool to guide development of greenhouse horticulture for two specific regions
    Blok, C. ; Leyh, R. ; Baeza Romero, E.J. ; Os, E.A. van; Salm, C. van der - \ 2020
    Acta Horticulturae 1268 (2020). - ISSN 0567-7572 - p. 27 - 34.
    Cultivation system - Decision support - Economics - Greenhouse type - Mediterranean

    Growers worldwide often lack means to find the economically soundest order of investing. Authorities face similar problems when deciding which developments to stimulate. For Dutch greenhouse horticulture, models for production, climate, revenue and costs, allow selection of an optimal investment order. This approach was widened into “Adaptive Greenhouse Methodology” which allows evaluation of worldwide climate and greenhouse technology combinations. However, running the models requires expert skills. Our goal was to deliver a simplified software tool, which would allow horticultural suppliers, researchers and growers to autonomously rank alternative investments, for a specific combination of region, greenhouse design and crop. The Investment Order Tool was developed in cooperation with selected horticultural supply companies for the regions Almeria in Spain and the Jordan Valley. In Spain, a flat roofed Parral type greenhouse was compared to an industrial multi-span greenhouse. In Jordan a single tunnel greenhouse was compared to an industrial multi-span greenhouse with passive crop based cooling. The Investment Order Tool uses a one-time run of the Adaptive Greenhouse Methodology based on local information. This data set allows further off-line calculations. All adaptions in greenhouse construction and cultivation system are defined as relative production changes from the local standard. The adaptations are provided with their specific costs and benefits. The investments compared include: reverse osmosis; substrates; nutrient dosing; climate-adapted cultivars; recirculation of drainage water; ventilation capacity; shading screens and thermal screens. The Investment Order Tool informed growers on the investment order with the highest return on investment and the investment order with the lowest demand for capital. Nursery specificity was realized by permitting user defined yield and market price level per month and by defining a first and second class for product quality. It is hoped the Investment Order Tool encourages growers and local authorities to base investment decisions on increasingly solid knowledge.

    Exploring the boundaries of the passive greenhouse in Jordan: A modelling approach
    Baeza Romero, E.J. ; Os, E.A. van; Salm, C. van der; Tsafaras, I. ; Blok, C. - \ 2020
    Acta Horticulturae 1268 (2020). - ISSN 0567-7572 - p. 43 - 50.
    Cooling - Fogging - Shading - Tomato - Whitewash

    Greenhouses are expanding fast in arid and semi-arid regions, among other reasons, because of the water savings that can be realized compared to open field cultivation. However, it is difficult for growers to recognize the optimum greenhouse design. Many competing aspects must be weighed against each other such as the structure, the cover and the climate control equipment. Obviously, the optimum design must be tailored for each specific crop and growing cycle and availability of resources (land, water, energy, labor, etc.). Simulation models can assist in this process, saving time and money. Wageningen University & Research, BU Greenhouse Horticulture has developed the Adaptive Greenhouse Methodology. It combines the use of greenhouse climate and resources simulation models, with crop growth and economic models, to solve the problem of designing the optimum greenhouse for each specific scenario in the world. In the present work we present the results of the application of this methodology to the specific case of the production of greenhouse soilless tomato in two regions in Jordan in the mid tech range: the highlands and the Jordan Valley. Results show that different mid tech designs could potentially provide yield levels of up to 35 and 27 kg m-2 in the Highlands and the Jordan Valley, respectively. The final design is similar in the two locations.

    Cardiorespiratory fitness, muscular fitness and mental health in older adolescents: A multi-level cross-sectional analysis
    Janssen, Amy ; Leahy, Angus A. ; Diallo, Thierno M.O. ; Smith, Jordan J. ; Kennedy, Sarah G. ; Eather, Narelle ; Mavilidi, Myrto F. ; Wagemakers, Annemarie ; Babic, Mark J. ; Lubans, David R. - \ 2020
    Preventive Medicine 132 (2020). - ISSN 0091-7435
    Physical activity interventions that promote cardiorespiratory (CRF) and muscular fitness (MF) may improve mental health in young adolescents. However, less is known about the links between fitness and mental health in older adolescents, as they are an understudied population. In addition, the association between MF and adolescents' mental health is less clear than it is for CRF. Our primary aim was to investigate whether MF is independently associated with mental health in a sample of older adolescents. Our secondary aim was to determine if the association between fitness and mental health was moderated by sex, socio-economic status (SES) or weight status. Participants were 670 students (16.0 [0.4] years, 44.6% female) from 20 secondary schools in New South Wales, Australia. Mental health (well-being and internalizing problems) was self-reported using the Short Warwick-Edinburgh Mental Wellbeing Scale and the Strengths and Difficulties Questionnaire. We assessed CRF using the Progressive Aerobic Cardiovascular Endurance Run and MF using the push-up and standing long jump tests. After controlling for CRF, MF was not associated with mental health. CRF was associated with well-being (β = 0.20, p < .001) and internalizing problems (β = −0.27, p < .001). The strength of association between CRF and mental health was stronger in girls, than boys. No interaction effects were observed for SES or weight status. Although cross-sectional, our findings provide further evidence of the potential benefits of CRF for adolescents' mental health (i.e., well-being and internalizing problems), particularly girls. However, MF may be less relevant for mental health among this population.
    Multi-environment analysis of sorghum breeding trials using additive and dominance genomic relationships
    Hunt, Colleen H. ; Hayes, Ben J. ; Eeuwijk, Fred A. van; Mace, Emma S. ; Jordan, David R. - \ 2020
    Theoretical and Applied Genetics 133 (2020). - ISSN 0040-5752 - p. 1009 - 1018.

    Key message: Multi-environment models using marker-based kinship information for both additive and dominance effects can accurately predict hybrid performance in different environments. Abstract: Sorghum is an important hybrid crop that is grown extensively in many subtropical and tropical regions including Northern NSW and Queensland in Australia. The highly varying weather patterns in the Australian summer months mean that sorghum hybrids exhibit a great deal of variation in yield between locations. To ultimately enable prediction of the outcome of crossing parental lines, both additive effects on yield performance and dominance interaction effects need to be characterised. This paper demonstrates that fitting a linear mixed model that includes both types of effects calculated using genetic markers in relationship matrices improves predictions. Genotype by environment interactions was investigated by comparing FA1 (single-factor analytic) and FA2 (two-factor analytic) structures. The G×E causes a change in hybrid rankings between trials with a difference of up to 25% of the hybrids in the top 10% of each trial. The prediction accuracies increased with the addition of the dominance term (over and above that achieved with an additive effect alone) by an average of 15% and a maximum of 60%. The percentage of dominance of the total genetic variance varied between trials with the trials with higher broad-sense heritability having the greater percentage of dominance. The inclusion of dominance in the factor analytic models improves the accuracy of the additive effects.Breeders selecting high yielding parents for crossing need to be aware of effects due to environment and dominance.

    Correction to: Unravelling the variability and causes of smallholder maize yield gaps in Ethiopia
    Assefa, Banchayehu Tessema ; Chamberlin, Jordan ; Reidsma, Pytrik ; Silva, João Vasco ; Ittersum, Martin K. van - \ 2020
    Food Security 12 (2020). - ISSN 1876-4517 - p. 489 - 490.

    The original version of this article unfortunately contained the following errors. (1) Title of co-author Pytrik Reidsma should be Associate Professor instead of Assistant Professor. (2) In Fig. 6, the explanations in the legend are switched. The corrected figure is shown here. (Figure presented.).

    Unravelling the variability and causes of smallholder maize yield gaps in Ethiopia
    Assefa, Banchayehu Tessema ; Chamberlin, Jordan ; Reidsma, Pytrik ; Silva, João Vasco ; Ittersum, Martin K. van - \ 2020
    Food Security 12 (2020)1. - ISSN 1876-4517 - p. 83 - 103.
    Production ecology - Smallholder agriculture - Stochastic frontier analysis - Sustainable intensification - Yield response to N - Zea mays L

    Ethiopia has achieved the second highest maize yield in sub-Saharan Africa. Yet, farmers’ maize yields are still much lower than on-farm and on-station trial yields, and only ca. 20% of the estimated water-limited potential yield. This article provides a comprehensive national level analysis of the drivers of maize yields in Ethiopia, by decomposing yield gaps into efficiency, resource and technology components, and accounting for a broad set of detailed input and crop management choices. Stochastic frontier analysis was combined with concepts of production ecology to estimate and explain technically efficient yields, the efficiency yield gap and the resource yield gap. The technology yield gap was estimated based on water-limited potential yields from the Global Yield Gap Atlas. The relative magnitudes of the efficiency, resource and technology yield gaps differed across farming systems; they ranged from 15% (1.6 t/ha) to 21% (1.9 t/ha), 12% (1.3 t/ha) to 25% (2.3 t/ha) and 54% (4.8 t/ha) to 73% (7.8 t/ha), respectively. Factors that reduce the efficiency yield gap include: income from non-farm sources, value of productive assets, education and plot distance from home. The resource yield gap can be explained by sub-optimal input use, from a yield perspective. The technology yield gap comprised the largest share of the total yield gap, partly due to limited use of fertilizer and improved seeds. We conclude that targeted but integrated policy design and implementation is required to narrow the overall maize yield gap and improve food security.

    Effectiveness of Panama as an intercontinental land bridge for large mammals
    Meyer, Ninon F.V. ; Moreno, Ricardo ; Sutherland, Christopher ; Torre, J.A. de la; Esser, Helen J. ; Jordan, Christopher A. ; Olmos, Melva ; Ortega, Josué ; Reyna-Hurtado, Rafael ; Valdes, Samuel ; Jansen, Patrick A. - \ 2020
    Conservation Biology 34 (2020)1. - ISSN 0888-8892 - p. 207 - 219.
    Bayesian statistics - community-level distribution - hierarchical occupancy modeling - landscape connectivity - Mesoamerican Biological Corridor - Neotropical forest

    Habitat fragmentation is a primary driver of wildlife loss, and establishment of biological corridors is a common strategy to mitigate this problem. A flagship example is the Mesoamerican Biological Corridor (MBC), which aims to connect protected forest areas between Mexico and Panama to allow dispersal and gene flow of forest organisms. Because forests across Central America have continued to degrade, the functioning of the MBC has been questioned, but reliable estimates of species occurrence were unavailable. Large mammals are suitable indicators of forest functioning, so we assessed their conservation status across the Isthmus of Panama, the narrowest section of the MBC. We used large-scale camera-trap surveys and hierarchical multispecies occupancy models in a Bayesian framework to estimate the occupancy of 9 medium to large mammals and developed an occupancy-weighted connectivity metric to evaluate species-specific functional connectivity. White-lipped peccary (Tayassu pecari), jaguar (Panthera onca), giant anteater (Myrmecophaga tridactyla), white-tailed deer (Odocoileus virginianus), and tapir (Tapirus bairdii) had low expected occupancy along the MBC in Panama. Puma (Puma concolor), red brocket deer (Mazama temama), ocelot (Leopardus pardalis), and collared peccary (Pecari tajacu), which are more adaptable, had higher occupancy, even in areas with low forest cover near infrastructure. However, the majority of species were subject to ≥1 gap that was larger than their known dispersal distances, suggesting poor connectivity along the MBC in Panama. Based on our results, forests in Darien, Donoso–Santa Fe, and La Amistad International Park are critical for survival of large terrestrial mammals in Panama and 2 areas need restoration.

    Protected Designation of Origin and Sustainability Characterization: The Case of PDO Cocoa Arriba
    Moreno-miranda, Carlos ; Jordán, Jeanette ; Moreno, Raúl ; Moreno, Pablo ; Solis, Jenny - \ 2019
    Agriculture 9 (2019)10. - ISSN 2077-0472
    The employment of Protected Designations of Origin (PDO) in agri-food products through recognized chains has a fundamental economic role in Ecuador. A substantial amount of research has focused on examining the crop performance of PDO products. However, there is a shift in the agri-food chain perspective towards more sustainable models. In this respect, social, economic, and institutional aspects are consequential and contribute to the agri-food sector development. The current rise in market opportunities at the local and international level drives support for them. This study aims to analyze socio-economic and governance components, in order to understand the PDO Cocoa Arriba (Theobroma cacao) chain sustainability performance and propose potential future strategies. Principal Components Analysis was used to contribute relevant insight. This framework applies accounts with a revision of primary and supporting activities. The investigation clustered pre-production, production, and post-production tiers. It also executed food chain mapping and identified chain actors. Results suggested several viable long-term strategies. Examples of these strategies include the enhancement of national regulation to assist chain actors, and the stimulus of young producers and empowerment of associations. The main contribution to the research was the application of governance mechanisms to comprehensively assess chain performance. Based on the results, we recommend incorporating new indicators to analyze the environmental and institutional components in detail
    Resource conversion by black soldier fly larvae: towards standardisation of methods and reporting
    Bosch, G. ; Oonincx, D.G.A.B. ; Jordan, H.R. ; Zhang, J. ; Loon, J.J.A. van; Huis, A. van; Tomberlin, Jeffery K. - \ 2019
    In: Book of Abstracts of the 70th Annual Meeting of the European Federation of Animal Science. - Wageningen Academic Publishers (EAAP book of abstracts No. 25 ) - ISBN 9789086863396 - p. 324 - 324.
    Standardisation of quantitative resource conversion studies with black soldier fly larvae
    Bosch, G. ; Oonincx, D.G.A.B. ; Jordan, H.R. ; Zhang, J. ; Loon, J.J.A. van; Huis, A. van; Tomberlin, Jeffery K. - \ 2019
    Journal of Insects as Food and Feed 6 (2019)2. - ISSN 2352-4588 - p. 95 - 109.
    Using larvae of the black soldier fly (Hermetia illucens; BSF) to convert low-value residual organic resources into high-value products like protein-rich animal feed ingredients and biofuel while managing organic waste has developed into a global industry. Considering the associated exponential increase in publications dealing with diet conversion efficiency by BSF larvae, it is timely to suggest procedures to arrive at an improved harmonization and reproducibility among studies. This means establishing protocols for describing the basic experiment design, fly colony origin, rearing procedures, reference and experimental feeding substrates, and sampling preparations including microbiota and chemical analyses. Such standardised protocols are instrumental to allow conversion efficiencies to be calculated. Some of these parameters are relatively easy to describe such as giving the origin and rearing conditions, while others are more challenging (e.g. description of microbe community). In this article we discuss and propose such procedures with the aim to arrive at standardisation of how future resource conversion studies with BSF larvae are conducted and how results are communicated.
    Genomic Prediction of Grain Yield and Drought-Adaptation Capacity in Sorghum Is Enhanced by Multi-Trait Analysis
    Velazco, Julio G. ; Jordan, David R. ; Mace, Emma S. ; Hunt, Colleen H. ; Malosetti, Marcos ; Eeuwijk, Fred A. van - \ 2019
    Frontiers in Plant Science 10 (2019). - ISSN 1664-462X
    auxiliary trait - blended kinship matrix - BLUP - genomic prediction - grain yield - multi-trait analysis - sorghum - stay-green

    Grain yield and stay-green drought adaptation trait are important targets of selection in grain sorghum breeding for broad adaptation to a range of environments. Genomic prediction for these traits may be enhanced by joint multi-trait analysis. The objectives of this study were to assess the capacity of multi-trait models to improve genomic prediction of parental breeding values for grain yield and stay-green in sorghum by using information from correlated auxiliary traits, and to determine the combinations of traits that optimize predictive results in specific scenarios. The dataset included phenotypic performance of 2645 testcross hybrids across 26 environments as well as genomic and pedigree information on their female parental lines. The traits considered were grain yield (GY), stay-green (SG), plant height (PH), and flowering time (FT). We evaluated the improvement in predictive performance of multi-trait G-BLUP models relative to single-trait G-BLUP. The use of a blended kinship matrix exploiting pedigree and genomic information was also explored to optimize multi-trait predictions. Predictive ability for GY increased up to 16% when PH information on the training population was exploited through multi-trait genomic analysis. For SG prediction, full advantage from multi-trait G-BLUP was obtained only when GY information was also available on the predicted lines per se, with predictive ability improvements of up to 19%. Predictive ability, unbiasedness and accuracy of predictions from conventional multi-trait G-BLUP were further optimized by using a combined pedigree-genomic relationship matrix. Results of this study suggest that multi-trait genomic evaluation combining routinely measured traits may be used to improve prediction of crop productivity and drought adaptability in grain sorghum.

    Author Correction: Reproducible, interactive, scalable and extensible microbiome data science using QIIME 2
    Bolyen, Evan ; Rideout, Jai Ram ; Dillon, Matthew R. ; Bokulich, Nicholas A. ; Abnet, Christian C. ; Al-Ghalith, Gabriel A. ; Alexander, Harriet ; Alm, Eric J. ; Arumugam, Manimozhiyan ; Asnicar, Francesco ; Bai, Yang ; Bisanz, Jordan E. ; Bittinger, Kyle ; Brejnrod, Asker ; Brislawn, Colin J. ; Brown, C.T. ; Callahan, Benjamin J. ; Caraballo-Rodríguez, Andrés Mauricio ; Chase, John ; Cope, Emily K. ; Silva, Ricardo Da; Diener, Christian ; Dorrestein, Pieter C. ; Douglas, Gavin M. ; Durall, Daniel M. ; Duvallet, Claire ; Edwardson, Christian F. ; Ernst, Madeleine ; Estaki, Mehrbod ; Fouquier, Jennifer ; Gauglitz, Julia M. ; Gibbons, Sean M. ; Gibson, Deanna L. ; Gonzalez, Antonio ; Gorlick, Kestrel ; Guo, Jiarong ; Hillmann, Benjamin ; Holmes, Susan ; Holste, Hannes ; Huttenhower, Curtis ; Huttley, Gavin A. ; Janssen, Stefan ; Jarmusch, Alan K. ; Jiang, Lingjing ; Kaehler, Benjamin D. ; Kang, Kyo Bin ; Keefe, Christopher R. ; Keim, Paul ; Kelley, Scott T. ; Knights, Dan ; Koester, Irina ; Kosciolek, Tomasz ; Kreps, Jorden ; Langille, Morgan G.I. ; Lee, Joslynn ; Ley, Ruth ; Liu, Yong Xin ; Loftfield, Erikka ; Lozupone, Catherine ; Maher, Massoud ; Marotz, Clarisse ; Martin, Bryan D. ; McDonald, Daniel ; McIver, Lauren J. ; Melnik, Alexey V. ; Metcalf, Jessica L. ; Morgan, Sydney C. ; Morton, Jamie T. ; Naimey, Ahmad Turan ; Navas-Molina, Jose A. ; Nothias, Louis Felix ; Orchanian, Stephanie B. ; Pearson, Talima ; Peoples, Samuel L. ; Petras, Daniel ; Preuss, Mary Lai ; Pruesse, Elmar ; Rasmussen, Lasse Buur ; Rivers, Adam ; Robeson, Michael S. ; Rosenthal, Patrick ; Segata, Nicola ; Shaffer, Michael ; Shiffer, Arron ; Sinha, Rashmi ; Song, Se Jin ; Spear, John R. ; Swafford, Austin D. ; Thompson, Luke R. ; Torres, Pedro J. ; Trinh, Pauline ; Tripathi, Anupriya ; Turnbaugh, Peter J. ; Ul-Hasan, Sabah ; Hooft, Justin J.J. van der; Vargas, Fernando ; Vázquez-Baeza, Yoshiki ; Vogtmann, Emily ; Hippel, Max von; Walters, William ; Wan, Yunhu ; Wang, Mingxun ; Warren, Jonathan ; Weber, Kyle C. ; Williamson, Charles H.D. ; Willis, Amy D. ; Xu, Zhenjiang Zech ; Zaneveld, Jesse R. ; Zhang, Yilong ; Zhu, Qiyun ; Knight, Rob ; Caporaso, J.G. - \ 2019
    Nature Biotechnology (2019). - ISSN 1087-0156

    In the version of this article initially published, some reference citations were incorrect. The three references to Jupyter Notebooks should have cited Kluyver et al. instead of Gonzalez et al. The reference to Qiita should have cited Gonzalez et al. instead of Schloss et al. The reference to mothur should have cited Schloss et al. instead of McMurdie & Holmes. The reference to phyloseq should have cited McMurdie & Holmes instead of Huber et al. The reference to Bioconductor should have cited Huber et al. instead of Franzosa et al. And the reference to the biobakery suite should have cited Franzosa et al. instead of Kluyver et al. The errors have been corrected in the HTML and PDF versions of the article.

    Reproducible, interactive, scalable and extensible microbiome data science using QIIME 2
    Bolyen, Evan ; Rideout, Jai Ram ; Dillon, Matthew R. ; Bokulich, Nicholas A. ; Abnet, Christian C. ; Al-Ghalith, Gabriel A. ; Alexander, Harriet ; Alm, Eric J. ; Arumugam, Manimozhiyan ; Asnicar, Francesco ; Bai, Yang ; Bisanz, Jordan E. ; Bittinger, Kyle ; Brejnrod, Asker ; Brislawn, Colin J. ; Brown, Titus C. ; Callahan, Benjamin J. ; Caraballo-Rodríguez, Andrés Mauricio ; Chase, John ; Cope, Emily K. ; Silva, Ricardo da; Diener, Christian ; Dorrestein, Pieter C. ; Douglas, Gavin M. ; Durall, Daniel M. ; Duvallet, Claire ; Edwardson, Christian F. ; Ernst, Madeleine ; Estaki, Mehrbod ; Fouquier, Jennifer ; Gauglitz, Julia M. ; Gibbons, Sean M. ; Gibson, Deanna L. ; Gonzalez, Antonio ; Gorlick, Kestrel ; Guo, Jiarong ; Hillmann, Benjamin ; Holmes, Susan ; Holste, Hannes ; Huttenhower, Curtis ; Huttley, Gavin A. ; Janssen, Stefan ; Jarmusch, Alan K. ; Jiang, Lingjing ; Kaehler, Benjamin D. ; Kang, Kyo Bin ; Keefe, Christopher R. ; Keim, Paul ; Kelley, Scott T. ; Knights, Dan ; Koester, Irina ; Kosciolek, Tomasz ; Kreps, Jorden ; Langille, Morgan G.I. ; Lee, Joslynn ; Ley, Ruth ; Liu, Yong Xin ; Loftfield, Erikka ; Lozupone, Catherine ; Maher, Massoud ; Marotz, Clarisse ; Martin, Bryan D. ; McDonald, Daniel ; McIver, Lauren J. ; Melnik, Alexey V. ; Metcalf, Jessica L. ; Morgan, Sydney C. ; Morton, Jamie T. ; Naimey, Ahmad Turan ; Navas-Molina, Jose A. ; Nothias, Louis Felix ; Orchanian, Stephanie B. ; Pearson, Talima ; Peoples, Samuel L. ; Petras, Daniel ; Preuss, Mary Lai ; Pruesse, Elmar ; Rasmussen, Lasse Buur ; Rivers, Adam ; Robeson, Michael S. ; Rosenthal, Patrick ; Segata, Nicola ; Shaffer, Michael ; Shiffer, Arron ; Sinha, Rashmi ; Song, Se Jin ; Spear, John R. ; Swafford, Austin D. ; Thompson, Luke R. ; Torres, Pedro J. ; Trinh, Pauline ; Tripathi, Anupriya ; Turnbaugh, Peter J. ; Ul-Hasan, Sabah ; Hooft, Justin J.J. van der; Vargas, Fernando ; Vázquez-Baeza, Yoshiki ; Vogtmann, Emily ; Hippel, Max von; Walters, William ; Wan, Yunhu ; Wang, Mingxun ; Warren, Jonathan ; Weber, Kyle C. ; Williamson, Charles H.D. ; Willis, Amy D. ; Xu, Zhenjiang Zech ; Zaneveld, Jesse R. ; Zhang, Yilong ; Zhu, Qiyun ; Knight, Rob ; Caporaso, J.G. - \ 2019
    Nature Biotechnology 37 (2019)8. - ISSN 1087-0156 - p. 852 - 857.
    Combining pedigree and genomic information to improve prediction quality: an example in sorghum
    Velazco, Julio G. ; Malosetti, Marcos ; Hunt, Colleen H. ; Mace, Emma S. ; Jordan, David R. ; Eeuwijk, Fred A. van - \ 2019
    Theoretical and Applied Genetics 132 (2019)7. - ISSN 0040-5752 - p. 2055 - 2067.

    Key message: The use of a kinship matrix integrating pedigree- and marker-based relationships optimized the performance of genomic prediction in sorghum, especially for traits of lower heritability. Abstract: Selection based on genome-wide markers has become an active breeding strategy in crops. Genomic prediction models can make use of pedigree information to account for the residual polygenic effects not captured by markers. Our aim was to evaluate the impact of using pedigree and genomic information on prediction quality of breeding values for different traits in sorghum. We explored BLUP models that use weighted combinations of pedigree and genomic relationship matrices. The optimal weighting factor was empirically determined in order to maximize predictive ability after evaluating a range of candidate weights. The phenotypic data consisted of testcross evaluations of sorghum parental lines across multiple environments. All lines were genotyped, and full pedigree information was available. The performance of the best predictive combined matrix was compared to that of models fitting the component matrices independently. Model performance was assessed using cross-validation technique. Fitting a combined pedigree–genomic matrix with the optimal weight always yielded the largest increases in predictive ability and the largest reductions in prediction bias relative to the simple G-BLUP. However, the weight that optimized prediction varied across traits. The benefits of including pedigree information in the genomic model were more relevant for traits with lower heritability, such as grain yield and stay-green. Our results suggest that the combination of pedigree and genomic relatedness can be used to optimize predictions of complex traits in crops when the additive variation is not fully explained by markers.

    Dietary supplementation of 11 different plant extracts on the antioxidant capacity of blood and selected tissues in lightweight lambs
    Leal, Leonel N. ; Jordán, María J. ; Bello, José M. ; Otal, Julio ; Hartog, Leo A. den; Hendriks, Wouter H. ; Martín-Tereso, Javier - \ 2019
    Journal of the Science of Food and Agriculture 99 (2019)9. - ISSN 0022-5142 - p. 4296 - 4303.
    kidney - lambs - liver - muscle - plant extracts - plasma

    BACKGROUND: Due to the growing public concern regarding the addition of chemical antioxidants to foods, focus has shifted towards natural alternatives. Because of their antioxidant potential, culinary herbs and spices have long been used to extend the shelf-life of foods. However, a better understanding of the fate of these products following intake is required to assess their use in lamb diets. RESULTS: Two hundred and eighty-eight Rasa Aragonesa male lambs (70 days old) were supplemented (5.0 g kg −1 compound feed) with bay, marjoram, oregano, rosemary, thyme, turmeric, cumin, caraway, dill, cinnamon and nutmeg extracts for 14 days before slaughter. Dietary supplementation with plant extracts had no effect on intake, growth performance or antioxidant activity in blood (TEAC values). In muscle, nutmeg supplementation increased (P < 0.05) the radical-scavenging capacity (TEAC), whereas a decrease in the radical-scavenging capacity was found for lambs supplemented with oregano, dill, cinnamon and nutmeg (ORAC values). In liver, nutmeg supplementation increased (P < 0.05) the antioxidant capacity (TEAC), whereas bay (ORAC), turmeric, cinnamon and nutmeg (DPPH values) decreased (P < 0.05) the radical-scavenging capacity of the tissue. In kidney, a lower (P < 0.05) radical-scavenging capacity (TEAC values) was found in lambs supplemented with oregano, cumin and caraway, whereas, turmeric, cumin, caraway, cinnamon and nutmeg increased (P < 0.05) the antioxidant capacity (ORAC values) in kidney. CONCLUSION: Supplementation of lamb diets with plant extracts affected radical-scavenging activity in muscle, liver and kidney. However, due to the divergent results of the different assays for the same tissue, it is not advisable to discriminate plant extracts using this approach.

    Disentangling the genetics of lean mass
    Karasik, David ; Zillikens, M.C. ; Hsu, Yi Hsiang ; Aghdassi, Ali ; Akesson, Kristina ; Amin, Najaf ; Barroso, Inês ; Bennett, David A. ; Bertram, Lars ; Bochud, Murielle ; Borecki, Ingrid B. ; Broer, Linda ; Buchman, Aron S. ; Byberg, Liisa ; Campbell, Harry ; Campos-Obando, Natalia ; Cauley, Jane A. ; Cawthon, Peggy M. ; Chambers, John C. ; Chen, Zhao ; Cho, Nam H. ; Choi, Hyung Jin ; Chou, Wen Chi ; Cummings, Steven R. ; Groot, Lisette C.P.G.M. De; Jager, Phillip L. De; Demuth, Ilja ; Diatchenko, Luda ; Econs, Michael J. ; Eiriksdottir, Gudny ; Enneman, Anke W. ; Eriksson, Joel ; Eriksson, Johan G. ; Estrada, Karol ; Evans, Daniel S. ; Feitosa, Mary F. ; Fu, Mao ; Gieger, Christian ; Grallert, Harald ; Gudnason, Vilmundur ; Lenore, Launer J. ; Hayward, Caroline ; Hofman, Albert ; Homuth, Georg ; Huffman, Kim M. ; Husted, Lise B. ; Illig, Thomas ; Ingelsson, Erik ; Ittermann, Till ; Jansson, John Olov ; Johnson, Toby ; Biffar, Reiner ; Jordan, Joanne M. ; Jula, Antti ; Karlsson, Magnus ; Khaw, Kay Tee ; Kilpeläinen, Tuomas O. ; Klopp, Norman ; Kloth, Jacqueline S.L. ; Koller, Daniel L. ; Kooner, Jaspal S. ; Kraus, William E. ; Kritchevsky, Stephen ; Kutalik, Zoltán ; Kuulasmaa, Teemu ; Kuusisto, Johanna ; Laakso, Markku ; Lahti, Jari ; Lang, Thomas ; Langdahl, Bente L. ; Lerch, Markus M. ; Lewis, Joshua R. ; Lill, Christina ; Lind, Lars ; Lindgren, Cecilia ; Liu, Yongmei ; Livshits, Gregory ; Ljunggren, Östen ; Loos, Ruth J.F. ; Lorentzon, Mattias ; Luan, Jian An ; Luben, Robert N. ; Malkin, Ida ; McGuigan, Fiona E. ; Medina-Gomez, Carolina ; Meitinger, Thomas ; Melhus, Håkan ; Mellström, Dan ; Michaëlsson, Karl ; Mitchell, Braxton D. ; Morris, Andrew P. ; Mosekilde, Leif ; Nethander, Maria ; Newman, Anne B. ; Oconnell, Jeffery R. ; Oostra, Ben A. ; Orwoll, Eric S. ; Palotie, Aarno ; Peacock, Munro ; Perola, Markus ; Peters, Annette ; Prince, Richard L. ; Psaty, Bruce M. ; Räikkönen, Katri ; Ralston, Stuart H. ; Ripatti, Samuli ; Rivadeneira, Fernando ; Robbins, John A. ; Rotter, Jerome I. ; Rudan, Igor ; Salomaa, Veikko ; Satterfield, Suzanne ; Schipf, Sabine ; Shin, Chan Soo ; Smith, Albert V. ; Smith, Shad B. ; Soranzo, Nicole ; Spector, Timothy D. ; StanÄ Áková, Alena ; Stefansson, Kari ; Steinhagen-Thiessen, Elisabeth ; Stolk, Lisette ; Streeten, Elizabeth A. ; Styrkarsdottir, Unnur ; Swart, Karin M.A. ; Thompson, Patricia ; Thomson, Cynthia A. ; Thorleifsson, Gudmar ; Thorsteinsdottir, Unnur ; Tikkanen, Emmi ; Tranah, Gregory J. ; Uitterlinden, André G. ; Duijn, Cornelia M. Van; Schoor, Natasja M. Van; Vandenput, Liesbeth ; Vollenweider, Peter ; Völzke, Henry ; Wactawski-Wende, Jean ; Walker, Mark ; J Wareham, Nicholas ; Waterworth, Dawn ; Weedon, Michael N. ; Wichmann, H.E. ; Widen, Elisabeth ; Williams, Frances M.K. ; Wilson, James F. ; Wright, Nicole C. ; Yerges-Armstrong, Laura M. ; Yu, Lei ; Zhang, Weihua ; Zhao, Jing Hua ; Zhou, Yanhua ; Nielson, Carrie M. ; Harris, Tamara B. ; Demissie, Serkalem ; Kiel, Douglas P. ; Ohlsson, Claes - \ 2019
    American Journal of Clinical Nutrition 109 (2019)2. - ISSN 0002-9165 - p. 276 - 278.
    body composition - body fat - meta-Analysis of genome-wide association studies - metabolic profile - skeletal muscle

    Background Lean body mass (LM) plays an important role in mobility and metabolic function. We previously identified five loci associated with LM adjusted for fat mass in kilograms. Such an adjustment may reduce the power to identify genetic signals having an association with both lean mass and fat mass. Objectives To determine the impact of different fat mass adjustments on genetic architecture of LM and identify additional LM loci. Methods We performed genome-wide association analyses for whole-body LM (20 cohorts of European ancestry with n = 38,292) measured using dual-energy X-ray absorptiometry) or bioelectrical impedance analysis, adjusted for sex, age, age 2, and height with or without fat mass adjustments (Model 1 no fat adjustment; Model 2 adjustment for fat mass as a percentage of body mass; Model 3 adjustment for fat mass in kilograms). Results Seven single-nucleotide polymorphisms (SNPs) in separate loci, including one novel LM locus (TNRC6B), were successfully replicated in an additional 47,227 individuals from 29 cohorts. Based on the strengths of the associations in Model 1 vs Model 3, we divided the LM loci into those with an effect on both lean mass and fat mass in the same direction and refer to those as "sumo wrestler" loci (FTO and MC4R). In contrast, loci with an impact specifically on LM were termed "body builder" loci (VCAN and ADAMTSL3). Using existing available genome-wide association study databases, LM increasing alleles of SNPs in sumo wrestler loci were associated with an adverse metabolic profile, whereas LM increasing alleles of SNPs in "body builder" loci were associated with metabolic protection. Conclusions In conclusion, we identified one novel LM locus (TNRC6B). Our results suggest that a genetically determined increase in lean mass might exert either harmful or protective effects on metabolic traits, depending on its relation to fat mass.

    A spatial framework for ex-ante impact assessment of agricultural technologies
    Andrade, José F. ; Rattalino Edreira, Juan I. ; Farrow, Andrew ; Loon, Marloes P. van; Craufurd, Peter Q. ; Rurinda, Jairos ; Zingore, Shamie ; Chamberlin, Jordan ; Claessens, Lieven ; Adewopo, Julius ; Ittersum, Martin K. van; Cassman, Kenneth G. ; Grassini, Patricio - \ 2019
    Global Food Security 20 (2019). - ISSN 2211-9124 - p. 72 - 81.
    Agricultural R&D - Impact assessment - Scaling out - Spatial framework

    Traditional agricultural research and extension relies on replicated field experiments, on-farm trials, and demonstration plots to evaluate and adapt agronomic technologies that aim to increase productivity, reduce risk, and protect the environment for a given biophysical and socio-economic context. To date, these efforts lack a generic and robust spatial framework for ex-ante assessment that: (i) provides strategic insight to guide decisions about the number and location of testing sites, (ii) define the target domain for scaling-out a given technology or technology package, and (iii) estimate potential impact from widespread adoption of the technology(ies) being evaluated. In this study, we developed a data-rich spatial framework to guide agricultural research and development (AR&D) prioritization and to perform ex-ante impact assessment. The framework uses “technology extrapolation domains”, which delineate regions with similar climate and soil type combined with other biophysical and socio-economic factors that influence technology adoption. We provide proof of concept for the framework using a maize agronomy project in three sub-Saharan Africa countries (Ethiopia, Nigeria, and Tanzania) as a case study. We used maize area and rural population coverage as indicators to estimate potential project impact in each country. The project conducted 496 nutrient omission trials located at both on-farm and research station sites across these three countries. Reallocation of test sites towards domains with a larger proportion of national maize area could increase coverage of maize area by 79–134% and of rural population by 14–33% in Nigeria and Ethiopia. This study represents a first step in developing a generic, transparent, and scientifically robust framework to estimate ex-ante impact of AR&D programs that aim to increase food production and reduce poverty and hunger.

    The agricultural knowledge and innovation system of Jordan’s horticultural sector : Current state and suggestions for improvement
    Sixt, Gregory ; Poppe, Krijn - \ 2019
    Wageningen : Wageningen Economic Research (Wageningen Economic Research report 2019-005) - ISBN 9789463435307 - 45
    The horticultural sector in Jordan is undergoing a crisis, due to a decline in export. Innovation can improve the performance of the sector. To this end, the government of Jordan should pursue an innovation policy with the Agricultural Knowledge and Innovation System (AKIS) as object of the governance. Based on a review of the AKIS in Jordan it is proposed that a Living Lab setting be used to gain experience with the management of a number of innovation projects and capacity building projects.
    Wageningen la fac qui veut nourrir le monde
    Noort, F.R. van - \ 2018
    Country profile Jordan
    Saaf, Ele Jan ; Brouwer, J.H. ; Peters, Bram ; Plataroti, Lavinia - \ 2018
    Wageningen Centre for Development Innovation - 8 p.
    This country profile, commissioned by The Netherlands Ministry of Foreign Affairs (Department of Inclusive Green Growth), gives a snapshot of what is happening in the closely interrelated themes Food & Nutrition Security, Water and Climate and Renewable Energy in Jordan. It provides basic statistics on Jordan’s performance on key indicators and indexes, but also analyses relevant national policies, current donor interventions, and the main trends on the abovementioned themes. Combined with an overview of Dutch support to Jordan, this profile concludes by suggesting potential priority result areas for The Netherlands.
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