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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Alternative Oxidase (AOX) Senses Stress Levels to Coordinate Auxin-Induced Reprogramming From Seed Germination to Somatic Embryogenesis—A Role Relevant for Seed Vigor Prediction and Plant Robustness
Mohanapriya, Gunasekaran ; Bharadwaj, Revuru ; Noceda, Carlos ; Costa, José Hélio ; Kumar, Sarma Rajeev ; Sathishkumar, Ramalingam ; Thiers, Karine Leitão Lima ; Santos Macedo, Elisete ; Silva, Sofia ; Annicchiarico, Paolo ; Groot, Steven P.C. ; Kodde, Jan ; Kumari, Aprajita ; Gupta, Kapuganti Jagadis ; Arnholdt-Schmitt, Birgit - \ 2019
Frontiers in Plant Science 10 (2019). - ISSN 1664-462X
developmental plasticity - endophytes - environmental stress - metabolic biomarker - plant performance prediction - seed technology

Somatic embryogenesis (SE) is the most striking and prominent example of plant plasticity upon severe stress. Inducing immature carrot seeds perform SE as substitute to germination by auxin treatment can be seen as switch between stress levels associated to morphophysiological plasticity. This experimental system is highly powerful to explore stress response factors that mediate the metabolic switch between cell and tissue identities. Developmental plasticity per se is an emerging trait for in vitro systems and crop improvement. It is supposed to underlie multi-stress tolerance. High plasticity can protect plants throughout life cycles against variable abiotic and biotic conditions. We provide proof of concepts for the existing hypothesis that alternative oxidase (AOX) can be relevant for developmental plasticity and be associated to yield stability. Our perspective on AOX as relevant coordinator of cell reprogramming is supported by real-time polymerase chain reaction (PCR) analyses and gross metabolism data from calorespirometry complemented by SHAM-inhibitor studies on primed, elevated partial pressure of oxygen (EPPO)–stressed, and endophyte-treated seeds. In silico studies on public experimental data from diverse species strengthen generality of our insights. Finally, we highlight ready-to-use concepts for plant selection and optimizing in vivo and in vitro propagation that do not require further details on molecular physiology and metabolism. This is demonstrated by applying our research & technology concepts to pea genotypes with differential yield performance in multilocation fields and chickpea types known for differential robustness in the field. By using these concepts and tools appropriately, also other marker candidates than AOX and complex genomics data can be efficiently validated for prebreeding and seed vigor prediction.

BrAPI-an application programming interface for plant breeding applications
Selby, Peter ; Abbeloos, Rafael ; Backlund, Jan Erik ; Basterrechea Salido, Martin ; Bauchet, Guillaume ; Benites-Alfaro, Omar E. ; Birkett, Clay ; Calaminos, Viana C. ; Carceller, Pierre ; Cornut, Guillaume ; Vasques Costa, Bruno ; Edwards, Jeremy D. ; Finkers, Richard ; Yanxin Gao, Star ; Ghaffar, Mehmood ; Glaser, Philip ; Guignon, Valentin ; Hok, Puthick ; Kilian, Andrzej ; König, Patrick ; Lagare, Jack Elendil B. ; Lange, Matthias ; Laporte, Marie Angélique ; Larmande, Pierre ; LeBauer, David S. ; Lyon, David A. ; Marshall, David S. ; Matthews, Dave ; Milne, Iain ; Mistry, Naymesh ; Morales, Nicolas ; Mueller, Lukas A. ; Neveu, Pascal ; Papoutsoglou, Evangelia ; Pearce, Brian ; Perez-Masias, Ivan ; Pommier, Cyril ; Ramírez-González, Ricardo H. ; Rathore, Abhishek ; Raquel, Angel Manica ; Raubach, Sebastian ; Rife, Trevor ; Robbins, Kelly ; Rouard, Mathieu ; Sarma, Chaitanya ; Scholz, Uwe ; Sempéré, Guilhem ; Shaw, Paul D. ; Simon, Reinhard ; Verouden, Maikel - \ 2019
Bioinformatics 35 (2019)20. - ISSN 1367-4803 - p. 4147 - 4155.

MOTIVATION: Modern genomic breeding methods rely heavily on very large amounts of phenotyping and genotyping data, presenting new challenges in effective data management and integration. Recently, the size and complexity of datasets have increased significantly, with the result that data are often stored on multiple systems. As analyses of interest increasingly require aggregation of datasets from diverse sources, data exchange between disparate systems becomes a challenge. RESULTS: To facilitate interoperability among breeding applications, we present the public plant Breeding Application Programming Interface (BrAPI). BrAPI is a standardized web service API specification. The development of BrAPI is a collaborative, community-based initiative involving a growing global community of over a hundred participants representing several dozen institutions and companies. Development of such a standard is recognized as critical to a number of important large breeding system initiatives as a foundational technology. The focus of the first version of the API is on providing services for connecting systems and retrieving basic breeding data including germplasm, study, observation, and marker data. A number of BrAPI-enabled applications, termed BrAPPs, have been written, that take advantage of the emerging support of BrAPI by many databases. AVAILABILITY AND IMPLEMENTATION: More information on BrAPI, including links to the specification, test suites, BrAPPs, and sample implementations is available at The BrAPI specification and the developer tools are provided as free and open source.

Rarity of monodominance in hyperdiverse Amazonian forests
Steege, Hans Ter; Henkel, Terry W. ; Helal, Nora ; Marimon, Beatriz S. ; Marimon-Junior, Ben Hur ; Huth, Andreas ; Groeneveld, Jürgen ; Sabatier, Daniel ; Souza Coelho, Luiz de; Andrade Lima Filho, Diogenes de; Salomão, Rafael P. ; Amaral, Iêda Leão ; Almeida Matos, Francisca Dionízia de; Castilho, Carolina V. ; Phillips, Oliver L. ; Guevara, Juan Ernesto ; Jesus Veiga Carim, Marcelo de; Cárdenas López, Dairon ; Magnusson, William E. ; Wittmann, Florian ; Irume, Mariana Victória ; Martins, Maria Pires ; Silva Guimarães, José Renan da; Molino, Jean François ; Bánki, Olaf S. ; Piedade, Maria Teresa Fernandez ; Pitman, Nigel C.A. ; Mendoza, Abel Monteagudo ; Ramos, José Ferreira ; Luize, Bruno Garcia ; Moraes de Leão Novo, Evlyn Márcia ; Núñez Vargas, Percy ; Silva, Thiago Sanna Freire ; Venticinque, Eduardo Martins ; Manzatto, Angelo Gilberto ; Reis, Neidiane Farias Costa ; Terborgh, John ; Casula, Katia Regina ; Honorio Coronado, Euridice N. ; Montero, Juan Carlos ; Feldpausch, Ted R. ; Duque, Alvaro ; Costa, Flávia R.C. ; Arboleda, Nicolás Castaño ; Schöngart, Jochen ; Killeen, Timothy J. ; Vasquez, Rodolfo ; Mostacedo, Bonifacio ; Demarchi, Layon O. ; Assis, Rafael L. ; Baraloto, Chris ; Engel, Julien ; Petronelli, Pascal ; Castellanos, Hernán ; Medeiros, Marcelo Brilhante de; Quaresma, Adriano ; Simon, Marcelo Fragomeni ; Andrade, Ana ; Camargo, José Luís ; Laurance, Susan G.W. ; Laurance, William F. ; Rincón, Lorena M. ; Schietti, Juliana ; Sousa, Thaiane R. ; Sousa Farias, Emanuelle de; Lopes, Maria Aparecida ; Magalhães, José Leonardo Lima ; Mendonça Nascimento, Henrique Eduardo ; Lima de Queiroz, Helder ; Aymard C, Gerardo A. ; Brienen, Roel ; Revilla, Juan David Cardenas ; Vieira, Ima Célia Guimarães ; Cintra, Bruno Barçante Ladvocat ; Stevenson, Pablo R. ; Feitosa, Yuri Oliveira ; Duivenvoorden, Joost F. ; Mogollón, Hugo F. ; Araujo-Murakami, Alejandro ; Ferreira, Leandro Valle ; Lozada, José Rafael ; Comiskey, James A. ; Toledo, José Julio de; Damasco, Gabriel ; Dávila, Nállarett ; Draper, Freddie ; García-Villacorta, Roosevelt ; Lopes, Aline ; Vicentini, Alberto ; Alonso, Alfonso ; Dallmeier, Francisco ; Gomes, Vitor H.F. ; Lloyd, Jon ; Neill, David ; Aguiar, Daniel Praia Portela de; Arroyo, Luzmila ; Carvalho, Fernanda Antunes ; Souza, Fernanda Coelho de; Amaral, Dário Dantas do; Feeley, Kenneth J. ; Gribel, Rogerio ; Pansonato, Marcelo Petratti ; Barlow, Jos ; Berenguer, Erika ; Ferreira, Joice ; Fine, Paul V.A. ; Guedes, Marcelino Carneiro ; Jimenez, Eliana M. ; Licona, Juan Carlos ; Peñuela Mora, Maria Cristina ; Villa, Boris ; Cerón, Carlos ; Maas, Paul ; Silveira, Marcos ; Stropp, Juliana ; Thomas, Raquel ; Baker, Tim R. ; Daly, Doug ; Dexter, Kyle G. ; Huamantupa-Chuquimaco, Isau ; Milliken, William ; Pennington, Toby ; Ríos Paredes, Marcos ; Fuentes, Alfredo ; Klitgaard, Bente ; Pena, José Luis Marcelo ; Peres, Carlos A. ; Silman, Miles R. ; Tello, J.S. ; Chave, Jerome ; Cornejo Valverde, Fernando ; Fiore, Anthony Di; Hilário, Renato Richard ; Phillips, Juan Fernando ; Rivas-Torres, Gonzalo ; Andel, Tinde R. van; Hildebrand, Patricio von; Noronha, Janaína Costa ; Barbosa, Edelcilio Marques ; Barbosa, Flávia Rodrigues ; Matos Bonates, Luiz Carlos de; Sá Carpanedo, Rainiellen de; Dávila Doza, Hilda Paulette ; Fonty, Émile ; GómeZárate Z, Ricardo ; Gonzales, Therany ; Gallardo Gonzales, George Pepe ; Hoffman, Bruce ; Junqueira, André Braga ; Malhi, Yadvinder ; Andrade Miranda, Ires Paula de; Pinto, Linder Felipe Mozombite ; Prieto, Adriana ; Jesus Rodrigues, Domingos de; Rudas, Agustín ; Ruschel, Ademir R. ; Silva, Natalino ; Vela, César I.A. ; Vos, Vincent Antoine ; Zent, Egleé L. ; Zent, Stanford ; Weiss Albuquerque, Bianca ; Cano, Angela ; Carrero Márquez, Yrma Andreina ; Correa, Diego F. ; Costa, Janaina Barbosa Pedrosa ; Flores, Bernardo Monteiro ; Galbraith, David ; Holmgren, Milena ; Kalamandeen, Michelle ; Nascimento, Marcelo Trindade ; Oliveira, Alexandre A. ; Ramirez-Angulo, Hirma ; Rocha, Maira ; Scudeller, Veridiana Vizoni ; Sierra, Rodrigo ; Tirado, Milton ; Umaña Medina, Maria Natalia ; Heijden, Geertje van der; Vilanova Torre, Emilio ; Vriesendorp, Corine ; Wang, Ophelia ; Young, Kenneth R. ; Ahuite Reategui, Manuel Augusto ; Baider, Cláudia ; Balslev, Henrik ; Cárdenas, Sasha ; Casas, Luisa Fernanda ; Farfan-Rios, William ; Ferreira, Cid ; Linares-Palomino, Reynaldo ; Mendoza, Casimiro ; Mesones, Italo ; Torres-Lezama, Armando ; Giraldo, Ligia Estela Urrego ; Villarroel, Daniel ; Zagt, Roderick ; Alexiades, Miguel N. ; Oliveira, Edmar Almeida de; Garcia-Cabrera, Karina ; Hernandez, Lionel ; Palacios Cuenca, Walter ; Pansini, Susamar ; Pauletto, Daniela ; Ramirez Arevalo, Freddy ; Sampaio, Adeilza Felipe ; Valderrama Sandoval, Elvis H. ; Valenzuela Gamarra, Luis ; Levesley, Aurora ; Pickavance, Georgia ; Melgaço, Karina - \ 2019
Scientific Reports 9 (2019). - ISSN 2045-2322

Tropical forests are known for their high diversity. Yet, forest patches do occur in the tropics where a single tree species is dominant. Such "monodominant" forests are known from all of the main tropical regions. For Amazonia, we sampled the occurrence of monodominance in a massive, basin-wide database of forest-inventory plots from the Amazon Tree Diversity Network (ATDN). Utilizing a simple defining metric of at least half of the trees ≥ 10 cm diameter belonging to one species, we found only a few occurrences of monodominance in Amazonia, and the phenomenon was not significantly linked to previously hypothesized life history traits such wood density, seed mass, ectomycorrhizal associations, or Rhizobium nodulation. In our analysis, coppicing (the formation of sprouts at the base of the tree or on roots) was the only trait significantly linked to monodominance. While at specific locales coppicing or ectomycorrhizal associations may confer a considerable advantage to a tree species and lead to its monodominance, very few species have these traits. Mining of the ATDN dataset suggests that monodominance is quite rare in Amazonia, and may be linked primarily to edaphic factors.

Credit, insurance and farmers’ liability: Evidence from a lab in the field experiment with coffee farmers in Costa Rica
Naranjo, María A. ; Pieters, Janneke ; Alpízar, Francisco - \ 2019
Journal of Economic Behavior and Organization 166 (2019). - ISSN 0167-2681 - p. 12 - 27.
Agriculture - Credit - Insurance - Liability

This paper examines the effect of farmers’ liability on demand for credit with and without insurance. We test predictions of a theoretical model in a lab in the field experiment with coffee farmers in Costa Rica. Farmers choose how much to invest in six different settings, described on the one hand by whether the loan is insured or not, and on the other by their liability. Our results show that the uptake of loans bundled with insurance is significantly higher than the uptake of loans without insurance, when farmers are liable for sure, and when there is uncertainty about their liability. In the case of limited liability, the uptake of credit is high irrespective of whether the loans are insured or not. Our results suggest that in order to increase the uptake of insurance as a strategy to increase private investment and reduce the vulnerability of farmers to shocks, it is important that farmers are liable with at least some probability.

Managing the farmscape for connectivity increases conservation value for tropical bird species with different forest-dependencies
Estrada-Carmona, N. ; Martínez-Salinas, A. ; DeClerck, F.A.J. ; Vílchez-Mendoza, S. ; Garbach, K. - \ 2019
Journal of Environmental Management 250 (2019). - ISSN 0301-4797
Agricultural landscapes - Agroforestry system - Circuitscape model - Costa Rica - Functional connectivity - Sustainable resource management

Land clearing for agricultural use is a primary driver of biodiversity loss and fragmentation of natural ecosystems. Restoring natural habitat connectivity by retaining quality habitats and increasing on-farm tree cover contributes to species' mobility and persistence in agricultural landscapes. Nonetheless, remarkably few studies have quantified the impacts of on-farm practices for species' mobility measured as functional connectivity within the context of farm and broader spatial levels of landscape organization. We tested how adding and removing trees in different configurations on a farm comprised of coffee plantations and cattle pastures can help evaluate species’ mobility at the farmscape level (an area comprising the farm plus a 1.5 km buffer area). We coupled bird capture data and scenario modeling to assess species mobility of five neotropical bird species with distinct life history characteristics representing a gradient of forest dependency. We used seven years of mist-netting data to estimate species habitat affinity and to predict species mobility using the Circuitscape model across a 4371 ha farmscape in Costa Rica. Circuitscape allowed us to estimate changes in movement probability and relative changes in resistance to movement that species experience during dispersal (measured as resistance distance and passage area through which species can move) under four farmscape management scenarios. The four land-use scenarios included: (a) the 2011 farmscape land-use composition and configuration, b) converting all existing live fences to post-and-wire fence lines in the farm c) converting simplified coffee agroforests to multistrata coffee agroforests in the farm, and d) placing multistrata live fences around the perimeter of every parcel and roads on the farm. Model results suggest that existing multistrata live fences maintain the sporadic movement of all five species irrespective of forest dependence. Likewise, adding multistrata live fences around individual fields presents a more efficient strategy for increasing species mobility than multistrata coffee agroforestry systems in the assessed farmscape, by doubling the passage areas available to all species, although it created labyrinths with “dead-ends” for two species. While retaining large habitat patches remains important for conservation, managing on-farm connectivity complements these efforts by increasing movement probability and reducing dispersal resistance for forest-dependent bird species.

Genome wide association studies and whole transcriptomic survey decipher the fruit texture regulation in apple towards the selection of novel superior accessions
Guardo, M. Di; Tadiello, A. ; Farneti, B. ; Busatto, N. ; Delledonne, M. ; Guerra, W. ; Letschka, T. ; Lozano, L. ; Velasco, R. ; Weg, E. Van de; Bink, M. ; Costa, F. - \ 2019
Acta Horticulturae 1242 (2019). - ISSN 0567-7572 - p. 441 - 446.
Ethylene - Fruit quality - GWAS - Marker assisted selection - Pedigree based analysis - Texture

Fruit quality is represented by a series of genetically controlled features that change throughout the entire ontogenic life. Among the several quality traits, texture plays a crucial role, impacting both consumers’ appreciation and postharvest performance. In order to decipher its regulation a multidisciplinary approach was employed. Initially, the texture performance was measured with a high resolution phenotyping device, represented by a texture analyzer equipped with an acoustic device. In the first attempt to dissect the fruit texture genetic control, two QTL mapping strategies were used. The first approach employed six bi-parental families linked by a common pedigree scheme, known as pedigree based analysis. The joint analysis of the phenotypic and genotypic data set through a Bayesian statistics identified a series of genomic regions related to both mechanical and acoustic signatures. These regions were further validated with a genome wide association study approach, which considered a much larger phenotypic and genotypic variation. To complement the genetic information, a whole transcriptome analysis was also carried out. To this end, two microarray platforms were designed and used to unravel the functional machinery ongoing during the fruit development and ripening phases, especially with regards to the plant hormone ethylene. In this study, the role of this hormone was dissected applying 1-MCP, a molecule competing with ethylene at receptor level. The combination of these resources provides a valuable source of information, essential to step forward in the comprehension of the genetic and physiological regulation of the fruit texture in apple. This knowledge would enable, in a close future, a more accurate and precise selection of the most favourable and valuable new apple accessions distinguished by a superior fruit quality.

Development and evaluation of a genome-wide Coffee 8.5K SNP array and its application for high-density genetic mapping and for investigating the origin of Coffea arabica L.
Merot-L'anthoene, Virginie ; Tournebize, Rémi ; Darracq, Olivier ; Rattina, Vimel ; Lepelley, Maud ; Bellanger, Laurence ; Tranchant-Dubreuil, Christine ; Coulée, Manon ; Pégard, Marie ; Metairon, Sylviane ; Fournier, Coralie ; Stoffelen, Piet ; Janssens, Steven B. ; Kiwuka, Catherine ; Musoli, Pascal ; Sumirat, Ucu ; Legnaté, Hyacinthe ; Kambale, Jean Léon ; Ferreira da Costa Neto, João ; Revel, Clara ; Kochko, Alexandre de; Descombes, Patrick ; Crouzillat, Dominique ; Poncet, Valérie - \ 2019
Plant Biotechnology Journal 17 (2019)7. - ISSN 1467-7644 - p. 1418 - 1430.
C. canephora - C. eugenioides - Coffea arabica origin - genetic map - single-nucleotide polymorphism - SNP array

Coffee species such as Coffea canephora P. (Robusta) and C. arabica L. (Arabica) are important cash crops in tropical regions around the world. C. arabica is an allotetraploid (2n = 4x = 44) originating from a hybridization event of the two diploid species C. canephora and C. eugenioides (2n = 2x = 22). Interestingly, these progenitor species harbour a greater level of genetic variability and are an important source of genes to broaden the narrow Arabica genetic base. Here, we describe the development, evaluation and use of a single-nucleotide polymorphism (SNP) array for coffee trees. A total of 8580 unique and informative SNPs were selected from C. canephora and C. arabica sequencing data, with 40% of the SNP located in annotated genes. In particular, this array contains 227 markers associated to 149 genes and traits of agronomic importance. Among these, 7065 SNPs (~82.3%) were scorable and evenly distributed over the genome with a mean distance of 54.4 Kb between markers. With this array, we improved the Robusta high-density genetic map by adding 1307 SNP markers, whereas 945 SNPs were found segregating in the Arabica mapping progeny. A panel of C. canephora accessions was successfully discriminated and over 70% of the SNP markers were transferable across the three species. Furthermore, the canephora-derived subgenome of C. arabica was shown to be more closely related to C. canephora accessions from northern Uganda than to other current populations. These validated SNP markers and high-density genetic maps will be useful to molecular genetics and for innovative approaches in coffee breeding.

Loss rates of honey bee colonies during winter 2017/18 in 36 countries participating in the COLOSS survey, including effects of forage sources
Gray, Alison ; Brodschneider, Robert ; Adjlane, Noureddine ; Ballis, Alexis ; Brusbardis, Valters ; Charrière, Jean Daniel ; Chlebo, Robert ; F. Coffey, Mary ; Cornelissen, Bram ; Amaro da Costa, Cristina ; Csáki, Tamás ; Dahle, Bjørn ; Danihlík, Jiří ; Dražić, Marica Maja ; Evans, Garth ; Fedoriak, Mariia ; Forsythe, Ivan ; Graaf, Dirk de; Gregorc, Aleš ; Johannesen, Jes ; Kauko, Lassi ; Kristiansen, Preben ; Martikkala, Maritta ; Martín-Hernández, Raquel ; Medina-Flores, Carlos Aurelio ; Mutinelli, Franco ; Patalano, Solenn ; Petrov, Plamen ; Raudmets, Aivar ; Ryzhikov, Vladimir A. ; Simon-Delso, Noa ; Stevanovic, Jevrosima ; Topolska, Grazyna ; Uzunov, Aleksandar ; Vejsnaes, Flemming ; Williams, Anthony ; Zammit-Mangion, Marion ; Soroker, Victoria - \ 2019
Journal of Apicultural Research 58 (2019)4. - ISSN 0021-8839 - p. 479 - 485.
Apis mellifera - beekeeping - citizen science - colony winter losses - forage sources - monitoring - mortality - survey

This short article presents loss rates of honey bee colonies over winter 2017/18 from 36 countries, including 33 in Europe, from data collected using the standardized COLOSS questionnaire. The 25,363 beekeepers supplying data passing consistency checks in total wintered 544,879 colonies, and reported 26,379 (4.8%, 95% CI 4.7–5.0%) colonies with unsolvable queen problems, 54,525 (10.0%, 95% CI 9.8–10.2%) dead colonies after winter and another 8,220 colonies (1.5%, 95% CI 1.4–1.6%) lost through natural disaster. This gave an overall loss rate of 16.4% (95% CI 16.1–16.6%) of honey bee colonies during winter 2017/18, but this varied greatly from 2.0 to 32.8% between countries. The included map shows relative risks of winter loss at regional level. The analysis using the total data-set confirmed findings from earlier surveys that smaller beekeeping operations with at most 50 colonies suffer significantly higher losses than larger operations (p <.001). Beekeepers migrating their colonies had significantly lower losses than those not migrating (p <.001), a different finding from previous research. Evaluation of six different forage sources as potential risk factors for colony loss indicated that intensive foraging on any of five of these plant sources (Orchards, Oilseed Rape, Maize, Heather and Autumn Forage Crops) was associated with significantly higher winter losses. This finding requires further study and explanation. A table is included giving detailed results of loss rates and the impact of the tested forage sources for each country and overall.

Characterization of Soybean yellow shoot virus, a New Member of the Family Potyviridae Infecting Soybean Plants in Brazil
Figueira, Antonia Dos Reis ; Geraldino-Duarte, Priscilla S. ; Pinzón Nuñez, Andrés Mauricio ; Lent, Jan van; Galvino-Costa, Suellen B.F. ; Farman, M. ; Goodin, Michael M. - \ 2019
Plant Disease 103 (2019)6. - ISSN 0191-2917 - p. 1172 - 1180.

A new virus species, belonging to the family Potyviridae and capable of infecting most of the soybean cultivars grown in Brazil, was collected in Lavras, Minas Gerais, Brazil, and named Soybean yellow shoot virus (SoyYSV). In this study, the complete 9,052-nucleotide genome of SoyYSV was determined and the structural, biological, and molecular properties of the virus were investigated. The SoyYSV genome encoded a single polyprotein that could be subsequently cleaved, generating 11 proteins. The SoyYSV genome shared 49% nucleotide and 36% amino acid sequence identity with Blackberry virus Y. However, the P1 protein of SoyYSV was much smaller and lacked the ALK1 domain characteristic of the genus Brambyvirus. Electron microscopy revealed flexuous filamentous virus particles, 760 to 780 nm in length, and cytoplasmic inclusions typical of those found in plant cells infected with Potyviridae species. In addition to soybean, SoyYSV infected species in the Amaranthaceae, Caricaceae, Fabaceae, and Solanaceae families. Among the most common potyviruses present in Brazil, only SoyYSV induced local necrotic lesions in Carica papaya L. SoyYSV was transmissible by Myzus persicae and Aphis gossypii but lacked the HC-Pro domain required for aphid transmission in other potyviruses. No seed transmission in soybean was observed.

Impact of maternal body mass index and gestational weight gain on pregnancy complications: an individual participant data meta-analysis of European, North American and Australian cohorts
Santos, S. ; Voerman, E. ; Amiano, P. ; Barros, H. ; Beilin, L.J. ; Bergström, A. ; Charles, M.A. ; Chatzi, L. ; Chevrier, C. ; Chrousos, G.P. ; Corpeleijn, E. ; Costa, O. ; Costet, N. ; Crozier, S. ; Devereux, G. ; Doyon, M. ; Eggesbø, M. ; Fantini, M.P. ; Farchi, S. ; Forastiere, F. ; Georgiu, V. ; Godfrey, K.M. ; Gori, D. ; Grote, V. ; Hanke, W. ; Hertz-Picciotto, I. ; Heude, B. ; Hivert, M.F. ; Hryhorczuk, D. ; Huang, R.C. ; Inskip, H. ; Karvonen, A.M. ; Kenny, L.C. ; Koletzko, B. ; Küpers, L.K. ; Lagström, H. ; Lehmann, I. ; Magnus, P. ; Majewska, R. ; Mäkelä, J. ; Manios, Y. ; McAuliffe, F.M. ; McDonald, S.W. ; Mehegan, J. ; Melén, E. ; Mommers, M. ; Morgen, C.S. ; Moschonis, G. ; Murray, D. ; Ní Chaoimh, C. ; Nohr, E.A. ; Nybo Andersen, A.M. ; Oken, E. ; Oostvogels, A.J.J.M. ; Pac, A. ; Papadopoulou, E. ; Pekkanen, J. ; Pizzi, C. ; Polanska, K. ; Porta, D. ; Richiardi, L. ; Rifas-Shiman, S.L. ; Roeleveld, N. ; Ronfani, L. ; Santos, A.C. ; Standl, M. ; Stigum, H. ; Stoltenberg, C. ; Thiering, E. ; Thijs, C. ; Torrent, M. ; Tough, S.C. ; Trnovec, T. ; Turner, S. ; Gelder, M.M.H.J. van; Rossem, L. van; Berg, A. von; Vrijheid, M. ; Vrijkotte, T.G.M. ; West, J. ; Wijga, A.H. ; Wright, J. ; Zvinchuk, O. ; Sørensen, T.I.A. ; Lawlor, D.A. ; Gaillard, R. ; Jaddoe, V.W.V. - \ 2019
BJOG : an international journal of obstetrics and gynaecology 126 (2019)8. - ISSN 1470-0328 - p. 984 - 995.
Birthweight - body mass index - pregnancy complications - preterm birth - weight gain

Objective: To assess the separate and combined associations of maternal pre-pregnancy body mass index (BMI) and gestational weight gain with the risks of pregnancy complications and their population impact. Design: Individual participant data meta-analysis of 39 cohorts. Setting: Europe, North America, and Oceania. Population: 265 270 births. Methods: Information on maternal pre-pregnancy BMI, gestational weight gain, and pregnancy complications was obtained. Multilevel binary logistic regression models were used. Main outcome measures: Gestational hypertension, pre-eclampsia, gestational diabetes, preterm birth, small and large for gestational age at birth. Results: Higher maternal pre-pregnancy BMI and gestational weight gain were, across their full ranges, associated with higher risks of gestational hypertensive disorders, gestational diabetes, and large for gestational age at birth. Preterm birth risk was higher at lower and higher BMI and weight gain. Compared with normal weight mothers with medium gestational weight gain, obese mothers with high gestational weight gain had the highest risk of any pregnancy complication (odds ratio 2.51, 95% CI 2.31– 2.74). We estimated that 23.9% of any pregnancy complication was attributable to maternal overweight/obesity and 31.6% of large for gestational age infants was attributable to excessive gestational weight gain. Conclusions: Maternal pre-pregnancy BMI and gestational weight gain are, across their full ranges, associated with risks of pregnancy complications. Obese mothers with high gestational weight gain are at the highest risk of pregnancy complications. Promoting a healthy pre-pregnancy BMI and gestational weight gain may reduce the burden of pregnancy complications and ultimately the risk of maternal and neonatal morbidity. Tweetable abstract: Promoting a healthy body mass index and gestational weight gain might reduce the population burden of pregnancy complications.

Genome-level responses to the environment : plant desiccation tolerance
Silva Artur, M.A. ; Dias Costa, M.C. ; Farrant, Jill M. ; Hilhorst, H.W.M. - \ 2019
Emerging Topics in Life Sciences 3 (2019)2. - ISSN 2397-8554 - p. 153 - 163.
Plants being sessile organisms are well equipped genomically to respond to environmental
stressors peculiar to their habitat. Evolution of plants onto land was enabled by the ability to
tolerate extreme water loss (desiccation), a feature that has been retained within genomes
but not universally expressed in most land plants today. In the majority of higher plants,
desiccation tolerance (DT) is expressed only in reproductive tissues (seeds and pollen), but
some 135 angiosperms display vegetative DT. Here, we review genome-level responses
associated with DT, pointing out common and yet sometimes discrepant features, the latter
relating to evolutionary adaptations to particular niches. Understanding DT can lead to the
ultimate production of crops with greater tolerance of drought than is currently realize
Individual preferences and farm-level decisions : experimental evidence from Costa Rica
Naranjo Barrantes, María Angélica - \ 2019
Wageningen University. Promotor(en): E.H. Bulte, co-promotor(en): J. Pieters. - Wageningen : Wageningen University - ISBN 9789463439367 - 147
Amazonian rainforest tree mortality driven by climate and functional traits
Aleixo, Izabela ; Norris, Darren ; Hemerik, Lia ; Barbosa, Antenor ; Prata, Eduardo ; Costa, Flávia ; Poorter, Lourens - \ 2019
Nature Climate Change 9 (2019)5. - ISSN 1758-678X - p. 384 - 388.

Tree mortality appears to be increasing in moist tropical forests 1 , with potentially important implications for global carbon and water cycles 2 . Little is known about the drivers of tree mortality in these diverse forests, partly because long-term data are lacking 3 . The relative importance of climatic factors and species functional traits as drivers of tropical tree mortality are evaluated using a unique dataset in which the survival of over 1,000 rainforest canopy trees from over 200 species has been monitored monthly over five decades in the Central Amazon. We found that drought, as well as heat, storms and extreme rainy years, increase tree mortality for at least two years after the climatic event. Specific functional groups (pioneers, softwoods and evergreens) had especially high mortality during extreme years. These results suggest that predicted climate change will lead to higher tree mortality rates, especially for short-lived species, which may result in faster carbon sequestration but lower carbon storage of tropical forests.

Apple whole genome sequences : recent advances and new prospects
Peace, Cameron P. ; Bianco, Luca ; Troggio, Michela ; Weg, Eric van de; Howard, Nicholas P. ; Cornille, Amandine ; Durel, Charles Eric ; Myles, Sean ; Migicovsky, Zoë ; Schaffer, Robert J. ; Costes, Evelyne ; Fazio, Gennaro ; Yamane, Hisayo ; Nocker, Steve van; Gottschalk, Chris ; Costa, Fabrizio ; Chagné, David ; Zhang, Xinzhong ; Patocchi, Andrea ; Gardiner, Susan E. ; Hardner, Craig ; Kumar, Satish ; Laurens, Francois ; Bucher, Etienne ; Main, Dorrie ; Jung, Sook ; Vanderzande, Stijn - \ 2019
Horticulture Research 6 (2019)1. - ISSN 2052-7276

In 2010, a major scientific milestone was achieved for tree fruit crops: publication of the first draft whole genome sequence (WGS) for apple (Malus domestica). This WGS, v1.0, was valuable as the initial reference for sequence information, fine mapping, gene discovery, variant discovery, and tool development. A new, high quality apple WGS, GDDH13 v1.1, was released in 2017 and now serves as the reference genome for apple. Over the past decade, these apple WGSs have had an enormous impact on our understanding of apple biological functioning, trait physiology and inheritance, leading to practical applications for improving this highly valued crop. Causal gene identities for phenotypes of fundamental and practical interest can today be discovered much more rapidly. Genome-wide polymorphisms at high genetic resolution are screened efficiently over hundreds to thousands of individuals with new insights into genetic relationships and pedigrees. High-density genetic maps are constructed efficiently and quantitative trait loci for valuable traits are readily associated with positional candidate genes and/or converted into diagnostic tests for breeders. We understand the species, geographical, and genomic origins of domesticated apple more precisely, as well as its relationship to wild relatives. The WGS has turbo-charged application of these classical research steps to crop improvement and drives innovative methods to achieve more durable, environmentally sound, productive, and consumer-desirable apple production. This review includes examples of basic and practical breakthroughs and challenges in using the apple WGSs. Recommendations for “what’s next” focus on necessary upgrades to the genome sequence data pool, as well as for use of the data, to reach new frontiers in genomics-based scientific understanding of apple.

Searching attractants for the detection of potato Epitrix species
Boavida, Conceicao ; Santos, Marcia ; Schuurman-de Bruin, A. ; Mumm, R. ; Barreto da Costa, Goncalo ; Booij, C.J.H. - \ 2019
Revista de Ciencias Agrarias 41 (2019)Especial. - ISSN 0871-018X - p. 125 - 132.
In order to identify volatile organic compounds (VOCs) attractive to Epitrix spp. adults, field and laboratory experiments were carried out in sequence. In the field, black nightshade potted plants attracted significantly more Epitrix
spp. adults than potato, aubergine, tomato and common lambsquarters. Following this result, headspace samples were collected from non-infested and from E. papa infested plants of potato, aubergine and black nightshade. VOC profiling by GC-MS analysis identified potential attractants which were tested as single compounds or as a mixture in a field experiment (1,3-butanediol, Z3-6:Ac/Linalool (1:1), (E)-β-farnesene and a blank control). Traps baited with Z3-6:Ac/ Linalool (1:1) attracted significantly more E. papa and E. cucumeris adults than the control. To find synergist substances to improve the attractiveness of this mixture, the choice of individual E. papa adults between this mixture alone or combined with several other plant VOCs, was sequentially tested in a Y-tube olfactometer. Adding (E)-β-ocimene to Z3-6:Ac/Linalool (1:3) increased the attractiveness of the mixture. This result was verified in two field experiments. The results were promising and encourage more research.
Applying the adverse outcome pathway (AOP) for food sensitization to support in vitro testing strategies
Lozano-Ojalvo, Daniel ; Benedé, Sara ; Antunes, Celia M. ; Bavaro, Simona L. ; Bouchaud, Grégory ; Costa, Ana ; Denery-Papini, Sandra ; Díaz-Perales, Araceli ; Garrido-Arandia, María ; Gavrovic-Jankulovic, Marija ; Hayen, Simone ; Martínez-Blanco, Mónica ; Molina, Elena ; Monaci, Linda ; Pieters, Raymond H.H. ; Villemin, Clelia ; Wichers, Harry J. ; Wróblewska, Barbara ; Willemsen, Linette E.M. ; Roggen, Erwin L. ; Bilsen, Jolanda H.M. van - \ 2019
Trends in Food Science and Technology 85 (2019). - ISSN 0924-2244 - p. 307 - 319.
Adverse outcome pathway - Dendritic cells - Epithelial cells - IgE-mediated food allergy - In vitro models - T and B cells

Background: Before introducing proteins from new or alternative dietary sources into the market, a compressive risk assessment including food allergic sensitization should be carried out in order to ensure their safety. We have recently proposed the adverse outcome pathway (AOP) concept to structure the current mechanistic understanding of the molecular and cellular pathways evidenced to drive IgE-mediated food allergies. This AOP framework offers the biological context to collect and structure existing in vitro methods and to identify missing assays to evaluate sensitizing potential of food proteins. Scope and approach: In this review, we provide a state-of-the-art overview of available in vitro approaches for assessing the sensitizing potential of food proteins, including their strengths and limitations. These approaches are structured by their potential to evaluate the molecular initiating and key events driving food sensitization. Key findings and conclusions: The application of the AOP framework offers the opportunity to anchor existing testing methods to specific building blocks of the AOP for food sensitization. In general, in vitro methods evaluating mechanisms involved in the innate immune response are easier to address than assays addressing the adaptive immune response due to the low precursor frequency of allergen-specific T and B cells. Novel ex vivo culture strategies may have the potential to become useful tools for investigating the sensitizing potential of food proteins. When applied in the context of an integrated testing strategy, the described approaches may reduce, if not replace, current animal testing approaches.

Gobernanza para la Adaptación basada en Ecosistemas (AbE) para pequeños caficultores de América Central
Vignola, Raffaele ; Otarola, Marco ; Alpizar, Francisco ; Rivera, Pavel - \ 2019
Agronomia mesoamericana 30 (2019)1. - ISSN 1021-7444 - p. 19 - 32.
climate change adaptation - environmental policies - network analysis - agriculture
Introduction. Agricultural practices based on good management of ecosystems are promoted as a good adaptation strategy for the productive activities of coffee smallholder farmers in the Central American region. The dissemination of information on innovations, techniques, instruments, etc. between organizations and producers is key to expand and consolidate the use of these practices. Objective. The objective of this study was to identify the structure of information-dissemination governance that can help expand and consolidate the use of Ecosystem-based Adaptation (EbA) practices in agriculture. Materials and methods. Three productive landscapes distributed in three countries
(Honduras, Guatemala and Costa Rica) were analysed, characterized by predominantly small-scale coffee growing farmers. For each of these landscapes, the actors that exchange information between the national scale and the level
of the producers were identified. Interviews were conducted to characterize the information flows and their possible relevance to promote EbA in the productive systems of coffee producers. Results. It was identified both key actors and gaps in the network of organizations that inhibit the transmission of information between scales and sectors. In Costa Rica, the capacity for intermediation of information across sectors and scales is spread between State entities and
competitive producer organizations. In Honduras, intermediation capacities are distributed among some civil society organizations that work at local levels closely with producers and governmental organizations that work at the national
level. In Guatemala, the intermediation capacities are mainly distributed among governmental, civil society and private organizations, mainly at the national level. Conclusion.The analysis of networks in these coffee landscapes suggests
that although all three countries have a similar institutionalization of the coffee sector, in two the dissemination of information to promote EbA would benefit at intermediate and local scales to promote learning among producers.
Can interaction specificity in the fungus-farming termite symbiosis be explained by nutritional requirements of the fungal crop?
Costa, Rafael R. da; Vreeburg, Sabine M.E. ; Shik, Jonathan Z. ; Aanen, Duur K. ; Poulsen, Michael - \ 2019
Fungal Ecology 38 (2019). - ISSN 1754-5048 - p. 54 - 61.
Biomass - Carbohydrates - Geometric framework - Interaction specificity - Macrotermes - Nutrition - Odontotermes - Protein - Symbiosis - Termitomyces

Fungus-growing termites are associated with genus-specific fungal symbionts, which they acquire via horizontal transmission. Selection of specific symbionts may be explained by the provisioning of specific, optimal cultivar growth substrates by termite farmers. We tested whether differences in in vitro performance of Termitomyces cultivars from nests of three termite species on various substrates are correlated with the interaction specificity of their hosts. We performed single-factor growth assays (varying carbon sources), and a two-factor geometric framework experiment (simultaneously varying carbohydrate and protein availability). Although we did not find qualitative differences between Termitomyces strains in carbon-source use, there were quantitative differences, which we analysed using principal component analysis. This showed that growth of Termitomyces on different carbon sources was correlated with termite host genus, rather than host species, while growth on different ratios and concentrations of protein and carbohydrate was correlated with termite host species. Our findings corroborate the interaction specificity between fungus-growing termites and Termitomyces cultivars and indicate that specificity between termite hosts and fungi is reflected both nutritionally and physiologically. However, it remains to be demonstrated whether those differences contribute to selection of specific fungal cultivars by termites at the onset of colony foundation.

Embolism resistance drives the distribution of Amazonian rainforest tree species along hydro-topographic gradients
Oliveira, Rafael S. ; Costa, Flavia R.C. ; Baalen, Emma van; Jonge, Arjen de; Bittencourt, Paulo R. ; Almanza, Yanina ; V. Barros, Fernanda de; Cordoba, Edher C. ; Fagundes, Marina V. ; Garcia, Sabrina ; Guimaraes, Zilza T.T.M. ; Hertel, Mariana ; Schietti, Juliana ; Rodrigues-Souza, Jefferson ; Poorter, Lourens - \ 2019
New Phytologist 221 (2019)3. - ISSN 0028-646X - p. 1457 - 1465.
drought vulnerability - forest resilience - functional ecology - hydrological niches - P - phosphorus - tropical forests - water table

Species distribution is strongly driven by local and global gradients in water availability but the underlying mechanisms are not clear. Vulnerability to xylem embolism (P50) is a key trait that indicates how species cope with drought and might explain plant distribution patterns across environmental gradients. Here we address its role on species sorting along a hydro-topographical gradient in a central Amazonian rainforest and examine its variance at the community scale. We measured P50 for 28 tree species, soil properties and estimated the hydrological niche of each species using an indicator of distance to the water table (HAND). We found a large hydraulic diversity, covering as much as 44% of the global angiosperm variation in P50. We show that P50: contributes to species segregation across a hydro-topographic gradient in the Amazon, and thus to species coexistence; is the result of repeated evolutionary adaptation within closely related taxa; is associated with species tolerance to P-poor soils, suggesting the evolution of a stress-tolerance syndrome to nutrients and drought; and is higher for trees in the valleys than uplands. The large observed hydraulic diversity and its association with topography has important implications for modelling and predicting forest and species resilience to climate change.

Data from: Maternal size and body condition predict the amount of post-fertilization maternal provisioning in matrotrophic fish
Hagmayer, A. ; Furness, Andrew I. ; Reznick, David N. ; Pollux, B.J.A. - \ 2018
live-bearing - matrotrophy - placenta - placentotrophy - superfetation - viviparity
Maternal effects often provide a mechanism for adaptive transgenerational phenotypic plasticity. The maternal phenotype can profoundly influence the potential for such environmentally-induced adjustments of the offspring phenotype, causing correlations between offspring and maternal traits. Here we study potential effects of the maternal phenotype on offspring provisioning prior to and during gestation in the matrotrophic live-bearing fish species Poeciliopsis retropinna. Specifically, we examine how maternal traits such as body fat, lean mass and length relate to pre- (i.e. allocation to the egg prior to fertilization) and post-fertilization (i.e. allocation to the embryo during pregnancy) maternal provisioning and how this ultimately affects offspring size and body composition at birth. We show that pre- and post-fertilization maternal provisioning is associated with maternal length and body fat, but not with maternal lean mass. Maternal length is proportionally associated with egg mass at fertilization and offspring mass at birth, notably without changing the ratio of pre- to post-fertilization maternal provisioning. This ratio, referred to as the matrotrophy index (MI), is often used to quantify the level of matrotrophy. By contrast, the proportion of maternal body fat is positively associated with post-fertilization, but not pre-fertilization, maternal provisioning and consequently is strongly positively correlated with the MI. We furthermore found that the composition of embryos changes throughout pregnancy. Females invest first in embryo lean mass, then allocate fat reserves to embryos very late in pregnancy. We argue that this delay in fat allocation may be adaptive, because it delays an unnecessary high reproductive burden to the mother during earlier stages of pregnancy, potentially leading to a more slender body shape and improved locomotor performance. In conclusion, our study suggests that (i) offspring size at birth is a plastic trait that is predicted by both maternal length and body fat, and (ii) the MI is a plastic trait that is predicted solely by the proportion of maternal body fat. It herewith provides new insights into the potential maternal causes and consequences of embryo provisioning during pregnancy in matrotrophic live-bearing species.
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