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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    Optimizing design to estimate genetic correlations between environments with common environmental effects
    Lozano-Jaramillo, Maria ; Komen, Hans ; Wientjes, Yvonne C.J. ; Mulder, Han A. ; Bastiaansen, John W.M. - \ 2020
    Journal of Animal Science 98 (2020)2. - ISSN 0021-8812
    breeding programs - genetic correlation - genotype by environment interaction - population structure

    Breeding programs for different species aim to improve performance by testing members of full-sib (FS) and half-sib (HS) families in different environments. When genotypes respond differently to changes in the environment, this is defined as genotype by environment (G × E) interaction. The presence of common environmental effects within families generates covariance between siblings, and these effects should be taken into account when estimating a genetic correlation. Therefore, an optimal design should be established to accurately estimate the genetic correlation between environments in the presence of common environmental effects. We used stochastic simulation to find the optimal population structure using a combination of FS and HS groups with different levels of common environmental effects. Results show that in a population with a constant population size of 2,000 individuals per environment, ignoring common environmental effects when they are present in the population will lead to an upward bias in the estimated genetic correlation of on average 0.3 when the true genetic correlation is 0.5. When no common environmental effects are present in the population, the lowest standard error (SE) of the estimated genetic correlation was observed with a mating ratio of one dam per sire, and 10 offspring per sire per environment. When common environmental effects are present in the population and are included in the model, the lowest SE is obtained with mating ratios of at least 5 dams per sire and with a minimum number of 10 offspring per sire per environment. We recommend that studies that aim to estimate the magnitude of G × E in pigs, chicken, and fish should acknowledge the potential presence of common environmental effects and adjust the mating ratio accordingly.

    Differential responses to salt stress in ion dynamics, growth and seed yield of European quinoa varieties
    Jaramillo Roman, Viviana ; Toom, Leonardus A. den; Castro Gamiz, Carlos ; Pijl, Niels van der; Visser, Richard G.F. ; Loo, Eibertus N. van; Linden, Gerard van der - \ 2020
    Environmental and Experimental Botany 177 (2020). - ISSN 0098-8472
    Chenopodium quinoa - Naexclusion - RGR - Salt stress tolerance - Survival and growth

    Quinoa is a nutritious seed crop with a great potential to grow in saline soils. Here, we studied ion concentrations in quinoa tissues throughout the life cycle of the plant, and linked ion dynamics to responses in growth parameters, seed yield and efficiency of photosynthesis under salinity (0–400 mM NaCl). Ion dynamics changed from high ion exclusion (>99 %, root contents lower than root medium and low accumulation of ions in the leaves) before flowering, to a build-up of ions during seed filling. This indicates a change in strategy in maintaining the necessary gradient of water potential from the root medium to the leaves. K+ concentrations in leaves also increased by more than 100 % in response to prolonged severe salt stress, which may point to a role of this ion in leaf osmotic adjustment. Accumulation of ions in epidermal bladder cells did not contribute substantially to Na+-exclusion as it was less than 6 % of the total Na+ taken up in leaves. Growth under salt stress was mostly impaired by anatomical adaptations (reduced SLA), while initial light use efficiency (Fv/Fm) and NAR were not affected. The variety Pasto showed a “survival strategy” to high salinity with higher ion exclusion and a higher reduction in transpiration than the other varieties, at the expense of lower biomass and seed yield.

    Using phenotypic distribution models to predict livestock performance
    Lozano Jaramillo, Maria ; Bastiaansen, J.W.M. ; Dessie, Tadelle ; Alemu, S.W. ; Komen, J. - \ 2019
    In: Book of Abstracts of the 70th Annual Meeting of the European Federation of Animal Science. - Wageningen Academic Publishers (EAAP Book of Abstracts ) - ISBN 9789086863396 - p. 658 - 658.
    Molecular characterization of Ecuadorian quinoa (Chenopodium quinoa Willd.) diversity : implications for conservation and breeding
    Salazar, Juan ; Jaramillo Roman, Viviana ; Gutierrez, Bernardo ; Loo, E.N. van; Lourdes Torres, María de; Torres, Andrés Francisco - \ 2019
    Euphytica 215 (2019)3. - ISSN 0014-2336
    Breeding - Ecuador - Genetic diversity - Population structure - Quinoa - SSR

    Quinoa (Chenopodium quinoa Willd.) is recognized as an important crop to improve global food security. It has gained international recognition because of the nutritional value of its seeds and its broad agronomic resilience. Although several studies have attempted to characterize the genetic diversity of quinoa, none have focused on evaluating germplasm from Ecuador; the latter considered a relevant subcenter of diversity for the species. In this study, 84 accessions representing the species’ cultivated range in the Ecuadorian Andes were characterized using 15 species-specific SSR markers. The extent of allelic richness (196 alleles) and genetic heterozygosity (H E = 0.71) detected for these accessions demonstrate that Ecuadorian quinoa is highly diverse. Phenetic analyzes structured Ecuadorian germplasm into 3 subgroups; each containing genotypes from all surveyed provinces. Average expected heterozygosity was high for all 3 subgroups (0.53 ≤ H E ≤ 0.72), and Nei-pairwise comparisons showed significant genetic divergence among them (0.31 ≤ Nei DST ≤ 0.84). The lack of a clear geographic pattern in the genetic structure of Ecuadorian quinoa led us to believe that the 3 reported subgroups constitute independent genetic lineages representing ancestral landrace populations which have been disseminated throughout Ecuador via informal seed networks. Nevertheless, a Wilcoxon test showed that at least one subgroup had been subject to intensive inbreeding and selection; and possibly corresponds to the local commercial variety INIAP-Tunkahuan. Our results show that ancestral quinoa diversity in Ecuador has prevailed despite the introduction of commercial varieties, and should be preserved for future use in breeding programs.

    Correction to: Molecular characterization of Ecuadorian quinoa (Chenopodium quinoa Willd.) diversity: implications for conservation and breeding
    Salazar, Juan ; Roman, Viviana Jaramillo ; Gutierrez, Bernardo ; Loo, Eibertus Nicolaas van; Lourdes Torres, María de; Torres, Andrés Francisco - \ 2019
    Euphytica 215 (2019)12. - ISSN 0014-2336

    Due to an unfortunate error of miscommunication, two of the co-authors of this manuscript were omitted from the original publication. The correct representation of the authors and their affiliations are listed here and should be treated as definitive. Juan Salazar1, Viviana Jaramillo Roman2, Bernardo Gutierrez1,3, Eibertus Nicolaas van Loo2, Mari´a de Lourdes Torres1, Andre´s Francisco Torres1,2 1. Laboratorio de Biotecnologi´a Vegetal, Colegio de Ciencias Biolo´gicas y Ambientales, Universidad San Francisco de Quito USFQ, Diego de Robles y Vi´a Interocea´nica, Cumbaya´, Ecuador 2. Wageningen UR Plant Breeding, Wageningen University and Research, PO Box 386, 6700 AJ Wageningen, The Netherlands 3. Department of Zoology, University of Oxford, 11a Mansfield Road, Oxford OX1 3SZ, UK Furthermore, the acknowledgments section has been adapted to match the changes in authorship. The corrected acknowledgements, presented below, are definitive: This research was funded with a Chancellor’s Grant (2015) from Universidad San Francisco de Quito USFQ (Quito-Ecuador). Germplasm access and research permit were granted by the Ministry of Environment of Ecuador (MAE-DNB-CM-2016- 0044). The authors would like to acknowledge the technical assistance offered by researchers at the Plant Biotechnology Laboratory (COCIBA, USFQ), as well as Dr. Leonardo Zurita for his assistance with georeferenced mapping. The authors would also like to acknowledge Dr. Gerard van der Linden (Wageningen University and Research) for supporting our efforts to search and collect quinoa germplasm throughout the Andes of Ecuador.

    Pathogen-induced activation of disease-suppressive functions in the endophytic root microbiome
    Carrión, Víctor J. ; Perez-Jaramillo, Juan ; Cordovez, Viviane ; Tracanna, Vittorio ; Hollander, Mattias De; Ruiz-Buck, Daniel ; Mendes, Lucas W. ; Ijcken, Wilfred F.J. van; Gomez-Exposito, Ruth ; Elsayed, Somayah S. ; Mohanraju, Prarthana ; Arifah, Adini ; Oost, John van der; Paulson, Joseph N. ; Mendes, Rodrigo ; Wezel, Gilles P. van; Medema, Marnix H. ; Raaijmakers, Jos M. - \ 2019
    Science 366 (2019)6465. - ISSN 0036-8075 - p. 606 - 612.

    Microorganisms living inside plants can promote plant growth and health, but their genomic and functional diversity remain largely elusive. Here, metagenomics and network inference show that fungal infection of plant roots enriched for Chitinophagaceae and Flavobacteriaceae in the root endosphere and for chitinase genes and various unknown biosynthetic gene clusters encoding the production of nonribosomal peptide synthetases (NRPSs) and polyketide synthases (PKSs). After strain-level genome reconstruction, a consortium of Chitinophaga and Flavobacterium was designed that consistently suppressed fungal root disease. Site-directed mutagenesis then revealed that a previously unidentified NRPS-PKS gene cluster from Flavobacterium was essential for disease suppression by the endophytic consortium. Our results highlight that endophytic root microbiomes harbor a wealth of as yet unknown functional traits that, in concert, can protect the plant inside out.

    Using phenotypic distribution models to predict livestock performance
    Lozano-Jaramillo, M. ; Alemu, S.W. ; Dessie, T. ; Komen, H. ; Bastiaansen, J.W.M. - \ 2019
    Scientific Reports 9 (2019)1. - ISSN 2045-2322

    Livestock production systems of the developing world use indigenous breeds that locally adapted to specific agro-ecologies. Introducing commercial breeds usually results in lower productivity than expected, as a result of unfavourable genotype by environment interaction. It is difficult to predict of how these commercial breeds will perform in different conditions encountered in e.g. sub-Saharan Africa. Here, we present a novel methodology to model performance, by using growth data from different chicken breeds that were tested in Ethiopia. The suitability of these commercial breeds was tested by predicting the response of body weight as a function of the environment across Ethiopia. Phenotype distribution models were built using machine learning algorithms to make predictions of weight in the local environmental conditions based on the productivity for the breed. Based on the predicted body weight, breeds were assigned as being most suitable in a given agro-ecology or region. We identified the most important environmental variables that explained the variation in body weight across agro-ecologies for each of the breeds. Our results highlight the importance of acknowledging the role of environment in predicting productivity in scavenging chicken production systems. The use of phenotype distribution models in livestock breeding is recommended to develop breeds that will better fit in their intended production environment.

    Predicting breed by environment interaction using ecological modelling
    Lozano-Jaramillo, María - \ 2019
    Wageningen University. Promotor(en): J. Komen, co-promotor(en): J.W.M. Bastiaansen; T. Dessie. - Wageningen : Wageningen University - ISBN 9789463950718 - 150

    In most of African countries, livestock production branches from an ancient tradition where nearly all rural and peri-urban families keep different indigenous breeds in scavenging systems. In sub-Saharan Africa, where these production systems are the most prominent, livestock mainly forages for resources that are highly dependent on the local environment and season. Even though these breeds are said to be adapted to the local conditions, their productivity is still low compared to commercial breeds. There have been several efforts from researchers, policy makers and livestock specialists to introduce commercial breeds to support the generation of food security and poverty alleviation. However, most of these attempts have failed because of the non-adaptability of introduced breeds to the local conditions. Typically there is no prior knowledge on the environmental sensitivity from these breeds to this new tropical environments. Throughout this thesis I use Geographic Information Systems (GIS) that describe the environment, and models used in ecology to investigate the match of animals with their environment. The aim of this thesis was to evaluate how the environment plays a role in shaping differences in breed performance across agro-ecological zones, and what implications this can have in genetic improvement of livestock.

    Several animal breeding studies tested breeds in different environments to evaluate whether genotypes respond differently to changes in the environment (i.e. G x E). To estimate if there is a re-ranking in breed/genotype performance between environments, a genetic correlation is estimated. To accurately estimate this correlation, an optimal mating design should be established. Breeding programs use full-sibs or half-sibs to perform testing in different environments. Within families, common environmental effects can be present generating a covariance between siblings, and should therefore be taken into account when estimating genetic correlations. In chapter 2, I used stochastic simulation to find the optimal population structure to accurately estimate the genetic correlation between environments using a combination of full-sibs and half-sibs groups under different levels of common environmental effects. Simulation results showed that when there are no common environmental effects present in the population, the mating ratio that gives the lowest standard error of the genetic correlation is of one female per male with 10 offspring per sire per environment. Not accounting for common environmental effects when these are present in the population will lead to an upward bias of the genetic correlation. Increasing the number of females per male to a minimum of 5, with 10 offspring per sire per environment will alleviate the impact of common environmental effects lowering the standard error of the genetic correlation. I suggest for studies that aim to estimate the magnitude of the G x E, to acknowledge the presence of common environmental effects and to take this into account when deciding the mating ratio.

    In chapter 3, using GIS and habitat distribution models a methodology to predict breed suitability for different agro-ecological zones was developed. The methodology was tested on the current distribution of two introduced chicken breeds in Ethiopia. Results show that this methodology is effective in predicting breed suitability for specific environmental conditions. For both chicken breeds the model predicts suitable areas beyond their current extent, hence suggesting areas for breed introduction. The most significant variables that explain the current breed distribution were similar to the environmental conditions from which the breeds originate.

    In chapter 3, only information on the location of the breeds was taken into account. This was extended in chapter 4, leading to an approach that predicts the productivity of the breeds. I present a methodology to model breed performance by using growth data from five different introduced chicken breeds in Ethiopia part of the African Chicken Genetic Gains project (ACGG; The suitability of these breeds was tested by predicting the response of body weight as a function of the environment in Ethiopia. Across the Ethiopian landscape, predicted body weights varied for all of the breeds. The variation in body weight was explained by different environmental variables, highlighting the importance of understanding the role of the environment in predicting breed productivity.

    In chapter 4, breed performance was predicted within a single country. In chapter 5 breed performance was predicted across countries. Growth data was used from two chicken breeds that were introduced in Ethiopia, Nigeria and Tanzania by the ACGG project. The aim was to assess if the data from one country could be used to predict the performance of the same breed in the other two countries. The variation found in breed performance could be attributed to each breeds’ environmental sensitivity. The environmental variables responsible for shaping the variation in performance were different for each breed in each country. The accuracy of the prediction models projected from one country to the other show they can be used to identify areas for successful breed introduction.

    In chapter 6 I discussed how the tools developed in this thesis can be used in animal breeding for different approaches. I suggest for different disciplines such as landscape genomics and ecology to work together with animal breeding to understand the role that the environment plays in shaping the observed phenotypic differences. This knowledge has implications for the development of breeding programs for different agro-ecologies, taking into account the continuous environmental variation. Furthermore, I recommend the use of these tools to generate knowledge on the impact of climate change on livestock to help generate mitigation plans and policy frameworks that will help in enhancing food security and preserving the current biodiversity.

    On integrating crowdsourced delivery in last-mile logistics: A simulation study to quantify its feasibility
    Guo, Xuezhen ; Lujan Jaramillo, Yngrid Jaqueline ; Bloemhof-Ruwaard, Jacqueline ; Claassen, G.D.H. - \ 2019
    Journal of Cleaner Production 241 (2019). - ISSN 0959-6526
    Crowdsourced delivery - E-commerce - Last miles - Sharing economy - Sustainable city logistics

    The fast-growing practice of e-commerce implies a strong increase in parcel deliveries, which in turn creates significant pressure on last-mile city logistics. Due to the important role the city transportation plays in energy use and greenhouse gas emission, effective last-mile solutions in cities must be developed to contribute to sustainability and a cleaner world economy. Crowdsourced delivery as an emerging “sharing economy” initiative can be an effective tool to mitigate the problems emerging from the last-mile city logistics. To valorise the benefits of crowdsourced delivery, a transition towards a hybrid city logistic system is required where crowdsourced delivery and the conventional delivery networks are closely integrated. Due to the lack of theoretical guidelines for crowdsourced delivery integration, this research develops a conceptual framework to facilitate last-mile city logistics transition adopting the multi-level socio-technical transition theory as the basis. The core of the conceptual framework is the “five basic principles” to be followed by stakeholders when designing intervening niche innovations at the current stage of system transition. To demonstrate the usability of the conceptual framework, an illustrative discrete event simulation study with specific settings that fits in with the current status of last-mile city logistics is conducted. Results show that incorporating crowdsourced delivery as a supplement to the conventional delivery network, following the five basic principles proposed by the conceptual framework can reduce the last-mile logistic costs. Moreover, the offline participation rate plays a key role in ensuring the feasibility of the new hybrid last-mile model. To conclude, the developed conceptual framework has a great potential of improving last-mile delivery in the era of e-commerce and having a critical scale of potential deliverer pool is the prerequisite for the successful application of crowdsourced deliveries.

    Micropropagation of Solanum quitoense var. quitoense by apical bud, petiole and hypocotyl culture
    Gutirrez, Bernardo ; Cobo, María Mercedes ; Orellana, Miguel ; Vega, Joely ; Arahana, Venancio ; Jaramillo, Viviana ; Lourdes Torres, María de - \ 2019
    Plant Biotechnology Reports 36 (2019)2. - ISSN 1342-4580 - p. 91 - 97.
    1-naphtaleneacetic acid (NAA) - 6-benzylaminopurine (BAP) - Andean crop - gibberellic acid (GA3) - in vitro culture - Solanum quitoense

    The development of in vitro propagation methods can improve the current commercial use and conservation of plants like naranjilla (Solanum quitoense), a distinctive Andean crop and key emerging agricultural product. In the present study, we report in vitro culture protocols for naranjilla apical buds, hypocotyls and petioles. In apical bud culture, MS medium supplemented with 0.10 mg l−1 1-naphtaleneacetic acid (NAA) produced longer plantlets with greater number of leaves. Hypocotyl culture yielded higher number of shoots when using older explants in MS medium supplemented with different combinations of NAA, 6-benzylaminopurine (BAP) and gibberellic acid (GA3). Petiole culture produced a significantly higher number of shoots per explant, with more abundant and bigger leaves, when using MS medium supplemented with 0.02 mg l−1 NAA, 4.50 mg l−1 BAP and 1.00 mg l−1 GA3. A factorial analysis reveals that the interaction between GA3 and NAA/BAP plays an important role in shoot regeneration. These results provide new tools for the in vitro regeneration of naranjilla plants, improving on previously reported protocols for this species by using alternative explant types and regeneration protocols.

    Modelling carbon stock and carbon sequestration ecosystem services for policy design: a comprehensive approach using a dynamic vegetation model
    Quijas, Sandra ; Boit, Alice ; Thonicke, Kirsten ; Murray-Tortarolo, Guillerma ; Mwampamba, Tuyeni ; Skutsch, Margaret ; Simões, Margareth ; Ascarrunz, Nataly ; Pena Claros, M. ; Jones, Laurence ; Arets, E.J.M.M. ; Jaramillo, Victor J. ; Lazos, Elena ; Toledo, Marisol ; Martorano, Lucieta G. ; Ferraz, Rodrigo ; Balvanera, Patricia - \ 2019
    Ecosystems and People 15 (2019)1. - ISSN 2639-5916 - p. 42 - 60.
    Ecosystem service (ES) models can only inform policy design adequately if they incorporate ecological processes. We used the Lund-Potsdam-Jena managed Land (LPJmL) model, to address following questions for Mexico, Bolivia and Brazilian Amazon: (i) How different are C stocks and C sequestration quantifications under standard (when soil and litter C and heterotrophic respiration are not considered) and comprehensive (including all C stock and heterotrophic respiration) approach? and (ii) How does the valuation of C stock and C sequestration differ in national payments for ES and global C funds or markets when comparing both approach? We found that up to 65% of C stocks have not been taken into account by neglecting to include C stored in soil and litter, resulting in gross underpayments (up to 500 times lower). Since emissions from heterotrophic respiration of organic material offset a large proportion of C gained through growth of living matter, we found that markets and decision-makers are inadvertently overestimating up to 100 times C sequestrated. New approaches for modelling C services relevant ecological process-based can help accounting for C in soil, litter and heterotrophic respiration and become important for the operationalization of agreements on climate change mitigation following the COP21 in 2015.
    Beerkan multi-runs for characterizing water infiltration and spatial variability of soil hydraulic properties across scales
    Lassabatere, Laurent ; Prima, Simone Di; Angulo-Jaramillo, Rafael ; Keesstra, Saskia ; Salesa, David - \ 2019
    Hydrological Sciences Journal 64 (2019)2. - ISSN 0262-6667 - p. 165 - 178.
    beerkan - BEST methods - field scale - multi-runs - spatial variability - transect scale

    A method is presented for characterizing the spatial variability of water infiltration and soil hydraulic properties at the transect and field scales. The method involves monitoring a set of 10 Beerkan runs distributed over a 1-m length of soil, and running BEST (Beerkan estimation of soil transfer parameters) methods to derive hydraulic parameters. The Beerkan multi-runs (BMR) method provides a significant amount of data at the transect scale, allowing the determination of correlations between water infiltration variables and hydraulic parameters, and the detection of specific runs affected by preferential flow or water repellence. The realization of several BMRs at several transects on the same site allows comparison of the variation between locations (spatial variability at the field scale) and at the transect scale (spatial variability at the metre scale), using analysis of variance. From the results, we determined the spatial variability of water infiltration and hydraulic parameters as well as its characteristic scale (transect versus field).

    Efficacy of non-pharmacological interventions to treat malnutrition in older persons : A systematic review and meta-analysis. The SENATOR project ONTOP series and MaNuEL knowledge hub project
    Correa-Pérez, Andrea ; Abraha, Iosef ; Cherubini, Antonio ; Collinson, Avril ; Dardevet, Dominique ; Groot, Lisette C.P.G.M. de; Schueren, Marian A.E. van der; Hebestreit, Antje ; Hickson, Mary ; Jaramillo-Hidalgo, Javier ; Lozano-Montoya, Isabel ; O'Mahony, Denis ; Soiza, Roy L. ; Visser, Marjolein ; Volkert, Dorothee ; Wolters, Maike ; Jentoft, Alfonso J.C. - \ 2019
    Ageing Research Reviews 49 (2019). - ISSN 1568-1637 - p. 27 - 48.
    Elderly, dietary supplementation - Protein energy malnutrition - Review, systematic

    Introduction: We aimed to perform a review of SRs of non-pharmacological interventions in older patients with well-defined malnutrition using relevant outcomes agreed by a broad panel of experts. Methods: PubMed, Cochrane, EMBASE, and CINHAL databases were searched for SRs. Primary studies from those SRs were included. Quality assessment was undertaken using Cochrane and GRADE criteria. Results: Eighteen primary studies from seventeen SRs were included. Eleven RCTs compared oral nutritional supplementation (ONS) with usual care. No beneficial effects of ONS treatment, after performing two meta-analysis in body weight changes (six studies), mean difference: 0.59 (95%CI -0.08, 1.96) kg, and in body mass index changes (two studies), mean difference: 0.31 (95%CI -0.17, 0.79) kg/m2 were found. Neither in MNA scores, muscle strength, activities of daily living, timed Up&Go, quality of life and mortality. Results of other intervention studies (dietary counselling and ONS, ONS combined with exercise, nutrition delivery systems) were inconsistent. The overall quality of the evidence was very low due to risk of bias and small sample size. Conclusions: This review has highlighted the lack of high quality evidence to indicate which interventions are effective in treating malnutrition in older people. High quality research studies are urgently needed in this area.

    Use of geographic information system tools to predict animal breed suitability for different agro-ecological zones
    Lozano-Jaramillo, M. ; Bastiaansen, J.W.M. ; Dessie, T. ; Komen, H. - \ 2019
    Animal 13 (2019)7. - ISSN 1751-7311 - p. 1536 - 1543.
    agro-ecology - breeding programs - distribution models - livestock - local adaptation

    Predicting breed-specific environmental suitability has been problematic in livestock production. Native breeds have low productivity but are thought to be more robust to perform under local conditions than exotic breeds. Attempts to introduce genetically improved exotic breeds are generally unsuccessful, mainly due to the antagonistic environmental conditions. Knowledge of the environmental conditions that are shaping the breed would be needed to determine its suitability to different locations. Here, we present a methodology to predict the suitability of breeds for different agro-ecological zones using Geographic Information Systems tools and predictive habitat distribution models. This methodology was tested on the current distribution of two introduced chicken breeds in Ethiopia: the Koekoek, originally from South Africa, and the Fayoumi, originally from Egypt. Cross-validation results show this methodology to be effective in predicting breed suitability for specific environmental conditions. Furthermore, the model predicts suitable areas of the country where the breeds could be introduced. The specific climatic parameters that explained the potential distribution of each of the breeds were similar to the environment from which the breeds originated. This novel methodology finds application in livestock programs, allowing for a more informed decision when designing breeding programs and introduction programs, and increases our understanding of the role of the environment in livestock productivity.

    UAV based soil salinity assessment of cropland
    Ivushkin, Konstantin ; Bartholomeus, Harm ; Bregt, Arnold K. ; Pulatov, Alim ; Franceschini, Marston H.D. ; Kramer, Henk ; Loo, Eibertus N. van; Jaramillo Roman, Viviana ; Finkers, Richard - \ 2019
    Geoderma 338 (2019). - ISSN 0016-7061 - p. 502 - 512.
    Hyperspectral - LiDAR - Quinoa - Remote sensing - Soil salinity - Thermography - UAV

    Increased soil salinity is a significant agricultural problem that decreases yields for common agricultural crops. Its dynamics require cost and labour effective measurement techniques and widely acknowledged methods are not present yet. We investigated the potential of Unmanned Aerial Vehicle (UAV) remote sensing to measure salt stress in quinoa plants. Three different UAV sensors were used: a WIRIS thermal camera, a Rikola hyperspectral camera and a Riegl VUX-SYS Light Detection and Ranging (LiDAR) scanner. Several vegetation indices, canopy temperature and LiDAR measured plant height were derived from the remote sensing data and their relation with ground measured parameters like salt treatment, stomatal conductance and actual plant height is analysed. The results show that widely used multispectral vegetation indices are not efficient in discriminating between salt affected and control quinoa plants. The hyperspectral Physiological Reflectance Index (PRI) performed best and showed a clear distinction between salt affected and treated plants. This distinction is also visible for LiDAR measured plant height, where salt treated plants were on average 10 cm shorter than control plants. Canopy temperature was significantly affected, though detection of this required an additional step in analysis – Normalised Difference Vegetation Index (NDVI) clustering. This step assured temperature comparison for equally vegetated pixels. Data combination of all three sensors in a Multiple Linear Regression model increased the prediction power and for the whole dataset R2 reached 0.46, with some subgroups reaching an R2 of 0.64. We conclude that UAV borne remote sensing is useful for measuring salt stress in plants and a combination of multiple measurement techniques is advised to increase the accuracy.

    Understanding the Effect of the Environmental Conditions on the Suitability of a Breed for Different Agro-Ecological Zones
    Lozano Jaramillo, Maria ; Bastiaansen, J.W.M. ; Dessie, Tadelle ; Komen, J. - \ 2018
    In: Proceedings of the World Congress on Genetics Applied to Livestock Production Auckland : IAVS / Massey University - 4 p.
    Predicting suitability of breeds for a production system can be challenging in livestock. Most attempts to introduce exotic breeds in low input systems were unsuccessful mainly due to the antagonistic environmental conditions. Knowledge of the environmental conditions that are shaping the breed would be needed to elucidate their suitability to different locations. Predictive habitat distribution models use the current climatic conditions of a breed to make
    predictions of the potential distribution of the breed. A methodology was developed to predict breed suitability for different agro-ecological zones based on GIS tools and PHD models. This methodology was tested on distribution data of two introduced chicken breeds in Ethiopia: the Koekoek, originally from South Africa, and the Fayoumi, originally from Egypt. Results from cross-validation based on the current distribution of the breeds showed this methodology to be effective in predicting breed specific environmental suitability. Furthermore, for both breeds the significant climatic factors that shape the breeds distribution
    were similar between the suggested distribution area, and the environment from which the breeds originated in South Africa and Egypt. This novel methodology applied to livestock research, allows for better decisions in introduction programs and the design of testing schemes, and increases our understanding of the role of the environment in livestock productivity.
    A comparison study of five different methods to measure carotenoids in biofortified yellow cassava (Manihot esculenta)
    Jaramillo, Angélica M. ; Londoño, Luis Fernando ; Orozco, Juan Camilo ; Patiño, Gelver ; Belalcazar, John ; Davrieux, Fabrice ; Talsma, Elise F. - \ 2018
    PLoS ONE 13 (2018)12. - ISSN 1932-6203

    The most commonly used method for measuring carotenoid concentration is high-performance liquid chromatography (HPLC). Nevertheless, easier, quicker, and less costly proxy methods exist. We aimed to determine the diagnostic performance of several proxy methods: the spectrophotometer, iCheck Carotene, and near-infrared spectroscopy using both a desktop (dNIRS) and a portable (pNIRS) device for the measurement of total carotenoid concentration (TCC) and all-trans-β-carotene concentration (trans-BC) in 30 fresh cassava (Manihot esculenta Crantz) storage roots in comparison with HPLC. The spectrophotometer presented the highest predictability for TCC, followed by iCheck, dNIRS, and pNIRS. The dNIRS showed the highest predictability and agreement for trans-BC. The pNIRS showed the poorest repeatability and greatest underestimations compared with HPLC. The agreement between all methods was lower for higher carotenoid concentration, with the exception of the spectrophotometer. According to our results, and for screening purposes, the measurement of carotenoids in fresh cassava roots can be carried out by spectrophotometer, iCheck Carotene and NIRS methods depending on the availability of equipment.

    The role of local adaptation in sustainable production of village chickens
    Bettridge, Judy M. ; Psifidi, Androniki ; Terfa, Zelalem G. ; Desta, Takele T. ; Lozano-Jaramillo, Maria ; Dessie, Tadelle ; Kaiser, Pete ; Wigley, Paul ; Hanotte, Olivier ; Christley, Robert M. - \ 2018
    Nature Sustainability 1 (2018)10. - ISSN 2398-9629 - p. 574 - 582.

    Village chickens are ubiquitous in smallholder farming systems, contributing to household, local and national economies under diverse environmental, economic and cultural settings. However, they are raised in challenging environments where productivity is low while mortality is high. There is much interest in utilizing indigenous genetic resources to produce a chicken that is resilient to its environment, while at the same time providing the basis of an economically sustainable enterprise. Globally, however, a wide variety of interventions have so far proved unable to deliver sustainable improvements. Here we show that regional differences in trait preferences and parasite burden are associated with distinct chicken gene pools, probably in response to interactions between natural and human-driven (economic and social) selection pressures. Drivers of regional differences include marketing opportunities, cultural preferences, agro-ecologies and parasite populations, and are evident in system adaptations, such as management practices, population dynamics and bird genotypes. Our results provide sound multidisciplinary evidence to support previous observations that sustainable poultry development interventions for smallholder farmers, including breeding programmes, should be locally tailored and designed for flexible implementation.

    Monitoreo climático: herramienta al servicio de la caficultura Colombiana
    Sarmiento, Ninibeth ; Ramírez, Carolina ; Jaramillo, Álvaro ; Restrepo, Alexander ; García López, Juan Carlos ; Wolters, W. ; Miguel Ayala, L. - \ 2018
    Bogota : APC Columbia - ISBN 9789588490298 - 110
    Transferencia de tecnología y extensión rural : Un modelo de la Federación Nacional de Cafeteros en el Proyecto Gestión Inteligente del Agua
    Jaramillo Cardona, Carlos Mario ; Wolters, W. ; Miguel Ayala, L. - \ 2018
    Bogota : APC Columbia - ISBN 9789588490250 - 59
    Development and analysis of the Soil Water Infiltration Global database
    Rahmati, Mehdi ; Weihermüller, Lutz ; Vanderborght, Jan ; Pachepsky, Yakov A. ; Mao, Lili ; Sadeghi, Seyed Hamidreza ; Moosavi, Niloofar ; Kheirfam, Hossein ; Montzka, Carsten ; Looy, Kris Van; Toth, Brigitta ; Hazbavi, Zeinab ; Yamani, Wafa Al; Albalasmeh, Ammar A. ; Alghzawi, M.Z. ; Angulo-Jaramillo, Rafael ; Antonino, Antônio Celso Dantas ; Arampatzis, George ; Armindo, Robson André ; Asadi, Hossein ; Bamutaze, Yazidhi ; Batlle-Aguilar, Jordi ; Béchet, Béatrice ; Becker, Fabian ; Blöschl, Günter ; Bohne, Klaus ; Braud, Isabelle ; Castellano, Clara ; Cerdà, Artemi ; Chalhoub, Maha ; Cichota, Rogerio ; Císlerová, Milena ; Clothier, Brent ; Coquet, Yves ; Cornelis, Wim ; Corradini, Corrado ; Coutinho, Artur Paiva ; Oliveira, Muriel Bastista De; Macedo, José Ronaldo De; Durães, Matheus Fonseca ; Emami, Hojat ; Eskandari, Iraj ; Farajnia, Asghar ; Flammini, Alessia ; Fodor, Nándor ; Gharaibeh, Mamoun ; Ghavimipanah, Mohamad Hossein ; Ghezzehei, Teamrat A. ; Giertz, Simone ; Hatzigiannakis, Evangelos G. ; Horn, Rainer ; Jiménez, Juan José ; Jacques, Diederik ; Keesstra, Saskia Deborah ; Kelishadi, Hamid ; Kiani-Harchegani, Mahboobeh ; Kouselou, Mehdi ; Jha, Madan Kumar ; Lassabatere, Laurent ; Li, Xiaoyan ; Liebig, Mark A. ; Lichner, Lubomír ; López, María Victoria ; Machiwal, Deepesh ; Mallants, Dirk ; Mallmann, Micael Stolben ; Oliveira Marques, Jean Dalmo De; Marshall, Miles R. ; Mertens, Jan ; Meunier, Félicien ; Mohammadi, Mohammad Hossein ; Mohanty, Binayak P. ; Pulido-Moncada, Mansonia ; Montenegro, Suzana ; Morbidelli, Renato ; Moret-Fernández, David ; Moosavi, Ali Akbar ; Mosaddeghi, Mohammad Reza ; Mousavi, Seyed Bahman ; Mozaffari, Hasan ; Nabiollahi, Kamal ; Neyshabouri, Mohammad Reza ; Ottoni, Marta Vasconcelos ; Ottoni Filho, Theophilo Benedicto ; Pahlavan-Rad, Mohammad Reza ; Panagopoulos, Andreas ; Peth, Stephan ; Peyneau, Pierre Emmanuel ; Picciafuoco, Tommaso ; Poesen, Jean ; Pulido, Manuel ; Reinert, Dalvan José ; Reinsch, Sabine ; Rezaei, Meisam ; Roberts, Francis Parry ; Robinson, David ; Rodrigo-Comino, Jesüs ; Rotunno Filho, Otto Corrêa ; Saito, Tadaomi ; Suganuma, Hideki ; Saltalippi, Carla ; Sándor, Renáta ; Schütt, Brigitta ; Seeger, Manuel ; Sepehrnia, Nasrollah ; Sharifi Moghaddam, Ehsan ; Shukla, Manoj ; Shutaro, Shiraki ; Sorando, Ricardo ; Stanley, Ajayi Asishana ; Strauss, Peter ; Su, Zhongbo ; Taghizadeh-Mehrjardi, Ruhollah ; Taguas, Encarnación ; Teixeira, Wenceslau Geraldes ; Vaezi, Ali Reza ; Vafakhah, Mehdi ; Vogel, Tomas ; Vogeler, Iris ; Votrubova, Jana ; Werner, Steffen ; Winarski, Thierry ; Yilmaz, Deniz ; Young, Michael H. ; Zacharias, Steffen ; Zeng, Yijian ; Zhao, Ying ; Zhao, Hong ; Vereecken, Harry - \ 2018
    Earth System Science Data 10 (2018)3. - ISSN 1866-3508 - p. 1237 - 1263.

    In this paper, we present and analyze a novel global database of soil infiltration measurements, the Soil Water Infiltration Global (SWIG) database. In total, 5023 infiltration curves were collected across all continents in the SWIG database. These data were either provided and quality checked by the scientists who performed the experiments or they were digitized from published articles. Data from 54 different countries were included in the database with major contributions from Iran, China, and the USA. In addition to its extensive geographical coverage, the collected infiltration curves cover research from 1976 to late 2017. Basic information on measurement location and method, soil properties, and land use was gathered along with the infiltration data, making the database valuable for the development of pedotransfer functions (PTFs) for estimating soil hydraulic properties, for the evaluation of infiltration measurement methods, and for developing and validating infiltration models. Soil textural information (clay, silt, and sand content) is available for 3842 out of 5023 infiltration measurements (∼76%) covering nearly all soil USDA textural classes except for the sandy clay and silt classes. Information on land use is available for 76ĝ€% of the experimental sites with agricultural land use as the dominant type (∼40%). We are convinced that the SWIG database will allow for a better parameterization of the infiltration process in land surface models and for testing infiltration models. All collected data and related soil characteristics are provided online in ∗.xlsx and ∗.csv formats for reference, and we add a disclaimer that the database is for public domain use only and can be copied freely by referencing it. Supplementary data are available at (Rahmati et al., 2018). Data quality assessment is strongly advised prior to any use of this database. Finally, we would like to encourage scientists to extend and update the SWIG database by uploading new data to it.

    Neutral and functionally important genes shed light on phylogeography and the history of high-altitude colonization in a widespread New World duck
    Lozano-Jaramillo, Maria ; McCracken, Kevin G. ; Cadena, Carlos Daniel - \ 2018
    Ecology and Evolution 8 (2018)13. - ISSN 2045-7758 - p. 6515 - 6528.
    adaptation - hypoxia - migration - natural selection

    Phylogeographic studies often infer historical demographic processes underlying species distributions based on patterns of neutral genetic variation, but spatial variation in functionally important genes can provide additional insights about biogeographic history allowing for inferences about the potential role of adaptation in geographic range evolution. Integrating data from neutral markers and genes involved in oxygen (O2)-transport physiology, we test historical hypotheses about colonization and gene flow across low- and high-altitude regions in the Ruddy Duck (Oxyura jamaicensis), a widely distributed species in the New World. Using multilocus analyses that for the first time include populations from the Colombian Andes, we also examined the hypothesis that Ruddy Duck populations from northern South America are of hybrid origin. We found that neutral and functional genes appear to have moved into the Colombian Andes from both North America and southern South America, and that high-altitude Colombian populations do not exhibit evidence of adaptation to hypoxia in hemoglobin genes. Therefore, the biogeographic history of Ruddy Ducks is likely more complex than previously inferred. Our new data raise questions about the hypothesis that adaptation via natural selection to high-altitude conditions through amino acid replacements in the hemoglobin protein allowed Ruddy Ducks to disperse south along the high Andes into southern South America. The existence of shared genetic variation with populations from both North America and southern South America as well as private alleles suggests that the Colombian population of Ruddy Ducks may be of old hybrid origin. This study illustrates the breadth of inferences one can make by combining data from nuclear and functionally important loci in phylogeography, and underscores the importance of complete range-wide sampling to study species history in complex landscapes.

    Laboratory testing of Beerkan infiltration experiments for assessing the role of soil sealing on water infiltration
    Prima, S. Di; Concialdi, P. ; Lassabatere, L. ; Angulo-Jaramillo, R. ; Pirastru, M. ; Cerdà, A. ; Keesstra, S. - \ 2018
    Catena 167 (2018). - ISSN 0341-8162 - p. 373 - 384.
    Beerkan infiltration experiment - BEST algorithms - Rainfall simulation - Saturated soil hydraulic conductivity - Soil sealing

    Soil surface sealing is a major cause of decreased infiltration rates and increased surface runoff and erosion during a rainstorm. The objective of this paper is to quantify the effect of surface sealing on infiltration for 3 layered soils with different textures for the upper layer and investigate the capability of BEST procedure to catch the formation of the seal and related consequences on water infiltration. Rainfall experiments were carried out to induce the formation of the seal. Meanwhile, Beerkan infiltration runs were carried out pouring water at different distances from the soil surface (BEST-H versus BEST-L runs, with a High and Low water pouring heights, respectively) for the same type of layered soils. Then, we determined saturated soil hydraulic conductivity, Ks, values from rainfall simulation and Beerkan infiltration experiments. Rainfall simulations carried out on soil layers having different depths allowed to demonstrate that infiltration processes were mainly driven by the seal and that Ks estimates were representative of the seal. Mean Ks values, estimated for the late-phase, ranged from 13.9 to 26.2 mm h−1. Soil sealing induced an increase in soil bulk density by 38.7 to 42.1%, depending on the type of soil. Rainfall-deduced Ks data were used as target values and compared with those estimated by the Beerkan runs. BEST-H runs proved more appropriate than BEST-L runs, those last triggering no seal formation. The predictive potential of the three BEST algorithms (BEST-slope, BEST-intercept and BEST-steady) to yield a proper Ks estimate for the seal was also investigated. BEST-slope yielded negative Ks values in 87% of the cases for BEST-H runs. Positive values were obtained in 100% of the cases with BEST-steady and BEST-intercept. However, poorer fits were obtained with the latter algorithm. The comparison of Ks estimates with rainfall-deduced estimates allowed to identify BEST-steady algorithm with BEST-H run as the best combination. The method proposed in this study could be used to easily measure the seal's saturated hydraulic conductivity of an initially undisturbed bare soil directly impacted by water with minimal experimental efforts, using small volumes of water and easily transportable equipment.

    Comparing transient and steady-state analysis of single-ring infiltrometer data for an abandoned field affected by fire in Eastern Spain
    Prima, Simone Di; Lassabatere, Laurent ; Rodrigo-Comino, Jesús ; Marrosu, Roberto ; Pulido, Manuel ; Angulo-Jaramillo, Rafael ; úbeda, Xavier ; Keesstra, Saskia ; Cerdà, Artemi ; Pirastru, Mario - \ 2018
    Water 10 (2018)4. - ISSN 2073-4441
    Bottomless bucket method - Data analysis procedures - Field-saturated soil hydraulic conductivity - Infiltration - Post-fire soil hydraulic characterization - Single-ring infiltrometer
    This study aimed at determining the field-saturated soil hydraulic conductivity, Kfs, of an unmanaged field affected by fire by means of single-ring infiltrometer runs and the use of transient and steady-state data analysis procedures. Sampling and measurements were carried out in 2012 and 2017 in a fire-affected field (burnt site) and in a neighboring non-affected site (control site). The predictive potential of different data analysis procedures (i.e., transient and steady-state) to yield proper Kfs estimates was investigated. In particular, the transient WU1 method and the BB, WU2 and OPD methods were compared. The cumulative linearization (CL) method was used to apply the WU1 method. Values of Kfs ranging from 0.87 to 4.21 mm·h-1 were obtained, depending on the considered data analysis method. The WU1 method did not yield significantly different Kfs estimates between the sampled sites throughout the five-year period, due to the generally poor performance of the CL method, which spoiled the soil hydraulic characterization. In particular, good fits were only obtained in 23% of the cases. The BB, WU2 and the OPD methods, with a characterization based exclusively on a stabilized infiltration process, yielded an appreciably lower variability of the Kfs data as compared with the WU1 method. It was concluded that steady-state methods were more appropriate for detecting slight changes of Kfs in post-fire soil hydraulic characterizations. Our results showed a certain degree of soil degradation at the burnt site with an immediate reduction of the soil organic matter and a progressive increase of the soil bulk density during the five years following the fire. This general impoverishment resulted in a slight but significant decrease in the field-saturated soil hydraulic conductivity.
    Comparing Beerkan infiltration tests with rainfall simulation experiments for hydraulic characterization of a sandy-loam soil
    Prima, Simone Di; Bagarello, Vincenzo ; Lassabatere, Laurent ; Angulo-Jaramillo, Rafael ; Bautista, Inmaculada ; Burguet, Maria ; Cerda Bolinches, Artemio ; Iovino, Massimo ; Prosdocimi, Massimo - \ 2017
    Hydrological Processes 31 (2017)20. - ISSN 0885-6087 - p. 3520 - 3532.
    Beerkan infiltration - height of water application - rainfall simulation - runoff - saturated soil hydraulic conductivity

    Saturated soil hydraulic conductivity, Ks, data collected by ponding infiltrometer methods and usual experimental procedures could be unusable for interpreting field hydrological processes and particularly rainfall infiltration. The Ks values determined by an infiltrometer experiment carried out by applying water at a relatively large distance from the soil surface could however be more appropriate to explain surface runoff generation phenomena during intense rainfall events. In this study, a link between rainfall simulation and ponding infiltrometer experiments was established for a sandy-loam soil. The height of water pouring for the infiltrometer run was chosen, establishing a similarity between the gravitational potential energy of the applied water, Ep, and the rainfall kinetic energy, Ek. To test the soundness of this procedure, the soil was sampled with the Beerkan estimation of soil transfer parameters procedure of soil hydraulic characterization and two heights of water pouring (0.03 m, i.e., usual procedure, and 0.34 m, yielding Ep = Ek). Then, a comparison between experimental steady-state infiltration rates, isR, measured with rainfall simulation experiments determining runoff production and Ks values for the two water pouring heights was carried out in order to discriminate between theoretically possible (isR ≥ Ks) and impossible (isR < Ks) situations. Physically possible Ks values were only obtained by applying water at a relatively large distance from the soil surface, because isR was equal to 20.0 mm h−1 and Ks values were 146.2–163.9 and 15.2–18.7 mm h−1 for a height of water pouring of 0.03 and 0.34 m, respectively. This result suggested the consistency between Beerkan runs with a high height of water pouring and rainfall simulator experiments. Soil compaction and mechanical aggregate breakdown were the most plausible physical mechanisms determining reduction of Ks with height. This study demonstrated that the height from which water is poured onto the soil surface is a key parameter in infiltrometer experiments and can be adapted to mimic the effect of high intensity rain on soil hydraulic properties.

    Linking rhizosphere microbiome composition of wild and domesticated Phaseolus vulgaris to genotypic and root phenotypic traits
    Pérez-Jaramillo, Juan E. ; Carrión, Víctor J. ; Bosse, Mirte ; Ferrão, Luiz F.V. ; Hollander, Mattias de; Garcia, Antonio Augusto Franco ; Ramírez, Camilo A. ; Mendes, Rodrigo ; Raaijmakers, Jos M. - \ 2017
    ISME Journal 11 (2017)10. - ISSN 1751-7362 - p. 2244 - 2257.
    Plant domestication was a pivotal accomplishment in human history, but also led to a reduction in genetic diversity of crop species compared to their wild ancestors. How this reduced genetic diversity affected plant-microbe interactions belowground is largely unknown. Here, we investigated the genetic relatedness, root phenotypic traits and rhizobacterial community composition of modern and wild accessions of common bean (Phaseolus vulgaris) grown in agricultural soil from the highlands of Colombia, one of the centers of common bean diversification. Diversity Array Technology-based genotyping and phenotyping of local common bean accessions showed significant genetic and root architectural differences between wild and modern accessions, with a higher specific root length for the wild accessions. Canonical Correspondence Analysis indicated that the divergence in rhizobacterial community composition between wild and modern bean accessions is associated with differences in specific root length. Along the bean genotypic trajectory, going from wild to modern, we observed a gradual decrease in relative abundance of Bacteroidetes, mainly Chitinophagaceae and Cytophagaceae, and an increase in relative abundance of Actinobacteria and Proteobacteria, in particular Nocardioidaceae and Rhizobiaceae, respectively. Collectively, these results establish a link between common bean domestication, specific root morphological traits and rhizobacterial community assembly.
    Impacts of thinning of a Mediterranean oak forest on soil properties influencing water infiltration
    Prima, Simone Di; Bagarello, Vincenzo ; Angulo-Jaramillo, Rafael ; Bautista, Inmaculada ; Cerda Bolinches, Artemio ; Campo, Antonio Del; González-Sanchis, María ; Iovino, Massimo ; Lassabatere, Laurent ; Maetzke, Federico - \ 2017
    Journal of Hydrology and Hydromechanics 65 (2017)3. - ISSN 0042-790X - p. 276 - 286.
    Forest soils - Saturated and near saturated hydraulic conductivity - Soil water repellency
    In Mediterranean ecosystems, special attention needs to be paid to forest-water relationships due to water scarcity. In this context, Adaptive Forest Management (AFM) has the objective to establish how forest resources have to be managed with regards to the efficient use of water, which needs maintaining healthy soil properties even after disturbance. The main objective of this investigation was to understand the effect of one of the AFM methods, namely forest thinning, on soil hydraulic properties. At this aim, soil hydraulic characterization was performed on two contiguous Mediterranean oak forest plots, one of them thinned to reduce the forest density from 861 to 414 tree per ha. Three years after the intervention, thinning had not affected soil water permeability of the studied plots. Both ponding and tension infiltration runs yielded not significantly different saturated, Ks, and unsaturated, K-20, hydraulic conductivity values at the thinned and control plots. Therefore, thinning had no an adverse effect on vertical water fluxes at the soil surface. Mean Ks values estimated with the ponded ring infiltrometer were two orders of magnitude higher than K-20 values estimated with the minidisk infiltrometer, revealing probably soil structure with macropores and fractures. The input of hydrophobic organic matter, as a consequence of the addition of plant residues after the thinning treatment, resulted in slight differences in terms of both water drop penetration time, WDPT, and the index of water repellency, R, between thinned and control plots. Soil water repellency only affected unsaturated soil hydraulic conductivity measurements. Moreover, K-20 values showed a negative correlation with both WDPT and R, whereas Ks values did not, revealing that the soil hydrophobic behavior has no impact on saturated hydraulic conductivity.
    High-throughput phenotyping and improvements in breeding cassava for increased carotenoids in the roots
    Belalcazar, John ; Dufour, Dominique ; Andersson, Meike S. ; Pizarro, Mónica ; Luna, Jorge ; Londoño, Luis ; Morante, Nelson ; Jaramillo, Angélica M. ; Pino, Lizbeth ; Becerra López-Lavalle, Luis A. ; Davrieux, Fabrice ; Talsma, Elise F. ; Ceballos, Hernán - \ 2016
    Crop Science 56 (2016)6. - ISSN 0011-183X - p. 2916 - 2925.

    Past research developed reliable equations to base selections for high β-carotene on nearinfrared spectroscopy (NIR) predictions (100 genotypes d−1) rather than with high-perfor-mance liquid chromatography (HPLC) (<10 samples d−1). During recent harvest, CIAT made selections based on NIR predictions for the first time. This innovation produced valuable information that will help other cassava (Manihot esculenta Crantz) breeding programs. A total of 284 samples were analyzed with NIR and HPLC for total β-carotene (TBC) and by the oven method for dry matter content (DMC). Results indicated that NIR reliably predicted TBC and DMC. In addition, 232 genotypes grown in preliminary yield trials (PYTs) were harvested at 8.5 and 10.5 mo after planting (one plant per genotype and age) and root quality traits analyzed (by NIR only). Repeatability of results at the two ages was excellent, suggesting reliable results from NIR. In contrast to previous reports, age of the plant did not influence carotenoids content in the roots. The availability of a high-throughput NIR protocol allowed comparing results (for the first time) from seedling and cloned plants from the same genotype. Results showed very little relationship for DMC between seedling and cloned plants (R2 = 0.09). There was a much better association for TBC (R2 = 0.48) between seedling and cloned plants. It is postulated that variation in the environmental conditions when seedling and cloned plants (from the same gen-otype) may be responsible for these weak associations. Important changes in selection strategies have been implemented to overcome problems related to a lengthy harvesting season.

    Towards bioeconomy development in Latin America and the Caribbean
    Trigo, E.J. ; Henry, G. ; Sanders, J.P.M. ; Schurr, U. ; Ingelbrecht, I. ; Revell, C. ; Santana, C. ; Rocha, P. - \ 2015
    In: Towards a Latin America and Caribbean knowledge based bio-economy in partnership with Europe / Hodson de Jaramillo, E., Bogota Colombia : Pontificia Universidad Javeriana - ISBN 9789587167429 - p. 15 - 41.
    Reported behavior, knowledge and awareness toward the potential for norovirus transmission by food handlers in Dutch catering companies and institutional settings in relation to the prevalence of norovirus
    Verhoef, Linda ; Jaramillo Gutierrez, Giovanna ; Koopmans, Marion ; Boxman, Ingeborg L.A. - \ 2013
    Food Control 34 (2013)2. - ISSN 0956-7135 - p. 420 - 427.
    Environmental samples - Environmental swabs - Food safety knowledge - Foodborne - Questionnaires

    Norovirus (NoV) in ready to eat food has recently been defined as one of the virus-food commodity combinations with greatest public health concern. The role of food handlers therein has well been recognized. The aim of this study was to identify gaps in food handlers' education and to investigate possible associations between reported behavior, knowledge and awareness of NoV, and environmental presence of NoV. For this, face-to-face interviews were conducted using structured questionnaires in 1023 catering companies (i.e. restaurants mainly), 101 non-hospital health care centers, 52 hospital central kitchens and in 102 hospital in-patient units. In addition, three surface swabs were taken at each setting. Multivariate logistic regression was performed on data restricted to NoV high season months only, in which NoV was present in 21/374 (6%) catering companies and 37/233 (16%) institutional settings (p<0.01). The two independent determinants of presence of NoV on environmental surfaces identified were being situated in an institutional setting and having an attitude to continue food handling while sick with vomiting complaints. Several gaps in education and training were identified, demonstrating that knowledge on NoV was low, although awareness of NoV was significantly higher among food handlers in institutional settings than in catering companies. This is the first time questionnaires and environmental testing have been combined in the same study to identify issues of improvement. Training on all important aspects of NoV according to the recently developed Codex Alimentarius guidelines to control viruses in food is strongly recommended.

    Land cover controls on river discharge in Sweden
    Velde, Y. van der; Vercauteren, N. ; Jaramillo, F. ; Dekker, S.C. ; Destouni, G. ; Lyon, S.W. - \ 2013
    Abstract As humans alter landscape, vegetation, climate and atmospheric composition, changes in the terrestrial water balance and fresh water resources are likely to occur. Understanding how climate, vegetation, humans and hydrology interact is key for accurate projections of future fresh water resources. In this study we focus on forest dominated Sweden where significant changes in climate and increasing human activity have co-occurred during the past 50 years. For 280 catchments in Sweden, we related runoff coefficients and change trends thereof to land-surface characteristics. With these relationships we created average and change trend maps for runoff and evapotranspiration across Sweden. All this information is summarized by plotting water use efficiency (actual evapotranspiration (ET)/precipitation) against energy use efficiency (actual ET/potential ET ) in a Budyko-type framework for areas with unique land cover across Sweden. This plot clearly shows that wetlands tend to have lower water and energy use efficiencies compared to “open waters”, forests and agriculture, and that agriculture and forests have comparable water and energy use efficiencies closest to those of “open waters”. These results demonstrate how a change in land cover driven by climate change or by humans is likely to alter land-cover-atmosphere interactions, thereby changing both the water and energy balance of catchments. Looking at runoff coefficient change trends during the last 50 years we see that forests tended to become more efficient in using water and energy (i.e. the fractions of water and energy converted into river runoff and heat decreased). As this behavior coincides with an increase in precipitation it signals an acceleration of the hydrological cycle of Swedish forests. In this presentation we will discuss these findings focusing on the impact of forests on river discharges and the implications for future water cycles.
    Computational protein design with electrostatic focusing: experimental characterization of a conditionally folded helical domain with a reduced amino acid alphabet
    Suarez Diez, M. ; Pujol, M. ; Matzapetakis, M. ; Jaramillo, A. ; Iranzo, O. - \ 2013
    Biotechnology Journal 8 (2013)7. - ISSN 1860-6768 - p. 855 - 864.
    solution nmr structure - structural basis - peptides - recognition - prediction - sequences - dynamics - energy - trifluoroethanol - optimization
    Automated methodologies to design synthetic proteins from first principles use energy computations to estimate the ability of the sequences to adopt a targeted structure. This approach is still far from systematically producing native-like sequences, due, most likely, to inaccuracies when modeling the interactions between the protein and its aqueous environment. This is particularly challenging when engineering small protein domains (with less polar pair interactions than with the solvent). We have re-designed a three-helix bundle, domain B, using a fixed backbone and a four amino acid alphabet. We have enlarged the rotamer library with conformers that increase the weight of electrostatic interactions within the design process without altering the energy function used to compute the folding free energy. Our synthetic sequences show less than 15% similarity to any Swissprot sequence. We have characterized our sequences in different solvents using circular dichroism and nuclear magnetic resonance. The targeted structure achieved is dependent on the solvent used. This method can be readily extended to larger domains. Our method will be useful for the engineering of proteins that become active only in a given solvent and for designing proteins in the context of hydrophobic solvents, an important fraction of the situations in the cell
    Interweaving monitoring activities and model development towards enhancing knowledge of the soil-plant-atmosphere continuum
    Romano, N. ; Angulo-Jaramillo, M. ; Javaux, M. ; Ploeg, M.J. van der - \ 2012
    Vadose Zone Journal 11 (2012)3. - ISSN 1539-1663 - 3 p.
    water - observatories - ecohydrology - systems
    The guest editors summarize the advances and challenges associated with monitoring and modeling of the soil–plant–atmosphere continuum. They introduce the contributions in the special section, with an emphasis on the scale addressed in each study. The study of water pathways from the soil to the atmosphere through plants—the so-called soil–plant–atmosphere continuum (SPAC)—has always been central to agronomy, hydrology, plant physiology, and other disciplines, using a wide range of approaches and tools. In recent years, we have been witnessing a rapid expansion of interweaving monitoring activities and model development related to SPAC in climatic, ecological, and applications other than the traditional agrohydrological, and it is therefore timely to review the current status of this topic and outline future directions of research. The initiative for the special section of Vadose Zone Journal on SPAC emanated from several sessions we recently organized in international conferences and meetings. With a view to the specific research questions covered in this special section, this article introduces and reviews SPAC underlying issues and then provides a brief overview of the invited contributions. We have grouped together the 15 contributions under three main sections related to the local, field, and landscape spatial scales of interests. Within these sections, the papers present their innovative results using different measuring techniques (from classic tensiometers and TDR sensors to more advanced and sophisticated equipment based on tomography and geophysics) and different modeling tools (from mechanistic models based on the Richards equation to more parametrically parsimonious hydrologic balance models). They provide a snapshot of the current state of the art while emphasizing the significant progress attained in this field of research. New technological developments and applications are also highlighted.
    Soil water repellency in arid and humid climates
    Jaramillo, D.F. ; Dekker, L.W. ; Ritsema, C.J. ; Hendrickx, J.M.H. - \ 2003
    In: Soil water repellency; occurrence, consequences, and amelioration / Ritsema, C.J., Dekker, L.W., Amsterdam : Elsevier - ISBN 9780444512697 - p. 93 - 98.
    Plaguicidas en el medio ambiente
    Stoorvogel, J.J. ; Jaramillo, R. ; Merino, R. ; Kosten, S. - \ 2003
    In: Los Plaguicidas. Impactos en produccion, salud y medio ambiente en Carchi, Ecuador / Yanggen, D., Crissman, C., Espinosa, P., Peru : Centro International de la Papa - ISBN 9789978222829 - p. 49 - 69.
    Carbofuran presence in soil leachate, groundwater, and surface water in the potato growing area in Carchi, Equador
    Jaramillo, R. ; Bowen, W. ; Stoorvogel, J.J. - \ 2001
    In: CIP Program Report 1999-2000 Lima : Int. Potato Center - p. 355 - 360.
    Occurrence of soil water repellency in arid and humid climates
    Jaramillo, D.F. ; Dekker, L.W. ; Ritsema, C.J. ; Hendrickx, J.M.H. - \ 2000
    Journal of Hydrology 231/232 (2000). - ISSN 0022-1694 - p. 105 - 111.
    bodemwater - hydratatie - afstoting - dehydratie - evaporatie - humide klimaatzones - soil water - hydration - repellency - dehydration - evaporation - humid zones
    Soil measurements during HAPEX-Sahel intensive observation period.
    Cuenca, R.H. ; Brouwer, J. ; Chanzy, A. ; Droogers, P. ; Galle, S. ; Gaze, S.R. ; Sicot, M. ; Stricker, J.N.M. ; Angulo-Jaramillo, R. ; Boyle, S.A. ; Bromley, J. ; Chebhouni, A.G. - \ 1997
    Journal of Hydrology 188/189 (1997). - ISSN 0022-1694 - p. 224 - 266.
    bodemwatergehalte - neerslag - hydrologie - sahel - soil water content - precipitation - hydrology - sahel
    This article describes measurements made at each site and for each vegetation cover as part of the soils program for the HAPEX-Sahel regional scale experiment. The measurements were based on an initial sampling scheme and included profile soil water content, surface soil water content, soil water potential, infiltration rates, additional measurements on core samples, and grain size analysis. The measurements were used to categorize the state of the surface and profile soil water regimes during the experiment and to derive functional relationships for the soil water characteristic curve, unsaturated hydraulic conductivity function, and infiltration function. Sample results for different supersites and different vegetation covers are presented showing soil water profiles and total soil water storage on days corresponding to the experimental 'Golden Days'. Sample results are also presented for spatial and temporal distribution of surface moisture content and infiltration tests. The results demonstrate that the major experimental objective of monitoring the supersites during the most rapid vegetative growth stage with the largest change of the surface energy balance following the rainy season was very nearly achieved. Separation of the effects of probable root activity and drainage of the soil profile is possible. The potential for localized advection between the bare soil and vegetation strips of the tiger bush sites is demonstrated.
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