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; https://africacgg.net/). 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
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