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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How to measure health improvement? : assessment of subtle shifts in metabolic phenotype
Fazelzadeh, Parastoo - \ 2017
Wageningen University. Promotor(en): A.H. Kersten; J.P.M. van Duynhoven, co-promotor(en): M.V. Boekschoten. - Wageningen : Wageningen University - ISBN 9789463430739 - 187
health promotion - improvement - measurement - metabolic profiling - elderly - obesity - microarrays - rna - peripheral blood mononuclear cells - gezondheidsbevordering - verbetering - meting - metabolische profilering - ouderen - obesitas - microarrays - rna - perifere mononucleaire bloedcellen

Human health is impacted by a complex network of interactions between biological pathways, mechanisms, processes, and organs, which need to be able to adapt to a continuously changing environment to maintain health. This adaptive ability is called ‘phenotypic flexibility’. It is thought that health is compromised and diseases develop when these adaptive processes fail. As the product of interactions between several factors such as genetic makeup, diet, lifestyle, environment and the gut microbiome, the ‘metabolic phenotype’ provides a readout of the metabolic state of an individual. Understanding these relationships will be one of a major challenges in nutrition and health research in the next decades. To address this challenge, the development of high-throughput omics tools combined with the application of elaborate statistical analyses will help characterize the complex relationship of (bio) chemicals in human systems and their interaction with other variables including environment and lifestyle to produce the measured phenotype. An important aim of this thesis was to identify phenotype shifts by looking at effect of prolonged resistance-type exercise training on skeletal muscle tissue in older subjects and the possible shift toward the features of younger subjects as a reference for a healthier phenotype. A second aim was to identify phenotype shifts by looking at the response to a challenge in obese subjects and the possible shift toward lean subjects as a reference for a healthier phenotype.

Chapter 2 and 3 of this thesis show how the significant remaining plasticity of ageing skeletal muscle can adapt to resistance-type exercise training. The data indicate that frail and healthy older subjects have two distinct phenotypes according to the skeletal muscle tissue metabolite profiles and that exercise training shifts aged muscle towards a younger phenotype. We showed that the effect of exercise on amino acid derived acylcarnitines (AAAC’s) in older subjects points towards decreased branched chain amino acid catabolism, likely due to compromised activation of the branched chain α-keto acid hydrogenase (BCKDH) complex. Furthermore, we found that the protocadherin gamma gene cluster might be involved in aged-muscle denervation and re-innervation. Finally, plasma was found to be a poor indicator of muscle metabolism, emphasizing the need for direct assessment of metabolites in muscle tissue.

Chapter 4 of this thesis examines whether a mixed meal challenge response provides a readout for a shift in phenotype upon weight loss in obese male subjects. We concluded that weight loss moderately affects the mixed meal challenge response of both plasma metabolome and transcriptome of peripheral blood mononuclear cells in obese subjects. Measurements at the fasted and postprandial state also provide us with a different type of information.

In Chapter 5 it is demonstrated that the global testing of pathways could provide a concise summary of the multiple univariate testing approach used in Chapter 4. In Chapter 6 it is discussed how the findings of this thesis increase our understanding of how to measure phenotypic flexibility as a proxy of health. In this thesis it is shown that the correlations between tissue and plasma metabolites are rather weak, emphasising the need to perform organ-specific studies. Availability of less invasive/painful sampling techniques and the use of small amounts of tissue would enable larger scale human studies on adipose tissue and skeletal muscle to more accurately define phenotypical shifts due to diet or lifestyle interventions. With respect to the assessment of phenotypical flexibility by omics approaches, significant complications can be expected in trying to relate plasma metabolism to PBMC gene expression. Organ-focussed approaches that integrate multiple omics levels using system biology approaches are considered to be a lot more promising.

Production efficiency of mussel bottom culture
Capelle, Jacob J. - \ 2017
Wageningen University. Promotor(en): Aad Smaal; P.M.J. Herman, co-promotor(en): Jeroen Wijsman. - Wageningen : Wageningen University - ISBN 9789463430869 - 240
mussels - mussel culture - bottom culture - efficiency - population dynamics - culture techniques - biomass production - improvement - shellfish culture - aquaculture - mossels - mosselteelt - bodemcultuur - efficiëntie - populatiedynamica - kweektechnieken - biomassa productie - verbetering - schaal- en schelpdierenteelt - aquacultuur

Mussel bottom culture is an extensive type of aquaculture; it depends on natural resources for feed, seed and space. It consists of the translocation of seed from natural beds to designed culture areas, where mussel farmers try to improve production efficiency. Production efficiency is measured by the relative biomass production (RBP) expressed as units of biomass harvested from one unit of biomass seeded, it increases with mussel growth and decreases with mussel mortality. Mussel bottom culture makes use of nature and also depends on nature. Cultured mussels are subject to similar environmental factors that influence growth and mortality on natural mussel beds, with additional effects of anthropogenic factors. In this thesis we focus on dynamics of mussel beds and the impact and effectivity of culture activities on mussel production yield. The major objectives are stated as: (1) to better understand the population dynamics of subtidal mussel populations, (2) to analyze what factors determine production efficiency in mussel bottom culture and how this can be improved. On natural mussel beds mussels organise in patterns that enhance food delivery and resilience of the bed. On culture plots mussels are seeded in concentric seeding patterns. Seeding techniques concentrate mussels locally within the culture plot area, resulting in high local mussel densities; this increases competition and limits the spatial re-organisation of mussels in the bed. Consequently, seeding on culture plots is followed by a large size and density dependent seeding loss that ranges from about 40% for seed from fishery to 69% for smaller SMC seed. This loss was the major factor in determining the maximum RBP. Losses in the grow-out stage were substantially lower, a subsequent density dependent loss was found for smaller mussels (<30 mm), and a non-density dependent loss for larger mussels (>30 mm). Shore crab predation is an important factor contributing to the higher losses at seeding. The effect of shore crab predation on mussel biomass production is higher than expected from previous studies. In an experiment on an intertidal culture plot in the Oosterschelde (NL), we observed that shore crab predation peaks directly after seeding and accounted for 33% of the total losses within five weeks after seeding. Spatial patterns in the survival rates of natural mussel beds in the Wadden Sea show better seed survival in areas with intermediate salinity (mean annual salinity 17.5-22.5 mg l-1). This suggests that mussel survival is negatively related to sea star distribution, which is largely controlled by salinity. Natural beds that escape predation are found at lower salinities and mussels on these beds showed low growth rates, also because of a lower food quality in these areas. Mussel culture strongly affects the population dynamics of the subtidal mussel population, through relaying of mussels from natural mussel beds to culture plots. Culture plots are located in more saline regions of the Wadden Sea (mean annual salinity 25.8 mg l-1), compared to natural mussel beds. This activity increased mussel growth and survival because food quality on culture plots is high and predation is prevented. As a result, average biomass production is higher on culture plots than on natural mussel beds and this difference increases over time. A more efficient seed use on the available area, that can be obtained by reducing seeding losses will increase RBP, maximum biomass production and increases maximum profit. Our results suggest that this can be achieved by seeding homogeneously in low densities.

Greening of Ethiopian Dairy Value Chains: evaluation of environmental impacts and identification of interventions for sustainable intensification of dairy value chains
Vries, Marion de; Yigrem, Sintayehu ; Vellinga, Theun - \ 2016
Wageningen : Wageningen UR Livestock Research (Livestock Research report 948) - 69
dairy herds - dairy performance - improvement - dairy industry - sustainability - nutrient use efficiency - environmental impact - intensification - ethiopia - melkveestapel - melkresultaten - verbetering - zuivelindustrie - duurzaamheid (sustainability) - nutriëntengebruiksefficiëntie - milieueffect - intensivering - ethiopië
QTL analysis for stomatal functioning in tetraploid Rosa x hybrida grown at high relative air humidity and its implications on postharvest longevity
Carvalho, D.R.A. ; Koning, C.F.S. ; Fanourakis, D. ; Vasconcelos, M.W. ; Carvalho, S.M.P. ; Heuvelink, E. ; Krens, F.A. ; Maliepaard, C.A. - \ 2015
Molecular Breeding 35 (2015). - ISSN 1380-3743 - 11 p.
marker-assisted selection - water relations - cut roses - in-vitro - traits - environments - conductance - sensitivity - improvement - resistance
High relative air humidity (RH = 85 %) during leaf development disturbs stomatal functioning leading to excessive water loss in conditions of high evaporative demand, resulting in severe reduction in postharvest longevity. In roses, this effect depends on the genotype, opening the possibility for breeding cultivars with more responsive stomata. In this study, we aim at identifying genomic regions associated with the control of water loss following growth at high RH. The F1 generation (108 offspring) and the two parents (P540 and P867) of a tetraploid cut rose population grown at high (85 %) RH were phenotyped for stomatal control to water loss by assessing the relative water content after 4 h of leaflet desiccation (RWC_4 h). The RWC_4 h varied between 7 and 62 % across the 110 studied individuals, with parents P540 and P867 showing 51 and 20 % RWC_4 h, respectively. Based on these data, a quantitative trait locus (QTL) analysis was performed. The impact of the identified QTLs on postharvest longevity of ten selected offspring was further evaluated. Three QTLs were identified: two major [positioned on linkage group 5 of the integrated consensus map (ICM 5) of both parents and on ICM 2 of the parent P867] and one putative minor (mapped to ICM 6 of both parents), explaining 32 % of the variability in the RWC_4 h. Low RWC_4 h was found to be a good proxy for eliminating the offspring with short vase life. This study constitutes a first step toward identifying the most likely regions for genes of interest controlling stomatal functioning in high RH-grown plants.
5 jaar Wageningen Potato Centre (WPC)
Brouwer, T.A. ; Tramper, M. ; Visser, R.G.F. - \ 2015
Wageningen : Wageningen UR
akkerbouw - aardappelen - wetenschappelijk onderzoek - landbouwbedrijven - proefbedrijven - kennisoverdracht - verbetering - arable farming - potatoes - scientific research - farms - pilot farms - knowledge transfer - improvement
Het kennisplatform Wageningen Potato Centre (WPC) is een initiatief van Wageningen UR om een brug te slaan tussen wetenschap en bedrijfsleven. Strategisch en fundamenteel wordt toegankelijk én toepasbaar gemaakt voor de partners van WPC.
Climate change impact and adaptation research requires integrated assessment and farming systems analysis: a case study in the Netherlands
Reidsma, P. ; Wolf, J. ; Kanellopoulos, A. ; Schaap, B.F. ; Mandryk, M. ; Verhagen, J. ; Ittersum, M.K. van - \ 2015
Environmental Research Letters 10 (2015)4. - ISSN 1748-9326
european-union - crop yields - agriculture - responses - models - wheat - variability - improvement - strategies - scenarios
Rather than on crop modelling only, climate change impact assessments in agriculture need to be based on integrated assessment and farming systems analysis, and account for adaptation at different levels. With a case study for Flevoland, the Netherlands, we illustrate that (1) crop models cannot account for all relevant climate change impacts and adaptation options, and (2) changes in technology, policy and prices have had and are likely to have larger impacts on farms than climate change. While crop modelling indicates positive impacts of climate change on yields of major crops in 2050, a semiquantitative and participatory method assessing impacts of extreme events shows that there are nevertheless several climate risks. A range of adaptation measures are, however, available to reduce possible negative effects at crop level. In addition, at farm level farmers can change cropping patterns, and adjust inputs and outputs. Also farm structural change will influence impacts and adaptation. While the 5th IPCC report is more negative regarding impacts of climate change on agriculture compared to the previous report, also for temperate regions, our results show that when putting climate change in context of other drivers, and when explicitly accounting for adaptation at crop and farm level, impacts may be less negative in some regions and opportunities are revealed. These results refer to a temperate region, but an integrated assessment may also change perspectives on climate change for other parts of the world.
Secure sustainable seafood from developing countries. Require improvements as conditions for market access
Sampson, G.S. ; Sanchirico, J.N. ; Roheim, C.A. ; Bush, S.R. ; Taylor, J.E. ; Allison, E.A. ; Anderson, J.L. ; Ban, N.C. ; Fujita, R. ; Jupiter, S. ; Wilson, J.R. - \ 2015
Science 348 (2015)6234. - ISSN 0036-8075 - p. 504 - 506.
marine stewardship council - msc certification - fisheries - improvement
Demand for sustainably certified wild-caught fish and crustaceans is increasingly shaping global seafood markets. Retailers such as Walmart in the United States, Sainsbury's in the United Kingdom, and Carrefour in France, and processors such as Canadianbased High Liner Foods, have promised to source all fresh, frozen, farmed, and wild seafood from sustainable sources by 2015 (1, 2). Credible arbiters of certifications, such as the Marine Stewardship Council (MSC), require detailed environmental and traceability standards. Although these standards have been met in many commercial fisheries throughout the developed world (3), developing country fisheries (DCFs) represent only 7% of ~220 total MSC-certified fisheries (4, 5). With the United Nations Food and Agriculture Organization reporting that developing countries account for ~50% of seafood entering international trade, this presents a fundamental challenge for marketers of sustainable seafood (see the photo).
The effect of rare alleles on estimated genomic relationships from whole genome sequence data
Eynard, S.E. ; Windig, J.J. ; Leroy, G. ; Binsbergen, R. van; Calus, M.P.L. - \ 2015
BMC Genetics 16 (2015). - ISSN 1471-2156
information - pedigree - conservation - populations - prediction - accuracy - cattle - coefficients - improvement - challenges
Relationships between individuals and inbreeding coefficients are commonly used for breeding decisions, but may be affected by the type of data used for their estimation. The proportion of variants with low Minor Allele Frequency (MAF) is larger in whole genome sequence (WGS) data compared to Single Nucleotide Polymorphism (SNP) chips. Therefore, WGS data provide true relationships between individuals and may influence breeding decisions and prioritisation for conservation of genetic diversity in livestock. This study identifies differences between relationships and inbreeding coefficients estimated using pedigree, SNP or WGS data for 118 Holstein bulls from the 1000 Bull genomes project. To determine the impact of rare alleles on the estimates we compared three scenarios of MAF restrictions: variants with a MAF higher than 5%, variants with a MAF higher than 1% and variants with a MAF between 1% and 5%. Results We observed significant differences between estimated relationships and, although less significantly, inbreeding coefficients from pedigree, SNP or WGS data, and between MAF restriction scenarios. Computed correlations between pedigree and genomic relationships, within groups with similar relationships, ranged from negative to moderate for both estimated relationships and inbreeding coefficients, but were high between estimates from SNP and WGS (0.49 to 0.99). Estimated relationships from genomic information exhibited higher variation than from pedigree. Inbreeding coefficients analysis showed that more complete pedigree records lead to higher correlation between inbreeding coefficients from pedigree and genomic data. Finally, estimates and correlations between additive genetic (A) and genomic (G) relationship matrices were lower, and variances of the relationships were larger when accounting for allele frequencies than without accounting for allele frequencies. Conclusions Using pedigree data or genomic information, and including or excluding variants with a MAF below 5% showed significant differences in relationship and inbreeding coefficient estimates. Estimated relationships and inbreeding coefficients are the basis for selection decisions. Therefore, it can be expected that using WGS instead of SNP can affect selection decision. Inclusion of rare variants will give access to the variation they carry, which is of interest for conservation of genetic diversity.
Weerbaarheid, ook tegen plantenvirussen!
Stijger, C.C.M.M. ; Verbeek, M. - \ 2015
Wageningen UR
gewasbescherming - tuinbouw - plagenbestrijding - virussen - bodemweerbaarheid - verbetering - conferenties - biologische bestrijding - plant protection - horticulture - pest control - viruses - soil suppressiveness - improvement - conferences - biological control
Minder virus (schade) in een economisch rendabele en duurzame teelt door: 1. Afbraak virusdeeltjes door bacteriën/schimmels. 2. Vatbaar wordt onvatbaar door genetische aanpassing van de plant. 3. Symptoomonderdrukking. Poster van PlantgezondheidEvent 12 maart 2015.
Introgression Browser: High throughput whole-genome SNP visualization
Aflitos, S.A. ; Sanchez Perez, G.F. ; Ridder, D. de; Fransz, P. ; Schranz, M.E. ; Jong, J.H.S.G.M. de; Peters, S.A. - \ 2015
The Plant Journal 82 (2015)1. - ISSN 0960-7412 - p. 174 - 182.
in-situ hybridization - alien chromosomes - recombination - tomato - markers - thaliana - potato - identification - organization - improvement
Breeding by introgressive hybridization is a pivotal strategy to broaden the genetic basis of crops. Usually, the desired traits are monitored in consecutive crossing generations by marker-assisted selection, but their analyses fail in chromosome regions where crossover recombinants are rare or not viable. Here, we present the Introgression Browser (IBROWSER), a bioinformatics tool aimed at visualizing introgressions at nucleotide or SNP accuracy. The software selects homozygous SNPs from Variant Call Format (VCF) information and filters out heterozygous SNPs, Multi-Nucleotide Polymorphisms (MNPs) and insertion-deletions (InDels). For data analysis IBROWSER makes use of sliding windows, but if needed it can generate any desired fragmentation pattern through General Feature Format (GFF) information. In an example of tomato (Solanum lycopersicum) accessions we visualize SNP patterns and elucidate both position and boundaries of the introgressions. We also show that our tool is capable of identifying alien DNA in a panel of the closely related S. pimpinellifolium by examining phylogenetic relationships of the introgressed segments in tomato. In a third example, we demonstrate the power of the IBROWSER in a panel of 597 Arabidopsis accessions, detecting the boundaries of a SNP-free region around a polymorphic 1.17 Mbp inverted segment on the short arm of chromosome 4. The architecture and functionality of IBROWSER makes the software appropriate for a broad set of analyses including SNP mining, genome structure analysis, and pedigree analysis. Its functionality, together with the capability to process large data sets and efficient visualization of sequence variation, makes IBROWSER a valuable breeding tool.
Various ways for successful Cultivar introduction in the market
Nuijten, H.A.C.P. ; Zeelenberg, A. ; Janmaat, L. ; Lammerts Van Bueren, E. - \ 2015
Louis Bolk Instituut
marketing - marketingkanalen - appels - gevalsanalyse - cultivars - ziekteresistentie - fruitteelt - agro-industriële ketens - verbetering - biologische productie - biologische landbouw - marketing channels - apples - case studies - disease resistance - fruit growing - agro-industrial chains - improvement - biological production - organic farming
In this brochure key obstacles and opportunities for market introduction of disease-resistant cultivars of apple and potato are described. Various solution pathways have been compared. The comparison focuses strongly on apple because many experiences have been gained with the introduction of scab resistant cultivars. Four solution pathways are described with four case studies.
Get a taste of new talented Robust potato cultivars
Lammerts Van Bueren, E. ; Janmaat, L. - \ 2015
Louis Bolk Instituut
marketing - aardappelen - consumptieaardappelen - verbetering - ziekteresistentie - biologische landbouw - phytophthora - cultivars - akkerbouw - potatoes - table potatoes - improvement - disease resistance - organic farming - arable farming
In the potato breeding programme Bioimpuls, the Louis Bolk Institute and Wageningen UR are working together with breeding companies and farmer-breeders to develop robust cultivars that are resistant to Phytophthora. Thanks to these new cultivars, organic growers now have more chance of yield security. The next step is to collaborate with organic wholesalers and retailers to make sure that the new cultivars reach the shop shelves and consumers’ plates. In the Netherlands, the organic market has already accepted new cultivars such as Bionica, Sarpo Mira and Carolus, but other cultivars are still relatively unknown, and additional promising cultivars will become available for the European market in the near future. Together, these cultivars will offer a complete assortment of boiling, baking and multi-purpose potatoes in various colours and shapes. The new talents are presented in this brochure.
Efficiency of selection for body weight in a cooperative village breeding program of Menz sheep under smallholder farming system
Gizaw, S. ; Getachew, T. ; Goshme, S. ; Valle-Zárate, A. ; Arendonk, J.A.M. van; Kemp, S. ; Mwai, O. ; Dessie, T. - \ 2014
Animal 8 (2014)8. - ISSN 1751-7311 - p. 1249 - 1254.
genetic-parameters - south-africa - improvement - traits - livestock - ethiopia - design
We evaluated the efficiency of selection for body weight in a cooperative village breeding program for Menz sheep of Ethiopia under smallholder farming system. The design of the program involved organizing villagers in a cooperative breeding group to implement selective breeding of their sheep. The program was jump-started through a one-time provision of elite rams from a central nucleus flock, but subsequent replacement rams were selected from within the village flocks. We also evaluated body weight trends in a village where cooperative breeding was not implemented and individual farmers managed their flocks under traditional breeding practices. Under traditional breeding practices, genetic progress over 8 years either stagnated or declined in all the weights recorded. In the cooperative villages, selection differentials of 2.44 and 2.45 kg were achieved in 2010 and 2011 selection seasons, respectively. Birth weight, 3-month weight and 6-month weight increased, respectively, by 0.49, 2.29 and 2.46 kg in the third-generation lambs over the base generation. Improved rams supplied from the central nucleus flock gave an initial genetic lift of 14.4% in the 6-month weight. This was higher than the gain achieved from selection in the village flocks, which was 5.2%. Our results showed that village-based genetic improvement in body weights under smallholder conditions could be feasible if appropriate designs are adopted and that commencing with elite central nucleus rams help jump-start village-based programs.
Breeding programs for smallholder sheep farming systems: I. Evaluation of alternative designs of breeding schemes
Gizaw, S. ; Rischkowsky, B. ; Valle-Zárate, A. ; Haile, A. ; Arendonk, J.A.M. van; Mwai, O. ; Dessie, T. - \ 2014
Journal of Animal Breeding and Genetics 131 (2014)5. - ISSN 0931-2668 - p. 341 - 349.
menz crossbred sheep - genetic-parameters - ethiopia - traits - improvement - population - selection - industry - growth - cattle
Village- and central nucleus-based schemes were simulated and evaluated for their relative bio-economic efficiencies, using Ethiopia's Menz sheep as example. The schemes were: village-based 2-tier (Scheme-1) and 1-tier (Scheme-2) cooperative village breeding schemes, dispersed village-based nuclei scheme (Scheme-3), conventional 2-tier central nucleus-based scheme (Scheme-4), and schemes linking a central nucleus and village multiplier nuclei with selection in central nucleus (Scheme-5) or in both central and village nuclei (Scheme-6). Among village-based schemes, Scheme-1 gave the highest genetic progress, while Scheme-2 was economically the most efficient with genetic gain in the breeding objective of Birr 5.6 and a profit of Birr 37.2/ewe/year. The central nucleus schemes were more efficient than the village schemes. Scheme-4 was the most efficient with genetic gain in the breeding objective of Birr 13.5 and a profit of Birr 71.2, but is operationally more difficult as it requires a very large central nucleus. The choice between village and central nucleus-based schemes would depend on local conditions (availability of infrastructure, logistics and technical knowhow and support). Linking central nucleus with village-based nuclei (Scheme-6) would be a feasible option to overcome the operational difficulties of the conventional central nucleus scheme. If a village-based breeding program is envisaged as should be the 1st step in most low-input systems, then Scheme-2 is the most efficient. To scale out to an entire Menz breed level, Scheme-3 would be recommended.
Optimizing the design of small-sized nucleus breeding programs for dairy cattle with minimal performance recording
Kariuki, C.M. ; Komen, J. ; Kahi, A.K. ; Arendonk, J.A.M. van - \ 2014
Journal of Dairy Science 97 (2014)12. - ISSN 0022-0302 - p. 7963 - 7974.
genome-wide selection - overlapping generations - predefined rate - prediction - schemes - kenya - improvement - efficiency
Dairy cattle breeding programs in developing countries are constrained by minimal and erratic pedigree and performance recording on cows on commercial farms. Small-sized nucleus breeding programs offer a viable alternative. Deterministic simulations using selection index theory were performed to determine the optimum design for small-sized nucleus schemes for dairy cattle. The nucleus was made up of 197 bulls and 243 cows distributed in 8 non-overlapping age classes. Each year 10 sires and 100 dams were selected to produce the next generation of male and female selection candidates. Conception rates and sex ratio were fixed at 0.90 and 0.50, respectively, translating to 45 male and 45 female candidates joining the nucleus per year. Commercial recorded dams provided information for genetic evaluation of selection candidates (bulls) in the nucleus. Five strategies were defined: nucleus records only [within-nucleus dam performance (DP)], progeny records in addition to nucleus records [progeny testing (PT)], genomic information only [genomic selection (GS)], dam performance records in addition to genomic information (GS+DP), and progeny records in addition to genomic information (GS+PT). Alternative PT, GS, GS+DP, and GS+PT schemes differed in the number of progeny per sire and size of reference population. The maximum number of progeny records per sire was 30, and the maximum size of the reference population was 5,000. Results show that GS schemes had higher responses and lower accuracies compared with other strategies, with the higher response being due to shorter generation intervals. Compared with similar sized progeny-testing schemes, genomic-selection schemes would have lower accuracies but these are offset by higher responses per year, which might provide additional incentive for farmers to participate in recording.
Using agronomic tools to improve pineapple quality and its uniformity in Benin
Fassinou Hotegni, V.N. - \ 2014
Wageningen University. Promotor(en): Paul Struik; Jack van der Vorst, co-promotor(en): Willemien Lommen. - Wageningen : Wageningen University - ISBN 9789462570382 - 302
ananas comosus - ananassen - fruitteelt - gewaskwaliteit - plantmateriaal - heterogeniteit - verbetering - gewasfysiologie - benin - ananas comosus - pineapples - fruit growing - crop quality - planting stock - heterogeneity - improvement - crop physiology - benin

Keywords: Ananas comosus; Benin; cultural practices; fruit quality; hapas; heterogeneity; planting material; slips; suckers; supply chain; variation in quality; variation within crop; vigour.

Poor average quality and uniformity in quality have become major issues in agri-food chains. This is also the case in the pineapple sector in Benin where less than 2% of the fresh pineapple is exported to international markets. The average quality of pineapple delivered to other markets, local and regional, is poor. The present thesis studied the improvement options in the pineapple sector which will help pineapple producers to produce higher pineapple quality for different markets, including international ones. This thesis aimed at (1) understanding how fresh pineapple supply chains are organised in Benin and identifying the bottlenecks for delivering the right pineapple to the right market; (2) increasing our knowledge on the agronomic tools used by pineapple producers to produce pineapple fruits; (3) understanding how agronomic factors affect pineapple quality and harvesting time, and (4) proposing and discussing the trade-offs between cultural practices. Research included analysis of supply chains and cropping systems and field experimentation.

To understand how fresh pineapple supply chains are organised, 54 semi-structured interviews were held with key informants and 173 structured interviews with actor groups. Results indicated six main actor groups in the fresh pineapple chains: primary producers, exporters, wholesalers (those selling at local markets and those selling at regional markets), processors, retailers, and middlemen. Two pineapple cultivars were grown: Sugarloaf and Smooth Cayenne, with Sugarloaf being dominant in local and regional markets and Smooth Cayenne in European markets. The main constraints hampering the effectivity of the chains were: the non-controlled conditions under which the pineapple was transported from one actor group to another, the lack of appropriate storage facilities at wholesaler’s and processor’s levels, the unavailability of boxes for export and the non-concordance between actor groups in which quality attributes and criteria they valued most. In addition, most respondents interviewed affirmed that the pineapple quality was highly heterogeneous, emphasising the need to understand how pineapple is grown in Benin and what the constraints for producing high pineapple quality are.

To find out the agronomic tools in use by pineapple producers in Benin, interviews were held with 100 producers in the pineapple production areas. Pineapple production practices proved diverse for both cultivars in planting density, flowering induction practice and fertiliser application. The production systems of the two pineapple cultivars differed in planting material used (slips in cv. Sugarloaf; hapas plus suckers in cv. Smooth Cayenne); the use of K2SO4 (not commonly used in cv. Sugarloaf and commonly used in cv. Smooth Cayenne); the number of fertiliser applications (lower in cv. Sugarloaf than in cv. Smooth Cayenne) and in the maturity synchronisation practice by means of Ethephon (not commonly used in cv. Sugarloaf and commonly used in cv. Smooth Cayenne). Constraints for high quality production were the unavailability of planting material, unavailability and high costs of fertilisers and the heterogeneity in planting material weight.

To understand how agronomic factors affect pineapple quality and harvesting time, four on-farm experiments were conducted in commercial pineapple fields. Results first indicated that the heterogeneity in fruit weight was a consequence of the heterogeneity in plant vigour at artificial flowering induction time. The plant vigour at flowering induction was mainly related with the infructescence weight and less or not with crown weight. Second, results indicated that artificial flowering induction gave fruits with lower infructescence weight and heavier crown than natural flowering induction. Artificial maturity induction reduced the total soluble solids (TSS) concentration in the fruits. Finally, results showed that the reason why a high proportion of fruits in cv. Sugarloaf was not exportable to Europe was the high value in the ratio crown: infructescence height (above 1.5); in cv. Smooth Cayenne, reasons were a ratio crown: infructescence height as well as a TSS below 12 ºBrix.

To come up with improvement options for high pineapple quality production with low heterogeneity in quality, the possibility of pruning slips on selective plants as means to improve uniformity in fruit quality was evaluated through two on-farm experiments on commercial fields with cv. Sugarloaf. Results revealed that pruning of slips did not significantly improve average fruit quality attributes and was not successful in achieving more uniform fruit quality at harvesting time. Through one experiment per pineapple cultivar, we investigated how fruit quality and its variation were affected by weight (in both pineapple cultivars) and type (in cv. Smooth Cayenne only) of planting material. Results showed that fruits from heavy planting material had heavier infructescence and fruit weights, longer infructescence height, but shorter crown height and smaller ratio crown: infructescence height than those from light planting material. In cv. Sugarloaf fruits from heavy planting material had higher variation in crown weight and lower variation in infructescence height than fruits from light and mixed (light plus heavy) planting materials. In cv. Smooth Cayenne, fruits from heavy planting material had a lower variation in fruit height than fruits from other classes of planting material. The type of planting material (in cv. Smooth Cayenne) had no effect on the average fruit quality attributes except on the crown height where fruits from hapas had shorter crowns than those from suckers. The type of planting material had in overall no significant effect on the variation in the fruit quality attributes.

The present study is a step towards the improvement of the whole pineapple sector in Benin. It identified constraints for high pineapple quality production but also tested and proposed improvement options for high pineapple quality production.

Influence of high solid concentrations on enzymatic wheat gluten hydrolysis and resulting functional properties
Hardt, N.A. ; Goot, A.J. van der; Boom, R.M. - \ 2013
Journal of Cereal Science 57 (2013)3. - ISSN 0733-5210 - p. 531 - 536.
ultrafiltration - protein - starch - improvement - fractions - peptides - systems - flour
Enzymatic hydrolysis at increased solid concentrations is beneficial with regard to energy and water consumption. This study examines the influence of the solid concentration on the enzymatic hydrolysis of wheat gluten and the resulting functional properties of the hydrolysate. Wheat gluten was mildly hydrolyzed at a solid concentration varying from 10% to 60% to degrees of hydrolysis (DH%) ranging from 3.2% to 10.2%. The gluten was susceptible to hydrolysis at all solid concentrations but the hydrolysis rate was influenced by increasing solid concentrations. Size-exclusion high-performance liquid chromatography revealed an increase in the ratio of peptides with a molecular mass >25 kDa for solid concentrations of 40% and 60%. The water solubility increased on hydrolysis and was independent of the solid concentration during proteolysis. The foam stability was not influenced by the solid concentration at low DH%. At DH% higher than 8%, high solid concentrations increased the foam stability, which might be related to the presence of more peptides with a molecular mass >25 kDa. In addition, we found increased reactor productivity. The results show the potential of hydrolyzing wheat gluten at high solid concentrations, which could lead to large savings for water and energy when applied industrially.
Genetic parameters for reproductive traits in female Nile tilapia (Oreochromis niloticus): I. Spawning success and time to spawn
Trong, T.Q. ; Arendonk, J.A.M. van; Komen, J. - \ 2013
Aquaculture 416-417 (2013). - ISSN 0044-8486 - p. 57 - 64.
challenge-test data - salmon salmo-salar - statistical-models - seed production - growth - improvement - prediction - resistance - broodfish - selection
Breeding programmes for Nile tilapia typically use nested mating designs with 2 females mated to 1 male to produce paternal half-sib families. This mating design can take up to 3 months or longer to produce the desired number of half-sib family groups. Prolonged family production increases common environmental effects, and negatively affects estimation of genetic parameters. In this paper we investigated the hypothesis that prolonged family production is a consequence of selection for growth in Nile tilapia. We compare two mating systems: group mating with 7 males and 15 females (MM) and group mating with a single male and 10 females (SM), using females from generation 12 of the GIFT sub-strain kept at RIA-2, Vietnam. Spawning success was modelled as a threshold trait (SPAWN) using a linear repeatability animal model and a generalised logit linear repeatability model. All animals that spawned before 32 days were labelled ‘spawn’ (1) and animals that did not spawn after 32 days were considered as ‘no-spawn’ (0). We then changed the threshold and estimated heritability at each threshold point; e.g. with a threshold at 20 days, all animals with ‘spawn’ records after 20 days are considered ‘no-spawn’. Overall, the MM experiment yielded a higher proportion of successful spawn records than the SM experiment. However, in both experiments 85% of the successful spawns were produced within 20 days. In the SM system, males frequently mated with more than one female during a mating period of 4 days. Heritability estimates for SPAWN were 0.20 to 0.22 for linear model and 0.14–0.18 for logit model with thresholds from 20 to 32 days. Estimates were consistent between linear and logit models. Estimates for ‘time to spawn’ were not different from zero (0.01 ± 0.02). Genetic correlations of SPAWN with harvest weight ranged from 0.48 to 0.52 for thresholds of 20–32 days. We conclude that Nile tilapia favour mating in groups and that spawning success as defined here is a heritable trait. Selection for harvest weight in GIFT should improve spawning success of Nile tilapia, provided the mating period is limited to 20–32 days. To facilitate the rapid production of paternal half-sibs, we recommend using a group mating design with single males and multiple females in a single tank.
Genetic parameters for reproductive traits in female Nile tilapia (Oreochromis niloticus): II. Fecundity and fertility
Trong, T.Q. ; Arendonk, J.A.M. van; Komen, J. - \ 2013
Aquaculture 416-417 (2013). - ISSN 0044-8486 - p. 72 - 77.
rainbow-trout - selection responses - body measurements - fillet traits - 6 generations - brown trout - growth - improvement - heritability - weight
Harvest weight is the main trait in Nile tilapia (Oreochromis niloticus) breeding programmes. The effects of selection for harvest weight on female reproductive traits are unknown. In this paper we estimate genetic parameters for reproductive traits and their correlation with harvest weight using females from the generation 12 of the GIFT strain of Nile tilapia in the Mekong Delta of Viet Nam. Spawning records were obtained from single pair mating as well as group mating experiments. The traits were categorised into two groups: fecundity-related traits and fertility-related traits. Fecundity traits were: number of eggs (NEGG), relative fecundity as the ratio of number of eggs to female spawning weight (RFEC), egg weight (EGGW) and egg diameter (EGGD); fertility traits were: number of fertilised eggs (FEGG), number of hatched eggs (HAT), number of swim-up fry (SWUP), and fertilisation rate (FER, in %). Heritability estimates for fecundity traits were low, ranging from 0.05 to 0.08. Heritability estimates for fertility traits were also low, ranging from 0.06 to 0.12. Genetic correlations for HW with NEGG and TEGGW were positive (0.51 and 0.42, respectively), while correlations for HW with RFEC, EGGW, and EGGD were negative (- 0.72, - 0.48, and - 0.50, respectively). The same trend was observed for body weight at spawning (SPW), but genetic correlations between SPW and fecundity traits were higher than those between HW and fecundity traits. Genetic correlations between HW and fertility traits were all moderate to high (0.46 to 0.69), except for FER (0.15 ± 0.24). Genetic correlations between SPW and fertility traits were even higher (0.69 to 0.93). We conclude that both HW and SPW have favourable genetic correlations with NEGG, RFEC, and SWUP, which are the desired characteristics for Nile tilapia seed production. Selection for HW does not affect these traits. However, Nile tilapia females selected for large HW tend to produce smaller eggs. We recommend monitoring the phenotypic and/or genetic trend in this trait, as smaller eggs might, on the longer term, lead to lower fry survival.
Improving the quality of crude palm oil: transdisciplinary research on artisanal processing in Kwabibirem District, Ghana
Osei-Amponsah, C. - \ 2013
Wageningen University. Promotor(en): Leontine Visser; M.K. Abekoe, co-promotor(en): Tjeerd-Jan Stomph; O. Sakyi-Dawson. - Wageningen : Wageningen UR - ISBN 9789461737588 - 146
palmoliën - kwaliteit - verbetering - verwerking - olieproducten - plattelandsontwikkeling - ghana - palm oils - quality - improvement - processing - oil products - rural development - ghana
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