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.

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Foreign investment, organizational innovation and transformation in food supply chains : evidence from the Ethiopian barley sector
Tefera, Delelegne Abera - \ 2017
University. Promotor(en): Onno Omta, co-promotor(en): Jos Bijman; Maja Slingerland. - Wageningen : Wageningen University - ISBN 9789463437165 - 217
foreign investment - organizations - innovations - management science - food supply - supply chain management - farmers - barley - economic sectors - ethiopia - east africa - buitenlandse investering - organisaties - innovaties - bedrijfswetenschap - voedselvoorziening - ketenmanagement - boeren - gerst - economische sectoren - ethiopië - oost-afrika

Driven by rapid urbanization, economic growth, and changes in consumption patterns, food chains in emerging and developing economies are experiencing a fundamental transformation process. This transformation is usually characterized by increased vertical coordination, growth of modern distribution channels (e.g. supermarkets), consolidation of retail markets, and an increase in export orientation. The rapid growth in demand of modern food with higher quality and safety attracts multinational enterprises to invest in agriculture and food processing in emerging economies. The appearance of multinationals in the food systems of developing countries has been claimed to have a positive impact on economic development and reduction of poverty. The multinationals have adopted modern supply chain management practices for securing a large volume and consistent supply of high quality products. They introduce new technologies that boost productivity and post-harvest management for product upgrading.

While so far most research on the modernization of food systems has focused on export chains, there is growing interest in the transformation of domestic and staple food chains. Upgrading domestic food chains is needed for a more efficient supply to fast growing urban markets and to sustain access to affordable food for the rapidly growing urban consumers in sub-Saharan Africa. As domestic food value chains are more inclusive than high-value export chains, upgrading these food chains can contribute more to poverty reduction and food security. However, much remains to be understood about the process of modernization in domestic food chains and its implications for rural development. The overarching aim of this dissertation was to deepen our understanding on how organizational innovations facilitate modernization of domestic food chains using case studies from the Ethiopian barley sector. In particular, the thesis examines the effectiveness and impacts of foreign direct investments (FDI), contract farming arrangements (CFAs), producer organizations (POs), and partnerships on the upgrading of malt barley value chains and welfare of local suppliers. To address this objective, we use a combination of qualitative and quantitative research approaches. Data were analyzed using parametric and non-parametric econometric models.

The findings from the empirical chapters show that: First, our analysis reveals that the appearance of foreign companies in the malt barley chain has brought important changes in the structure and economics of the barley value chain, resulting in the development of a modern chain next to the conventional chain. It is also shown that participation in modern supply chains is determined by a range of factors that include farmer and farm characteristics. Second, the results show that participation in modern supply chains has a positive and significant impact on commercialization, intensification, quality improvement and farm gate prices, ultimately resulting in increased farmer income and spillovers towards productivity of other food crops. Third, we found that POs perform diverse economic functions to enhance rural development , but tighter coordination in food value chains demands alignment of chain activities among actors which leads to changes in the strategies and functions of POs. Fourth, we showed that POs have a positive impact on farm productivity and smallholder income. However, this positive impact of POs come at the expense of inclusiveness, i.e. POs are less inclusive. Thus, there is a tension between business performance and inclusiveness of POs. Moreover, the results show that the motivation to participate in a PO is determined by demographic and economic factors. Lastly, we found that the determinants of quality improvement at farm level are socioeconomic, technological and institutional factors. Specifically, the identified factors are farmers’ level of education, age (as a proxy for farming experience), entrepreneurial attitude, PO membership, CFA participation, and type of improved seed varieties. The thesis concludes that enhancing the modernization of food value chains involving smallholders requires organizational innovation that facilitate coordination and collaborative activities among chain actors.

Brewing with fractionated barley
Donkelaar, L.H.G. van - \ 2016
University. Promotor(en): Remko Boom; Atze Jan van der Goot. - Wageningen : Wageningen University - ISBN 9789462577343 - 152 p.
brewing - brewing quality - barley - fractionation - endosperm - beers - malt - filtration - industrial wastes - process optimization - food process engineering - bierbereiding - brouwkwaliteit - gerst - fractionering - bieren - mout - filtratie - industrieel afval - procesoptimalisatie - levensmiddelenproceskunde

Brewing with fractionated barley

Beer is a globally consumed beverage, which is produced from malted barley, water, hops and yeast. In recent years, the use of unmalted barley and exogenous enzymes have become more popular because they enable simpler processing and reduced environmental impact. Raw barley, however, contains less endogenous enzymes and more undesired components for the use of beer brewing, compared to malted barley.

The overall aim of this thesis is to investigate how barley can be fractionated to optimize the use of resources for the beer brewing process, while maintaining the quality of the brewed beer. A resource use efficiency analysis was performed to verify the presumed benefits on the environmental sustainability of the proposed process change. The work was based on the hypothesis that fractionation of the unprocessed barley will reduce the amount of undesired components, which leads to improvements in the brewing process based on partial or no malting. Fractionation can be performed by milling and separation, which requires physical disentanglement of the components. This fractionation can be influenced by properties of the components of the material, such as the glass transition temperature (Stuart et al.). Fractionation by abrasive milling, also known as pearling, is another possibility: here one makes use of the spatial distribution of components in the kernels. In case of barley for brewing this technique is especially promising as most of the undesired components are in the outer layer of the kernel. In addition, the removal of bran from the barley reduces the amount of water needed in the process. It will also reduce the volume of spent grains, hence reducing wastes and energy required for drying the spent grains. A disadvantage of pearling is however that it lowers the ability of the barley kernel to produce enzymes. This leads to the need of the addition of exogenous enzymes, as is the case when the malting step is omitted.

Chapter 2 describes the glass-to-rubber transition of protein and starch isolated from the barley endosperm, for different moisture levels. The hypothesis for this chapter is that dry fractionation by milling is facilitated by milling conditions in which the protein is in a rubbery state and the starch in a glassy state. Two methods were used to measure the Tg; differential scanning calorimetry (DSC) and thermo-mechanical compression tests (TMCT). The methods gave different results due to the differences in moisture content range, and heating rates, which may lead to conformational changes of the protein. The value of the Tg of partially crystalline materials, such as starch in barley, was not unambiguous when using TMCT because the mechanical effect of expansion of these materials was smaller. For both results, the Tg lines were modelled using the Gordon-Taylor equation. Based on sorption isotherms, it was concluded that moisture does not distribute evenly over the protein and starch in the kernel. Starch absorbs more moisture than protein at given water activities. This required a correction of the Tg lines. After this correction, the glass transition lines of starch and protein were closer together. The expectation is therefore that achieving good separation between the components based on having one glassy component and one rubbery component is challenging.

For this reason, another dry fractionation technique, pearling, was considered. Chapter 3 describes the chemical composition of the barley and of fractions removed by pearling. Pearling was shown to selectively remove insoluble fibre, ash, protein and polyphenols, while the β-amylase activity and starch content of the remaining kernel was hardly affected. For example, removing the outer 5% of the kernel reduced insoluble arabinoxylans (15%), insoluble fibres (23%), ash (19%), polyphenols (11%) and water holding capacity of the non-starch components (25%), while only lowering starch content by 0.20%. The water holding capacity of the barley fractions was strongly related to the fibre content. This indicates that when the fibre content in the mash was reduced by pearling, the spent grains will take up less water, leading to less wort and sugar losses in this waste stream, and hence better use of the raw materials and less wastes.

Chapter 4 compares a traditional brewing process to an enzyme-assisted brewing process with respect to their resource use efficiency, which is one aspect of the sustainability of the processes. The use of exogenous enzymes is found to be more efficient than producing enzymes through the malting process. The exergetic efficiency of the conventional malting process was 77%. The main losses stem from the use of natural gas for removal of moisture from the barley in the kilning process, and from the loss of starch in the germination process. In case of the use of exogenous enzymes, it was concluded that the chemical exergy content of the enzymes was not a good measure for the exergy content of the enzymes. Instead, we proposed to use the cumulative exergetic consumption in the enzyme production rather than just the chemical exergy content of the enzymes. This cumulative exergetic consumption in the production of the enzymes was ± 30 times higher than their standard chemical exergy. This shows that the cumulative exergetic costs of minor components should be taken into account if a process uses them in significant quantities. This can be done by extending the system boundaries to include the production process of the purified components. The exergy efficiency of the enzyme formulation production process ranges between 20% and 42% depending on whether the by-product of the fermentation broth was considered as useful as the enzyme product. Even though the cumulative exergy consumption of the process was 30 times the standard chemical exergy of the dry enzyme, the total exergy input (i.e. both wasted and destroyed) for the production of 100 kg of beer was still larger for the conventional malting process (441 MJ) than for the enzyme-assisted process (354 MJ). In addition, beer produced using exogenous enzymes reduces the use of water by 7%, of raw materials by 14%, and of natural gas by 78%. Thus, the exergy loss of the enzyme production process is more than compensated by the prevention of exergy loss in the total beer brewing process.

Chapter 5 describes brewing tests using malted, unmalted and pearled, unmalted barley kernels. Brewing with unmalted barley saves material, energy and water in the malting stage but may result in complications during processing. Pearling mitigates these problems. Exogenous enzymes were used to compensate for the low enzyme activity in unmalted barley. Lautertun filtration and mash filtration were considered as filtration methods. Principle component analysis was performed on the chemical composition of the wort and the various spent grains, to investigate the effect of the malt-to-barley ratio, the degree of pearling and the filter method. A mash filter is optimal for this type of process, and we identified a window of operation in which optimal use is made of the raw materials while maintaining the end product quality, judged on basis of 4 quality parameters.

The concluding chapter 6 presents a general discussion of all results described in this thesis. In addition, the benefits of pearling over that of milling and fractionation, and the effect of pearling on milling properties were discussed. Furthermore, it explores the advantages in environmental sustainability that can be achieved by pearling. Pearling as a pre-treatment for malting reduces the enzyme activity of germinating barley, and therefore the mash quality.

This thesis provides insights in how pre-treatment of barley can make beer brewing more efficient in the use of resources. It stresses the need to optimally use all material streams in a process, to be able to design an environmentally sustainable process, and it shows that efficient resource use is key for achieving this. Additionally the value of enzymes as processing aids was discussed. A clear result is that one needs to include the resource use in the production of enzymes or other processing aids, when analyzing the environmental sustainability of a process, since this can be significant in the overall process.

Estimation of the in situ degradation of the washout fraction of starch by using a modified in situ protocol and in vitro measurements
Jonge, L.H. de; Laar, H. van; Dijkstra, J. - \ 2015
Animal 9 (2015)9. - ISSN 1751-7311 - p. 1465 - 1472.
dairy-cows - digestion - rumen - gas - degradability - barley - vivo - digestibility - feedstuff - cultivars
The in situ degradation of the washout fraction of starch in six feed ingredients (i.e. barley, faba beans, maize, oats, peas and wheat) was studied by using a modified in situ protocol and in vitro measurements. In comparison with the washing machine method, the modified protocol comprises a milder rinsing method to reduce particulate loss during rinsing. The modified method markedly reduced the average washout fraction of starch in these products from 0.333 to 0.042 g/g. Applying the modified rinsing method, the fractional degradation rate (k d ) of starch in barley, oats and wheat decreased from on average 0.327 to 0.144 h-1 whereas for faba beans, peas and maize no differences in k d were observed compared with the traditional washing machine rinsing. For barley, maize and wheat, the difference in non-fermented starch in the residue between both rinsing methods during the first 4 h of incubation increased, which indicates secondary particle loss. The average effective degradation of starch decreased from 0.761 to 0.572 g/g when using the new rinsing method and to 0.494 g/g when applying a correction for particulate matter loss during incubation. The in vitro k d of starch in the non-washout fraction did not differ from that in the total product. The calculated ratio between the k d of starch in the washout and non-washout fraction was on average 1.59 and varied between 0.96 for oats and 2.39 for maize. The fractional rate of gas production was significantly different between the total product and the non-washout fraction. For all products, except oats, this rate of gas production was larger for the total product compared with the non-washout fraction whereas for oats the opposite was observed. The rate of increase in gas production was, especially for grains, strongly correlated with the in vitro k d of starch. The results of the present study do not support the assumption used in several feed evaluation systems that the degradation of the washout fraction of starch in the rumen is much faster than that of the non-washout fraction.
Beheersing aarfusarium en bladvlekkenziekte in zomergerst
Evenhuis, A. ; Schepers, H.T.A.M. - \ 2015
Wageningen : Praktijkonderzoek Plant & Omgeving (Applied Plant Research), part of Wageningen UR Business Unit AGV - 24
akkerbouw - graangewassen - hordeum vulgare - gerst - schimmelziekten - fusarium - gibberella zeae - bladvlekkenziekte - bestrijdingsmethoden - proeven - detectie - fungiciden - arable farming - grain crops - barley - fungal diseases - leaf spotting - control methods - trials - detection - fungicides
Aarfusarium leidt tot kwaliteitsverlies in graangewassen. Aarfusarium in granen wordt veroorzaakt door verschillende ziekteverwekkers van het geslacht Fusarium: De belangrijkste veroorzaker van aarfusarium is F. graminearum. De schimmel infecteert de aar tijdens de bloeiperiode, onder vochtige omstandigheden. Is het tijdens de bloei droog dan is er weinig kans op Fusarium. Is het tijdens en voor de bloei nat dan vergroot dat de kans op aarfusarium. Als een partij tarwe of gerst te zwaar geïnfecteerd is kan dat leiden tot een lagere bakkwaliteit, respectievelijk een lagere brouwkwaliteit. In opdracht van het Productschap Akkerbouw is onderzoek gedaan naar de bestrijding van Fusarium in de teelt van brouwgerst. Het onderzoek is uitgevoerd in samenwerking met de gewasbeschermingsindustrie.
Glutenvrij ? Pils onde de loep
Sleutels, I. ; Meer, I.M. van der; Broeck, H.C. van den - \ 2014
Voedingsmiddelentechnologie 7 (2014). - ISSN 0042-7934 - p. 10 - 11.
gluten - coeliakie - glutenvrije diëten - bieren - alcoholische dranken - gerst - lc-ms - analytische methoden - coeliac syndrome - gluten free diets - beers - alcoholic beverages - barley - liquid chromatography-mass spectrometry - analytical methods
Gluten meten in gehydrolyseerde en gefermenteerde voedingsmiddelen – zoals pils – is lastig. De door de Codex Alimentarius gevalideerde test onderschat het gehalte gluten in deze producten. Een uitgebreide LC-MS/MS-analyse geeft gedetailleerde informatie over de aanwezige coeliakie-stimulerende gluten in pils. Met deze gegevens is een geschikte test te ontwikkelen.
Canopy architectural and physiological characterization of near-isogenic wheat lines differing in the tiller inhibition gene tin
Moeller, C. ; Evers, J.B. ; Rebetzke, G. - \ 2014
Frontiers in Plant Science 5 (2014). - ISSN 1664-462X - 14 p.
triticum-aestivum - spring wheat - grain-yield - nitrogen relationships - agronomic evaluation - solar-radiation - plant-density - red ratio - barley - growth
Tillering is a core constituent of plant architecture, and influences light interception to affect plant and crop performance. Near-isogenic lines (NILs) varying for a tiller inhibition (tin) gene and representing two genetic backgrounds were investigated for tillering dynamics, organ size distribution, leaf area, light interception, red: far-red ratio, and chlorophyll content. Tillering ceased earlier in the tin lines to reduce the frequencies of later primary and secondary tillers compared to the free-tillering NILs, and demonstrated the genetically lower tillering plasticity of tin-containing lines. The distribution of organ sizes along shoots varied between NILs contrasting for tin. Internode elongation commenced at a lower phytomer, and the peduncle was shorter in the tin lines. The flag leaves of tin lines were larger, and the longest leaf blades were observed at higher phytomers in the tin than in free-tillering lines. Total leaf area was reduced in tin lines, and non-tin lines invested more leaf area at mid-canopy height. The tiller economy (ratio of seed-bearing shoots to numbers of shoots produced) was 10% greater in the tin lines (0.73–0.76) compared to the free-tillering sisters (0.62–0.63). At maximum tiller number, the red: far-red ratio (light quality stimulus that is thought to induce the cessation of tillering) at the plant-base was 0.18–0.22 in tin lines and 0.09–0.11 in free-tillering lines at levels of photosynthetic active radiation of 49–53% and 30–33%, respectively. The tin lines intercepted less radiation compared to their free-tillering sisters once genotypic differences in tiller numbers had established, and maintained green leaf area in the lower canopy later into the season. Greater light extinction coefficients (k) in tin lines prior to, but reduced k after, spike emergence indicated that differences in light interception between NILs contrasting in tin cannot be explained by leaf area alone but that geometric and optical canopy properties contributed. The careful characterization of specifically-developed NILs is refining the development of a physiology-based model for tillering to improve understanding of the value of architectural traits for use in cereal improvement.
Maize yield and quality in response to plant density and application of a novel plant growth regulator
Zhang, Q. ; Zhang, L. ; Evers, J.B. ; Werf, W. van der; Zhang, W. ; Duan, L. - \ 2014
Field Crops Research 164 (2014). - ISSN 0378-4290 - p. 82 - 89.
zea-mays l. - irrigated maize - spring wheat - grain-yield - corn - ethephon - height - climate - barley - ethyl
Farmers in China have gradually increased plant density in maize to achieve higher yields, but this has increased risk of lodging due to taller and weaker stems at higher plant densities. Plant growth regulators can be used to reduce lodging risk. In this study, for the first time, the performance of a mixture of the plant growth regulators ethephon and diethyl aminoethyl hexanoate (DA-6), called EDAH is tested at different plant densities and in different cultivars. Grain yield, yield components and grain quality as well as plant height and lodging percentage were determined in two years (2012 and 2013), using two maize hybrids, ZD 958 and Pioneer 335 at densities of 4.5, 6.0, 7.5 and 9.0 plants m-2 with and without foliar application of EDAH at 7 expanded leaves stage. EDAH significantly increased grain yield (by 7.8–8.0%), kernel number per ear (by 2.9–4.0%) and 1000-kernel weight (by 3.3–5.1%). Lodging percentage increased with plant density and was decreased by EDAH application in 2013. Optimal density was 7.5 plants m-2. The number of ears per unit ground area increased linearly with plant density, but number of kernels per ear and kernel weight showed an optimum. The two tested cultivars differed in yield and quality. No effects of EDAH on grain quality parameters (protein, oil and starch content) were found. We conclude that EDAH can improve lodging resistance and yield in maize, and that the yield effect of EDAH also occurs if lodging is not reduced.
Development and validation of a 20K Single Nucleotide Polymorphism (SNP) whole genome genotyping array for apple (Malus × domestica Borkh)
Bianco, L. ; Cestaro, A. ; Sargent, D.J. ; Guardo, M. Di; Jansen, J. ; Weg, W.E. van de - \ 2014
PLoS One 9 (2014)10. - ISSN 1932-6203 - 9 p.
linkage map - construction - cultivars - alignment - accurate - barley
High-density SNP arrays for genome-wide assessment of allelic variation have made high resolution genetic characterization of crop germplasm feasible. A medium density array for apple, the IRSC 8 K SNP array, has been successfully developed and used for screens of bi-parental populations. However, the number of robust and well-distributed markers contained on this array was not sufficient to perform genome-wide association analyses in wider germplasm sets, or Pedigree-Based Analysis at high precision, because of rapid decay of linkage disequilibrium. We describe the development of an Illumina Infinium array targeting 20 K SNPs. The SNPs were predicted from re-sequencing data derived from the genomes of 13 Malus × domestica apple cultivars and one accession belonging to a crab apple species (M. micromalus). A pipeline for SNP selection was devised that avoided the pitfalls associated with the inclusion of paralogous sequence variants, supported the construction of robust multi-allelic SNP haploblocks and selected up to 11 entries within narrow genomic regions of ±5 kb, termed focal points (FPs). Broad genome coverage was attained by placing FPs at 1 cM intervals on a consensus genetic map, complementing them with FPs to enrich the ends of each of the chromosomes, and by bridging physical intervals greater than 400 Kbps. The selection also included ~3.7 K validated SNPs from the IRSC 8 K array. The array has already been used in other studies where ~15.8 K SNP markers were mapped with an average of ~6.8 K SNPs per full-sib family. The newly developed array with its high density of polymorphic validated SNPs is expected to be of great utility for Pedigree-Based Analysis and Genomic Selection. It will also be a valuable tool to help dissect the genetic mechanisms controlling important fruit quality traits, and to aid the identification of marker-trait associations suitable for the application of Marker Assisted Selection in apple breeding programs.
Towards map-based cloning of partial resistance QTLs of barley to Puccinia hordei
Yeo, F.K.S. - \ 2014
University. Promotor(en): Richard Visser, co-promotor(en): Rients Niks. - Wageningen : Wageningen University - ISBN 9789462570733 - 185
hordeum vulgare - gerst - ziekteresistentie - plantenziekteverwekkende schimmels - puccinia hordei - partiële resistentie - loci voor kwantitatief kenmerk - genkartering - plantenveredeling - barley - disease resistance - plant pathogenic fungi - partial resistance - quantitative trait loci - gene mapping - plant breeding

Partial resistance of barley to Puccinia hordei and near-nonhost resistance to non-adapted rust fungi inherit polygenically. The two types of resistance seem to share some genes and have a similar prehaustorial mechanism of resistance, but partial resistance is less strong than near-nonhost resistance of barley. Partial resistance to adapted, “host”, rust fungi seems, therefore, like a weak form of nonhost resistance to non-adapted rust fungi. If partial resistance and nonhost resistance are indeed based on the same principles, one can understand nonhost resistance by studying partial resistance and vice versa. To study partial and nonhost resistance, as well as their association, the candidate gene(s) for resistance must be cloned and characterized for their action.

Five resistance quantitative trait loci (QTLs) for partial resistance (Rphq2, Rphq3, Rphq4, Rphq11 and Rphq16) and one nonhost resistance QTL (Rnhq) were selected to pursue map-based cloning. First, the effect of the QTLs was verified in near-isogenic lines (NILs). The NILs of Rphq2, Rphq3, Rphq4 and Rnhq (QTL-NILs) were available in L94 genetic background. L94 is extremely susceptible to Puccinia hordei, and, at seedling stage, somewhat susceptible to certain non-adapted rust fungi. The experimental barley line SusPtrit is also susceptible to P. hordei but, at seedling stage, also very susceptible to at least nine species of non-adapted rust fungi. In Chapter 3, we developed NILs in SusPtrit background for Rphq2, Rphq3, Rphq11, Rphq16 and two alleles of Rnhq, viz. L94 and Vada alleles. The effect of each QTL in L94 and SusPtrit genetic backgrounds was tested not only against different isolates of P. hordei but also against different species and isolates of non-adapted rust fungi. The QTL-NILs suggested that the effects of the partial resistance genes depended on rust species and rust isolates. Some introgressions conferred resistance to a broader spectrum of rust species and isolates than others, the broadest being the Rphq11-introgression. The NILs may overestimate the spectrum of effectiveness of the partial resistance genes because some NILs contain inadvertent donor genome in the background and the introgressed QTL region may contain several linked resistance genes, each with a narrow resistance spectrum. The introgression would then confer a resistance spectrum that is the combination of the spectra of several linked resistance genes. Allowing for the possibility of linkage of narrow-spectrum resistance genes, our study suggests that some genes may be involved in partial as well as nonhost resistance. Data also suggest that genetic background may play a role in the resistance conferred by the QTL-introgression.

The NILs also allow fine-mapping of the QTL as was done for Rphq2 in a previous study. In Chapter 4, we target to fine-map another two partial resistance QTLs of our interest, viz. Rphq11 and Rphq16. We, however, did not use the NILs for fine-mapping of Rphq11 and Rphq16. Instead, after validating the effect of Rphq11 and Rphq16 using the early breeding materials for developing NILs of Rphq11 and Rphq16, we developed fixed QTL-recombinants (i.e. homozygous recombinants at the Rphq11/Rphq16 QTL alleles, homozygous susceptible at the non-targeted QTL alleles). The genomic background of fixed QTL-recombinants was still segregating, but expected not to be relevant for the resistance level. Rphq11 was fine-mapped into a 0.2 cM genetic interval and a 1.4 cM genetic interval for Rphq16, before the NILs were ready. The strongest candidate gene for Rphq11 is a phospholipid hydroperoxide glutathione peroxidase (PHGPx). This gene corresponds to the new Rphq11 peak marker – WBE129, located within the refined 0.2 cM genetic intervals and was one of the candidate genes for Rphq11 identified through e-QTL mapping on Steptoe/Morex challenged with the same rust isolate. There was no clear candidate gene identified for Rphq16.

A QTL has to be fine-mapped into a sufficiently narrow genetic window to make physical mapping feasible. Rphq2 with a genetic window of 0.1 cM is ready for physical mapping. In Chapter 5, we have constructed two non-gridded Bacterial Artificial Chromosome (BAC) libraries of barley from Vada and SusPtrit. Based on the insert sizes of the BAC clones, the estimated genome coverage of the Vada BAC library is 2.6x and of the SusPtrit BAC library 3.7x. The genome coverage of Vada is comparable to the BAC library of Morex, HVVMRXALLhB and SusPtrit to HVVMRXALLeA. The estimation of genome coverage based on microsatellite markers indicates, however, Vada and SusPtrit BAC libraries to have 5.0x and 6.8x genome coverage, respectively. Based on genome insert size, the BAC library of Vada gives at least 93% probability of identifying a clone corresponding to any sequence of Vada and for the BAC library of SusPtrit a probability of 98% is expected. Together, the two BAC libraries give more than 99% probability of recovering any specific sequence from the barley genome. A tiling path of three BAC clones was constructed for Vada, which cover the Rphq2 genetic window. The physical window of Rphq2 in Vada BAC contig is approximately 195 Kbp. For SusPtrit, the three BAC clones forming the contig did not cover the entire genetic window of Rphq2. The physical length bridged by them is approximately 226 Kbp. The TriAnnot pipeline annotated 12 genes in both the Vada and the SusPtrit contig, but only four of the annotated genes are shared between Vada and SusPtrit. The candidate genes for Rphq2 might be a resistance factor in Vada or a susceptibility factor in SusPtrit. The peroxidases and kinases are good candidates to represent Rphq2. It is possible that one of the peroxidase or kinase gene members in the physical window of Rphq2 explains the resistance phenotype observed. Another possibility is that peroxidase or kinase gene members function as a complex QTL. A member of the Seven in absentia protein family (SINA) can be a candidate as well. The gene families to which previously cloned genes for partial resistance belong were not found to be represented in the Rphq2 region.

We propose to perform functional analysis of candidate genes through Agrobacterium-mediated stable transformation of the resistance allele into a susceptible genotype, such as SusPtrit. Unfortunately, SusPtrit is, as so many barley accessions, not amenable to Agrobacterium-mediated transformation. In Chapter 2, we developed a doubled haploid (DH) mapping population (n=122) by crossing SusPtrit with Golden Promise to develop a ‘Golden SusPtrit’, i.e., a barley line combining SusPtrit’s high susceptibility to non-adapted rust fungi with the high amenability of Golden Promise for transformation. Using the DH population, we identified nine genomic regions occupied by QTLs against four non-adapted rust fungi and P. hordei isolate 1.2.1 (Ph.1.2.1). From 12 DH lines that were most susceptible to the tested non-adapted rust fungi, we selected four DHs for an Agrobacterium-mediated transformation efficiency test. We obtained a DH line (SG062N) with transformation efficiency of 11 to 17 transformants per 100 immature embryos. The level of susceptibility of SG062N to non-adapted rust fungi is either similar to or higher than the level of susceptibility of SusPtrit. Against P. hordei, the latency period conferred by SG062N at seedling stage is as short as that conferred by SusPtrit. SG062N, designated ‘Golden SusPtrit’, will be a valuable experimental line that could replace SusPtrit in future nonhost and partial resistance studies, especially for stable transformation using candidate genes that may determine the differences in resistance levels against adapted and non-adapted rust fungi.

Identification of candidate genes required for susceptibility to powdery or downy mildew in cucumber
Schouten, H.J. ; Krauskopf, J. ; Visser, R.G.F. ; Bai, Y. - \ 2014
Euphytica 200 (2014)3. - ISSN 0014-2336 - p. 475 - 486.
quantitative trait loci - sativus l. - disease resistance - mlo-gene - qtl analysis - cell-death - arabidopsis - defense - protein - barley
Powdery mildew (PM, caused by Podosphaera fusca) and downy mildew (DM, caused by Pseudoperonospora cubensis) are important diseases of cucumber (Cucumis sativus). Breeding for resistance has been undertaken since the 1940s, but underlying resistance genes have not been functionally analysed yet. The published genome sequence of cucumber catalyses the search for such genes. Genetic studies have indicated that resistances to PM and DM in cucumber are often inherited recessively, which indicates the presence of susceptibility genes (S-genes). Therefore we analyzed the cucumber genome for homologs of functionally proven S-genes known from other plant species. We identified 13 MLO-like genes in cucumber, three of which cluster in Clade V, the clade that contains all known MLO-like susceptibility genes to powdery mildews in other dicots. The expression of one of these three genes, CsaMLO1, located on chromosome 1, was upregulated after PM inoculation. It co-localizes with a QTL for PM resistance previously identified. Also homologs of the susceptibility genes PMR4 and PMR5 are located at this QTL. The second MLO-like gene from Clade V (CsaMLO8) resides in a recessively inherited major QTL for PM resistance at the bottom of chromosome 5, together with a PMR6-like gene. Two major QTL for DM recessive resistance at the top of chromosome 5 co-localize with CsaDMR6-2, which is homologous to the DMR6 susceptibility gene in Arabidopsis. This study has identified several candidate genes for susceptibility to PM and DM in cucumber that may explain QTL for recessively inherited resistance, reported earlier.
Characterization of the MLO gene family in Rosaceae and gene expression analysis in Malus domestica
Pessina, S. ; Pavan, S.N.C. ; Catalano, D. ; Gallotta, A. ; Visser, R.G.F. ; Bai, Y. ; Malnoy, M. ; Schouten, H.J. - \ 2014
BMC Genomics 15 (2014)618. - ISSN 1471-2164 - 23 p.
powdery mildew resistance - barley - identification - protein - defense - genome - orthologs - evolution - prunus - plants
Background Powdery mildew (PM) is a major fungal disease of thousands of plant species, including many cultivated Rosaceae. PM pathogenesis is associated with up-regulation of MLO genes during early stages of infection, causing down-regulation of plant defense pathways. Specific members of the MLO gene family act as PM-susceptibility genes, as their loss-of-function mutations grant durable and broad-spectrum resistance. Results We carried out a genome-wide characterization of the MLO gene family in apple, peach and strawberry, and we isolated apricot MLO homologs through a PCR-approach. Evolutionary relationships between MLO homologs were studied and syntenic blocks constructed. Homologs that are candidates for being PM susceptibility genes were inferred by phylogenetic relationships with functionally characterized MLO genes and, in apple, by monitoring their expression following inoculation with the PM causal pathogen Podosphaera leucotricha. Conclusions Genomic tools available for Rosaceae were exploited in order to characterize the MLO gene family. Candidate MLO susceptibility genes were identified. In follow-up studies it can be investigated whether silencing or a loss-of-function mutations in one or more of these candidate genes leads to PM resistance.
Gebruiksnorm brouwgerst hoger
Timmer, R.D. - \ 2014
Boerderij 99 (2014)39. - ISSN 0006-5617 - p. 32 - 32.
akkerbouw - gerst - veldproeven - brouwgranen - bemesting - stikstofmeststoffen - rassen (planten) - eiwitgehalte - normen - opbrengst - proeven op proefstations - arable farming - barley - field tests - brewers' grains - fertilizer application - nitrogen fertilizers - varieties - protein content - standards - outturn - station tests
80 Kilo stikstof per hectare is eigenlijk te weinig om kwalitatief goede brouwgerst te telen. Ruud Timmer van het PPO te Lelystad en brouwers pleiten voor een hogere gebruiksnorm. Onderzoek naar rassen voor de mouterijen is gewenst.
Steeds preciezer met de sensor
Houweling, P. van; PPO Akkerbouw, Groene Ruimte en Vollegrondsgroente, - \ 2014
Akker magazine 10 (2014)4. - ISSN 1875-9688 - p. 18 - 21.
akkerbouw - aardappelen - loofvernietiging - sensors - bemesting - stikstofmeststoffen - gerst - spuitapparaten - pleksgewijs spuiten - bladbespuiting - precisielandbouw - arable farming - potatoes - haulm destruction - fertilizer application - nitrogen fertilizers - barley - sprayers - spot spraying - foliar spraying - precision agriculture
Maurits Bax uit Luyksgestel werkt met de Yara N-sensor. Zo spuit hij minder dan een derde van de voorgeschreven dosering voor loofdodingsmiddel in aardappelen. Andere toepassingen zijn minder praktijkrijp, zoals aardappelen bijmesten. Daarvoor lijkt een app, ontwikkeld door het PPO, uitkomst te gaan bieden. PPO Lelystad begeleidt het project waar Bax aan mee doet. De teler kreeg de afgelopen twee teeltseizoenen voor zijn aardappelen een adviesgift van PPO op basis van twee systemen: de BemestingsNavigator aardappel van Altic en een systeem dat PPO ontwikkelt. De volgende toepassing was voor het spuiten van halmverstevigers in zomergerst.
Simultaneous real-time PCR quantification of Fusarium asiaticum, F ussurianum and F vorosii, representing the Asian clade of the F graminearum species complex
Fernandez-Ortuno, D. ; Waalwijk, C. ; Lee, T.A.J. van der; Fan, J. ; West, J.S. ; Fraaije, B.A. - \ 2013
International Journal of Food Microbiology 166 (2013)1. - ISSN 0168-1605 - p. 148 - 154.
head blight pathogen - gibberella-zeae - genealogical concordance - southern brazil - wheat - diversity - barley - quantification - populations - mycotoxins
Due to the repeated discovery of new members of the Fusarium graminearum species complex (FGSC), some of the F. graminearum sensu stricto (s.s.)-specific qPCR assays developed to date have since been shown to be non-specific. In this study, a probe-based qPCR method was developed, targeting a sterol 14-alpha demethylase (CYP51) paralogue, CYP51C unique to the genus Fusarium, for the simultaneous detection of F. asiaticum, F. ussurianum and F. vorosii. Specificity of the assay was demonstrated for a wide range of Fusarium species, including all tested FGSC members (n=6), originating from different hosts and geographic regions. Alongside a previously published assay for detection of F. graminearum, we were able to show that members of the Asian clade of the FGSC (i.e. F. asiaticum, F. ussurianum and F. vorosii) were the primary etiological agent in wheat seeds samples originating from Central-East China. The grain samples from the UK tested negative for the presence of the FGSC's Asian clade and positive for presence of F. graminearum. It is likely that only F. graminearum s.s. is present in the UK, but the presence of other FGSC members cannot be ruled out and need further investigation
Geographic differences in trichothecene chemotypes of Fusarium graminearum in the Northwest and North of Iran
Davari, M. ; Wei, S.H. ; Babay-Ahari, A. ; Arzanlou, M. ; Waalwijk, C. ; Lee, T.A.J. van der; Zare, R. ; Ende, A.H.G.G. van den; Hoog, G.S. de; Diepeningen, A.D. van - \ 2013
World Mycotoxin Journal 6 (2013)2. - ISSN 1875-0710 - p. 137 - 150.
head blight pathogen - dna-sequence database - species complex - genealogical concordance - wheat - populations - mycotoxins - barley - deoxynivalenol - diversity
The diversity and prevalence of Fusarium species and their chemotypes on wheat in the North-West and North of Iran was determined. Wheat in these areas is severely affected by Fusarium head blight, with Fusarium graminearum as prevalent species causing 96% of the infections in the North-West and 50% in the Northern provinces. Fungal isolates were identified based on morphological characters and sequences of the internal transcribed spacer region, and parts of translation elongation factor 1-alpha and RNA polymerase subunit II sequences. Phylogenetic and phylogeographic analyses show little haplotype variation between the F. graminearum strains collected from the different locations, but the isolates differ significantly in their trichothecene chemotypes as determined with a multilocus genotyping assay. E graminearum strains producing 15-acetyldeoxynivalenol were abundant in Ardabil (North-West of Iran), while in Golestan province (North of Iran) at the other side of the Caspian Sea especially nivalenol producing strains and a variety of other Fusarium species were observed. Strains producing 3-acetyldeoxynivalenol were rarely found in both areas. This is the first detailed study on Fusarium infections in Iranian wheat, showing large differences in prevalent etiological agents and in mycotoxin chemotypes geographically.
Farmer’s seed sources and seed quality: 2. seed health
Bishaw, Z. ; Struik, P.C. ; Gastel, A.J.G. van - \ 2013
International Journal of Plant Production 7 (2013)4. - ISSN 1735-6814 - p. 637 - 658.
wheat seed - borne diseases - management - system - barley
The study assessed the health quality of wheat (Triticum aestivum L.) and barley (Hordeum vulgare L.) seed samples collected from formal and informal sector in Ethiopia and Syria. In Ethiopia, several seed-borne fungi were found on wheat samples: Cochliobolus sativum, Fusarium avenaceum, F. graminearum, F. nivale, F. poae and Septoria nodorum. C. sativum was predominant with 84% of samples infected (frequency) and 1.85% mean infection level (rate) followed by F. graminearum with 74% and 1.54%, respectively. Certified seed consistently showed less infection for most seed-borne pathogens. In Syria, 68% and 14%, respectively, of wheat samples were infected with common bunt (Tilletia spp) and loose smut (Ustilago tritici). Mean loose smut infection rate was 0.79%. In barley, 85% of samples were infected with covered smut (Ustilago hordei) and 83% with loose smut (Ustilago nuda). Mean loose smut infection rate was 18%. Wheat seed health was better than of barley in terms of frequency and rate of infection. In Ethiopia, significant difference (P
Results of a proficiency test for multi-mycotoxin determination in maize by using methods based on LC-MS/(MS)
Solfrizzo, M. ; Girolamo, A. De; Lattanzio, V.M.T. ; Visconti, A. ; Stroka, J. ; Alldrick, A. ; Egmond, H.P. van - \ 2013
Quality Assurance and Safety of Crops & Foods 5 (2013)1. - ISSN 1757-8361 - p. 15 - 48.
immunoaffinity column cleanup - liquid-chromatography - grains - barley
Liquid chromatography coupled with single or tandem mass spectrometry (LC-MS/(MS)) is routinely used for the simultaneous determination of mycotoxins in food and feed although official methods using this technique have not yet been adopted by the European Committee for Standardization and the Association of Analytical Communities. A proficiency test (PT) was conducted for the simultaneous determination of up to 11 mycotoxins (aflatoxin B-1 (AFB(1)), aflatoxin B-2 (AFB(2)), aflatoxin G(1) (AFG(1)), aflatoxin G(2) (AFG(2)), ochratoxin A (OTA), deoxynivalenol (DON), T-2 toxin (T-2), HT-2 toxin (HT-2), zearalenone (ZEA), fumonisin B-1 (FB1) and fumonisin B-2 (FB2)) in maize using LC-MS/(MS) to benchmark laboratories currently using this technique and to obtain information on currently used methodologies and method-related performances. Each participant received the following: instructions; a comprehensive questionnaire; a mixed mycotoxins calibration solution; a spiking solution (AFB(1), AFB(2), AFG(1) and AFG(2), OTA, DON, T-2, HT-2, ZEA, FB1 and FB2); and two test materials, namely a contaminated maize sample and a blank maize sample to be spiked with a spiking solution containing 11 mycotoxins. Laboratory results were rated with z-scores. Of the 64 laboratories enrolled in the PT, 41 laboratories from 14 countries returned 43 sets of results for various combinations of analytes. The majority of laboratories (61%) reported results for all 11 mycotoxins, whereas the remaining laboratories reported results for a restricted combination (from 2 to 10 analytes). For contaminated maize and spiked maize the percentage of satisfactory z-score values (vertical bar z vertical bar 3) was obtained for FB1 (31%), FB2 (32%), AFB(1) (32%) and AFB(2) (32%) in contaminated maize and for DON (35%), FB1 (63%) and FB2 (52%) in spiked maize. Mean recovery results were acceptable for all mycotoxins (74% to 109%), except for fumonisins, where these were unacceptably high (159% for FB1 and 163% for FB2). A robust and reliable method for simultaneous determination of 11 mycotoxins in maize could not be identified from the results of this PT. Additional experimental work is necessary to set up a method suitable for inter-laboratory validation. The results of this PT and the relevant method's details can be useful to identify methodology strengths and weaknesses.
Koji – where East meets West in fermentation
Yang Zhu, Yang ; Tramper, J. - \ 2013
Biotechnology Advances 31 (2013)8. - ISSN 0734-9750 - p. 1448 - 1457.
japanese soy-sauce - aspergillus-oryzae - soybean products - genomics - industry - allergen - biology - barley - flavor - assay
Almost all biotechnological processes originate from traditional food fermentations, i.e. the many indigenous processes that can be found already in the written history of thousands of years ago. We still consume many of these fermented foods and beverages on a daily basis today. The evolution of these traditional processes, in particular since the 19th century, stimulated and influenced the development of modern biotechnological processes. In return, the development of modern biotechnology and related advanced techniques will no doubt improve the process, the product quality and the safety of our favourite fermented foods and beverages. In this article, we describe the relationship between these traditional food fermentations and modern biotechnology. Using Koji and its derived product soy sauce as examples, we address the mutual influences that will provide us with a better future concerning the quality, safety and nutritional effect of many fermented food products.
Multi-trait and multi-environment QTL analyses of yield and a set of physiological traits in pepper
Alimi, N.A. ; Bink, M.C.A.M. ; Dieleman, J.A. ; Magán, J.J. ; Wubs, A.M. ; Palloix, A. ; Eeuwijk, F.A. van - \ 2013
Theoretical and Applied Genetics 126 (2013)10. - ISSN 0040-5752 - p. 2597 - 2625.
mixed-model approach - capsicum-annuum - complex traits - fruit size - loci - populations - barley - maize - covariables - regression
For many agronomic crops, yield is measured simultaneously with other traits across multiple environments. The study of yield can benefit from joint analysis with other traits and relations between yield and other traits can be exploited to develop indirect selection strategies. We compare the performance of three multi-response QTL approaches based on mixed models: a multi-trait approach (MT), a multi-environment approach (ME), and a multi-trait multi-environment approach (MTME). The data come from a multi-environment experiment in pepper, for which 15 traits were measured in four environments. The approaches were compared in terms of number of QTLs detected for each trait, the explained variance, and the accuracy of prediction for the final QTL model. For the four environments together, the superior MTME approach delivered a total of 47 regions containing putative QTLs. Many of these QTLs were pleiotropic and showed quantitative QTL by environment interaction. MTME was superior to ME and MT in the number of QTLs, the explained variance and accuracy of predictions. The large number of model parameters in the MTME approach was challenging and we propose several guidelines to help obtain a stable final QTL model. The results confirmed the feasibility and strengths of novel mixed model QTL methodology to study the architecture of complex traits.
Loss of Function in Mlo Orthologs Reduces Susceptibility of Pepper and Tomato to Powdery Mildew Disease Caused by Leveillula taurica
Zheng, Z. ; Nonomura, T. ; Appiano, M. ; Pavan, S.N.C. ; Matsuda, Y. ; Toyoda, H. ; Wolters, A.M.A. ; Visser, R.G.F. ; Bai, Y. - \ 2013
PLoS One 8 (2013)7. - ISSN 1932-6203 - 14 p.
real-time pcr - capsicum-annuum - subcellular-localization - nonhost resistance - gene-expression - oryza-sativa - cell-death - barley - family - identification
Powdery mildew disease caused by Leveillula taurica is a serious fungal threat to greenhouse tomato and pepper production. In contrast to most powdery mildew species which are epiphytic, L. taurica is an endophytic fungus colonizing the mesophyll tissues of the leaf. In barley, Arabidopsis, tomato and pea, the correct functioning of specific homologues of the plant Mlo gene family has been found to be required for pathogenesis of epiphytic powdery mildew fungi. The aim of this study was to investigate the involvement of the Mlo genes in susceptibility to the endophytic fungus L. taurica. In tomato (Solanum lycopersicum), a loss-of-function mutation in the SlMlo1 gene results in resistance to powdery mildew disease caused by Oidium neolycopersici. When the tomato Slmlo1 mutant was inoculated with L. taurica in this study, it proved to be less susceptible compared to the control, S. lycopersicum cv. Moneymaker. Further, overexpression of SlMlo1 in the tomato Slmlo1 mutant enhanced susceptibility to L. taurica. In pepper, the CaMlo2 gene was isolated by applying a homology-based cloning approach. Compared to the previously identified CaMlo1 gene, the CaMlo2 gene is more similar to SlMlo1 as shown by phylogenetic analysis, and the expression of CaMlo2 is up-regulated at an earlier time point upon L. taurica infection. However, results of virus-induced gene silencing suggest that both CaMlo1 and CaMlo2 may be involved in the susceptibility of pepper to L. taurica. The fact that overexpression of CaMlo2 restored the susceptibility of the tomato Slmlo1 mutant to O. neolycopersici and increased its susceptibility to L. taurica confirmed the role of CaMlo2 acting as a susceptibility factor to different powdery mildews, though the role of CaMlo1 as a co-factor for susceptibility cannot be excluded.
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