Staff Publications

Staff Publications

  • external user (warningwarning)
  • Log in as
  • language uk
  • About

    '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.

    We have a manual that explains all the features 

Records 1 - 20 / 37

  • help
  • print

    Print search results

  • export

    Export search results

  • alert
    We will mail you new results for this query: q=Fitzgerald
Check title to add to marked list
Spatial distribution of the potential forest biomass availability in Europe
Verkerk, P.J. ; Fitzgerald, Joanne Brighid ; Datta, Pawan ; Dees, M. ; Hengeveld, G.M. ; Lindner, M. ; Zudin, S. - \ 2019
Forest Ecosystems 6 (2019). - ISSN 2095-6355
Background
European forests are considered a crucial resource for supplying biomass to a growing bio-economy in Europe. This study aimed to assess the potential availability of forest biomass from European forests and its spatial distribution. We tried to answer the questions (i) how is the potential forest biomass availability spatially distributed across Europe and (ii) where are hotspots of potential forest biomass availability located?
Methods
The spatial distribution of woody biomass potentials was assessed for 2020 for stemwood, residues (branches and harvest losses) and stumps for 39 European countries. Using the European Forest Information SCENario (EFISCEN) model and international forest statistics, we estimated the theoretical amount of biomass that could be available based on the current and future development of the forest age-structure, growing stock and increment and forest management regimes. We combined these estimates with a set of environmental (site productivity, soil and water protection and biodiversity protection) and technical (recovery rate, soil bearing capacity) constraints, which reduced the amount of woody biomass that could potentially be available. We mapped the potential biomass availability at the level of administrative units and at the 10 km × 10 km grid level to gain insight into the spatial distribution of the woody biomass potentials.
Results
According to our results, the total availability of forest biomass ranges between 357 and 551 Tg dry matter per year. The largest potential supply of woody biomass per unit of land can be found in northern Europe (southern Finland and Sweden, Estonia and Latvia), central Europe (Austria, Czech Republic, and southern Germany), Slovenia, southwest France and Portugal. However, large parts of these potentials are already used to produce materials and energy. The distribution of biomass potentials that are currently unused only partially coincides with regions that currently have high levels of wood production.
Conclusions
Our study shows how the forest biomass potentials are spatially distributed across the European continent, thereby providing insight into where policies could focus on an increase of the supply of woody biomass from forests. Future research on potential biomass availability from European forests should also consider to what extent forest owners would be willing to mobilise additional biomass from their forests and at what costs the estimated potentials could be mobilised.
Lactobacillus mucosae DPC 6426 as a bile-modifying and immunomodulatory microbe
Ryan, Paul M. ; Stolte, Ellen H. ; London, Lis E.E. ; Wells, Jerry M. ; Long, Sarah L. ; Joyce, Susan A. ; Gahan, Cormac G.M. ; Fitzgerald, Gerald F. ; Ross, R.P. ; Caplice, Noel M. ; Stanton, Catherine - \ 2019
BMC Microbiology 19 (2019)1. - ISSN 1471-2180
Bile acid - Bile salt hydrolase (BSH) - CVD - Exopolysaccharide - Hypercholesterolaemia

Background: Lactobacillus mucosae DPC 6426 has previously demonstrated potentially cardio-protective properties, in the form of dyslipidaemia and hypercholesterolemia correction in an apolipoprotein-E deficient mouse model. This study aims to characterise the manner in which this microbe may modulate host bile pool composition and immune response, in the context of cardiovascular disease. Lactobacillus mucosae DPC 6426 was assessed for bile salt hydrolase activity and specificity. The microbe was compared against several other enteric strains of the same species, as well as a confirmed bile salt hydrolase-active strain, Lactobacillus reuteri APC 2587. Results: Quantitative bile salt hydrolase assays revealed that enzymatic extracts from Lactobacillus reuteri APC 2587 and Lactobacillus mucosae DPC 6426 demonstrate the greatest activity in vitro. Bile acid profiling of porcine and murine bile following incubation with Lactobacillus mucosae DPC 6426 confirmed a preference for hydrolysis of glyco-conjugated bile acids. In addition, the purified exopolysaccharide and secretome of Lactobacillus mucosae DPC 6426 were investigated for immunomodulatory capabilities using RAW264.7 macrophages. Gene expression data revealed that both fractions stimulated increases in interleukin-6 and interleukin-10 gene transcription in the murine macrophages, while the entire secretome was necessary to increase CD206 transcription. Moreover, the exopolysaccharide elicited a dose-dependent increase in nitric oxide and interleukin-10 production from RAW264.7 macrophages, concurrent with increased tumour necrosis factor-α secretion at all doses. Conclusions: This study indicates that Lactobacillus mucosae DPC 6426 modulates both bile pool composition and immune system tone in a manner which may contribute significantly to the previously identified cardio-protective phenotype.

Climate change impact and adaptation for wheat protein
Asseng, Senthold ; Martre, Pierre ; Maiorano, Andrea ; Rötter, Reimund P. ; O’Leary, Garry J. ; Fitzgerald, Glenn J. ; Girousse, Christine ; Motzo, Rosella ; Giunta, Francesco ; Babar, M.A. ; Reynolds, Matthew P. ; Kheir, Ahmed M.S. ; Thorburn, Peter J. ; Waha, Katharina ; Ruane, Alex C. ; Aggarwal, Pramod K. ; Ahmed, Mukhtar ; Balkovič, Juraj ; Basso, Bruno ; Biernath, Christian ; Bindi, Marco ; Cammarano, Davide ; Challinor, Andrew J. ; Sanctis, Giacomo De; Dumont, Benjamin ; Eyshi Rezaei, Ehsan ; Fereres, Elias ; Ferrise, Roberto ; Garcia-Vila, Margarita ; Gayler, Sebastian ; Gao, Yujing ; Horan, Heidi ; Hoogenboom, Gerrit ; Izaurralde, R.C. ; Jabloun, Mohamed ; Jones, Curtis D. ; Kassie, Belay T. ; Kersebaum, Kurt Christian ; Klein, Christian ; Koehler, Ann Kristin ; Liu, Bing ; Minoli, Sara ; Montesino San Martin, Manuel ; Müller, Christoph ; Naresh Kumar, Soora ; Supit, Iwan ; Tao, Fulu ; Wolf, Joost ; Zhang, Zhao ; Ewert, Frank - \ 2019
Global Change Biology 25 (2019)1. - ISSN 1354-1013 - p. 155 - 173.
climate change adaptation - climate change impact - food security - grain protein - wheat

Wheat grain protein concentration is an important determinant of wheat quality for human nutrition that is often overlooked in efforts to improve crop production. We tested and applied a 32-multi-model ensemble to simulate global wheat yield and quality in a changing climate. Potential benefits of elevated atmospheric CO2 concentration by 2050 on global wheat grain and protein yield are likely to be negated by impacts from rising temperature and changes in rainfall, but with considerable disparities between regions. Grain and protein yields are expected to be lower and more variable in most low-rainfall regions, with nitrogen availability limiting growth stimulus from elevated CO2. Introducing genotypes adapted to warmer temperatures (and also considering changes in CO2 and rainfall) could boost global wheat yield by 7% and protein yield by 2%, but grain protein concentration would be reduced by −1.1 percentage points, representing a relative change of −8.6%. Climate change adaptations that benefit grain yield are not always positive for grain quality, putting additional pressure on global wheat production.

Multimodel ensembles improve predictions of crop–environment–management interactions
Wallach, Daniel ; Martre, Pierre ; Liu, Bing ; Asseng, Senthold ; Ewert, Frank ; Thorburn, Peter J. ; Ittersum, Martin van; Aggarwal, Pramod K. ; Ahmed, Mukhtar ; Basso, Bruno ; Biernath, Christian ; Cammarano, Davide ; Challinor, Andrew J. ; Sanctis, Giacomo De; Dumont, Benjamin ; Eyshi Rezaei, Ehsan ; Fereres, Elias ; Fitzgerald, Glenn J. ; Gao, Y. ; Garcia-Vila, Margarita ; Gayler, Sebastian ; Girousse, Christine ; Hoogenboom, Gerrit ; Horan, Heidi ; Izaurralde, Roberto C. ; Jones, Curtis D. ; Kassie, Belay T. ; Kersebaum, Christian C. ; Klein, Christian ; Koehler, Ann Kristin ; Maiorano, Andrea ; Minoli, Sara ; Müller, Christoph ; Naresh Kumar, Soora ; Nendel, Claas ; O'Leary, Garry J. ; Palosuo, Taru ; Priesack, Eckart ; Ripoche, Dominique ; Rötter, Reimund P. ; Semenov, Mikhail A. ; Stöckle, Claudio ; Stratonovitch, Pierre ; Streck, Thilo ; Supit, Iwan ; Tao, Fulu ; Wolf, Joost ; Zhang, Zhao - \ 2018
Global Change Biology 24 (2018)11. - ISSN 1354-1013 - p. 5072 - 5083.
climate change impact - crop models - ensemble mean - ensemble median - multimodel ensemble - prediction

A recent innovation in assessment of climate change impact on agricultural production has been to use crop multimodel ensembles (MMEs). These studies usually find large variability between individual models but that the ensemble mean (e-mean) and median (e-median) often seem to predict quite well. However, few studies have specifically been concerned with the predictive quality of those ensemble predictors. We ask what is the predictive quality of e-mean and e-median, and how does that depend on the ensemble characteristics. Our empirical results are based on five MME studies applied to wheat, using different data sets but the same 25 crop models. We show that the ensemble predictors have quite high skill and are better than most and sometimes all individual models for most groups of environments and most response variables. Mean squared error of e-mean decreases monotonically with the size of the ensemble if models are added at random, but has a minimum at usually 2–6 models if best-fit models are added first. Our theoretical results describe the ensemble using four parameters: average bias, model effect variance, environment effect variance, and interaction variance. We show analytically that mean squared error of prediction (MSEP) of e-mean will always be smaller than MSEP averaged over models and will be less than MSEP of the best model if squared bias is less than the interaction variance. If models are added to the ensemble at random, MSEP of e-mean will decrease as the inverse of ensemble size, with a minimum equal to squared bias plus interaction variance. This minimum value is not necessarily small, and so it is important to evaluate the predictive quality of e-mean for each target population of environments. These results provide new information on the advantages of ensemble predictors, but also show their limitations.

Distribution of month of birth of individuals with autism spectrum disorder differs from the general population in the Netherlands
Ciéslińska, Anna ; Simmelink, Jannicke ; Teodorowicz, M. ; Verhoef, J.C.M. ; Tobi, H. ; Savelkoul, H.F.J. - \ 2017
In: Autism - Paradigms, Recent Research and Clinical Applications / Fitzgerald, M., Yip, J., InTech - ISBN 9789535130796 - 43 p.
The prevalence of autism spectrum disorders (ASDs) is causally dependent on genetic and environmental influences. We investigated whether autism spectrum disorders are associated with month of birth compared to the general population using a retrospective study, comparing ASD cases (n = 3478) with the general population (n = 2,716,876) born between 1995 and 2008. Associations were examined using χ2 tests and Walter and Elwood’s seasonality χ2 tests for the total ASD group, and separately for autistic disorder and Asperger syndrome. For the total ASD group, the distribution of month of birth was different compared to the general population (p < 0.0001), with July as the highest contributor, and a season-of-birth effect was found for this group (p = 0.02). For the autistic disorder group, the months of birth distribution were different (p = 0.01), with July as the highest contributor. No season-of-birth effect over the year was found (p = 0.09). No association was found for the months of birth of individuals with Asperger syndrome (p = 0.06), with no seasonal trend over the year (p = 0.60). In conclusion, a drop in sun exposure during the first trimester of pregnancy might explain the peak in July births and the associated risk for ASD development.
A multidisciplinary phenotyping and genotyping analysis of a mapping population enables quality to be combined with yield in rice
Calingacion, Mariafe ; Mumm, Roland ; Tan, Kevin ; Quiatchon-Baeza, Lenie ; Concepcion, Jeanaflor C.T. ; Hageman, Jos A. ; Prakash, Sangeeta ; Fitzgerald, Melissa ; Hall, Robert D. - \ 2017
Frontiers in Molecular Biosciences 4 (2017)MAY. - ISSN 2296-889X
Aroma - GC-MS analysis - Metabolomics - QTL - Rice - Segregating population - Sensory - Yield
In this study a mapping population (F8) of ca 200 progeny from a cross between the commercial rice varieties Apo and IR64 has been both genotyped and phenotyped. A genotyping-by-sequencing approach was first used to identify 2,681 polymorphic SNP markers which gave dense coverage of the genome with a good distribution across all 12 chromosomes. The coefficient of parentage was also low, at 0.13, confirming that the parents are genetically distant from each other. The progeny, together with both parents, were grown under irrigated and water restricted conditions in a randomised block design. All grain was harvested to determine variation in yield across the population. The grains were then polished following standard procedures prior to performing the phenotyping analyses. A Gas Chromatography-Mass Spectrometry approach was used to determine the volatile biochemical profiles of each line and after data curation and processing, discriminatory metabolites were putatively identified based on in-house and commercial spectral libraries. These data were used to predict the potential role of these metabolites in determining differences in aroma between genotypes. A number of QTLs for yield and for individual metabolites have been identified. Following these combined multi-disciplinary analyses, it proved possible to identify a number of lines which appeared to combine the favourable aroma attributes of IR64 with the favourable (higher) yield potential of Apo. As such, these lines are excellent candidates to assess further as potential genotypes to work up into a new variety of rice which has both good yield and good quality, thus meeting the needs of both farmer and consumer alike.
Solution to the current price crisis in the pig sector
Hoste, Robert - \ 2016
Comparative Genomics of Campylobacter fetus from Reptilesand Mammals Reveals Divergent Evolution in Host-Associated Lineages
Gilbert, Maarten J. ; Miller, William G. ; Yee, Emma ; Zomer, Aldert ; Graaf-Van Bloois, Linda Van Der; Fitzgerald, C. ; Forbes, Ken J. ; Méric, Guillaume ; Sheppard, S. ; Wagenaar, J.A. ; Duim, Birgitta - \ 2016
Genome Biology and Evolution 8 (2016)6. - ISSN 1759-6653 - p. 2006 - 2019.
Campylobacter fetus currently comprises three recognized subspecies, which display distinct host association. Campylobacter fetus subsp. fetus and C. fetus subsp. venerealis are both associated with endothermic mammals, primarily ruminants, whereas C. fetus subsp. testudinum is primarily associated with ectothermic reptiles. Both C. fetus subsp. testudinum and C. fetus subsp. fetus have been associated with severe infections, often with a systemic component, in immunocompromised humans. To study the genetic factors associated with the distinct host dichotomy in C. fetus, whole-genome sequencing and comparison of mammal- and reptile-associated C. fetus was performed. The genomes of C. fetus subsp. testudinum isolated from either reptiles or humans were compared with elucidate the genetic factors associated with pathogenicity in humans. Genomic comparisons showed conservation of gene content and organization among C. fetus subspecies, but a clear distinction between mammal- and reptile-associated C. fetus was observed. Several genomic regions appeared to be subspecies specific, including a putative tricarballylate catabolism pathway, exclusively present in C. fetus subsp. testudinum strains. Within C. fetus subsp. testudinum, sapA, sapB, and sapAB type strains were observed. The recombinant locus iamABC (mlaFED) was exclusively associated with invasive C. fetus subsp. testudinum strains isolated from humans. A phylogenetic reconstruction was consistent with divergent evolution in host-associated strains and the existence of a barrier to lateral gene transfer between mammal- and reptile-associated C. fetus. Overall, this study shows that reptile-associated C. fetus subsp. testudinum is genetically divergent from mammal-associated C. fetus subspecies.
Eco-districts : can they accelerate urban climate planning?
Fitzgerald, Joan ; Lenhart, Jennifer - \ 2016
Environment and Planning C. Government and Policy 34 (2016)2. - ISSN 0263-774X - p. 364 - 380.
climate adaptation - climate mitigation - environmental governance - environmental policy - local climate action

Despite signing the Mayors Climate Change Agreement, few US cities have made significant progress in either climate mitigation or adaptation. For the most part, European cities have been more effective, albeit with assistance from the European Union and their national governments. Several of the most successful European cities have implemented eco-districts, which have offered many lessons for overall sustainability planning. Using Malmö, Sweden as a case study, we ask how planners and elected officials learned from implementing an eco-district, focusing on experimentation with new technologies and approaches to planning. We identify how “double-loop learning”, a term coined by Argyris and Shön, was at play in changing planning practice. As eco-districts are catching on in North American cities, there is much to be learned from European practice.

Multi-platform metabolomics analyses of a broad collection of fragrant and non-fragrant rice varieties reveals the high complexity of grain quality characteristics
Mumm, R. ; Hageman, J.A. ; Calingacion, M.N. ; Vos, C.H. de; Jonker, H.H. ; Erban, A. ; Kopka, J. ; Hansen, T.H. ; Laursen, K.H. ; Schjoerring, J.K. ; Ward, J.L. ; Beale, M.H. ; Jongee, S. ; Rauf, A. ; Habibi, F. ; Indrasari, S.D. ; Sakhan, S. ; Ramli, A. ; Romero, M. ; Reinke, R. ; Ohtsubo, K. ; Boualaphanh, C. ; Fitzgerald, M.A. ; Hall, R.D. - \ 2016
Metabolomics 12 (2016)2. - ISSN 1573-3882 - 19 p.
The quality of rice in terms not only of its nutritional value but also in terms of its aroma and flavour is becoming increasingly important in modern rice breeding
where global targets are focused on both yield stability and grain quality. In the present paper we have exploited advanced, multi-platform metabolomics approaches to determine the biochemical differences in 31 rice varieties from a diverse range of genetic backgrounds and origin. All were grown under the specific local conditions for which they have been bred and all aspects of varietal identification and sample purity have been guaranteed by local experts from each country. Metabolomics analyses using 6 platforms have revealed the extent of biochemical differences (and similarities) between the chosen rice genotypes.
Comparison of fragrant rice varieties showed a difference in the metabolic profiles of jasmine and basmati varieties. However with no consistent separation of the germplasm class. Storage of grains had a significant effect on the
metabolome of both basmati and jasmine rice varieties but changes were different for the two rice types. This shows how metabolic changes may help prove a causal relationship with developing good quality in basmati rice or
incurring quality loss in jasmine rice in aged grains. Such metabolomics approaches are leading to hypotheses on the potential links between grain quality attributes, biochemical composition and genotype in the context of breeding for improvement. With this knowledge we shall establish a
stronger, evidence-based foundation upon which to build targeted strategies to support breeders in their quest for improved rice varieties.
Delving deeper into technological innovations to understand differences in rice quality
Calingacion, M.N. ; Fang, L. ; Quiatchon-Baeza, L. ; Mumm, R. ; Riedel, A. ; Hall, R.D. ; Fitzgerald, M.A. - \ 2015
Rice 8 (2015). - ISSN 1939-8433 - 10 p.
odor-active compounds - oryza-sativa l. - stage drought stress - grain-yield - genetic backgrounds - mass-spectrometry - direct selection - scented rice - cultivars - varieties
Increasing demand for better quality rice varieties, which are also more suited to growth under sub-optimal cultivation conditions, is driving innovation in rice research. Here we have used a multi-disciplinary approach, involving SNP-based genotyping together with phenotyping based on yield analysis, metabolomic analysis of grain volatiles, and sensory panel analysis to determine differences between two contrasting rice varieties, Apo and IR64. Plants were grown under standard and drought-induced conditions. Results revealed important differences between the volatile profiles of the two rice varieties and we relate these differences to those perceived by the sensory panel. Apo, which is the more drought tolerant variety, was less affected by the drought condition concerning both sensory profile and yield; IR64, which has higher quality but is drought sensitive, showed greater differences in these characteristics in response to the two growth conditions. Metabolomics analyses using GCxGC-MS, followed by multivariate statistical analyses of the data, revealed a number of discriminatory compounds between the varieties, but also effects of the difference in cultivation conditions. Results indicate the complexity of rice volatile profile, even of non-aromatic varieties, and how metabolomics can be used to help link changes in aroma profile with the sensory phenotype. Our outcomes also suggest valuable multi-disciplinary approaches which can be used to help define the aroma profile in rice, and its underlying genetic background, in order to support breeders in the generation of improved rice varieties combining high yield with high quality, and tolerance of both these traits to climate change.
Empowering breeding programs with new approaches to overcome constraints for selecting superior quality traits of rice
Calingacion, M.N. - \ 2015
Wageningen University. Promotor(en): Robert Hall; M.A. Fitzgerald, co-promotor(en): Roland Mumm. - Wageningen : Wageningen University - ISBN 9789462572188 - 198
oryza sativa - rijst - rassen (planten) - cultivars - genetische diversiteit - gewaskwaliteit - aroma - geur en smaak - consumentenvoorkeuren - plantenveredeling - veredelingsprogramma's - oryza sativa - rice - varieties - cultivars - genetic diversity - crop quality - aroma - flavour - consumer preferences - plant breeding - breeding programmes

Empowering breeding programs with new approaches to overcome constraints for selecting superior quality traits of rice

Mariafe N. Calingacion

Most rice breeding programs have focused on improving agronomic traits such as yield, while enhancing grain quality traits such as flavour and aroma, especially of non-fragrant rices, has not been given high priority. In this study, we utilised a multi-disciplinary approach to understand better quality traits of aroma and flavour in rice grains, and to determine whether good flavour in the grain could be combined with stress tolerant genotypes.

To understand what factors drive rice preferences, an extensive survey among members of the International Network for Quality Rice who are local experts in grain quality evaluation programs in 25 countries was conducted (Chapter 2). The objective was to identify the grain quality characteristics of the popular rice varieties in each region. Eighteen combinations of size and shape of the grain, amylose content (AC), gelatinisation temperature (GT) and fragrance were identified. These trait combinations reveal the complexity of consumer preferences. The two most popular combinations both have long and slender grains, while one has low amylose, low GT and is aromatic, and the other has intermediate AC and intermediate GT and is non-aromatic. Further evaluation of varieties having the same combination of grain quality traits showed that consumers readily identify differences between these varieties. For example, BRS Primavera and IR64 that are popular in Brazil and in the Philippines, respectively, have the same combination of all 18 traits, however, panellists of sensory evaluation can easily perceive differences in aroma and flavour of BRS Primavera and IR64. This emphasises that the current tools we have available to assess rice quality are unable to capture all the quality traits consumers are looking for in rice.

In Chapter 3, a novel multiplatform metabolomic and ionomic approach with genome-wide genotyping was utilised to investigate the effect of different nitrogen fertiliser regimes on the biochemical profile of three premium waxy rice varieties, Hom Nang Nouane (HNN), Kai Noi Leuanag (KNL) and Tha Sa No (TSN) from Lao PDR. The current tools used to phenotype grain quality such as GT, values from viscosity curves, and hardness and stickiness, were unable to differentiate between HNN, KNL and TSN either on the basis of nitrogen treatment nor genotype. However, metabolite profiling of metabolites and minerals followed by multivariate statistical methods readily separated the genotypes on each platform, and discriminatory compounds that were identified were relevant to consumers in terms of flavour, taste and nutrition. However, despite yield differences, nitrogen treatment did not significantly affect the overall metabolite and mineral profiles of the samples. Using 1536 single nucleotide polymorphism (SNP) loci, the Euclidean distance between each variety was calculated and compared to the distance between each variety for each metabolomic platform. Procrustes analysis was used to rotate and scale the variety mean scores on the metabolite principal components to give the best fit to the genetic principal coordinates. Comparing the triangles whereby each vertex of the triangle is a variety and the length of each side is equal to the scaled Euclidean distance, mineral elements, polar metabolites and volatile compounds all associate very well with the genetic distance between each variety. This study highlights that multiple metabolomic platforms are potential phenotyping tools to characterise rice quality in a comprehensive and efficient way, and in a way that provides data that is relevant to consumers.

To gain insights on the influence of water availability to the metabolomic profile of drought tolerant rice, two contrasting varieties, Apo and IR64, and a mapping population derived from them were extensively characterised in Chapters 4 and 5. Apo is drought tolerant but has unacceptable grain quality while IR64 is drought susceptible with premium grain quality. Apo and IR64 were grown under irrigated and drought conditions. Yield of Apo from both water conditions was higher than yield of IR64 under the same conditions. Moreover, metabolite profiling and sensory analysis showed that grains of Apo were not affected by drought conditions i.e. panellists perceived no difference in the aroma of Apo from both conditions and Principal Components Analysis (PCA) of the volatiles showed one cluster of Apo from both conditions. However, grains of IR64 formed two clusters based on water condition in the PCA and panellists were able to perceive ‘water-like metallic’ aroma in IR64 that was grown under drought conditions but this was not detected in grains from the irrigated treatment. This suggests that response to water stress in the metabolomic profile of the grain is variety dependent.

In Chapter 5, a mapping population derived from Apo and IR64 was grown, with the parents, under irrigated and drought conditions. The yield of more than half of the population was higher than the yield of Apo and IR64 under both irrigated and drought conditions; this indicates significant transgressive segregation. Using a dense linkage map based on genotyping by sequencing data, quantitative trait loci (QTL) analysis of drought stress identified one major QTL on chromosome 3 that is likely to be qDTY3.1 which was previously detected in a population derived from Apo as the drought tolerant parent. All the lines of the population carrying this QTL showed significantly higher yield under drought than those without it, indicating the potential importance of this QTL in drought tolerance.

Metabolite profiling and sensory analysis were also conducted in the grains of the population. More than a hundred volatiles were detected in the headspace of rice samples and PC1 and PC2 explained 55.6% of the variation in the metabolite profiles with many of the lines clustering in between the Apo and IR64 parent values. Six novel metabolite QTLs for volatile compounds were identified - 1 QTL was detected in chromosome 1 for 3,7-dimethyl-octen-1-ol, 1 QTL for hexanol in chromosome 2, and 4 QTLs for pentanol, hexanol, hexanal, and heptanone in chromosome 3. Interestingly, three lines were observed by the panellists to have similar aroma as IR64 while four lines were observed to have similar aroma as that perceived in Apo. Lines 20, 164 and 28 were perceived by the panellists to have high levels of corn, dairy and sweet aromatic features. Moreover, the yield of these 3 lines under both irrigated and drought conditions was similar to that of the Apo parent under the same conditions with Line 28 yielding the highest under drought and has the QTL associated with yield under drought on chromosome 3.

Finally, the potential of metabolomics as a phenotyping tool in characterising grain quality is further highlighted in Chapter 6. Combining metabolomics with high throughput genotyping and sensory analysis offers new breadth of approach in understanding grain quality of rice. Three lines identified that carry IR64 quality along with high yield in both irrigation and drought, are recommended to enter a rice breeding program at the stage of advanced replicated and multi-location testing. By using advanced tools of phenotyping and genotyping, with validation by sensory panels, these three advanced lines have been selected in just three years.

Campylobacter fetus subsp. testudinum subsp. nov., isolated from humans and reptiles
Fitzgerald, C. ; Tu, Z.C. ; Patrick, M. ; Stiles, T. ; Lawson, A.J. ; Santovenia, M. ; Gilbert, M.J. ; Bergen, M. von; Joyce, K. ; Pruckler, J. ; Stroika, S. ; Duim, B. ; Miller, W.G. ; Loparev, V. ; Sinnige, J.C. ; Fields, P.I. ; Tauxe, R.V. ; Blaser, M.J. ; Wagenaar, J.A. - \ 2014
International Journal of Systematic and Evolutionary Microbiology 64 (2014). - ISSN 1466-5026 - p. 2944 - 2948.
genus campylobacter - pcr assay - differentiation - identification - strains - origins
A polyphasic study was undertaken to determine the taxonomic position of 13 Campylobacter fetus-like strains from humans (n=8) and reptiles (n=5). The results of matrix-assisted laser desorption ionization time-of-flight (MALDI-TOF) MS and genomic data from sap analysis, 16S rRNA gene and hsp60 sequence comparison, pulsed-field gel electrophoresis, amplified fragment length polymorphism analysis, DNA-DNA hybridization and whole genome sequencing demonstrated that these strains are closely related to C. fetus but clearly differentiated from recognized subspecies of C. fetus. Therefore, this unique cluster of 13 strains represents a novel subspecies within the species C. fetus, for which the name Campylobacter fetus subsp. testudinum subsp. nov. is proposed, with strain 03-427(T) (=ATCC BAA-2539(T)=LMG 27499(T)) as the type strain. Although this novel taxon could not be differentiated from C. fetus subsp. fetus and C. fetus subsp. venerealis using conventional phenotypic tests, MALDI-TOF MS revealed the presence of multiple phenotypic biomarkers which distinguish Campylobacter fetus subsp. testudinum subsp. nov. from recognized subspecies of C. fetus.
Climate change and European forests: What do we know, what are the uncertainties, and what are the implications for forest management?
Lindner, M. ; Fitzgerald, J.B. ; Zimmermann, N.E. ; Reyer, C. ; Delzon, S. ; Maaten, E. van der; Schelhaas, M. ; Lasch, P. ; Eggers, J. ; Maaten-Theunissen, M. van der; Suckow, F. ; Psomas, A. ; Pouler, B. ; Hanewinkel, M. - \ 2014
Journal of Environmental Management 146 (2014). - ISSN 0301-4797 - p. 69 - 83.
water-use efficiency - change impacts - elevated co2 - change risks - face sites - scots pine - drought - carbon - shift - trees
The knowledge about potential climate change impacts on forests is continuously expanding and some changes in growth, drought induced mortality and species distribution have been observed. However despite a significant body of research, a knowledge and communication gap exists between scientists and non-scientists as to how climate change impact scenarios can be interpreted and what they imply for European forests. It is still challenging to advise forest decision makers on how best to plan for climate change as many uncertainties and unknowns remain and it is difficult to communicate these to practitioners and other decision makers while retaining emphasis on the importance of planning for adaptation. In this paper, recent developments in climate change observations and projections, observed and projected impacts on European forests and the associated uncertainties are reviewed and synthesised with a view to understanding the implications for forest management. Current impact assessments with simulation models contain several simplifications, which explain the discrepancy between results of many simulation studies and the rapidly increasing body of evidence about already observed changes in forest productivity and species distribution. In simulation models uncertainties tend to cascade onto one another; from estimating what future societies will be like and general circulation models (GCMs) at the global level, down to forest models and forest management at the local level. Individual climate change impact studies should not be uncritically used for decision-making without reflection on possible shortcomings in system understanding, model accuracy and other assumptions made. It is important for decision makers in forest management to realise that they have to take long-lasting management decisions while uncertainty about climate change impacts are still large. We discuss how to communicate about uncertainty - which is imperative for decision making - without diluting the overall message. Considering the range of possible trends and uncertainties in adaptive forest management requires expert knowledge and enhanced efforts for providing science-based decision support.
Large scale variation in copy number in chicken breeds
Crooijmans, Richard ; Fife, Mark S. ; Fitzgerald, Tomas ; Strickland, Shurnevia ; Cheng, Hans H. ; Kaiser, Pete ; Redon, Richard ; Groenen, Martien - \ 2013
Gallus gallus - GSE47623 - PRJNA215849
Background: Detecting genetic variation is a critical step in elucidating the molecular mechanisms underlying phenotypic diversity. Until recently, such detection has mostly focused on single nucleotide polymorphisms (SNPs) because of the ease in screening complete genomes. Another type of variant, copy number variation (CNV), is emerging as a significant contributor to phenotypic variation in many species.
Large scale variation in DNA copy number in chicken breeds
Crooijmans, R.P.M.A. ; Fife, M. ; FitzGerald, R.J. ; strickland, S. ; Groenen, M. - \ 2013
BMC Genomics 14 (2013). - ISSN 1471-2164
human genome - structural variation - mareks-disease - evolution - map - genes - resistance - feather - loci - pcr
Background Detecting genetic variation is a critical step in elucidating the molecular mechanisms underlying phenotypic diversity. Until recently, such detection has mostly focused on single nucleotide polymorphisms (SNPs) because of the ease in screening complete genomes. Another type of variant, copy number variation (CNV), is emerging as a significant contributor to phenotypic variation in many species. Here we describe a genome-wide CNV study using array comparative genomic hybridization (aCGH) in a wide variety of chicken breeds. Results We identified 3,154 CNVs, grouped into 1,556 CNV regions (CNVRs). Thirty percent of the CNVs were detected in at least 2 individuals. The average size of the CNVs detected was 46.3 kb with the largest CNV, located on GGAZ, being 4.3 Mb. Approximately 75% of the CNVs are copy number losses relatively to the Red Jungle Fowl reference genome. The genome coverage of CNVRs in this study is 60 Mb, which represents almost 5.4% of the chicken genome. In particular large gene families such as the keratin gene family and the MHC show extensive CNV. Conclusions A relative large group of the CNVs are line-specific, several of which were previously shown to be related to the causative mutation for a number of phenotypic variants. The chance that inter-specific CNVs fall into CNVRs detected in chicken is related to the evolutionary distance between the species. Our results provide a valuable resource for the study of genetic and phenotypic variation in this phenotypically diverse species.
Mapping the risk to European forests with a changing climate
Gardiner, B. ; Schelhaas, M.J. ; Nicoll, B. - \ 2013
In: Adapting to climate change in European forests – Results of the MOTIVE project / Fitzgerald, J., Lindner, M., Sofia : Pensoft Publishers - ISBN 9789546426901 - p. 28 - 33.
Veluwe case study
Schelhaas, M.J. - \ 2013
In: Adapting to climate change in European forests – Results of the MOTIVE project / Fitzgerald, J., Lindner, M., Sofia : Pensoft Publishers - ISBN 9789546426901 - p. 68 - 71.
How fast can European forests adapt to a changing climate?
Hengeveld, G.M. ; Schelhaas, M.J. ; Reyer, C. ; Zimmermann, N.E. ; Cullmann, D.A. ; Nabuurs, G.J. - \ 2013
In: Adapting to climate change in European forests – Results of the MOTIVE project / Fitzgerald, J., Lindner, M., Sofia : Pensoft Publishers - ISBN 9789546426901 - p. 80 - 82.
The potential of rice to offer solutions for malnutrition and chronic diseases
Dipti, S.S. ; Bergman, C. ; Indrasari, S.D. ; Herath, T. ; Hall, R.D. ; Lee, H. ; Habibi, F. ; Zaczuk Bassinello, P. ; Graterol, E. ; Ferraz, J. ; Fitzgerald, M. - \ 2012
Rice 5 (2012). - ISSN 1939-8433
It is internationally accepted that malnutrition and chronic diseases in developing countries are key limitations to achieving the Millennium Development Goals. In many developing countries, rice is the primary source of nutrition. In those countries, the major forms of malnutrition are Fe-induced anaemia, Zn deficiency and Vitamin A deficiency, whereas the major chronic disease challenges are Type II diabetes, cardiovascular disease and some cancers. There is a growing corpus of evidence regarding both limitations and opportunities as to how rice could be an effective vehicle by which to tackle key nutrition and health related problems in countries with limited resources. Rice breeding programs are able to focus on developing new varieties carrying enhanced amounts of either Fe, Zn or beta-carotene because of large public investment, and the intuitive link between providing a mineral/vitamin to cure a deficiency in that mineral/vitamin. By contrast, there has been little investment in progressing the development of particular varieties for potential impact on chronic diseases. In this review article we focus on the broad battery of evidence linking rice-related nutritional limitations to their impact on a variety of human health issues. We discuss how rice might offer sometimes even simple solutions to rectifying key problems through targeted biofortification strategies and finally, we draw attention to how recent technological (-omics) developments may facilitate untold new opportunities for more rapidly generating improved rice varieties specifically designed to meet the current and future nutritional needs of a rapidly expanding global population.
Check title to add to marked list
<< previous | next >>

Show 20 50 100 records per page

 
Please log in to use this service. Login as Wageningen University & Research user or guest user in upper right hand corner of this page.