Staff Publications

Staff Publications

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    'Staff publications' is the digital repository of Wageningen University & Research

    'Staff publications' contains references to publications authored by Wageningen University staff from 1976 onward.

    Publications authored by the staff of the Research Institutes are available from 1995 onwards.

    Full text documents are added when available. The database is updated daily and currently holds about 240,000 items, of which 72,000 in open access.

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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.
Metabolomic and elemental profiling of melon fruit quality as affected by genotype and environment
Bernillon, S. ; Biais, B. ; Deborde, C. ; Maucort, M. ; Cabasson, C. ; Gibon, Y. ; Hansen, T. ; Husted, S. ; Vos, R.C.H. de; Mumm, R. ; Jonker, H. ; Ward, J.L. ; Miller, S.J. ; Baker, J.M. ; Burger, J. ; Tadmor, Y. ; Beale, M.H. ; Schjoerring, J.K. ; Schaffer, A. ; Rolin, D. ; Hall, R.D. ; Moing, A. - \ 2013
Metabolomics 9 (2013)1. - ISSN 1573-3882 - p. 57 - 77.
cucumis-melo - tomato fruit - chemical-composition - functional genomics - plant metabolomics - mass-spectrometry - aroma volatiles - nitrate ratio - grape berry - amino-acid
Melon (Cucumis melo L.) is a global crop in terms of economic importance and nutritional quality. The aim of this study was to explore the variability in metabolite and elemental composition of several commercial varieties of melon in various environmental conditions. Volatile and non-volatile metabolites as well as mineral elements were profiled in the flesh of mature fruit, employing a range of complementary analytical technologies. More than 1,000 metabolite signatures and 19 mineral elements were determined. Data analyses revealed variations related to factors such as variety, growing season, contrasting agricultural management practices (greenhouse vs. field with or without fruit thinning) and planting date. Two hundred and ninety-one analytes discriminated two contrasting varieties, one from the var. inodorous group and the other from the var. cantaloupensis group. Two hundred and eighty analytes discriminated a short shelf-life from a mid-shelf-life variety within the var. cantaloupensis group. Three hundred and twenty-seven analytes discriminated two seasons, and two hundred and fifty-two analytes discriminated two contrasting agricultural management practices. The affected compound families greatly depended on the factor studied. The compositional variability of identified or partially identified compounds was used to study metabolite and mineral element co-regulation using correlation networks. The results confirm that metabolome and mineral element profiling are useful diagnostic tools to characterize the quality of fruits cultivated under commercial conditions. They can also provide knowledge on fruit metabolism and the mechanisms of plant response to environmental modifications, thereby paving the way for metabolomics-guided improvement of cultural practices for better fruit quality.
An inter-laboratory comparison demonstrates that [H-1]-NMR metabolite fingerprinting is a robust technique for collaborative plant metabolomic data collection.
Ward, J.L. ; Baker, J.M. ; Miller, S.J. ; Deborde, C. ; Maucourt, M. ; Biais, B. ; Rolin, D. ; Moing, A. ; Moco, S.I.A. ; Vervoort, J.J.M. ; Lommen, A. ; Schafer, H. ; Humpfer, E. ; Beale, M.H. - \ 2010
Metabolomics 6 (2010)2. - ISSN 1573-3882 - p. 263 - 273.
minimum reporting standards - nmr-spectroscopy - h-1-nmr spectroscopy - mass-spectrometry - metabonomics
In any metabolomics experiment, robustness and reproducibility of data collection is of vital importance. These become more important in collaborative studies where data is to be collected on multiple instruments. With minimisation of variance in sample preparation and instrument performance it is possible to elucidate even subtle differences in metabolite fingerprints due to genotype or biological treatment. In this paper we report on an inter laboratory comparison of plant derived samples by [1H]-NMR spectroscopy across five different sites and within those sites utilising instruments with different probes and magnetic field strengths of 9.4 T (400 MHz), 11.7 T (500 MHz) and 14.1 T (600 MHz). Whilst the focus of the study is on consistent data collection across laboratories, aspects of sample stability and the requirement for sample rotation within the NMR magnet are also discussed. Comparability of the datasets from participating laboratories was exceptionally good and the data were amenable to comparative analysis by multivariate statistics. Field strength differences can be adjusted for in the data pre-processing and multivariate analysis demonstrating that [1H]-NMR fingerprinting is the ideal technique for large scale plant metabolomics data collection requiring the participation of multiple laboratories.
System-wide molecular evidence for phenotypic buffering in Arabidopsis
Fu, J. ; Keurentjes, J.J.B. ; Bouwmeester, H.J. ; America, T. ; Verstappen, F. ; Ward, J.L. ; Beale, M.H. ; Vos, C.H. de; Dijkstra, M. ; Scheltema, R.A. ; Johannes, F. ; Koornneef, M. ; Vreugdenhil, D. ; Breitling, R. ; Jansen, R.C. - \ 2009
Nature Genetics 41 (2009)2. - ISSN 1061-4036 - p. 166 - 167.
biological robustness - genetic genomics - networks - expression - disease
We profiled 162 lines of Arabidopsis for variation in transcript, protein and metabolite abundance using mRNA microarrays, two-dimensional polyacrylamide gel electrophoresis, gas chromatography time-of-flight mass spectrometry, liquid chromatography quadrupole time-of-flight mass spectrometry, and proton nuclear magnetic resonance. We added all publicly available phenotypic data from the same lines and mapped quantitative trait loci (QTL) for 40,580 molecular and 139 phenotypic traits. We found six QTL hot spots with major, system-wide effects, suggesting there are six breakpoints in a system otherwise buffered against many of the 500,000 SNPs
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