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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An integrated method for calculating DEM-based RUSLE LS
Wang, Meng ; Baartman, Jantiene E.M. ; Zhang, Hongming ; Yang, Qinke ; Li, Shuqin ; Yang, Jiangtao ; Cai, Cheng ; Wang, Meili ; Ritsema, Coen J. ; Geissen, Violette - \ 2018
Earth Science Informatics (2018). - ISSN 1865-0473 - 12 p.
Geographic information system (GIS) - LS factor - Revised universal soil loss equation (RUSLE) - Soil erosion

The improvement of resolution of digital elevation models (DEMs) and the increasing application of the Revised Universal Soil Loss Equation (RUSLE) over large areas have created problems for the efficiency of calculating the LS factor for large data sets. The pretreatment for flat areas, flow accumulation, and slope-length calculation have traditionally been the most time-consuming steps. However, obtaining these features are generally usually considered as separate steps, and calculations still tend to be time-consuming. We developed an integrated method to improve the efficiency of calculating the LS factor. The calculation model contains algorithms for calculating flow direction, flow accumulation, slope length, and the LS factor. We used the Deterministic 8 method to develop flow-direction octrees (FDOTs), flat matrices (FMs) and first-in-first-out queues (FIFOQs) tracing the flow path. These data structures were much more time-efficient for calculating the slope length inside the flats, the flow accumulation, and the slope length linearly by traversing the FDOTs from their leaves to their roots, which can reduce the search scope and data swapping. We evaluated the accuracy and effectiveness of this integrated algorithm by calculating the LS factor for three areas of the Loess Plateau in China and SRTM DEM of China. The results indicated that this tool could substantially improve the efficiency of LS-factor calculations over large areas without reducing accuracy.

Phylogenomics reveals multiple losses of nitrogen-fixing root nodule symbiosis
Griesmann, Maximilian ; Chang, Yue ; Liu, Xin ; Song, Yue ; Haberer, Georg ; Crook, Matthew B. ; Billault-Penneteau, Benjamin ; Lauressergues, Dominique ; Keller, Jean ; Imanishi, Leandro ; Roswanjaya, Yuda Purwana ; Kohlen, Wouter ; Pujic, Petar ; Battenberg, Kai ; Alloisio, Nicole ; Liang, Yuhu ; Hilhorst, Henk ; Salgado, Marco G. ; Hocher, Valerie ; Gherbi, Hassen ; Svistoonoff, Sergio ; Doyle, Jeff J. ; He, Shixu ; Xu, Yan ; Xu, Shanyun ; Qu, Jing ; Gao, Qiang ; Fang, Xiaodong ; Fu, Yuan ; Normand, Philippe ; Berry, Alison M. ; Wall, Luis G. ; Ané, Jean Michel ; Pawlowski, Katharina ; Xu, Xun ; Yang, Huanming ; Spannagl, Manuel ; Mayer, Klaus F.X. ; Wong, Gane Ka Shu ; Parniske, Martin ; Delaux, Pierre Marc ; Cheng, Shifeng - \ 2018
Science (2018). - ISSN 0036-8075 - 18 p.

The root nodule symbiosis of plants with nitrogen-fixing bacteria impacts global nitrogen cycles and food production but is restricted to a subset of genera within a single clade of flowering plants. To explore the genetic basis for this scattered occurrence, we sequenced the genomes of ten plant species covering the diversity of nodule morphotypes, bacterial symbionts and infection strategies. In a genome-wide comparative analysis of a total of 37 plant species, we discovered signatures of multiple independent loss-of-function events in the indispensable symbiotic regulator NODULE INCEPTION (NIN) in ten out of 13 genomes of non-nodulating species within this clade. The discovery that multiple independent losses shaped the present day distribution of nitrogen-fixing root nodule symbiosis in plants reveals a phylogenetically wider distribution in evolutionary history and a so far underestimated selection pressure against this symbiosis.

The tomato MAX1 homolog, SlMAX1, is involved in the biosynthesis of tomato strigolactones from carlactone
Zhang, Yanxia ; Cheng, Xi ; Wang, Yanting ; Díez-Simón, Carmen ; Flokova, Kristyna ; Bimbo, Andrea ; Bouwmeester, Harro J. ; Ruyter-Spira, Carolien - \ 2018
New Phytologist 219 (2018)1. - ISSN 0028-646X - p. 297 - 309.
cytochrome P450 (CYP) - didehydro-orobanchol isomers - MORE AXILLARY GROWTH 1 (MAX1) - orobanchol - solanacol - tomato strigolactones
Strigolactones (SLs) are rhizosphere signalling molecules exuded by plants that induce seed germination of root parasitic weeds and hyphal branching of arbuscular mycorrhiza. They are also phytohormones regulating plant architecture. MORE AXILLARY GROWTH 1 (MAX1) and its homologs encode cytochrome P450 (CYP) enzymes that catalyse the conversion of the strigolactone precursor carlactone to canonical strigolactones in rice (Oryza sativa), and to an SL-like compound in Arabidopsis. Here, we characterized the tomato (Solanum lycopersicum) MAX1 homolog, SlMAX1. The targeting induced local lesions in genomes method was used to obtain Slmax1 mutants that exhibit strongly reduced production of orobanchol, solanacol and didehydro-orobanchol (DDH) isomers. This results in a severe strigolactone mutant phenotype in vegetative and reproductive development. Transient expression of SlMAX1 – together with SlD27, SlCCD7 and SlCCD8 – in Nicotiana benthamiana showed that SlMAX1 catalyses the formation of carlactonoic acid from carlactone. Plant feeding assays showed that carlactone, but not 4-deoxy-orobanchol, is the precursor of orobanchol, which in turn is the precursor of solanacol and two of the three DDH isomers. Inhibitor studies suggest that a 2-oxoglutarate-dependent dioxygenase is involved in orobanchol biosynthesis from carlactone and that the formation of solanacol and DDH isomers from orobanchol is catalysed by CYPs.
A genetically and functionally diverse group of non-diazotrophic Bradyrhizobium spp. colonizes the root endophytic compartment of Arabidopsis thaliana
Schneijderberg, Martinus ; Schmitz, Lucas ; Cheng, Xu ; Polman, Sharon ; Franken, Carolien ; Geurts, Rene ; Bisseling, Ton - \ 2018
BMC Plant Biology 18 (2018)1. - ISSN 1471-2229
Arabidopsis - Bradyrhizobium - Endophytic compartment - Root colonization
Background: Diazotrophic Bradyrhizobium spp. are well known for their ability to trigger nodule formation on a variety of legume species. In nodules, Bradyrhizobium utilizes plant-derived carbohydrates in exchange for fixed nitrogen. The genes essential for the nodulation and nitrogen-fixation trait are clustered in a genomic region, which is known as the 'symbiotic island'. Recently, novel non-diazotrophic Bradyrhizobium spp. have been found to be highly abundant in soils, suggesting that these species can also have a 'free-living' life history. However, whether non-diazotrophic Bradyrhizobium spp. can live in association with plants remains elusive. Results: In this study, we show that Bradyrhizobium spp. are common root endophytes of non-legume plant species - including Arabidopsis thaliana (Arabidopsis) - grown in an ecological setting. From a single Arabidopsis root, four Bradyrhizobium sp. strains (designated MOS001 to MOS004) were isolated. Comparative genome analysis revealed that these strains were genetically and functionally highly diverse, but did not harbour the nodulation and the nitrogen fixation gene clusters. Comparative colonization experiments, with MOS strains and nitrogen-fixing symbiotic strains, revealed that all tested Bradyrhizobium spp. can colonize the root endophytic compartment of Arabidopsis. Conclusion: This study provides evidence that both diazotrophic and non-diazotrophic Bradyrhizobium spp. colonize the root endophytic compartment of a wide variety of plant species, including the model species Arabidopsis. This demonstrates that plant roots form a major ecological niche for Bradyrhizobium spp., which might be ancestral to the evolution of the nodulation and nitrogen-fixation trait in this genus.
Thrips advisor : Exploiting thrips-induced defences to combat pests on crops
Steenbergen, Merel ; Abd-El-Haliem, Ahmed ; Bleeker, Petra ; Dicke, Marcel ; Escobar-Bravo, Rocio ; Cheng, Gang ; Haring, Michel A. ; Kant, Merijn R. ; Kappers, Iris ; Klinkhamer, Peter G.L. ; Leiss, Kirsten A. ; Legarrea, Saioa ; Macel, Mirka ; Mouden, Sanae ; Pieterse, Corné M.J. ; Sarde, Sandeep J. ; Schuurink, Robert C. ; Vos, Martin De; Wees, Saskia C.M. Van; Broekgaarden, Colette - \ 2018
Journal of Experimental Botany 69 (2018)8. - ISSN 0022-0957 - p. 1837 - 1848.
Cell-content feeder - effectors - herbivorous insect - phytohormone signalling - plant defence - specialized metabolites - thrips - virus - volatiles

Plants have developed diverse defence mechanisms to ward off herbivorous pests. However, agriculture still faces estimated crop yield losses ranging from 25% to 40% annually. These losses arise not only because of direct feeding damage, but also because many pests serve as vectors of plant viruses. Herbivorous thrips (Thysanoptera) are important pests of vegetable and ornamental crops worldwide, and encompass virtually all general problems of pests: they are highly polyphagous, hard to control because of their complex lifestyle, and they are vectors of destructive viruses. Currently, control management of thrips mainly relies on the use of chemical pesticides. However, thrips rapidly develop resistance to these pesticides. With the rising demand for more sustainable, safer, and healthier food production systems, we urgently need to pinpoint the gaps in knowledge of plant defences against thrips to enable the future development of novel control methods. In this review, we summarize the current, rather scarce, knowledge of thrips-induced plant responses and the role of phytohormonal signalling and chemical defences in these responses. We describe concrete opportunities for breeding resistance against pests such as thrips as a prototype approach for next-generation resistance breeding.

The group I alphabaculovirus-specific protein, AC5, is a novel component of the occlusion body but is not associated with ODVS or the PIF complex
Wang, Xi ; Chen, Cheng ; Zhang, Nan ; Li, Jiang ; Deng, Fei ; Wang, Hualin ; Vlak, Just M. ; Hu, Zhihong ; Wang, Manli - \ 2018
Journal of General Virology 99 (2018)4. - ISSN 0022-1317 - p. 585 - 595.
Ac5 - Baculovirus - Function - Group I alphabaculovirus - Occlusion body - PIF complex
Autographa californica nucleopolyhedrovirus (AcMNPV) orf5 (ac5) is a group I alphabaculovirus-specific gene of unknown function, although the protein (AC5) was previously reported to be associated with the per os infectivity factor (PIF) complex. The purpose of this study was to study the dynamics of AC5 during AcMNPV infection and to verify whether it is indeed a component of the PIF complex. Transcription and expression analyses suggested that ac5 is a late viral gene. An ac5-deleted recombinant AcMNPV was generated by homologous recombination. A one-step growth curve assay indicated that ac5 was not required for budded virus (BV) production in Sf9 cells. Scanning electron microscopy and transmission electron microscopy demonstrated that the deletion of ac5 did not affect occlusion body (OB) morphology, and nor did it affect the insertion of occlusion-derived virus (ODV) into OBs. Partially denaturing SDS-PAGE and a co-immunoprecipitation assay clearly showed that AC5 was not a component of the PIF complex, while the deletion of ac5 did not affect the formation and presence of the PIF complex. Further analyses showed, however, that AC5 was an OB-specific protein, but it was not detected as a component of BVs or ODVs. Bioassay experiments showed that the oral infectivity of ac5-deleted AcMNPV to third instar Spodoptera exigua larvae was not significantly different from that of the ac5-repaired virus. In conclusion, AC5 is an intrinsic protein of OBs, instead of being a component of the PIF complex, and is not essential for either BV or ODV infection. AC5 is awaiting the assignment of another hitherto unknown function.
Arbuscular mycorrhizal fungi negatively affect nitrogen acquisition and grain yield of maize in a N deficient soil
Wang, Xin Xin ; Wang, Xiaojing ; Sun, Yu ; Cheng, Yang ; Liu, Shitong ; Chen, Xinping ; Feng, Gu ; Kuyper, Thomas W. - \ 2018
Frontiers in Microbiology 9 (2018)MAR. - ISSN 1664-302X
Arbuscular mycorrhizal fungi - Benomyl - Competition - Maize - Nitrogen uptake
Arbuscular mycorrhizal fungi (AMF) play a crucial role in enhancing the acquisition of immobile nutrients, particularly phosphorus. However, because nitrogen (N) is more mobile in the soil solution and easier to access by plants roots, the role of AMF in enhancing N acquisition is regarded as less important for host plants. Because AMF have a substantial N demand, competition for N between AMF and plants particularly under low N condition is possible. Thus, it is necessary to know whether or not AMF affect N uptake of plants and thereby affect plant growth under field conditions. We conducted a 2-year field trial and pot experiments in a greenhouse by using benomyl to suppress colonization of maize roots by indigenous AMF at both low and high N application rates. Benomyl reduced mycorrhizal colonization of maize plants in all experiments. Benomyl-treated maize had a higher shoot N concentration and content and produced more grain under field conditions. Greenhouse pot experiments showed that benomyl also enhanced maize growth and N concentration and N content when the soil was not sterilized, but had no effect on maize biomass and N content when the soil was sterilized but a microbial wash added, providing evidence that increased plant performance is at least partly caused by direct effects of benomyl on AMF. We conclude that AMF can reduce N acquisition and thereby reduce grain yield of maize in N-limiting soils.
Genetically engineering Crambe abyssinica- A potentially high-value oil crop for salt land improvement
Qi, W. ; Tinnenbroek-Capel, I.E.M. ; Salentijn, E.M.J. ; Zhang, Zhao ; Huang, Bangquan ; Cheng, Jihua ; Shao, Hongbo ; Visser, R.G.F. ; Krens, F.A. ; Loo, E.N. van - \ 2018
Land Degradation and Development 29 (2018)4. - ISSN 1085-3278 - p. 1096 - 1106.
Crambe abyssinica (crambe) is a new industrial oil crop that can grow on saline soil and tolerates salty water irrigation. Genetically engineered crambe in which the seed‐oil composition is manipulated for more erucic acid and less polyunsaturated fatty acid (PUFA) would be highly beneficial to industry. In this research, lysophosphatidic acid acyltransferase 2 RNA interference (CaLPAT2‐RNAi) was introduced into the crambe genome to manipulate its oil composition. The result showed in comparison with wild type, CaLPAT2‐RNAi could significantly reduce linoleic and linolenic acid content, simultaneously increasing erucic acid content. Systematic metabolism engineering was then carried out to further study CaLPAT2‐RNAi, combined with the overexpression of Brassica napus fatty acid elongase (BnFAE), Limnanthes douglasii LPAT (LdLPAT), and RNAi of endogenous fatty acid desaturase 2 (CaFAD2‐RNAi). Oil composition analysis on the tranformants' seeds showed that (a) with CaFAD2‐RNAi, PUFA content could be dramatically decreased, in comparison with BnFAE + LdLPAT + CaFAD2‐RNAi, and BnFAE + LdLPAT + CaFAD2‐RNAi + CaLPAT2‐RNAi seeds showed lower linolenic acid content; (b) BnFAE + LdLPAT + CaFAD2‐RNAi + CaLPAT2‐RNAi could increase the erucic acid content in crambe seed oil from less than 66.6% to 71.6%, whereas the highest erucic acid content of BnFAE + LdLPAT + CaFAD2‐RNAi was 79.2%; (c) although the four‐gene combination could not increase the erucic acid content of seed oil to a higher level than the others, it led to increased carbon resource deposited into C22:1 and C18:1 moieties and lower PUFA. Summarily, the present research indicates that suppression of LPAT2 is a new, promising strategy for seed‐oil biosynthesis pathway engineering, which would increase the value of crambe oil.
The role of complementarity and selection effects in P acquisition of intercropping systems
Li, Xiao Fei ; Wang, Cheng Bao ; Zhang, Wei Ping ; Wang, Le Hua ; Tian, Xiu Li ; Yang, Si Cun ; Jiang, Wan Li ; Ruijven, Jasper van; Li, Long - \ 2018
Plant and Soil 422 (2018)1-2. - ISSN 0032-079X - p. 479 - 493.
Crop diversity - Interspecific facilitation - Niche differentiation - Overyielding - Phosphorus
Background and aims: Enhanced crop productivity by intercropping is commonly assumed to be driven by resource complementarity. However, relatively few studies have directly measured resource acquisition to assess potential mechanisms underlying enhanced performance of intercropping. Methods: A long-term field experiment with three P application rates (0, 40, 80 kg P ha−1 yr.−1) and four maize-based intercropping systems was used to assess P acquisition and P fertilizer recovery efficiency (PRE) for three consecutive years. To identify underlying mechanisms, the additive partitioning method was applied to determine complementarity (CE) and selection effects (SE) in P acquisition of intercropping. Results: Average P acquisition increased by 28.4% and 27.6% compared to their monocultures in faba bean/maize and chickpea/maize intercropping, respectively. However, P acquisition was generally not enhanced and even reduced in the last year in soybean/maize and oilseed rape/maize intercropping. Enhanced P acquisition was due to positive CE in faba bean/maize, and to positive CE and SE in chickpea/maize intercropping. Conclusions: Increased resource acquisition via CE and/or SE depended on the particular crop combination in intercropping systems. Application of the additive partitioning method to intercropping may help to identify underlying mechanisms of overyielding and carefully select crop combinations to enable more efficient resource use.
Nitrogen removal performance and microbial community changes in subsurface wastewater infiltration systems (SWISs) at low temperature with different bioaugmentation strategies
Liu, Chunjing ; Xie, Jianzhi ; Song, Manli ; Gao, Zhiling ; Zheng, Dongxing ; Liu, Xia ; Ning, Guohui ; Cheng, Xu ; Bruning, Harry - \ 2018
Bioresource Technology 250 (2018). - ISSN 0960-8524 - p. 603 - 610.
Aerobic denitrification - Bacterial community structure - Embedding bioaugmentation - Low temperature - Subsurface wastewater infiltration system
Poor nitrogen removal efficiency (mainly nitrate, NO3 −-N) at low temperatures strongly limits application of subsurface wastewater infiltration systems (SWISs). Seven psychrophilic strains (heterotrophic nitrifying bacteria and aerobic denitrifying bacteria) were isolated and added to SWISs to investigate the effect of embedding and direct-dosing bioaugmentation strategies on sewage treatment performance at low temperature. Both bioaugmentation strategies improved ammonium (NH4 +-N) removal efficiencies, and the embedding strategy also exhibited satisfactory NO3 −-N and total nitrogen (TN) removal efficiencies. Pyrosequencing results of the bacterial 16S rRNA gene indicated that the embedding strategy significantly decreased the indigenous soil microbial diversity (p <.05) and altered the bacterial community structure, significantly increasing the relative abundance of Clostridia, which have good nitrate-reducing activity.
Three modelling approaches to predict deoxynivalenol contamination levels in winter wheat in the Netherlands.
Liu, Cheng - \ 2017
Higher plasticity in feeding preference of a generalist than a specialist : Experiments with two closely related Helicoverpa species
Wang, Yan ; Ma, Ying ; Zhou, Dong Sheng ; Gao, Su Xia ; Zhao, Xin Cheng ; Tang, Qing Bo ; Wang, Chen Zhu ; Loon, Joop J.A. van - \ 2017
Scientific Reports 7 (2017). - ISSN 2045-2322
Herbivorous insects have been categorized as generalists or specialists depending on the taxonomic relatedness of the plants they use as food or oviposition substrates. The plasticity in host plant selection behavior of species belonging to the two categories received little attention. In the present work, fifth instar caterpillars of the generalist herbivore Helicoverpa armigera and its closely related species, the specialist Helicoverpa assulta, were fed on common host plants or artificial diet, after which their feeding preference was assessed individually by using dual - and triple- plant choice assays. Results show both the two Helicoverpa species have a preference hierarchy for host plants. Compared to the fixed preference hierarchy of the specialist H. assulta, the generalist H. armigera exhibited extensive plasticity in feeding preference depending on the host plant experienced during larval development. Whereas the specialist H. assulta exhibited a rigid preference in both dual and triple-plant choice assays, our findings demonstrate that the generalist H. armigera expressed stronger preferences in the dual-plant choice assay than in the triple-plant choice assay. Our results provide additional evidence supporting the neural constraints hypothesis which predicts that generalist herbivores make less accurate decisions than specialists when selecting plants.
The Evolution, Characteristic and Inspiration of the Higher Education Quality Assurance System in the Netherlands
Cheng, Xieshe ; Biemans, H.J.A. - \ 2017
- p. 90 - 94.
Genome-wide analysis of bacterial determinants of plant growth promotion and induced systemic resistance by Pseudomonas fluorescens
Cheng, X. ; Etalo, Desalegn W. ; Mortel, J.E. van de; Dekkers, E. ; Nguyen, Linh ; Medema, M.H. ; Raaijmakers, J.M. - \ 2017
Environmental Microbiology 19 (2017)11. - ISSN 1462-2912 - p. 4638 - 4656.
Pseudomonas fluorescens strain SS101 (Pf.SS101) promotes growth of Arabidopsis thaliana, enhances greening and lateral root formation, and induces systemic resistance (ISR) against the bacterial pathogen Pseudomonas syringae pv. tomato (Pst). Here, targeted and untargeted approaches were adopted to identify bacterial determinants and underlying mechanisms involved in plant growth promotion and ISR by Pf.SS101. Based on targeted analyses, no evidence was found for volatiles, lipopeptides and siderophores in plant growth promotion by Pf.SS101. Untargeted, genome-wide analyses of 7488 random transposon mutants of Pf.SS101 led to the identification of 21 mutants defective in both plant growth promotion and ISR. Many of these mutants, however, were auxotrophic and impaired in root colonization. Genetic analysis of three mutants followed by site-directed mutagenesis, genetic complementation and plant bioassays revealed the involvement of the phosphogluconate dehydratase gene edd, the response regulator gene colR and the adenylsulfate reductase gene cysH in both plant growth promotion and ISR. Subsequent comparative plant transcriptomics analyses strongly suggest that modulation of sulfur assimilation, auxin biosynthesis and transport, steroid biosynthesis and carbohydrate metabolism in Arabidopsis are key mechanisms linked to growth promotion and ISR by Pf.SS101.
PCR and omics based techniques to study the diversity, ecology and biology of anaerobic fungi : Insights, challenges and opportunities
Edwards, Joan E. ; Forster, Robert J. ; Callaghan, Tony M. ; Dollhofer, Veronika ; Dagar, Sumit S. ; Cheng, Yanfen ; Chang, Jongsoo ; Kittelmann, Sandra ; Fliegerova, Katerina ; Puniya, Anil K. ; Henske, John K. ; Gilmore, Sean P. ; O'Malley, Michelle A. ; Griffith, Gareth W. ; Smidt, Hauke - \ 2017
Frontiers in Microbiology 8 (2017). - ISSN 1664-302X - 27 p.
(meta) transcriptomics - Anaerobic fungi - Genomics - Metabolomics - Neocallimastigomycota - Phylogeny - Proteomics - Rumen

Anaerobic fungi (phylum Neocallimastigomycota) are common inhabitants of the digestive tract of mammalian herbivores, and in the rumen, can account for up to 20% of the microbial biomass. Anaerobic fungi play a primary role in the degradation of lignocellulosic plant material. They also have a syntrophic interaction with methanogenic archaea, which increases their fiber degradation activity. To date, nine anaerobic fungal genera have been described, with further novel taxonomic groupings known to exist based on culture-independent molecular surveys. However, the true extent of their diversity may be even more extensively underestimated as anaerobic fungi continue being discovered in yet unexplored gut and non-gut environments. Additionally many studies are now known to have used primers that provide incomplete coverage of the Neocallimastigomycota. For ecological studies the internal transcribed spacer 1 region (ITS1) has been the taxonomic marker of choice, but due to various limitations the large subunit rRNA (LSU) is now being increasingly used. How the continued expansion of our knowledge regarding anaerobic fungal diversity will impact on our understanding of their biology and ecological role remains unclear; particularly as it is becoming apparent that anaerobic fungi display niche differentiation. As a consequence, there is a need to move beyond the broad generalization of anaerobic fungi as fiber-degraders, and explore the fundamental differences that underpin their ability to exist in distinct ecological niches. Application of genomics, transcriptomics, proteomics and metabolomics to their study in pure/mixed cultures and environmental samples will be invaluable in this process. To date the genomes and transcriptomes of several characterized anaerobic fungal isolates have been successfully generated. In contrast, the application of proteomics and metabolomics to anaerobic fungal analysis is still in its infancy. A central problem for all analyses, however, is the limited functional annotation of anaerobic fungal sequence data. There is therefore an urgent need to expand information held within publicly available reference databases. Once this challenge is overcome, along with improved sample collection and extraction, the application of these techniques will be key in furthering our understanding of the ecological role and impact of anaerobic fungi in the wide range of environments they inhabit.

Exploring the resistance against root parasitic plants in Arabidopsis and tomato
Cheng, Xi - \ 2017
University. Promotor(en): H.J. Bouwmeester, co-promotor(en): Carolien Ruyter-Spira. - Wageningen : Wageningen University - ISBN 9789463437004 - 305
plants - parasitic plants - arabidopsis thaliana - solanum lycopersicum - host parasite relationships - plant growth regulators - resistance - planten - parasitaire planten - gastheer parasiet relaties - plantengroeiregulatoren - weerstand
Root parasitic plant species such as broomrapes (Orobanche and Phelipanche spp.) and witchweeds (Striga spp.) are notorious agricultural weeds. They cause damage to crops by depriving them of water, nutrients and assimilates via a vascular connection. The difficulty in controlling root parasitic weeds is largely due to their intricate lifecycle and partially underground lifestyle. Their life cycle includes processes such as germination of the seed, the formation of the vascular connection with the host, the growth and development of the parasite after attachment and the emergence of shoots and flowers aboveground. The germination of many parasitic plants is induced by strigolactones that were recently shown to also be signalling compounds that stimulate mycorrhizal symbiosis. In addition, in the past few years, their role in plant development and plant defense has been established revealing them as a new class of plant hormones that exert their function likely in interaction with other hormones.
Pyrrolizidine alkaloid variation in Senecio vulgaris populations from native and invasive ranges
Cheng, Dandan ; Nguyen, Viet Thang ; Ndihokubwayo, Noel ; Ge, Jiwen ; Mulder, Patrick P.J. - \ 2017
PeerJ 2017 (2017)8. - ISSN 2167-8359
Biological invasion - Diversity - Liquid chromatography-tanderm mass spectrometry (LC-MS/MS) - Qualitative defense - Secondary metabolite - Shift Defense Hypothesis (SDH)

Biological invasion is regarded as one of the greatest environmental problems facilitated by globalization. Some hypotheses about the invasive mechanisms of alien invasive plants consider the plant-herbivore interaction and the role of plant defense in this interaction. For example, the ``Shift Defense Hypothesis'' (SDH) argues that introduced plants evolve higher levels of qualitative defense chemicals and decreased levels of quantitative defense, as they are released of the selective pressures from specialist herbivores but still face attack from generalists. Common groundsel (Senecio vulgaris), originating from Europe, is a cosmopolitan invasive plant in temperate regions. As in other Senecio species, S. vulgaris contains pyrrolizidine alkaloids (PAs) as characteristic qualitative defense compounds. In this study, S. vulgaris plants originating from native and invasive ranges (Europe and China, respectively) were grown under identical conditions and harvested upon flowering. PA composition and concentration in shoot and root samples were determined using Liquid Chromatography-Tandem Mass Spectrometry (LC-MS/MS). We investigated the differences between native and invasive S. vulgaris populations with regard to quantitative and qualitative variation of PAs. We identified 20 PAs, among which senecionine, senecionine N-oxide, integerrimine Noxide and seneciphylline N-oxide were dominant in the roots. In the shoots, in addition to the four PAs dominant in roots, retrorsine N-oxide, spartioidine N-oxide and two non-identified PAs were also prevalent. The roots possessed a lower PA diversity but a higher total PA concentration than the shoots. Most individual PAs as well as the total PA concentration were strongly positively correlated between the roots and shoots. Both native and invasive S. vulgaris populations shared the pattern described above. However, there was a slight trend indicating lower PA diversity and lower total PA concentration in invasive S. vulgaris populations than native populations, which is not consistent with the prediction of SDH.

Large-scale GWAS identifies multiple loci for hand grip strength providing biological insights into muscular fitness
Willems, Sara M. ; Wright, D.J. ; Day, Felix R. ; Trajanoska, Katerina ; Joshi, P.K. ; Morris, John A. ; Matteini, Amy M. ; Garton, Fleur C. ; Grarup, Niels ; Oskolkov, Nikolay ; Thalamuthu, Anbupalam ; Mangino, Massimo ; Liu, Jun ; Demirkan, Ayse ; Lek, Monkol ; Xu, Liwen ; Wang, Guan ; Oldmeadow, Christopher ; Gaulton, Kyle J. ; Lotta, Luca A. ; Miyamoto-Mikami, Eri ; Rivas, Manuel A. ; White, Tom ; Loh, Po Ru ; Aadahl, Mette ; Amin, Najaf ; Attia, John R. ; Austin, Krista ; Benyamin, Beben ; Brage, Søren ; Cheng, Yu Ching ; Ciȩszczyk, Paweł ; Derave, Wim ; Eriksson, Karl Fredrik ; Eynon, Nir ; Linneberg, Allan ; Lucia, Alejandro ; Massidda, Myosotis ; Mitchell, Braxton D. ; Miyachi, Motohiko ; Murakami, Haruka ; Padmanabhan, Sandosh ; Pandey, Ashutosh ; Papadimitriou, Ioannis ; Rajpal, Deepak K. ; Sale, Craig ; Schnurr, Theresia M. ; Sessa, Francesco ; Shrine, Nick ; Tobin, Martin D. ; Varley, Ian ; Wain, Louise V. ; Wray, Naomi R. ; Lindgren, Cecilia M. ; MacArthur, Daniel G. ; Waterworth, Dawn M. ; McCarthy, Mark I. ; Pedersen, Oluf ; Khaw, Kay Tee ; Kiel, Douglas P. ; Pitsiladis, Yannis ; Fuku, Noriyuki ; Franks, Paul W. ; North, Kathryn N. ; Duijn, C.M. Van; Mather, Karen A. ; Hansen, Torben ; Hansson, Ola ; Spector, Tim D. ; Murabito, Joanne M. ; Richards, J.B. ; Rivadeneira, Fernando ; Langenberg, Claudia ; Perry, John R.B. ; Wareham, Nick J. ; Scott, Robert A. ; Oei, Ling ; Zheng, Hou Feng ; Forgetta, Vincenzo ; Leong, Aaron ; Ahmad, Omar S. ; Laurin, Charles ; Mokry, Lauren E. ; Ross, Stephanie ; Elks, Cathy E. ; Bowden, Jack ; Warrington, Nicole M. ; Murray, Anna ; Ruth, Katherine S. ; Tsilidis, Konstantinos K. ; Medina-Gómez, Carolina ; Estrada, Karol ; Bis, Joshua C. ; Chasman, Daniel I. ; Demissie, Serkalem ; Enneman, Anke W. ; Hsu, Yi Hsiang ; Ingvarsson, Thorvaldur ; Kähönen, Mika ; Kammerer, Candace ; Lacroix, Andrea Z. ; Li, Guo ; Liu, Ching Ti ; Liu, Yongmei ; Lorentzon, Mattias ; Mägi, Reedik ; Mihailov, Evelin ; Milani, Lili ; Moayyeri, Alireza ; Nielson, Carrie M. ; Sham, Pack Chung ; Siggeirsdotir, Kristin ; Sigurdsson, Gunnar ; Stefansson, Kari ; Trompet, Stella ; Thorleifsson, Gudmar ; Vandenput, Liesbeth ; Velde, Nathalie Van Der; Viikari, Jorma ; Xiao, Su Mei ; Zhao, Jing Hua ; Evans, Daniel S. ; Cummings, Steven R. ; Cauley, Jane ; Duncan, Emma L. ; Groot, Lisette C.P.G.M. De; Esko, Tonu ; Gudnason, Vilmundar ; Harris, Tamara B. ; Jackson, Rebecca D. ; Jukema, J.W. ; Ikram, Arfan M.A. ; Karasik, David ; Kaptoge, Stephen ; Kung, Annie Wai Chee ; Lehtimäki, Terho ; Lyytikäinen, Leo Pekka ; Lips, Paul ; Luben, Robert ; Metspalu, Andres ; Meurs, Joyce B. van; Minster, Ryan L. ; Orwoll, Erick ; Oei, Edwin ; Psaty, Bruce M. ; Raitakari, Olli T. ; Ralston, Stuart W. ; Ridker, Paul M. ; Robbins, John A. ; Smith, Albert V. ; Styrkarsdottir, Unnur ; Tranah, Gregory J. ; Thorstensdottir, Unnur ; Uitterlinden, Andre G. ; Zmuda, Joseph ; Zillikens, M.C. ; Ntzani, Evangelia E. ; Evangelou, Evangelos ; Ioannidis, John P.A. ; Evans, David M. ; Ohlsson, Claes - \ 2017
Nature Communications 8 (2017). - ISSN 2041-1723
Hand grip strength is a widely used proxy of muscular fitness, a marker of frailty, and predictor of a range of morbidities and all-cause mortality. To investigate the genetic determinants of variation in grip strength, we perform a large-scale genetic discovery analysis in a combined sample of 195,180 individuals and identify 16 loci associated with grip strength (P<5 × 10-8) in combined analyses. A number of these loci contain genes implicated in structure and function of skeletal muscle fibres (ACTG1), neuronal maintenance and signal transduction (PEX14, TGFA, SYT1), or monogenic syndromes with involvement of psychomotor impairment (PEX14, LRPPRC and KANSL1). Mendelian randomization analyses are consistent with a causal effect of higher genetically predicted grip strength on lower fracture risk. In conclusion, our findings provide new biological insight into the mechanistic underpinnings of grip strength and the causal role of muscular strength in age-related morbidities and mortality.
Missing Food, Missing Data? A Critical Review of Global Food Losses and Food Waste Data
Xue, Li ; Liu, Gang ; Parfitt, Julian ; Liu, Xiaojie ; Herpen, Erica van; Stenmarck, Åsa ; O'Connor, Clementine ; Östergren, Karin ; Cheng, Shengkui - \ 2017
Environmental Science and Technology 51 (2017)12. - ISSN 0013-936X - p. 6618 - 6633.

Food losses and food waste (FLW) have become a global concern in recent years and emerge as a priority in the global and national political agenda (e.g., with Target 12.3 in the new United Nations Sustainable Development Goals). A good understanding of the availability and quality of global FLW data is a prerequisite for tracking progress on reduction targets, analyzing environmental impacts, and exploring mitigation strategies for FLW. There has been a growing body of literature on FLW quantification in the past years; however, significant challenges remain, such as data inconsistency and a narrow temporal, geographical, and food supply chain coverage. In this paper, we examined 202 publications which reported FLW data for 84 countries and 52 individual years from 1933 to 2014. We found that most existing publications are conducted for a few industrialized countries (e.g., the United Kingdom and the United States), and over half of them are based only on secondary data, which signals high uncertainties in the existing global FLW database. Despite these uncertainties, existing data indicate that per-capita food waste in the household increases with an increase of per-capita GDP. We believe that more consistent, in-depth, and primary-data-based studies, especially for emerging economies, are badly needed to better inform relevant policy on FLW reduction and environmental impacts mitigation.

Young inversion with multiple linked QTLs under selection in a hybrid zone
Lee, Cheng-Ruei ; Wange, Baosheng ; Mojica, Julius P. ; Mandakova, Terezie ; Prasad, K.V.S.K. ; Goicoechea, J.L. ; Perera, Nadeesha ; Hellsten, Uffe ; Hundley, Hope N. ; Johnson, J. ; Grimwood, J. ; Barry, Kerrie ; Fairclough, Stephen ; Jenkins, Jerry W. ; Yu, Yeisoo ; Kudrna, D. ; Zhang, Jianwei ; Talag, Jayson ; Golser, Wolfgang ; Ghattas, Kathryn ; Schranz, Eric ; Wing, Rod A. ; Lysak, Martin A. ; Schmutz, Jeremy - \ 2017
Ecology and Evolution 1 (2017)5. - ISSN 2045-7758 - 11 p.

Fixed chromosomal inversions can reduce gene flow and promote speciation in two ways: by suppressing recombination and by carrying locally favoured alleles at multiple loci. However, it is unknown whether favoured mutations slowly accumulate on older inversions or if young inversions spread because they capture pre-existing adaptive quantitative trait loci (QTLs). By genetic mapping, chromosome painting and genome sequencing, we have identified a major inversion controlling ecologically important traits in Boechera stricta. The inversion arose since the last glaciation and subsequently reached local high frequency in a hybrid speciation zone. Furthermore, the inversion shows signs of positive directional selection. To test whether the inversion could have captured existing, linked QTLs, we crossed standard, collinear haplotypes from the hybrid zone and found multiple linked phenology QTLs within the inversion region. These findings provide the first direct evidence that linked, locally adapted QTLs may be captured by young inversions during incipient speciation.

Chromosome inversions play an important role in local adaptation and speciation1,2, and selectively important inversions have been identified in many species3,4. Selection due to different environmental factors or stages in the life cycle1 may favour inversions carrying locally adapted alleles at several loci. In addition, established inversions are predicted to accumulate selectively important genetic differences, which may contribute to reproductive isolation during speciation1.

Although few studies have identified the actual loci that influence selection on inversions2,4,5, rearrangements may be favoured due to gene alterations near breakpoints6, chromatin changes7 or combinations of advantageous, co-adapted alleles8. Inversions suppress recombination, so locally advantageous alleles may segregate together, causing higher fitness than recombinant haplotypes9. Most evolutionary studies have focused on widespread, older inversions, so we have little knowledge of the evolutionary processes that guide their initial increase in frequency. For example, do inversions drift to higher frequency, and then acquire new advantageous mutations after they are common? Or are multiple linked, advantageous alleles captured in a new inversion, allowing them to spread together? Analysis of younger inversions may elucidate the evolutionary forces controlling the initial spread of chromosome inversions, which therefore influence their role in adaptation and speciation4,8.

Related species often differ for chromosome inversions that carry locally favoured alleles at multiple loci10,11. A key distinction among models for the evolution of inversions is whether early frequency increase is due to genetic drift or natural selection. Genetic drift might predominate initially, with subsequent accumulation of advantageous variants12. Alternatively, the Kirkpatrick–Barton model9 argues that linked, locally adapted alleles exist first, and subsequently are captured within a new, selectively favoured inversion13. In this ‘inversion-late’ evolutionary sequence1,5, linked quantitative trait loci (QTLs), similar to the ancestral haplotype that gave rise to the inversion, may still exist in non-inverted genotypes9. Here, we test these predictions of the Kirkpatrick–Barton model. First, we introduce ecologically diverged subspecies of Boechera stricta. Next, we examine a young inversion to infer the selective forces controlling its early increase in frequency. Finally, we cross collinear, standard genotypes from the hybrid zone to ask whether old, linked QTLs can be found within the inversion region.
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