Publications by authors named "Basten L Snoek"

26 Publications

  • Page 1 of 1

Transcriptome Signatures in WCS417 Shed Light on Role of Root-Secreted Coumarins in -Mutualist Communication.

Microorganisms 2021 Mar 11;9(3). Epub 2021 Mar 11.

Plant-Microbe Interactions, Department of Biology, Science4Life, Utrecht University, Padualaan 8, 3584 CH Utrecht, The Netherlands.

WCS417 is a root-colonizing bacterium with well-established plant-beneficial effects. Upon colonization of roots, WCS417 evades local root immune responses while triggering an induced systemic resistance (ISR) in the leaves. The early onset of ISR in roots shows similarities with the iron deficiency response, as both responses are associated with the production and secretion of coumarins. Coumarins can mobilize iron from the soil environment and have a selective antimicrobial activity that impacts microbiome assembly in the rhizosphere. Being highly coumarin-tolerant, WCS417 induces the secretion of these phenolic compounds, likely to improve its own niche establishment, while providing growth and immunity benefits for the host in return. To investigate the possible signaling function of coumarins in the mutualistic -WCS417 interaction, we analyzed the transcriptome of WCS417 growing in root exudates of coumarin-producing Col-0 and the coumarin-biosynthesis mutant . We found that coumarins in F6'H1-dependent root exudates significantly affected the expression of 439 bacterial genes (8% of the bacterial genome). Of those, genes with functions related to transport and metabolism of carbohydrates, amino acids, and nucleotides were induced, whereas genes with functions related to cell motility, the bacterial mobilome, and energy production and conversion were repressed. Strikingly, most genes related to flagellar biosynthesis were down-regulated by F6'H1-dependent root exudates and we found that application of selected coumarins reduces bacterial motility. These findings suggest that coumarins' function in the rhizosphere as semiochemicals in the communication between the roots and WCS417. Collectively, our results provide important novel leads for future functional analysis of molecular processes in the establishment of plant-mutualist interactions.
View Article and Find Full Text PDF

Download full-text PDF

Source
http://dx.doi.org/10.3390/microorganisms9030575DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC8000642PMC
March 2021

The chemical compound 'Heatin' stimulates hypocotyl elongation and interferes with the Arabidopsis NIT1-subfamily of nitrilases.

Plant J 2021 Mar 26. Epub 2021 Mar 26.

Molecular Plant Physiology, Institute of Environmental Biology, Utrecht University, Padualaan 8, Utrecht, 3584 CH, the Netherlands.

Temperature passively affects biological processes involved in plant growth. Therefore, it is challenging to study the dedicated temperature signalling pathways that orchestrate thermomorphogenesis, a suite of elongation growth-based adaptations that enhance leaf-cooling capacity. We screened a chemical library for compounds that restored hypocotyl elongation in the pif4-2-deficient mutant background at warm temperature conditions in Arabidopsis thaliana to identify modulators of thermomorphogenesis. The small aromatic compound 'Heatin', containing 1-iminomethyl-2-naphthol as a pharmacophore, was selected as an enhancer of elongation growth. We show that ARABIDOPSIS ALDEHYDE OXIDASES redundantly contribute to Heatin-mediated hypocotyl elongation. Following a chemical proteomics approach, the members of the NITRILASE1-subfamily of auxin biosynthesis enzymes were identified among the molecular targets of Heatin. Our data reveal that nitrilases are involved in promotion of hypocotyl elongation in response to high temperature and Heatin-mediated hypocotyl elongation requires the NITRILASE1-subfamily members, NIT1 and NIT2. Heatin inhibits NIT1-subfamily enzymatic activity in vitro and the application of Heatin accordingly results in the accumulation of NIT1-subfamily substrate indole-3-acetonitrile in vivo. However, levels of the NIT1-subfamily product, bioactive auxin (indole-3-acetic acid), were also significantly increased. It is likely that the stimulation of hypocotyl elongation by Heatin might be independent of its observed interaction with NITRILASE1-subfamily members. However, nitrilases may contribute to the Heatin response by stimulating indole-3-acetic acid biosynthesis in an indirect way. Heatin and its functional analogues present novel chemical entities for studying auxin biology.
View Article and Find Full Text PDF

Download full-text PDF

Source
http://dx.doi.org/10.1111/tpj.15250DOI Listing
March 2021

Soil microbial legacies differ following drying-rewetting and freezing-thawing cycles.

ISME J 2021 04 6;15(4):1207-1221. Epub 2021 Jan 6.

Department of Biology, University of Copenhagen, Universitetsparken 15, 2100, Copenhagen, Denmark.

Climate change alters frequencies and intensities of soil drying-rewetting and freezing-thawing cycles. These fluctuations affect soil water availability, a crucial driver of soil microbial activity. While these fluctuations are leaving imprints on soil microbiome structures, the question remains if the legacy of one type of weather fluctuation (e.g., drying-rewetting) affects the community response to the other (e.g., freezing-thawing). As both phenomenons give similar water availability fluctuations, we hypothesized that freezing-thawing and drying-rewetting cycles have similar effects on the soil microbiome. We tested this hypothesis by establishing targeted microcosm experiments. We created a legacy by exposing soil samples to a freezing-thawing or drying-rewetting cycle (phase 1), followed by an additional drying-rewetting or freezing-thawing cycle (phase 2). We measured soil respiration and analyzed soil microbiome structures. Across experiments, larger CO pulses and changes in microbiome structures were observed after rewetting than thawing. Drying-rewetting legacy affected the microbiome and CO emissions upon the following freezing-thawing cycle. Conversely, freezing-thawing legacy did not affect the microbial response to the drying-rewetting cycle. Our results suggest that drying-rewetting cycles have stronger effects on soil microbial communities and CO production than freezing-thawing cycles and that this pattern is mediated by sustained changes in soil microbiome structures.
View Article and Find Full Text PDF

Download full-text PDF

Source
http://dx.doi.org/10.1038/s41396-020-00844-3DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC8115648PMC
April 2021

Dissecting the eQTL Micro-Architecture in .

Front Genet 2020 3;11:501376. Epub 2020 Nov 3.

Laboratory of Nematology, Wageningen University & Research, Wageningen, Netherlands.

The study of expression quantitative trait loci (eQTL) using natural variation in inbred populations has yielded detailed information about the transcriptional regulation of complex traits. Studies on eQTL using recombinant inbred lines (RILs) led to insights on and regulatory loci of transcript abundance. However, determining the underlying causal polymorphic genes or variants is difficult, but ultimately essential for the understanding of regulatory networks of complex traits. This requires insight into whether associated loci are single eQTL or a combination of closely linked eQTL, and how this QTL micro-architecture depends on the environment. We addressed these questions by testing for independent replication of previously mapped eQTL in using new data from introgression lines (ILs). Both populations indicate that the overall heritability of gene expression, number, and position of eQTL differed among environments. Across environments we were able to replicate 70% of the - and 40% of the -eQTL using the ILs. Testing eight different simulation models, we suggest that additive effects explain up to 60-93% of RIL/IL heritability for all three environments. Closely linked eQTL explained up to 40% of RIL/IL heritability in the control environment whereas only 7% in the heat-stress and recovery environments. In conclusion, we show that reproducibility of eQTL was higher for vs. eQTL and that the environment affects the eQTL micro-architecture.
View Article and Find Full Text PDF

Download full-text PDF

Source
http://dx.doi.org/10.3389/fgene.2020.501376DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7670075PMC
November 2020

Community-level interactions between plants and soil biota during range expansion.

J Ecol 2020 Sep 12;108(5):1860-1873. Epub 2020 Jun 12.

Netherlands Institute of Ecology Wageningen The Netherlands.

Plant species that expand their range in response to current climate change will encounter soil communities that may hinder, allow or even facilitate plant performance. It has been shown repeatedly for plant species originating from other continents that these plants are less hampered by soil communities from the new than from the original range. However, information about the interactions between intra-continental range expanders and soil communities is sparse, especially at community level.Here we used a plant-soil feedback experiment approach to examine if the interactions between range expanders and soil communities change during range expansion. We grew communities of range-expanding and native plant species with soil communities originating from the original and new range of range expanders. In these conditioned soils, we determined the composition of fungi and bacteria by high-throughput amplicon sequencing of the ITS region and the 16S rRNA gene respectively. Nematode community composition was determined by microscopy-based morphological identification. Then we tested how these soil communities influence the growth of subsequent communities of range expanders and natives.We found that after the conditioning phase soil bacterial, fungal and nematode communities differed by origin and by conditioning plant communities. Despite differences in bacterial, fungal and nematode communities between original and new range, soil origin did not influence the biomass production of plant communities. Both native and range expanding plant communities produced most above-ground biomass in soils that were conditioned by plant communities distantly related to them. . Communities of range-expanding plant species shape specific soil communities in both original and new range soil. Plant-soil interactions of range expanders in communities can be similar to the ones of their closely related native plant species.
View Article and Find Full Text PDF

Download full-text PDF

Source
http://dx.doi.org/10.1111/1365-2745.13409DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7508040PMC
September 2020

Network Analysis Prioritizes and as the Candidate Genes for Major eQTL Hotspots in Seed Germination of .

G3 (Bethesda) 2020 11 5;10(11):4215-4226. Epub 2020 Nov 5.

Bioinformatics Group, Wageningen University, NL-6708 PB Wageningen, The Netherlands

Seed germination is characterized by a constant change of gene expression across different time points. These changes are related to specific processes, which eventually determine the onset of seed germination. To get a better understanding on the regulation of gene expression during seed germination, we performed a quantitative trait locus mapping of gene expression (eQTL) at four important seed germination stages (primary dormant, after-ripened, six-hour after imbibition, and radicle protrusion stage) using Bay x Sha recombinant inbred lines (RILs). The mapping displayed the distinctness of the eQTL landscape for each stage. We found several eQTL hotspots across stages associated with the regulation of expression of a large number of genes. Interestingly, an eQTL hotspot on chromosome five collocates with hotspots for phenotypic and metabolic QTL in the same population. Finally, we constructed a gene co-expression network to prioritize the regulatory genes for two major eQTL hotspots. The network analysis prioritizes transcription factors and as the most likely regulatory genes for the hotspot. Together, we have revealed that the genetic regulation of gene expression is dynamic along the course of seed germination.
View Article and Find Full Text PDF

Download full-text PDF

Source
http://dx.doi.org/10.1534/g3.120.401477DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7642920PMC
November 2020

Quantitative mapping of transcriptome and proteome dynamics during polarization of human iPSC-derived neurons.

Elife 2020 09 17;9. Epub 2020 Sep 17.

Cell Biology, Neurobiology and Biophysics, Department of Biology, Faculty of Science, Utrecht University, Utrecht, Netherlands.

The differentiation of neuronal stem cells into polarized neurons is a well-coordinated process which has mostly been studied in classical non-human model systems, but to what extent these findings are recapitulated in human neurons remains unclear. To study neuronal polarization in human neurons, we cultured hiPSC-derived neurons, characterized early developmental stages, measured electrophysiological responses, and systematically profiled transcriptomic and proteomic dynamics during these steps. The neuron transcriptome and proteome shows extensive remodeling, with differential expression profiles of ~1100 transcripts and ~2200 proteins during neuronal differentiation and polarization. We also identified a distinct axon developmental stage marked by the relocation of axon initial segment proteins and increased microtubule remodeling from the distal (stage 3a) to the proximal (stage 3b) axon. This developmental transition coincides with action potential maturation. Our comprehensive characterization and quantitative map of transcriptome and proteome dynamics provides a solid framework for studying polarization in human neurons.
View Article and Find Full Text PDF

Download full-text PDF

Source
http://dx.doi.org/10.7554/eLife.58124DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7498259PMC
September 2020

Detection of QTLs for genotype × environment interactions in tomato seeds and seedlings.

Plant Cell Environ 2020 08 11;43(8):1973-1988. Epub 2020 Jun 11.

Wageningen Seed Lab, Laboratory of Plant Physiology, Wageningen University, Wageningen, The Netherlands.

Seed quality and seedling establishment are the most important factors affecting successful crop development. They depend on the genetic background and are acquired during seed maturation and therefor, affected by the maternal environment under which the seeds develop. There is little knowledge about the genetic and environmental factors that affect seed quality and seedling establishment. The aim of this study is to identify the loci and possible molecular mechanisms involved in acquisition of seed quality and how these are controlled by adverse maternal conditions. For this, we used a tomato recombinant inbred line (RIL) population consisting of 100 lines which were grown under two different nutritional environmental conditions, high phosphate and low nitrate. Most of the seed germination traits such as maximum germination percentage (G ), germination rate (t ) and uniformity (U ) showed ample variation between genotypes and under different germination conditions. This phenotypic variation leads to identification of quantitative trait loci (QTLs) which were dependent on genetic factors, but also on the interaction with the maternal environment (QTL × E). Further studies of these QTLs may ultimately help to predict the effect of different maternal environmental conditions on seed quality and seedling establishment which will be very useful to improve the production of high-performance seeds.
View Article and Find Full Text PDF

Download full-text PDF

Source
http://dx.doi.org/10.1111/pce.13788DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7496158PMC
August 2020

Field cricket genome reveals the footprint of recent, abrupt adaptation in the wild.

Evol Lett 2020 Feb 19;4(1):19-33. Epub 2019 Dec 19.

School of Biology University of St Andrews St Andrews Fife KY16 9TH United Kingdom.

Evolutionary adaptation is generally thought to occur through incremental mutational steps, but large mutational leaps can occur during its early stages. These are challenging to study in nature due to the difficulty of observing new genetic variants as they arise and spread, but characterizing their genomic dynamics is important for understanding factors favoring rapid adaptation. Here, we report genomic consequences of recent, adaptive song loss in a Hawaiian population of field crickets (). A discrete genetic variant, , appeared and spread approximately 15 years ago. erases sound-producing veins on male wings. These silent flatwing males are protected from a lethal, eavesdropping parasitoid fly. We sequenced, assembled and annotated the cricket genome, produced a linkage map, and identified a quantitative trait locus covering a large region of the X chromosome. Gene expression profiling showed that is associated with extensive genome-wide effects on embryonic gene expression. We found that flatwing male crickets express feminized chemical pheromones. This male feminizing effect, on a different sexual signaling modality, is genetically associated with the genotype. Our findings suggest that the early stages of evolutionary adaptation to extreme pressures can be accompanied by greater genomic and phenotypic disruption than previously appreciated, and highlight how abrupt adaptation might involve suites of traits that arise through pleiotropy or genomic hitchhiking.
View Article and Find Full Text PDF

Download full-text PDF

Source
http://dx.doi.org/10.1002/evl3.148DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7006468PMC
February 2020

WormQTL2: an interactive platform for systems genetics in Caenorhabditis elegans.

Database (Oxford) 2020 01;2020

Bioinformatics Group, Wageningen University, Droevendaalsesteeg 1, NL-6708 PB Wageningen, The Netherlands.

Quantitative genetics provides the tools for linking polymorphic loci to trait variation. Linkage analysis of gene expression is an established and widely applied method, leading to the identification of expression quantitative trait loci (eQTLs). (e)QTL detection facilitates the identification and understanding of the underlying molecular components and pathways, yet (e)QTL data access and mining often is a bottleneck. Here, we present WormQTL2, a database and platform for comparative investigations and meta-analyses of published (e)QTL data sets in the model nematode worm C. elegans. WormQTL2 integrates six eQTL studies spanning 11 conditions as well as over 1000 traits from 32 studies and allows experimental results to be compared, reused and extended upon to guide further experiments and conduct systems-genetic analyses. For example, one can easily screen a locus for specific cis-eQTLs that could be linked to variation in other traits, detect gene-by-environment interactions by comparing eQTLs under different conditions, or find correlations between QTL profiles of classical traits and gene expression. WormQTL2 makes data on natural variation in C. elegans and the identified QTLs interactively accessible, allowing studies beyond the original publications. Database URL: www.bioinformatics.nl/WormQTL2/.
View Article and Find Full Text PDF

Download full-text PDF

Source
http://dx.doi.org/10.1093/database/baz149DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6971878PMC
January 2020

Transcriptome resilience predicts thermotolerance in Caenorhabditis elegans.

BMC Biol 2019 12 10;17(1):102. Epub 2019 Dec 10.

Laboratory of Nematology, Wageningen University, Droevendaalsesteeg 1, Wageningen, 6708 PB, The Netherlands.

Background: The detrimental effects of a short bout of stress can persist and potentially turn lethal, long after the return to normal conditions. Thermotolerance, which is the capacity of an organism to withstand relatively extreme temperatures, is influenced by the response during stress exposure, as well as the recovery process afterwards. While heat-shock response mechanisms have been studied intensively, predicting thermal tolerance remains a challenge.

Results: Here, we use the nematode Caenorhabditis elegans to measure transcriptional resilience to heat stress and predict thermotolerance. Using principal component analysis in combination with genome-wide gene expression profiles collected in three high-resolution time series during control, heat stress, and recovery conditions, we infer a quantitative scale capturing the extent of stress-induced transcriptome dynamics in a single value. This scale provides a basis for evaluating transcriptome resilience, defined here as the ability to depart from stress-expression dynamics during recovery. Independent replication across multiple highly divergent genotypes reveals that the transcriptional resilience parameter measured after a spike in temperature is quantitatively linked to long-term survival after heat stress.

Conclusion: Our findings imply that thermotolerance is an intrinsic property that pre-determines long-term outcome of stress and can be predicted by the transcriptional resilience parameter. Inferring the transcriptional resilience parameters of higher organisms could aid in evaluating rehabilitation strategies after stresses such as disease and trauma.
View Article and Find Full Text PDF

Download full-text PDF

Source
http://dx.doi.org/10.1186/s12915-019-0725-6DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6905072PMC
December 2019

HISTONE DEACETYLASE 9 stimulates auxin-dependent thermomorphogenesis in by mediating H2A.Z depletion.

Proc Natl Acad Sci U S A 2019 12 25;116(50):25343-25354. Epub 2019 Nov 25.

Molecular Plant Physiology, Institute of Environmental Biology, Utrecht University, 3584 CH Utrecht, The Netherlands;

Many plant species respond to unfavorable high ambient temperatures by adjusting their vegetative body plan to facilitate cooling. This process is known as thermomorphogenesis and is induced by the phytohormone auxin. Here, we demonstrate that the chromatin-modifying enzyme HISTONE DEACETYLASE 9 (HDA9) mediates thermomorphogenesis but does not interfere with hypocotyl elongation during shade avoidance. HDA9 is stabilized in response to high temperature and mediates histone deacetylation at the locus, a rate-limiting enzyme in auxin biosynthesis, at warm temperatures. We show that HDA9 permits net eviction of the H2A.Z histone variant from nucleosomes associated with , allowing binding and transcriptional activation by PHYTOCHROME INTERACTING FACTOR 4, followed by auxin accumulation and thermomorphogenesis.
View Article and Find Full Text PDF

Download full-text PDF

Source
http://dx.doi.org/10.1073/pnas.1911694116DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6911240PMC
December 2019

Genetic background modifies phenotypic and transcriptional responses in a C. elegans model of α-synuclein toxicity.

BMC Genomics 2019 Mar 20;20(1):232. Epub 2019 Mar 20.

Biomolecular Research Group, School of Human and Life Sciences, Canterbury Christ Church University, North Holmes Road, Canterbury, CT1 1QU, UK.

Background: Accumulation of protein aggregates are a major hallmark of progressive neurodegenerative disorders such as Parkinson's disease and Alzheimer's disease. Transgenic Caenorhabditis elegans nematodes expressing the human synaptic protein α-synuclein in body wall muscle show inclusions of aggregated protein, which affects similar genetic pathways as in humans. It is not however known how the effects of α-synuclein expression in C. elegans differs among genetic backgrounds. Here, we compared gene expression patterns and investigated the phenotypic consequences of transgenic α-synuclein expression in five different C. elegans genetic backgrounds.

Results: Transcriptome analysis indicates that α-synuclein expression effects pathways associated with nutrient storage, lipid transportation and ion exchange and that effects vary depending on the genetic background. These gene expression changes predict that a range of phenotypes will be affected by α-synuclein expression. We confirm this, showing that α-synuclein expression delayed development, reduced lifespan, increased rate of matricidal hatching, and slows pharyngeal pumping. Critically, these phenotypic effects depend on the genetic background and coincide with the core changes in gene expression.

Conclusions: Together, our results show genotype-specific effects and core alterations in both gene expression and in phenotype in response to α-synuclein expression. We conclude that the effects of α-synuclein expression are substantially modified by the genetic background, illustrating that genetic background needs to be considered in C. elegans models of neurodegenerative disease.
View Article and Find Full Text PDF

Download full-text PDF

Source
http://dx.doi.org/10.1186/s12864-019-5597-1DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6427842PMC
March 2019

A multi-parent recombinant inbred line population of C. elegans allows identification of novel QTLs for complex life history traits.

BMC Biol 2019 03 12;17(1):24. Epub 2019 Mar 12.

Laboratory of Nematology, Wageningen University, Droevendaalsesteeg 1, NL-6708 PB, Wageningen, The Netherlands.

Background: The nematode Caenorhabditis elegans has been extensively used to explore the relationships between complex traits, genotypes, and environments. Complex traits can vary across different genotypes of a species, and the genetic regulators of trait variation can be mapped on the genome using quantitative trait locus (QTL) analysis of recombinant inbred lines (RILs) derived from genetically and phenotypically divergent parents. Most RILs have been derived from crossing two parents from globally distant locations. However, the genetic diversity between local C. elegans populations can be as diverse as between global populations and could thus provide means of identifying genetic variation associated with complex traits relevant on a broader scale.

Results: To investigate the effect of local genetic variation on heritable traits, we developed a new RIL population derived from 4 parental wild isolates collected from 2 closely located sites in France: Orsay and Santeuil. We crossed these 4 genetically diverse parental isolates to generate a population of 200 multi-parental RILs and used RNA-seq to obtain sequence polymorphisms identifying almost 9000 SNPs variable between the 4 genotypes with an average spacing of 11 kb, doubling the mapping resolution relative to currently available RIL panels for many loci. The SNPs were used to construct a genetic map to facilitate QTL analysis. We measured life history traits such as lifespan, stress resistance, developmental speed, and population growth in different environments, and found substantial variation for most traits. We detected multiple QTLs for most traits, including novel QTLs not found in previous QTL analysis, including those for lifespan and pathogen responses. This shows that recombining genetic variation across C. elegans populations that are in geographical close proximity provides ample variation for QTL mapping.

Conclusion: Taken together, we show that using more parents than the classical two parental genotypes to construct a RIL population facilitates the detection of QTLs and that the use of wild isolates facilitates the detection of QTLs. The use of multi-parent RIL populations can further enhance our understanding of local adaptation and life history trade-offs.
View Article and Find Full Text PDF

Download full-text PDF

Source
http://dx.doi.org/10.1186/s12915-019-0642-8DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6417139PMC
March 2019

The interaction between genotype and maternal nutritional environments affects tomato seed and seedling quality.

J Exp Bot 2019 05;70(10):2905-2918

Wageningen Seed Lab, Laboratory of Plant Physiology, Wageningen University, Droevendaalsesteeg, PB Wageningen, The Netherlands.

Seed and seedling traits are affected by the conditions of the maternal environment, such as light, temperature, and nutrient availability. In this study, we have investigated whether different maternally applied nitrate and phosphate concentrations affect the seed and seedling performance of two closely related tomato species: Solanum lycopersicum cv. Money maker and Solanum pimpinellifolium accession CGN14498. We observed large differences for seed and seedling traits between the two species. Additionally, we have shown that for nitrate most of the seed and seedling traits were significantly affected by genotype-environment interactions (G×E). The effect of the maternal environment was clearly visible in the primary metabolites of the dry seeds. For example, we could show that the amount of γ-aminobutyric acid (GABA) in Money maker seeds was affected by the differences in the maternal environments and was positively correlated with seed germination under high temperature. Overall, compared with phosphate, nitrate had a larger effect on seed and seedling performance in tomato. In general, the different responses to the maternal environments of the two tomato species showed a major role for G×E in shaping seed and seedling traits.
View Article and Find Full Text PDF

Download full-text PDF

Source
http://dx.doi.org/10.1093/jxb/erz101DOI Listing
May 2019

Competition and predation as possible causes of bacterial rarity.

Environ Microbiol 2019 04 18;21(4):1356-1368. Epub 2019 Mar 18.

Department of Terrestrial Ecology, Netherlands Institute of Ecology (NIOO-KNAW), P.O. Box 50, 6700 AB, Wageningen, The Netherlands.

We assembled communities of bacteria and exposed them to different nutrient concentrations with or without predation by protists. Taxa that were rare in the field were less abundant at low nutrient concentrations than common taxa, independent of predation. However, some taxa that were rare in the field became highly abundant in the assembled communities, especially under ample nutrient availability. This high abundance points at a possible competitive advantage of some rare bacterial taxa under nutrient-rich conditions. In contrast, the abundance of most rare bacterial taxa decreased at low resource availability. Since low resource availability will be the prevailing situation in most soils, our data suggests that under those conditions poor competitiveness for limiting resources may contribute to bacterial rarity. Interestingly, taxa that were rare in the field and most successful under predator-free conditions in the lab also tended to be more reduced by predation than common taxa. This suggests that predation contributes to rarity of bacterial taxa in the field. We further discuss whether there may be a trade-off between competitiveness and predation resistance. The substantial variability among taxa in their responses to competition and predation suggests that other factors, for example abiotic conditions and dispersal ability, also influence the local abundance of soil bacteria.
View Article and Find Full Text PDF

Download full-text PDF

Source
http://dx.doi.org/10.1111/1462-2920.14569DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6850713PMC
April 2019

Abundantly Present miRNAs in Milk-Derived Extracellular Vesicles Are Conserved Between Mammals.

Front Nutr 2018 18;5:81. Epub 2018 Sep 18.

Department of Biochemistry and Cell Biology, Faculty of Veterinary Medicine Utrecht University, Utrecht, Netherlands.

Mammalian milk is not only a source of nutrition for the newborn, but also contains various components that regulate further development. For instance, milk is an abundant source of microRNAs (miRNAs), which are evolutionary conserved small non-coding RNAs that are involved in post-transcriptional regulation of target mRNA. MiRNAs present in milk can occur in extracellular vesicles (EVs), which are nanosized membrane vesicles released by many cell types as a means of intercellular communication. The membrane of EVs protects enclosed miRNAs from degradation and harbors molecules that allow specific targeting to recipient cells. Although several studies have investigated the miRNA content in milk EVs from individual species, little is known about the evolutionary conserved nature of EV-associated miRNAs among different species. In this study, we profiled the miRNA content of purified EVs from human and porcine milk. These data were compared to published studies on EVs from human, cow, porcine, and panda milk to assess the overlap in the top 20 most abundant miRNAs. Interestingly, several abundant miRNAs were shared between species (e.g., let-7 family members let-7a, let-7b, let-7f, and miR-148a). Moreover, these miRNAs have been implicated in immune-related functions and regulation of cell growth and signal transduction. The conservation of these miRNA among species, not only in their sequence homology, but also in their incorporation in milk EVs of several species, suggests that they are evolutionarily selected to regulate cell function in the newborn.
View Article and Find Full Text PDF

Download full-text PDF

Source
http://dx.doi.org/10.3389/fnut.2018.00081DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6153340PMC
September 2018

Natural genetic variation in identified genomic loci controlling metabolite levels.

Genome Res 2018 09 14;28(9):1296-1308. Epub 2018 Aug 14.

Laboratory Genetic Metabolic Diseases, Amsterdam UMC, University of Amsterdam, Amsterdam Gastroenterology and Metabolism, 1105 AZ Amsterdam, The Netherlands.

Metabolic homeostasis is sustained by complex biological networks that respond to nutrient availability. Genetic and environmental factors may disrupt this equilibrium, leading to metabolic disorders, including obesity and type 2 diabetes. To identify the genetic factors controlling metabolism, we performed quantitative genetic analysis using a population of 199 recombinant inbred lines (RILs) in the nematode We focused on the genomic regions that control metabolite levels by measuring fatty acid (FA) and amino acid (AA) composition in the RILs using targeted metabolomics. The genetically diverse RILs showed a large variation in their FA and AA levels with a heritability ranging from 32% to 82%. We detected strongly co-correlated metabolite clusters and 36 significant metabolite quantitative trait loci (mQTL). We focused on mQTL displaying highly significant linkage and heritability, including an mQTL for the FA C14:1 on Chromosome I, and another mQTL for the FA C18:2 on Chromosome IV. Using introgression lines (ILs), we were able to narrow down both mQTL to a 1.4-Mbp and a 3.6-Mbp region, respectively. RNAi-based screening focusing on the Chromosome I mQTL identified several candidate genes for the C14:1 mQTL, including , Y87G2A.2, , , and Overall, this systems approach provides us with a powerful platform to study the genetic basis of metabolism. Furthermore, it allows us to investigate interventions such as nutrients and stresses that maintain or disturb the regulatory network controlling metabolic homeostasis, and identify gene-by-environment interactions.
View Article and Find Full Text PDF

Download full-text PDF

Source
http://dx.doi.org/10.1101/gr.232322.117DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6120624PMC
September 2018

Network Analyses Can Advance Above-Belowground Ecology.

Trends Plant Sci 2018 09 30;23(9):759-768. Epub 2018 Jul 30.

Department of Terrestrial Ecology, Netherlands Institute of Ecology (NIOO-KNAW), P.O. Box 50, 6700 AB, Wageningen, The Netherlands; Laboratory of Nematology, Wageningen University, P.O. Box 8123, 6700 ES, Wageningen, The Netherlands.

An understanding of above-belowground (AG-BG) ecology is important for evaluating how plant interactions with enemies, symbionts, and decomposers affect species diversity and will respond to global changes. However, research questions and experiments often focus on only a limited number of interactions, creating an incomplete picture of how entire communities may be involved in AG-BG community ecology. Therefore, a pressing challenge is to formulate hypotheses of AG-BG interactions when considering communities in their full complexity. Here we discuss how network analyses can be a powerful tool to progress AG-BG research, link across scales from individual to community and ecosystem, visualize community interactions between the two (AG and BG) subsystems, and develop testable hypotheses.
View Article and Find Full Text PDF

Download full-text PDF

Source
http://dx.doi.org/10.1016/j.tplants.2018.06.009DOI Listing
September 2018

The Arabidopsis bZIP transcription factor family-an update.

Curr Opin Plant Biol 2018 10 1;45(Pt A):36-49. Epub 2018 Jun 1.

Department of Pharmaceutical Biology, Julius-von-Sachs-Institute, Biocenter, Julius-Maximilians-Universität Würzburg, Würzburg 97082, Germany. Electronic address:

The basic (region) leucine zippers (bZIPs) are evolutionarily conserved transcription factors in eukaryotic organisms. Here, we have updated the classification of the Arabidopsis thaliana bZIP-family, comprising 78 members, which have been assorted into 13 groups. Arabidopsis bZIPs are involved in a plethora of functions related to plant development, environmental signalling and stress response. Based on the classification, we have highlighted functional and regulatory aspects of selected well-studied bZIPs, which may serve as prototypic examples for the particular groups.
View Article and Find Full Text PDF

Download full-text PDF

Source
http://dx.doi.org/10.1016/j.pbi.2018.05.001DOI Listing
October 2018

Drought Legacy Effects on the Composition of Soil Fungal and Prokaryote Communities.

Front Microbiol 2018 7;9:294. Epub 2018 Mar 7.

Department of Terrestrial Ecology, Netherlands Institute of Ecology, Wageningen, Netherlands.

It is increasingly acknowledged that climate change is influencing terrestrial ecosystems by increased drought and rainfall intensities. Soil microbes are key drivers of many processes in terrestrial systems and rely on water in soil pores to fulfill their life cycles and functions. However, little is known on how drought and rainfall fluctuations, which affect the composition and structure of microbial communities, persist once original moisture conditions have been restored. Here, we study how simulated short-term drying and re-wetting events shape the community composition of soil fungi and prokaryotes. In a mesocosm experiment, soil was exposed to an extreme drought, then re-wetted to optimal moisture (50% WHC, water holding capacity) or to saturation level (100% WHC). Composition, community structure and diversity of microbes were measured by sequencing ITS and 16S rRNA gene amplicons 3 weeks after original moisture content had been restored. Drying and extreme re-wetting decreased richness of microbial communities, but not evenness. Abundance changes were observed in only 8% of prokaryote OTUs, and 25% of fungal OTUs, whereas all other OTUs did not differ between drying and re-wetting treatments. Two specific legacy response groups (LRGs) were observed for both prokaryotes and fungi. OTUs belonging to the first LRG decreased in relative abundance in soil with a history of drought, whereas OTUs that increased in soil with a history of drought formed a second LRG. These microbial responses were spread among different phyla. Drought appeared to be more important for the microbial community composition than the following extreme re-wetting. 16S profiles were correlated with both inorganic N concentration and basal respiration and ITS profiles correlated with fungal biomass. We conclude that a drying and/or an extreme re-wetting history can persist in soil microbial communities via specific response groups composed of members with broad phylogenetic origins, with possible functional consequences on soil processes and plant species. As a large fraction of OTUs responding to drying and re-wetting belonged to the rare biosphere, our results suggest that low abundant microbial species are potentially important for ecosystem responses to extreme weather events.
View Article and Find Full Text PDF

Download full-text PDF

Source
http://dx.doi.org/10.3389/fmicb.2018.00294DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5845876PMC
March 2018

Ras/MAPK Modifier Loci Revealed by eQTL in .

G3 (Bethesda) 2017 09 7;7(9):3185-3193. Epub 2017 Sep 7.

Laboratory of Nematology, Wageningen University and Research, 6708PB, The Netherlands

The oncogenic Ras/MAPK pathway is evolutionarily conserved across metazoans. Yet, almost all our knowledge on this pathway comes from studies using single genetic backgrounds, whereas mutational effects can be highly background dependent. Therefore, we lack insight in the interplay between genetic backgrounds and the Ras/MAPK-signaling pathway. Here, we used a RIL population containing a gain-of-function mutation in the Ras/MAPK-pathway gene and measured how gene expression regulation is affected by this mutation. We mapped eQTL and found that the majority (∼73%) of the 1516 detected -eQTL were not specific for the mutation, whereas most (∼76%) of the 898 detected -eQTL were associated with the mutation. We detected six eQTL -bands specific for the interaction between the genetic background and the mutation, one of which colocalized with the polymorphic Ras/MAPK modifier Comparison between transgenic lines expressing allelic variants of showed the involvement of in 79% of the -eQTL for genes mapping to this -band. Together, our results have revealed hidden loci affecting Ras/MAPK signaling using sensitized backgrounds in These loci harbor putative polymorphic modifier genes that would not have been detected using mutant screens in single genetic backgrounds.
View Article and Find Full Text PDF

Download full-text PDF

Source
http://dx.doi.org/10.1534/g3.117.1120DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5592943PMC
September 2017

Contribution of trans regulatory eQTL to cryptic genetic variation in C. elegans.

BMC Genomics 2017 06 29;18(1):500. Epub 2017 Jun 29.

Laboratory of Nematology, Wageningen University and Research, Droevendaalsesteeg 1, 6708PB, Wageningen, The Netherlands.

Background: Cryptic genetic variation (CGV) is the hidden genetic variation that can be unlocked by perturbing normal conditions. CGV can drive the emergence of novel complex phenotypes through changes in gene expression. Although our theoretical understanding of CGV has thoroughly increased over the past decade, insight into polymorphic gene expression regulation underlying CGV is scarce. Here we investigated the transcriptional architecture of CGV in response to rapid temperature changes in the nematode Caenorhabditis elegans. We analyzed regulatory variation in gene expression (and mapped eQTL) across the course of a heat stress and recovery response in a recombinant inbred population.

Results: We measured gene expression over three temperature treatments: i) control, ii) heat stress, and iii) recovery from heat stress. Compared to control, exposure to heat stress affected the transcription of 3305 genes, whereas 942 were affected in recovering animals. These affected genes were mainly involved in metabolism and reproduction. The gene expression pattern in recovering animals resembled both the control and the heat-stress treatment. We mapped eQTL using the genetic variation of the recombinant inbred population and detected 2626 genes with an eQTL in the heat-stress treatment, 1797 in the control, and 1880 in the recovery. The cis-eQTL were highly shared across treatments. A considerable fraction of the trans-eQTL (40-57%) mapped to 19 treatment specific trans-bands. In contrast to cis-eQTL, trans-eQTL were highly environment specific and thus cryptic. Approximately 67% of the trans-eQTL were only induced in a single treatment, with heat-stress showing the most unique trans-eQTL.

Conclusions: These results illustrate the highly dynamic pattern of CGV across three different environmental conditions that can be evoked by a stress response over a relatively short time-span (2 h) and that CGV is mainly determined by response related trans regulatory eQTL.
View Article and Find Full Text PDF

Download full-text PDF

Source
http://dx.doi.org/10.1186/s12864-017-3899-8DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5492678PMC
June 2017

Genetic Dissection of Morphometric Traits Reveals That Phytochrome B Affects Nucleus Size and Heterochromatin Organization in .

G3 (Bethesda) 2017 08 7;7(8):2519-2531. Epub 2017 Aug 7.

Molecular Plant Physiology, Institute of Environmental Biology, Utrecht University, 3584 CH, The Netherlands

Microscopically visible chromatin is partitioned into two major components in nuclei. On one hand, chromocenters are conspicuous foci of highly condensed "heterochromatic" domains that contain mostly repeated sequences. On the other hand, less condensed and gene-rich "euchromatin" emanates from these chromocenters. This differentiation, together with the dynamic nature of chromatin compaction in response to developmental and environmental stimuli, makes a powerful system for studying chromatin organization and dynamics. Heterochromatin dynamics can be monitored by measuring the Heterochromatin Index, , the proportion of nuclei displaying well-defined chromocenters, or the DNA fraction of chromocenters (relative heterochromatin fraction). Both measures are composite traits, thus their values represent the sum of effects of various underlying morphometric properties. We exploited genetic variation between natural occurring accessions to determine the genetic basis of individual nucleus and chromocenter morphometric parameters (area, perimeter, density, roundness, and heterogeneity) that together determine chromatin compaction. Our novel reductionist genetic approach revealed quantitative trait loci (QTL) for all measured traits. Genomic colocalization among QTL was limited, which suggests a complex genetic regulation of chromatin compaction. Yet genomic intervals of QTL for nucleus size (area and perimeter) both overlap with a known QTL for heterochromatin compaction that is explained by natural polymorphism in the red/far-red light and temperature receptor Phytochrome B. Mutant analyses and genetic complementation assays show that Phytochrome B is a negative regulator of nucleus size, revealing that perception of climatic conditions by a Phytochrome-mediated hub is a major determinant for coordinating nucleus size and heterochromatin compaction.
View Article and Find Full Text PDF

Download full-text PDF

Source
http://dx.doi.org/10.1534/g3.117.043539DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5555459PMC
August 2017

reGenotyper: Detecting mislabeled samples in genetic data.

PLoS One 2017 13;12(2):e0171324. Epub 2017 Feb 13.

Groningen Bioinformatics Centre, University of Groningen, Groningen, The Netherlands.

In high-throughput molecular profiling studies, genotype labels can be wrongly assigned at various experimental steps; the resulting mislabeled samples seriously reduce the power to detect the genetic basis of phenotypic variation. We have developed an approach to detect potential mislabeling, recover the "ideal" genotype and identify "best-matched" labels for mislabeled samples. On average, we identified 4% of samples as mislabeled in eight published datasets, highlighting the necessity of applying a "data cleaning" step before standard data analysis.
View Article and Find Full Text PDF

Download full-text PDF

Source
http://journals.plos.org/plosone/article?id=10.1371/journal.pone.0171324PLOS
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5305221PMC
August 2017

AraQTL - workbench and archive for systems genetics in Arabidopsis thaliana.

Plant J 2017 Mar 13;89(6):1225-1235. Epub 2017 Feb 13.

Laboratory of Nematology, Wageningen University, Droevendaalsesteeg 1, Wageningen, NL-6708 PB, The Netherlands.

Genetical genomics studies uncover genome-wide genetic interactions between genes and their transcriptional regulators. High-throughput measurement of gene expression in recombinant inbred line populations has enabled investigation of the genetic architecture of variation in gene expression. This has the potential to enrich our understanding of the molecular mechanisms affected by and underlying natural variation. Moreover, it contributes to the systems biology of natural variation, as a substantial number of experiments have resulted in a valuable amount of interconnectable phenotypic, molecular and genotypic data. A number of genetical genomics studies have been published for Arabidopsis thaliana, uncovering many expression quantitative trait loci (eQTLs). However, these complex data are not easily accessible to the plant research community, leaving most of the valuable genetic interactions unexplored as cross-analysis of these studies is a major effort. We address this problem with AraQTL (http://www.bioinformatics.nl/Ara QTL/), an easily accessible workbench and database for comparative analysis and meta-analysis of all published Arabidopsis eQTL datasets. AraQTL provides a workbench for comparing, re-using and extending upon the results of these experiments. For example, one can easily screen a physical region for specific local eQTLs that could harbour candidate genes for phenotypic QTLs, or detect gene-by-environment interactions by comparing eQTLs under different conditions.
View Article and Find Full Text PDF

Download full-text PDF

Source
http://dx.doi.org/10.1111/tpj.13457DOI Listing
March 2017