Papers by Joost Keurentjes
In compatible interactions between plants and viruses that result in systemic infection, symptom ... more In compatible interactions between plants and viruses that result in systemic infection, symptom development is a major phenotypic trait. However, host determinants governing this trait are mostly unknown, and the mechanisms underlying it are still poorly understood. In a previous study on the Arabidopsis thaliana¿Plum pox virus (PPV) pathosystem, we showed a large degree of variation in symptom development among susceptible accessions. In particular, Cvi-1 (Cape Verde islands) accumulates viral particules but remains symptomless, Col-0 (Columbia) sometimes shows weak symptoms compared with Ler (Landsberg erecta), which always shows severe symptoms. Genetic analyses of Col × Ler and Cvi × Ler F2 and recombinant inbred line (RIL) populations suggested that symptom development as well as viral accumulation traits are polygenic and quantitative. Three of the symptom quantitative trait loci (QTL) identified could be confirmed in near-isogenic lines, including PSI1 (PPV symptom induction...
Genetics, 2007
In Arabidopsis recombinant inbred line (RIL) populations are widely used for quantitative trait l... more In Arabidopsis recombinant inbred line (RIL) populations are widely used for quantitative trait locus (QTL) analyses. However, mapping analyses with this type of population can be limited because of the masking effects of major QTL and epistatic interactions of multiple QTL. An alternative type of immortal experimental population commonly used in plant species are sets of introgression lines. Here we introduce the development of a genomewide coverage near-isogenic line (NIL) population of Arabidopsis thaliana, by introgressing genomic regions from the Cape Verde Islands (Cvi) accession into the Landsberg erecta (Ler) genetic background. We have empirically compared the QTL mapping power of this new population with an already existing RIL population derived from the same parents. For that, we analyzed and mapped QTL affecting six developmental traits with different heritability. Overall, in the NIL population smaller-effect QTL than in the RIL population could be detected although th...
Plants develop an enhanced defensive capacity against a broad spectrum of plant pathogens after c... more Plants develop an enhanced defensive capacity against a broad spectrum of plant pathogens after colonization of the roots by selected strains of nonpathogenic biocontrol bacteria. In Arabidopsis thaliana, this induced systemic resistance (ISR) functions independently of salicylic acid but requires an intact response to the plant hormones jasmonic acid (JA) and ethylene. To further investigate the roles of JA and ethylene in the ISR signalling pathway, the levels of these signalling molecules were determined in A. thaliana upon induction of ISR by Pseudomonas¯uorescens WCS417r and subsequent challenge inoculation with Pseudomonas syringae pv. tomato DC3000. Upon treatment of the roots with ISR-inducing WCS417r bacteria, neither the JA content, nor the level of ethylene evolution was altered in systemically resistant leaves. In®ltration of leaves with WCS417r triggered the JA-and ethylene-dependent ISR pathway, but did not cause local changes in the production of either of these signalling molecules. These results indicate that rhizobacteria-mediated ISR is not based on the induction of changes in the biosynthesis of either JA or ethylene. However, in ISR-expressing plants the capacity to convert 1-aminocyclopropane-1-carboxylate (ACC) to ethylene was signi®cantly enhanced, providing a greater potential to produce ethylene upon pathogen attack. *
Nature genetics, 2006
Variation for metabolite composition and content is often observed in plants. However, it is poor... more Variation for metabolite composition and content is often observed in plants. However, it is poorly understood to what extent this variation has a genetic basis. Here, we describe the genetic analysis of natural variation in the metabolite composition in Arabidopsis thaliana. Instead of focusing on specific metabolites, we have applied empirical untargeted metabolomics using liquid chromatography-time of flight mass spectrometry (LC-QTOF MS). This uncovered many qualitative and quantitative differences in metabolite accumulation between A. thaliana accessions. Only 13.4% of the mass peaks were detected in all 14 accessions analyzed. Quantitative trait locus (QTL) analysis of more than 2,000 mass peaks, detected in a recombinant inbred line (RIL) population derived from the two most divergent accessions, enabled the identification of QTLs for about 75% of the mass signals. More than one-third of the signals were not detected in either parent, indicating the large potential for modifi...
Nature protocols, 2014
Hybrid crop varieties are traditionally produced by selecting and crossing parental lines to eval... more Hybrid crop varieties are traditionally produced by selecting and crossing parental lines to evaluate hybrid performance. Reverse breeding allows doing the opposite: selecting uncharacterized heterozygotes and generating parental lines from them. With these, the selected heterozygotes can be recreated as F1 hybrids, greatly increasing the number of hybrids that can be screened in breeding programs. Key to reverse breeding is the suppression of meiotic crossovers in a hybrid plant to ensure the transmission of nonrecombinant chromosomes to haploid gametes. These gametes are subsequently regenerated as doubled-haploid (DH) offspring. Each DH carries combinations of its parental chromosomes, and complementing pairs can be crossed to reconstitute the initial hybrid. Achiasmatic meiosis and haploid generation result in uncommon phenotypes among offspring owing to chromosome number variation. We describe how these features can be dealt with during a reverse-breeding experiment, which can ...
Genome Biology, 2008
Plant carbohydrate metabolism <p>Multiparallel QTL analysis of 15 <it>Arabidopsis</it> primary ca... more Plant carbohydrate metabolism <p>Multiparallel QTL analysis of 15 <it>Arabidopsis</it> primary carbohydrate metabolism enzymes reveals that traits affecting primary metabolism are often correlated.</p> Abstract Background: Plant primary carbohydrate metabolism is complex and flexible, and is regulated at many levels. Changes of transcript levels do not always lead to changes in enzyme activities, and these do not always affect metabolite levels and fluxes. To analyze interactions between these three levels of function, we have performed parallel genetic analyses of 15 enzyme activities involved in primary carbohydrate metabolism, transcript levels for their encoding structural genes, and a set of relevant metabolites. Quantitative analyses of each trait were performed in the Arabidopsis thaliana Ler × Cvi recombinant inbred line (RIL) population and subjected to correlation and quantitative trait locus (QTL) analysis.
European Journal of Plant Pathology, 2001
Plants develop an enhanced defensive capacity against a broad spectrum of plant pathogens after c... more Plants develop an enhanced defensive capacity against a broad spectrum of plant pathogens after colonization of the roots by selected strains of nonpathogenic biocontrol bacteria. In Arabidopsis thaliana, this induced systemic resistance (ISR) functions independently of salicylic acid but requires an intact response to the plant hormones jasmonic acid (JA) and ethylene. To further investigate the roles of JA and ethylene in the ISR signalling pathway, the levels of these signalling molecules were determined in A. thaliana upon induction of ISR by Pseudomonas¯uorescens WCS417r and subsequent challenge inoculation with Pseudomonas syringae pv. tomato DC3000. Upon treatment of the roots with ISR-inducing WCS417r bacteria, neither the JA content, nor the level of ethylene evolution was altered in systemically resistant leaves. In®ltration of leaves with WCS417r triggered the JA-and ethylene-dependent ISR pathway, but did not cause local changes in the production of either of these signalling molecules. These results indicate that rhizobacteria-mediated ISR is not based on the induction of changes in the biosynthesis of either JA or ethylene. However, in ISR-expressing plants the capacity to convert 1-aminocyclopropane-1-carboxylate (ACC) to ethylene was signi®cantly enhanced, providing a greater potential to produce ethylene upon pathogen attack. *
We here describe the MetaNetwork protocol to reconstruct metabolic networks using metabolite abun... more We here describe the MetaNetwork protocol to reconstruct metabolic networks using metabolite abundance data from segregating populations. MetaNetwork maps metabolite quantitative trait loci (mQTLs) underlying variation in metabolite abundance in individuals of a segregating population using a two-part model to account for the often observed spike in the distribution of metabolite abundance data. MetaNetwork predicts and visualizes potential associations between metabolites using correlations of mQTL profiles, rather than of abundance profiles. Simulation and permutation procedures are used to assess statistical significance. Analysis of about 20 metabolite mass peaks from a mass spectrometer takes a few minutes on a desktop computer. Analysis of 2,000 mass peaks will take up to 4 days. In addition, MetaNetwork is able to integrate high-throughput data from subsequent metabolomics, transcriptomics and proteomics experiments in conjunction with traditional phenotypic data. This way MetaNetwork will contribute to a better integration of such data into systems biology. 7 0 0 2 © natureprotocols / m o c . e r u t a n . w w w / / : p t t h NATURE PROTOCOLS | VOL.2 NO.3 | 2007 | 685 PROTOCOL
Genetics, 2014
Heritability is a central parameter in quantitative genetics, both from an evolutionary and a bre... more Heritability is a central parameter in quantitative genetics, both from an evolutionary and a breeding perspective. For plant traits heritability is traditionally estimated by comparing within and between genotype variability. This approach estimates broad-sense heritability, and does not account for different genetic relatedness. With the availability of high-density markers there is growing interest in marker based estimates of narrow-sense heritability, using mixed models in which genetic relatedness is estimated from genetic markers. Such estimates have received much attention in human genetics but are rarely reported for plant traits. A major obstacle is that current methodology and software assume a single phenotypic value per genotype, hence requiring genotypic means. An alternative that we propose here, is to use mixed models at individual plant or plot level. Using statistical arguments, simulations and real data we investigate the feasibility of both approaches, and how these affect genomic prediction with G-BLUP and genome-wide association studies. Heritability estimates obtained from genotypic means had very large standard errors and were sometimes biologically unrealistic. Mixed models at individual plant or plot level produced more realistic estimates, and for simulated traits standard errors were up to 13 times smaller. Genomic prediction was also improved by using these mixed models, with up to a 49% increase in accuracy. For GWAS on simulated traits, the use of individual plant data gave almost no increase in power. The new methodology is applicable to any complex trait where multiple replicates of individual genotypes can be scored. This includes important agronomic crops, as well as bacteria and fungi.
Phytopathology, 2003
de Boer, M., Bom, P., Kindt, F., Keurentjes, J. J. B., van der Sluis, I., van Loon, L. C., and Ba... more de Boer, M., Bom, P., Kindt, F., Keurentjes, J. J. B., van der Sluis, I., van Loon, L. C., and Bakker, P. A. H. M. 2003. Control of Fusarium wilt of radish by combining Pseudomonas putida strains that have different disease-suppressive mechanisms. Phytopathology 93:626-632.
Proceedings of the National Academy of Sciences of the United States of America, 2007
Accessions of a plant species can show considerable genetic differences that are analyzed effecti... more Accessions of a plant species can show considerable genetic differences that are analyzed effectively by using recombinant inbred line (RIL) populations. Here we describe the results of genome-wide expression variation analysis in an RIL population of Arabidopsis thaliana. For many genes, variation in expression could be explained by expression quantitative trait loci (eQTLs). The nature and consequences of this variation are discussed based on additional genetic parameters, such as heritability and transgression and by examining the genomic position of eQTLs versus gene position, polymorphism frequency, and gene ontology. Furthermore, we developed an approach for genetic regulatory network construction by combining eQTL mapping and regulator candidate gene selection. The power of our method was shown in a case study of genes associated with flowering time, a well studied regulatory network in Arabidopsis. Results that revealed clusters of coregulated genes and their most likely reg...
Proceedings of The National Academy of Sciences, 2009
Rising demand for food and bioenergy makes it imperative to breed for increased crop yield. Veget... more Rising demand for food and bioenergy makes it imperative to breed for increased crop yield. Vegetative plant growth could be driven by resource acquisition or developmental programs. Metabolite profiling in 94 Arabidopsis accessions revealed that biomass correlates negatively with many metabolites, especially starch. Starch accumulates in the light and is degraded at night to provide a sustained supply of carbon
Trends in Plant Science, 2011
Molecular biologists typically restrict systems biology to cellular levels. By contrast, ecologis... more Molecular biologists typically restrict systems biology to cellular levels. By contrast, ecologists define biological systems as communities of interacting individuals at different trophic levels that process energy, nutrient and information flows. Modern plant breeding needs to increase agricultural productivity while decreasing the ecological footprint. This requires a holistic systems biology approach that couples different aggregation levels while considering the variables that affect these biological systems from cell to community. The challenge is to generate accurate experimental data that can be used together with modelling concepts and techniques that allow experimentally verifying in silico predictions. The coupling of aggregation levels in plant sciences, termed Integral Quantification of Biological Organization (IQ BiO ), might enhance our abilities to generate new desired plant phenotypes.
THE PLANT CELL ONLINE, 2009
Nearly 100 genes and functional polymorphisms underlying natural variation in plant development a... more Nearly 100 genes and functional polymorphisms underlying natural variation in plant development and physiology have been identified. In crop plants, these include genes involved in domestication traits, such as those related to plant architecture, fruit and seed structure and morphology, as well as yield and quality traits improved by subsequent crop breeding. In wild plants, comparable traits have been dissected mainly in Arabidopsis thaliana. In this review, we discuss the major contributions of the analysis of natural variation to our understanding of plant development and physiology, focusing in particular on the timing of germination and flowering, plant growth and morphology, primary metabolism, and mineral accumulation. Overall, functional polymorphisms appear in all types of genes and gene regions, and they may have multiple mutational causes. However, understanding this diversity in relation to adaptation and environmental variation is a challenge for which tools are now available.
Proceedings of the National Academy of Sciences, 2006
The possible role of the sucrose-splitting enzymes sucrose synthase and invertase in elongating r... more The possible role of the sucrose-splitting enzymes sucrose synthase and invertase in elongating roots and hypocotyls of Arabidopsis was tested by using a combination of histochemical methods and quantitative trait locus (QTL) analysis. Lengths of roots and hypocotyls correlated better with invertase activities than with sucrose synthase activities. The highest correlations were observed with activities in the elongating zones of roots. The genetic basis of these correlations was studied by using QTL analysis. Several loci, affecting invertase activity, colocated with loci that had an effect on root or hypocotyl length. Further fine mapping of a major locus for root length, but not for hypocotyl length (top chromosome 1), consistently showed colocation with the locus for invertase activity containing a gene coding for a vacuolar invertase. The analysis of a functional knockout line confirmed the role of this invertase in root elongation, whereas other invertase genes might play a role in hypocotyl elongation. Thus, we show the power of QTL analysis, combined for morphological and biochemical traits, followed by fine-mapping and mutant analysis, in unraveling the function of genes and their role in growth and development.
Plant, Cell and Environment, 2005
Water limitation is one of the most important factors limiting crop productivity world-wide and h... more Water limitation is one of the most important factors limiting crop productivity world-wide and has likely been an important selective regime influencing the evolution of plant physiology. Understanding the genetic and physiological basis of drought adaptation is therefore important for improving crops as well as for understanding the evolution of wild species. Here, results are presented from quantitative trait loci (QTL) mapping of flowering time (a drought escape mechanism) and carbon stable isotope ratio (d d d d 13 C) (a drought-avoidance mechanism) in Arabidopsis thaliana. Whole-genome scans were performed using multiple-QTL models for both additive and epistatic QTL effects. We mapped five QTL affecting flowering time and five QTL affecting d d d d 13 C, but two genomic regions contained QTL with effects on both traits, suggesting a potential pleiotropic relationship. In addition, we observed QTL-QTL interaction for both traits. Two d d d d 13 C QTL were captured in nearisogenic lines to further characterize their physiological basis. These experiments revealed allelic effects on d d d d 13 C through the upstream trait of stomatal conductance with subsequent consequences for whole plant transpiration efficiency and water loss. Our findings document considerable natural genetic variation in whole-plant, drought resistance physiology of Arabidopsis and highlight the value of quantitative genetic approaches for exploring functional relationships regulating physiology.
PLANT PHYSIOLOGY, 2012
Recent advances in -omics technologies such as transcriptomics, metabolomics, and proteomics alon... more Recent advances in -omics technologies such as transcriptomics, metabolomics, and proteomics along with genotypic profiling have permitted dissection of the genetics of complex traits represented by molecular phenotypes in nonmodel species. To identify the genetic factors underlying variation in primary metabolism in potato (Solanum tuberosum), we have profiled primary metabolite content in a diploid potato mapping population, derived from crosses between S. tuberosum and wild relatives, using gas chromatography-time of flight-mass spectrometry. In total, 139 polar metabolites were detected, of which we identified metabolite quantitative trait loci for approximately 72% of the detected compounds. In order to obtain an insight into the relationships between metabolic traits and classical phenotypic traits, we also analyzed statistical associations between them. The combined analysis of genetic information through quantitative trait locus coincidence and the application of statistical learning methods provide information on putative indicators associated with the alterations in metabolic networks that affect complex phenotypic traits.
PLANT PHYSIOLOGY, 2010
Plants display enormous diversity in their metabolism. Although the biosynthesis and function of ... more Plants display enormous diversity in their metabolism. Although the biosynthesis and function of the myriads of plant metabolites has been studied for decades, we have little understanding of the interactions between metabolites, metabolite signaling, interactions with development and the role of metabolism in genotype-to-phenotype relationships. Technologies for the analysis of metabolites have made tremendous progress in recent years, both in terms of the number of metabolites that are identified and of throughput. Recent developments allow the construction of metabolic networks, and study of the role of these networks in plant growth and development. In this review, we discuss what types of information can be obtained from measurements of metabolites and what requirements they have with respect comprehensiveness of coverage and precision of identification and quantification, and outline procedures that can be implemented to validate the measurements. We then discuss what sorts of perturbations can be used to disturb metabolic networks, including environmental and physiological treatments, chemicals, reverse genetics and the use of natural genetic diversity. www.plant.org on April 27, 2016 -Published by www.plantphysiol.org Downloaded from K (2008) Prime: A web site that assembles tools for metabolomics and transcriptomics. In Silico Biol 8: 339-345 Alonso-Blanco C, Aarts MG, Bentsink L, Keurentjes JJB, Reymond M, Vreugdenhil D, Koornneef M (2009) What has natural variation taught us about plant development, physiology, and adaptation? Plant Cell 21: 1877-1896 Antoniewicz MR, Kelleher JK, Stephanopoulos G (2007) Accurate assessment of amino acid mass isotopomer distributions for metabolic flux analysis. Anal. Chem. 79: 7554-7559 Arrivault S, Guenther M, Ivakov A, Feil R, Vosloh D, van Dongen JT, Sulpice R, Stitt M (2009) Use of reverse-phase liquid chromatography, linked to tandem mass spectrometry, to profile the calvin cycle and other metabolic intermediates in arabidopsis rosettes at different carbon dioxide concentrations. Plant J. 59: 824-839 Balasubramanian S, Schwartz C, Singh A, Warthmann N, Kim MC, Maloof JN, Loudet O, Trainer GT, Dabi T, Borevitz JO, Chory J, Weigel D (2009) Qtl mapping in new arabidopsis thaliana advanced intercross-recombinant inbred lines. PLoS One 4: e4318 Barton DB, Pappl B, Delneri D , Oliver SB, Rattrav M, Bergman CM (2008) Systems biology of energetic and atomic costs in the yeast transcriptome, proteome, and metabolome. Nature Precedings. hdl:10101/npre.2008.1841.2 Barton NH (2000) Genetic hitchhiking. Phil. Trans. R. Soc. B 355: 1553-1562 Bassham JA (2003) Mapping the carbon reduction cycle: A personal retrospective. Photosynthesis Res. 76: 37-52 Bassham JA, Krause GH (1969) Free energy changes and metabolic regulation in steady-state photosynthetic carbon reduction. Biochim. Biophys. Acta 189: 207-221 Bennett BD, Yuan J, Kimball EH, Rabinowitz JD (2002) Absolute quantitation of intracellular metaboliteconcentrations by an isotope ratio-based approach. Nat. Protoc. 3, 1299-1311 Bennett BD, Kimball EH, Gao M, Osterhout R, Van Dien SJ, Rabinowitz JD (2009) Absolute metabolite concentrations and implied enzyme active site occupancy in escherichia coli. Nat. Chem. Biol. 5: 593-599 Benson AA (2002) Following the path of carbon in photosynthesis: A personal story. Photosynthesis Res. 73: 31-49 Bikard D, Patel D, Le Mette C, Giorgi V, Camilleri C, Bennett MJ, Loudet O (2009) Divergent evolution of duplicate genes leads to genetic incompatibilities within a.
PLANT PHYSIOLOGY, 2010
Gene expression differences between individuals within a species can be largely explained by diff... more Gene expression differences between individuals within a species can be largely explained by differences in genetic background. The effect of genetic variants (alleles) of genes on expression can be studied in a multifactorial way by the application of genetical genomics or expression quantitative trait locus mapping. In this paper, we present a strategy to construct regulatory networks by the application of genetical genomics in combination with transcript profiling of mutants that are disrupted in single genes. We describe the network identification downstream of the receptor-like kinase ERECTA in Arabidopsis (Arabidopsis thaliana). Extending genetical genomics on the Landsberg erecta/Cape Verde Islands (Ler/Cvi) recombinant inbred population with expression profiling of monogenic mutants enabled the identification of regulatory networks in the so far elusive ERECTA signal transduction cascade. We provide evidence that ERECTA is the causal gene for the major hotspot for transcript regulation in the Arabidopsis Ler/Cvi recombinant inbred population. We further propose additional genetic variation between Ler and Cvi in loci of the signaling pathway downstream of ERECTA and suggest candidate genes underlying these loci. Integration of publicly available microarray expression data of other monogenic mutants allowed us to link ERECTA to a downstream mitogen-activated protein kinase signaling cascade. Our study shows that microarray data of monogenic mutants can be effectively used in combination with genetical genomics data to enhance the identification of genetic regulatory networks.
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Papers by Joost Keurentjes