@article{MeyerKustererLisecetal.2009, author = {Meyer, Rhonda Christiane and Kusterer, Barbara and Lisec, Jan and Steinfath, Matthias and Becher, Martina and Scharr, Hanno and Melchinger, Albrecht E. and Selbig, Joachim and Schurr, Ulrich and Willmitzer, Lothar and Altmann, Thomas}, title = {QTL analysis of early stage heterosis for biomass in Arabidopsis}, series = {Theoretical and applied genetics}, volume = {129}, journal = {Theoretical and applied genetics}, number = {2}, publisher = {Springer Nature}, address = {Berlin}, issn = {1432-2242}, doi = {10.1007/s00122-009-1074-6}, pages = {227 -- 237}, year = {2009}, abstract = {The main objective of this study was to identify genomic regions involved in biomass heterosis using QTL, generation means, and mode-of-inheritance classification analyses. In a modified North Carolina Design III we backcrossed 429 recombinant inbred line and 140 introgression line populations to the two parental accessions, C24 and Col-0, whose F 1 hybrid exhibited 44\% heterosis for biomass. Mid-parent heterosis in the RILs ranged from -31 to 99\% for dry weight and from -58 to 143\% for leaf area. We detected ten genomic positions involved in biomass heterosis at an early developmental stage, individually explaining between 2.4 and 15.7\% of the phenotypic variation. While overdominant gene action was prevalent in heterotic QTL, our results suggest that a combination of dominance, overdominance and epistasis is involved in biomass heterosis in this Arabidopsis cross.}, language = {en} } @article{SteinfathGaertnerLisecetal.2009, author = {Steinfath, Matthias and G{\"a}rtner, Tanja and Lisec, Jan and Meyer, Rhonda Christiane and Altmann, Thomas and Willmitzer, Lothar and Selbig, Joachim}, title = {Prediction of hybrid biomass in Arabidopsis thaliana by selected parental SNP and metabolic markers}, series = {Theoretical and applied genetics : TAG ; international journal of plant breeding research}, volume = {120}, journal = {Theoretical and applied genetics : TAG ; international journal of plant breeding research}, publisher = {Springer}, address = {Berlin}, issn = {0040-5752}, doi = {10.1007/s00122-009-1191-2}, pages = {239 -- 247}, year = {2009}, abstract = {A recombinant inbred line (RIL) population, derived from two Arabidopsis thaliana accessions, and the corresponding testcrosses with these two original accessions were used for the development and validation of machine learning models to predict the biomass of hybrids. Genetic and metabolic information of the RILs served as predictors. Feature selection reduced the number of variables (genetic and metabolic markers) in the models by more than 80\% without impairing the predictive power. Thus, potential biomarkers have been revealed. Metabolites were shown to bear information on inherited macroscopic phenotypes. This proof of concept could be interesting for breeders. The example population exhibits substantial mid-parent biomass heterosis. The results of feature selection could therefore be used to shed light on the origin of heterosis. In this respect, mainly dominance effects were detected.}, language = {en} } @article{LissoAltmannMuessig2006, author = {Lisso, Janina and Altmann, Thomas and M{\"u}ssig, Carsten}, title = {The AtNFXL1 gene encodes a NF-X1 type zinc finger protein required for growth under salt stress}, series = {FEBS letters : the journal for rapid publication of short reports in molecular biosciences}, volume = {580}, journal = {FEBS letters : the journal for rapid publication of short reports in molecular biosciences}, number = {22}, publisher = {Elsevier}, address = {Amsterdam}, issn = {0014-5793}, doi = {10.1016/j.febslet.2006.07.079}, pages = {4851 -- 4856}, year = {2006}, abstract = {The human NF-X1 protein and homologous proteins in eukaryotes represent a class of transcription factors which are characterised. by NF-X1 type zinc finger motifs. The Arabidopsis genome encodes two NF-X1 homologs, which we termed AtNFXL1 and AtNFXL2. Growth and survival was impaired in atnfxl1 knock-out mutants and AtNFXL1-antisense plants under salt stress in comparison to wild-type plants. In contrast, 35S: :AtNFXL1 plants showed higher survival rates. The AtNFXL2 protein potentially plays an antagonistic role. The Arabidopsis NF-X1 type zinc finger proteins likely are part of regulatory mechanisms, which protect major processes such as photosynthesis.}, language = {en} } @article{LissoAltmannMuessig2006, author = {Lisso, Janina and Altmann, Thomas and M{\"u}ssig, Carsten}, title = {Metabolic changes in fruits of the tomato d(x) mutant}, series = {Phytochemistry : an international journal of plant biochemistry}, volume = {67}, journal = {Phytochemistry : an international journal of plant biochemistry}, number = {20}, publisher = {Elsevier}, address = {Oxford}, issn = {0031-9422}, doi = {10.1016/j.phytochem.2006.07.008}, pages = {2232 -- 2238}, year = {2006}, language = {en} } @article{TorjekWituckaWallMeyeretal.2006, author = {Torjek, Otto and Witucka-Wall, Hanna and Meyer, Rhonda C. and von Korff, Maria and Kusterer, Barbara and Rautengarten, Carsten and Altmann, Thomas}, title = {Segregation distortion in Arabidopsis C24/Col-0 and Col-0/C24 recombinant inbred line populations is due to reduced fertility caused by epistatic interaction of two loci}, series = {Theoretical and applied genetics}, volume = {113}, journal = {Theoretical and applied genetics}, publisher = {Springer}, address = {Berlin}, issn = {0040-5752}, doi = {10.1007/s00122-006-0402-3}, pages = {1551 -- 1561}, year = {2006}, abstract = {A new large set of reciprocal recombinant inbred lines (RILs) was created between the Arabidopsis accessions Col-0 and C24 for quantitative trait mapping approaches, consisting of 209 Col-0 x C24 and 214 C24 x Col-0 F-7 RI lines. Genotyping was performed using 110 evenly distributed framework single nucleotide polymorphism markers, yielding a genetic map of 425.70 cM, with an average interval of 3.87 cM. Segregation distortion (SD) was observed in several genomic regions during the construction of the genetic map. Linkage disequilibrium analysis revealed an association between a distorted region at the bottom of chromosome V and a non-distorted region on chromosome IV. A detailed analysis of the RILs for these two regions showed that an SD occurred when homozygous Col-0 alleles on chromosome IV coincided with homozygous C24 alleles at the bottom of chromosome V. Using nearly isogenic lines segregating for the distorted region we confirmed that this genotypic composition leads to reduced fertility and fitness.}, language = {en} } @article{EdlichMuthMurayaAltmannetal.2016, author = {Edlich-Muth, Christian and Muraya, Moses M. and Altmann, Thomas and Selbig, Joachim}, title = {Phenomic prediction of maize hybrids}, series = {Biosystems : journal of biological and information processing sciences}, volume = {146}, journal = {Biosystems : journal of biological and information processing sciences}, publisher = {Elsevier}, address = {Oxford}, issn = {0303-2647}, doi = {10.1016/j.biosystems.2016.05.008}, pages = {102 -- 109}, year = {2016}, abstract = {Phenomic experiments are carried out in large-scale plant phenotyping facilities that acquire a large number of pictures of hundreds of plants simultaneously. With the aid of automated image processing, the data are converted into genotype-feature matrices that cover many consecutive days of development. Here, we explore the possibility of predicting the biomass of the fully grown plant from early developmental stage image-derived features. We performed phenomic experiments on 195 inbred and 382 hybrid maizes varieties and followed their progress from 16 days after sowing (DAS) to 48 DAS with 129 image-derived features. By applying sparse regression methods, we show that 73\% of the variance in hybrid fresh weight of fully-grown plants is explained by about 20 features at the three-leaf-stage or earlier. Dry weight prediction explained over 90\% of the variance. When phenomic features of parental inbred lines were used as predictors of hybrid biomass, the proportion of variance explained was 42 and 45\%, for fresh weight and dry weight models consisting of 35 and 36 features, respectively. These models were very robust, showing only a small amount of variation in performance over the time scale of the experiment. We also examined mid-parent heterosis in phenomic features. Feature heterosis displayed a large degree of variance which resulted in prediction performance that was less robust than models of either parental or hybrid predictors. Our results show that phenomic prediction is a viable alternative to genomic and metabolic prediction of hybrid performance. In particular, the utility of early-stage parental lines is very encouraging. (C) 2016 Elsevier Ireland Ltd. All rights reserved.}, language = {en} } @article{CwiekKupczynskaAltmannArendetal.2016, author = {´Cwiek-Kupczynska, Hanna and Altmann, Thomas and Arend, Daniel and Arnaud, Elizabeth and Chen, Dijun and Cornut, Guillaume and Fiorani, Fabio and Frohmberg, Wojciech and Junker, Astrid and Klukas, Christian and Lange, Matthias and Mazurek, Cezary and Nafissi, Anahita and Neveu, Pascal and van Oeveren, Jan and Pommier, Cyril and Poorter, Hendrik and Rocca-Serra, Philippe and Sansone, Susanna-Assunta and Scholz, Uwe and van Schriek, Marco and Seren, {\"U}mit and Usadel, Bjorn and Weise, Stephan and Kersey, Paul and Krajewski, Pawel}, title = {Measures for interoperability of phenotypic data: minimum information requirements and formatting}, series = {Plant Methods}, volume = {12}, journal = {Plant Methods}, publisher = {BioMed Central}, address = {London}, issn = {1746-4811}, doi = {10.1186/s13007-016-0144-4}, pages = {18}, year = {2016}, abstract = {Background: Plant phenotypic data shrouds a wealth of information which, when accurately analysed and linked to other data types, brings to light the knowledge about the mechanisms of life. As phenotyping is a field of research comprising manifold, diverse and time-consuming experiments, the findings can be fostered by reusing and combining existing datasets. Their correct interpretation, and thus replicability, comparability and interoperability, is possible provided that the collected observations are equipped with an adequate set of metadata. So far there have been no common standards governing phenotypic data description, which hampered data exchange and reuse. Results: In this paper we propose the guidelines for proper handling of the information about plant phenotyping experiments, in terms of both the recommended content of the description and its formatting. We provide a document called "Minimum Information About a Plant Phenotyping Experiment", which specifies what information about each experiment should be given, and a Phenotyping Configuration for the ISA-Tab format, which allows to practically organise this information within a dataset. We provide examples of ISA-Tab-formatted phenotypic data, and a general description of a few systems where the recommendations have been implemented. Conclusions: Acceptance of the rules described in this paper by the plant phenotyping community will help to achieve findable, accessible, interoperable and reusable data.}, language = {en} } @article{BurkartWacoJosefssonDilkesetal.2012, author = {Burkart-Waco, Diana and Josefsson, Caroline and Dilkes, Brian and Kozloff, Nora and Torjek, Otto and Meyer, Rhonda C. and Altmann, Thomas and Comai, Luca}, title = {Hybrid incompatibility in arabidopsis is determined by a Multiple-Locus genetic network}, series = {Plant physiology : an international journal devoted to physiology, biochemistry, cellular and molecular biology, biophysics and environmental biology of plants}, volume = {158}, journal = {Plant physiology : an international journal devoted to physiology, biochemistry, cellular and molecular biology, biophysics and environmental biology of plants}, number = {2}, publisher = {American Society of Plant Physiologists}, address = {Rockville}, issn = {0032-0889}, doi = {10.1104/pp.111.188706}, pages = {801 -- 812}, year = {2012}, abstract = {The cross between Arabidopsis thaliana and the closely related species Arabidopsis arenosa results in postzygotic hybrid incompatibility, manifested as seed death. Ecotypes of A. thaliana were tested for their ability to produce live seed when crossed to A. arenosa. The identified genetic variation was used to map quantitative trait loci (QTLs) encoded by the A. thaliana genome that affect the frequency of postzygotic lethality and the phenotypes of surviving seeds. Seven QTLs affecting the A. thaliana component of this hybrid incompatibility were identified by crossing a Columbia x C24 recombinant inbred line population to diploid A. arenosa pollen donors. Additional epistatic loci were identified based on their pairwise interaction with one or several of these QTLs. Epistatic interactions were detected for all seven QTLs. The two largest additive QTLs were subjected to fine-mapping, indicating the action of at least two genes in each. The topology of this network reveals a large set of minor-effect loci from the maternal genome controlling hybrid growth and viability at different developmental stages. Our study establishes a framework that will enable the identification and characterization of genes and pathways in A. thaliana responsible for hybrid lethality in the A. thaliana x A. arenosa interspecific cross.}, language = {en} } @article{MeyerWituckaWallBecheretal.2012, author = {Meyer, Rhonda C. and Witucka-Wall, Hanna and Becher, Martina and Blacha, Anna Maria and Boudichevskaia, Anastassia and D{\"o}rmann, Peter and Fiehn, Oliver and Friedel, Svetlana and von Korff, Maria and Lisec, Jan and Melzer, Michael and Repsilber, Dirk and Schmidt, Renate and Scholz, Matthias and Selbig, Joachim and Willmitzer, Lothar and Altmann, Thomas}, title = {Heterosis manifestation during early Arabidopsis seedling development is characterized by intermediate gene expression and enhanced metabolic activity in the hybrids}, series = {The plant journal}, volume = {71}, journal = {The plant journal}, number = {4}, publisher = {Wiley-Blackwell}, address = {Hoboken}, issn = {0960-7412}, doi = {10.1111/j.1365-313X.2012.05021.x}, pages = {669 -- 683}, year = {2012}, abstract = {Heterosis-associated cellular and molecular processes were analyzed in seeds and seedlings of Arabidopsis thaliana accessions Col-0 and C24 and their heterotic hybrids. Microscopic examination revealed no advantages in terms of hybrid mature embryo organ sizes or cell numbers. Increased cotyledon sizes were detectable 4 days after sowing. Growth heterosis results from elevated cell sizes and numbers, and is well established at 10 days after sowing. The relative growth rates of hybrid seedlings were most enhanced between 3 and 4 days after sowing. Global metabolite profiling and targeted fatty acid analysis revealed maternal inheritance patterns for a large proportion of metabolites in the very early stages. During developmental progression, the distribution shifts to dominant, intermediate and heterotic patterns, with most changes occurring between 4 and 6 days after sowing. The highest incidence of heterotic patterns coincides with establishment of size differences at 4 days after sowing. In contrast, overall transcript patterns at 4, 6 and 10 days after sowing are characterized by intermediate to dominant patterns, with parental transcript levels showing the largest differences. Overall, the results suggest that, during early developmental stages, intermediate gene expression and higher metabolic activity in the hybrids compared to the parents lead to better resource efficiency, and therefore enhanced performance in the hybrids.}, language = {en} } @article{AndorfMeyerSelbigetal.2012, author = {Andorf, Sandra and Meyer, Rhonda C. and Selbig, Joachim and Altmann, Thomas and Repsilber, Dirk}, title = {Integration of a systems biological network analysis and QTL results for biomass heterosis in arabidopsis thaliana}, series = {PLoS one}, volume = {7}, journal = {PLoS one}, number = {11}, publisher = {PLoS}, address = {San Fransisco}, issn = {1932-6203}, doi = {10.1371/journal.pone.0049951}, pages = {10}, year = {2012}, abstract = {To contribute to a further insight into heterosis we applied an integrative analysis to a systems biological network approach and a quantitative genetics analysis towards biomass heterosis in early Arabidopsis thaliana development. The study was performed on the parental accessions C24 and Col-0 and the reciprocal crosses. In an over-representation analysis it was tested if the overlap between the resulting gene lists of the two approaches is significantly larger than expected by chance. Top ranked genes in the results list of the systems biological analysis were significantly over-represented in the heterotic QTL candidate regions for either hybrid as well as regarding mid-parent and best-parent heterosis. This suggests that not only a few but rather several genes that influence biomass heterosis are located within each heterotic QTL region. Furthermore, the overlapping resulting genes of the two integrated approaches were particularly enriched in biomass related pathways. A chromosome-wise over-representation analysis gave rise to the hypothesis that chromosomes number 2 and 4 probably carry a majority of the genes involved in biomass heterosis in the early development of Arabidopsis thaliana.}, language = {en} } @article{SchmidTorjekMeyeretal.2006, author = {Schmid, Karl J. and Torjek, Otto and Meyer, Rhonda C. and Schmuths, Heike and Hoffmann, Matthias H. and Altmann, Thomas}, title = {Evidence for a large-scale population structure of Arabidopsis thaliana from genome-wide single nucleotide polymorphism markers}, doi = {10.1007/s00122-006-0212-7}, year = {2006}, abstract = {Population-based methods for the genetic mapping of adaptive traits and the analysis of natural selection require that the population structure and demographic history of a species are taken into account. We characterized geographic patterns of genetic variation in the model plant Arabidopsis thaliana by genotyping 115 genome-wide single nucleotide polymorphism (SNP) markers in 351 accessions from the whole species range using a matrix-assisted laser desorption/ionization time-of-flight assay, and by sequencing of nine unlinked short genomic regions in a subset of 64 accessions. The observed frequency distribution of SNPs is not consistent with a constant-size neutral model of sequence polymorphism due to an excess of rare polymorphisms. There is evidence for a significant population structure as indicated by differences in genetic diversity between geographic regions. Accessions from Central Asia have a low level of polymorphism and an increased level of genome-wide linkage disequilibrium (LD) relative to accessions from the Iberian Peninsula and Central Europe. Cluster analysis with the structure program grouped Eurasian accessions into K=6 clusters. Accessions from the Iberian Peninsula and from Central Asia constitute distinct populations, whereas Central and Eastern European accessions represent admixed populations in which genomes were reshuffled by historical recombination events. These patterns likely result from a rapid postglacial recolonization of Eurasia from glacial refugial populations. Our analyses suggest that mapping populations for association or LD mapping should be chosen from regional rather than a species-wide sample or identified genetically as sets of individuals with similar average genetic distances}, language = {en} } @article{ChildsWituckaWallGuentheretal.2010, author = {Childs, Liam H. and Witucka-Wall, Hanna and Guenther, Torsten and Sulpice, Ronan and Korff, Maria V. and Stitt, Mark and Walther, Dirk and Schmid, Karl J. and Altmann, Thomas}, title = {Single feature polymorphism (SFP)-based selective sweep identification and association mapping of growth- related metabolic traits in Arabidopsis thaliana}, issn = {1471-2164}, doi = {10.1186/1471-2164-11-188}, year = {2010}, abstract = {Background: Natural accessions of Arabidopsis thaliana are characterized by a high level of phenotypic variation that can be used to investigate the extent and mode of selection on the primary metabolic traits. A collection of 54 A. thaliana natural accession-derived lines were subjected to deep genotyping through Single Feature Polymorphism (SFP) detection via genomic DNA hybridization to Arabidopsis Tiling 1.0 Arrays for the detection of selective sweeps, and identification of associations between sweep regions and growth-related metabolic traits. Results: A total of 1,072,557 high-quality SFPs were detected and indications for 3,943 deletions and 1,007 duplications were obtained. A significantly lower than expected SFP frequency was observed in protein-, rRNA-, and tRNA-coding regions and in non- repetitive intergenic regions, while pseudogenes, transposons, and non-coding RNA genes are enriched with SFPs. Gene families involved in plant defence or in signalling were identified as highly polymorphic, while several other families including transcription factors are depleted of SFPs. 198 significant associations between metabolic genes and 9 metabolic and growth-related phenotypic traits were detected with annotation hinting at the nature of the relationship. Five significant selective sweep regions were also detected of which one associated significantly with a metabolic trait. Conclusions: We generated a high density polymorphism map for 54 A. thaliana accessions that highlights the variability of resistance genes across geographic ranges and used it to identify selective sweeps and associations between metabolic genes and metabolic phenotypes. Several associations show a clear biological relationship, while many remain requiring further investigation.}, language = {en} } @article{SulpicePylIshiharaetal.2009, author = {Sulpice, Ronan and Pyl, Eva-Theresa and Ishihara, Hirofumi and Trenkamp, Sandra and Steinfath, Matthias and Witucka-Wall, Hanna and Gibon, Yves and Usadel, Bj{\"o}rn and Poree, Fabien and Piques, Maria Conceicao and von Korff, Maria and Steinhauser, Marie Caroline and Keurentjes, Joost J. B. and Guenther, Manuela and Hoehne, Melanie and Selbig, Joachim and Fernie, Alisdair R. and Altmann, Thomas and Stitt, Mark}, title = {Starch as a major integrator in the regulation of plant growth}, issn = {0027-8424}, doi = {10.1073/pnas.0903478106}, year = {2009}, abstract = {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 for growth. Multivariate analysis revealed that starch is an integrator of the overall metabolic response. We hypothesized that this reflects variation in a regulatory network that balances growth with the carbon supply. Transcript profiling in 21 accessions revealed coordinated changes of transcripts of more than 70 carbon-regulated genes and identified 2 genes (myo-inositol-1- phosphate synthase, a Kelch-domain protein) whose transcripts correlate with biomass. The impact of allelic variation at these 2 loci was shown by association mapping, identifying them as candidate lead genes with the potential to increase biomass production.}, language = {en} } @article{LisecSteinfathMeyeretal.2009, author = {Lisec, Jan and Steinfath, Matthias and Meyer, Rhonda C. and Selbig, Joachim and Melchinger, Albrecht E. and Willmitzer, Lothar and Altmann, Thomas}, title = {Identification of heterotic metabolite QTL in Arabidopsis thaliana RIL and IL populations}, issn = {0960-7412}, doi = {10.1111/j.1365-313X.2009.03910.x}, year = {2009}, abstract = {Two mapping populations of a cross between the Arabidopsis thaliana accessions Col-0 and C24 were cultivated and analyzed with respect to the levels of 181 metabolites to elucidate the biological phenomenon of heterosis at the metabolic level. The relative mid-parent heterosis in the F-1 hybrids was <20\% for most metabolic traits. The first mapping population consisting of 369 recombinant inbred lines (RILs) and their test cross progeny with both parents allowed us to determine the position and effect of 147 quantitative trait loci (QTL) for metabolite absolute mid-parent heterosis (aMPH). Furthermore, we identified 153 and 83 QTL for augmented additive (Z(1)) and dominance effects (Z(2)), respectively. We identified putative candidate genes for these QTL using the ARACYC database (http://www.arabidopsis.org/ biocyc), and calculated the average degree of dominance, which was within the dominance and over-dominance range for most metabolites. Analyzing a second population of 41 introgression lines (ILs) and their test crosses with the recurrent parent, we identified 634 significant differences in metabolite levels. Nine per cent of these effects were classified as over-dominant, according to the mode of inheritance. A comparison of both approaches suggested epistasis as a major contributor to metabolite heterosis in Arabidopsis. A linear combination of metabolite levels was shown to significantly correlate with biomass heterosis (r = 0.62).}, language = {en} } @article{MuessigLissoCollGarciaetal.2006, author = {M{\"u}ssig, Carsten and Lisso, Janina and Coll-Garcia, Danahe and Altmann, Thomas}, title = {Molecular analysis of brassinosteroid action}, doi = {10.1055/s-2005-873043}, year = {2006}, abstract = {Brassinosteroids (BRs) are steroidal plant hormones with important regulatory roles in various physiological processes, including growth, xylem differentiation, disease resistance, and stress tolerance. Several components of the BR signal transduction pathway have been identified. The extracellular domains of receptor kinases such as BRI1 perceive BRs and transduce the signal via intracellular kinase domains. Within the cell further kinases and phosphatases determine the phosphorylation status of transcription factors such as BES1 and BZR1. These factors mediate major BR effects. Studies of BR-regulated genes shed light on the molecular mode of BR action. Genes encoding cell-wall-modifying enzymes, enzymes of the BR biosynthetic pathway, transcription factors, and proteins involved in primary and secondary metabolism are subject to BR-regulation. Gene expression data also point at interactions with other phytohormones and a role of BR in stress responses. This article gives a survey of the BR-signaling pathway. Two BR-responsive genes, OPR3 and EXO, are described in detail}, language = {en} } @article{AltmannThimmEssigmannetal.2001, author = {Altmann, Thomas and Thimm, O. and Essigmann, B. and Kloska, Sebastian and Buckhout, Thomas J.}, title = {Response of arabidopsis to iron deficiency stress as revealed by microarray analysis}, year = {2001}, language = {en} } @article{AltmannMuessig2001, author = {Altmann, Thomas and M{\"u}ssig, Carsten}, title = {Brassinosteroid signaling in plants}, year = {2001}, language = {en} } @article{AltmannNarang2001, author = {Altmann, Thomas and Narang, R. A.}, title = {Phosphate accquisition heterosis in Arabidopsis thaliana : a morphological and physiological analysis}, year = {2001}, language = {en} } @article{AltmannKossmann2001, author = {Altmann, Thomas and Koßmann, Jens}, title = {Photosynthesis and primary metabolism}, issn = {1360-1385}, year = {2001}, language = {en} } @article{AltmannFiehnKloska2001, author = {Altmann, Thomas and Fiehn, Oliver and Kloska, Sebastian}, title = {Integrated studies on plant biology using multiparallel techniques}, year = {2001}, language = {en} } @article{AltmannUdvardiEssigmannetal.2002, author = {Altmann, Thomas and Udvardi, M. K. and Essigmann, B. and Colebatch, G. and Kloska, Sebastian and Smith, P. and Trevaskis, B.}, title = {Lotus japonicus functional genomics : cDNA microarray analysis uncovers novel nodulins}, isbn = {0-85199-591-8}, year = {2002}, language = {en} } @article{AltmannBrandtKloskaetal.2002, author = {Altmann, Thomas and Brandt, Stephan Peter and Kloska, Sebastian and Kehr, Julia}, title = {Using array hybridization to monitore gene expression at the single cell level}, year = {2002}, language = {en} } @article{AltmannvonGrollBerger2002, author = {Altmann, Thomas and von Groll, Uritza and Berger, Dieter}, title = {The subtilisin-like serine protease SDD1 mediates cell-cell signaling during Arabidopsis stomatal development}, year = {2002}, language = {en} } @article{AltmannMuessigFischer2002, author = {Altmann, Thomas and M{\"u}ssig, Carsten and Fischer, Sabine}, title = {Brassinosteroid-regulated gene expression}, year = {2002}, language = {en} } @article{AltmannBasseKerschbameretal.2002, author = {Altmann, Thomas and Basse, Christoph W. and Kerschbamer, Christine and Brustmann, Markus and Kahmann, Regine}, title = {Evidence for a Ustilago maydis steroid 5 alpha-reductase by functional expression in Arabidopsis det2-1 mutants}, year = {2002}, language = {en} } @article{AltmannSchlueterKoepkeetal.2002, author = {Altmann, Thomas and Schl{\"u}ter, U. and K{\"o}pke, D. and M{\"u}ssig, Carsten}, title = {Analysis of carbohydrate metabolism of CPD antisense plants and the brassinosteroid-deficient cbb1 mutant}, year = {2002}, language = {en} } @article{Altmann2002, author = {Altmann, Thomas}, title = {Methodik der funktionellen Genomanalyse : wie mit Mikroarrays die Aktivit{\"a}t vieler Gene erfasst wird}, year = {2002}, language = {de} } @article{AltmannColebatchKloskaetal.2002, author = {Altmann, Thomas and Colebatch, G. and Kloska, Sebastian and Trevaskis, B. and Freund, S. and Udvardi, M. K.}, title = {Novel aspects of symbiotic nitrogen fixation uncovered by transcript profiling with cDNA arrays}, year = {2002}, language = {en} } @article{MuessigAltmann2003, author = {M{\"u}ssig, Carsten and Altmann, Thomas}, title = {Genomic brassinosteroid effects}, year = {2003}, abstract = {Detailed analysis of brassinosteroid (BR)-regulated genes can provide evidence of the molecular basis of BR effects. Classical techniques (such as subtractive cDNA cloning) as well as cDNA and oligonucleotide microarrays have been applied to identify genes which are upregulated or downregulated after BR treatment or are differently expressed in BR-deficient or -insensitive mutants compared with wild type plants. Genes encoding cell-wall-modifying enzymes, enzymes of the BR biosynthetic pathway, auxin response factors, and transcription factors are subject to BR regulation. Effects on several other metabolic pathways and interactions with other phytohormones have been reported as well, although some of these effects may depend on certain environmental conditions (for example, light/dark or stress), the developmental stage of the plants, and tissue types. The identification of components of the BR signal transduction pathway revealed different modes of transcriptional control in animals and plants. Steroid signaling in plants comprises the plasma membrane receptor kinases BRI1 and BAK1 and intracellular protein phosphorylations. Thus, BR signaling in plants is reminiscent of growth factor and TGF-beta signal transduction in animals. The phosphorylation cascade could be a basis of extensive signaling cross-talk and thereby explain the complexity of BR responses}, language = {en} } @article{MuessigAltmann2003, author = {M{\"u}ssig, Carsten and Altmann, Thomas}, title = {Changes in gene expression in response to altered SHL transcript levels}, year = {2003}, abstract = {The nuclear SHL protein is composed of a N-terminal BAH domain and a C-terminal PHD finger. Both domains are found in transcriptional regulators and chromatin-modifying proteins. Arabidopsis plants over-expressing SHL showed earlier flowering and senescence phenotype. To identify SHL regulated genes, expression profiles of 35S::SHL plants were established with Affymetrix ATH1 microarrays. About 130 genes showed reduced transcript levels, and about 45 genes showed increased transcript levels in 35S:: SHL plants. The up-regulated genes included AGL20 and AGL9, which most likely cause the early flowering phenotype of 35S:: SHL plants. Late-flowering SHL-antisense lines showed reduced AGL20 mRNA levels, suggesting that AGL20 gene expression depends on the SHL protein. The stronger expression of senescence- and defence-related genes (such as DIN2, DIN11 and PR-1) is in line with the early senescence phenotype of SHL-over- expressing plants. SHL-down-regulated genes included stress response genes and the PSR3.2 gene (encoding a beta- glucosidase). SHL over-expression did not alter the tissue specificity of PSR3.2 gene expression, but resulted in reduced transcript levels in both shoots and roots. Plants with glucocorticoid-inducible SHL over-expression were established and used for expression profiling as well. A subset of genes was identified, which showed consistent changes in the inducible system and in plants with constitutive SHL over-expression}, language = {en} } @article{MuessigShinAltmann2003, author = {M{\"u}ssig, Carsten and Shin, G.-H. and Altmann, Thomas}, title = {Brassinosteroids promote root growth in Arabidopsis}, year = {2003}, language = {en} } @article{AltmannToerjekBergeretal.2003, author = {Altmann, Thomas and T{\"o}rjek, Otto and Berger, Dieter and Meyer, Rhonda C. and M{\"u}ssig, Carsten and Schmidt, K. J. and Sorensen, T. R. and Weisshaar, Bernd and Olds-Mitchell, T.}, title = {Establishment of a high-efficiency SNP-based framework marker set for Arabidopsis}, year = {2003}, language = {en} } @article{AltmannSchlueterMuschaketal.2003, author = {Altmann, Thomas and Schl{\"u}ter, U. and Muschak, M. and Berger, Dieter}, title = {Photosynthetic performance of an Arabidopsis mutant with elevated stomatal density (sdd1-1) under different light regimes}, year = {2003}, language = {en} } @article{AltmannSchmidSoerensenetal.2003, author = {Altmann, Thomas and Schmid, K. J. and S{\"o}rensen, Rossleff T. and Stracke, R. and T{\"o}rjek, Otto and Mitchel-Olds, T. and Weisshaar, Bernd}, title = {Large-scale identification and analysis of genome-wide single-nucleotide polymorphisms for mapping in Arabidopsis thaliana}, year = {2003}, language = {en} } @article{AltmannvonGroll2003, author = {Altmann, Thomas and von Groll, Uritza}, title = {Stomatal cell biology}, year = {2003}, language = {en} } @article{AltmannTaylorKingetal.2003, author = {Altmann, Thomas and Taylor, Janet and King, Ross. D. and Fiehn, Oliver}, title = {Application of metabolomics to plant genotype discrimination using statistics and machine learning}, year = {2003}, language = {en} } @article{MeyerToerjekBecheretal.2004, author = {Meyer, Rhonda C. and T{\"o}rj{\´e}k, Otto and Becher, Monika and Altmann, Thomas}, title = {Heterosis of biomass production in Arabidopsis : Establishment during early development}, year = {2004}, abstract = {Heterosis has been widely used in agriculture to increase yield and to broaden adaptability of hybrid varieties and is applied to an increasing number of crop species. We performed a systematic survey of the extent and degree of heterosis for dry biomass in 63 Arabidopsis accessions crossed to three reference lines (Col-0, C24, and Nd). We detected a high heritability (69\%) for biomass production in Arabidopsis. Among the 169 crosses analyzed, 29 exhibited significant mid-parent-heterosis for shoot biomass. Furthermore, we analyzed two divergent accessions, C24 and Col-0, the F-1 hybrids of which were shown to exhibit hybrid vigor, in more detail. In the combination Col-0/C24, heterosis for biomass was enhanced at higher light intensities; we found 51\% to 66\% mid-parent-heterosis at low and intermediate light intensities (60 and 120 mumol m(-2) s(-1)), and 161\% at high light intensity (240 mumol m(-2) s(-1)). While at the low and intermediate light intensities relative growth rates of the hybrids were higher only in the early developmental phase (0-15 d after sowing [DAS]), at high light intensity the hybrids showed increased relative growth rates over the entire vegetative phase (until 25 DAS). An important finding was the early onset of heterosis for biomass; in the cross Col-0/C24, differences between parental and hybrid lines in leaf size and dry shoot mass could be detected as early as 10 DAS. The widespread occurrence of heterosis in the model plant Arabidopsis opens the possibility to investigate the genetic basis of this phenomenon using the tools of genetical genomics}, language = {en} } @article{HilsonAllemeerschAltmannetal.2004, author = {Hilson, Pierre and Allemeersch, Joke and Altmann, Thomas and Aubourg, Sebastien and Avon, Alexandra and Beynon, Jim and Bhalerao, Rishikesh P. and Bitton, Frederique and Caboche, Michel and Cannoot, Bernard and Chardakov, Vasil and Cognet-Holliger, Cecile and Colot, Vincent and Crowe, Mark and Darimont, Caroline and Durinck, Steffen and Eickhoff, Holger and deLongevialle, Andeol Falcon and Farmer, Edward E. and Grant, Murray and Kuiper, Martin T. R. and Lehrach, Hans and Leon, Celine and Leyva, Antonio and Lundeberg, Joakim and Lurin, Claire and Moreau, Yves}, title = {Versatile gene-specific sequence tags for arabidopsis functional genomics : transcript profiling and reserve genetics applications}, year = {2004}, abstract = {Microarray transcript profiling and RNA interference are two new technologies crucial for large-scale gene function studies in multicellular eukaryotes. Both rely on sequence-specific hybridization between complementary nucleic acid strands, inciting us to create a collection of gene-specific sequence tags (GSTs) representing at least 21,500 Arabidopsis genes and which are compatible with both approaches. The GSTs were carefully selected to ensure that each of them shared no significant similarity with any other region in the Arabidopsis genome. They were synthesized by PCR amplification from genomic DNA. Spotted microarrays fabricated from the GSTs show good dynamic range, specificity, and sensitivity in transcript profiling experiments. The GSTs have also been transferred to bacterial plasmid vectors via recombinational cloning protocols. These cloned GSTs constitute the ideal starting point for a variety of functional approaches, including reverse genetics. We have subcloned GSTs on a large scale into vectors designed for gene silencing in plant cells. We show that in planta expression of GST hairpin RNA results in the expected phenotypes in silenced Arabidopsis lines. These versatile GST resources provide novel and powerful tools for functional genomics}, language = {en} } @article{GollGarciaMazuchAltmannetal.2004, author = {Goll-Garcia, D. and Mazuch, J. and Altmann, Thomas and M{\"u}ssig, Carsten}, title = {Exordium regulates brassinosteroid-responsive genes}, year = {2004}, abstract = {In a screen for potential mediators of brassinosteroid (BR) effects, the EXORDIUM (EXO) protein was identified as a regulator of BR-responsive genes. The EXO gene was characterized as a BR-up-regulated gene. EXO overexpression under the control of the 35SCaMV promoter resulted in increased transcript levels of the BR-up-regulated KCS1, Exp5, delta-TIP, and AGP4 genes, which likely are involved in the mediation of BR-promoted growth. 35S::EXO lines grown in soil or in synthetic medium showed increased vegetative growth in comparison to wild-type plants, resembling the growth phenotype of BR-treated plants. Thus, the EXO protein most likely promotes growth via the modulation of gene expression patterns. (C) 2004 Federation of European Biochemical Societies. Published by Elsevier B.V. All rights reserved}, language = {en} } @article{MeyerMuessigAltmann2004, author = {Meyer, Rhonda C. and M{\"u}ssig, Carsten and Altmann, Thomas}, title = {Genetic Diversity : Creation of novel genetic variants of arabidopsis}, isbn = {3-00-011587-0}, year = {2004}, language = {en} } @article{ScheibleToerjekAltmann2004, author = {Scheible, W. R. and T{\"o}rj{\´e}k, Otto and Altmann, Thomas}, title = {From markers to cloned genes : map based cloning}, isbn = {3-540-20689-2}, year = {2004}, language = {en} } @article{BergerToerjekAltmann2004, author = {Berger, Dieter and T{\"o}rjek, Otto and Altmann, Thomas}, title = {Establishment of high-efficiency mapping tools}, isbn = {3-00-011587-0}, year = {2004}, language = {en} } @article{LissoSteinhaeuserAltmannetal.2005, author = {Lisso, Janina and Steinhaeuser, Dirk and Altmann, Thomas and Kopka, Joachim and M{\"u}ssig, Carsten}, title = {Identification of brassinosteroid-related genes by means of transcript co-response analyses}, issn = {0305-1048}, year = {2005}, abstract = {The comprehensive systems-biology database (CSB.DB) was used to reveal brassinosteroid (BR)-related genes from expression profiles based on co-response analyses. Genes exhibiting simultaneous changes in transcript levels are candidates of common transcriptional regulation. Combining numerous different experiments in data matrices allows ruling out outliers and conditional changes of transcript levels. CSB.DB was queried for transcriptional co-responses with the BR-signalling components BRI1 and BAK1: 301 out of 9694 genes represented in the nasc0271 database showed co-responses with both genes. As expected, these genes comprised pathway-involved genes (e.g. 72 BR-induced genes), because the BRI1 and BAK1 proteins are required for BR-responses. But transcript co-response takes the analysis a step further compared with direct approaches because BR-related non BR-responsive genes were identified. Insights into networks and the functional context of genes are provided, because factors determining expression patterns are reflected in correlations. Our findings demonstrate that transcript co-response analysis presents a valuable resource to uncover common regulatory patterns of genes. Different data matrices in CSB.DB allow examination of specific biological questions. All matrices are publicly available through CSB.DB. This work presents one possible roadmap to use the CSB.DB resources}, language = {en} } @article{RautengartenSteinhaeuserBussisetal.2005, author = {Rautengarten, Carsten and Steinhaeuser, Dirk and Bussis, D and Stintzi, A and Schaller, A and Kopka, Joachim and Altmann, Thomas}, title = {Inferring hypotheses on functional relationships of genes : Analysis of the Arabidopsis thaliana subtilase gene family}, year = {2005}, abstract = {The gene family of subtilisin-like serine proteases (subtilases) in Arabidopsis thaliana comprises 56 members, divided into six distinct subfamilies. Whereas the members of five subfamilies are similar to pyrolysins, two genes share stronger similarity to animal kexins. Mutant screens confirmed 144 T-DNA insertion lines with knockouts for 55 out of the 56 subtilases. Apart from SDD1, none of the confirmed homozygous mutants revealed any obvious visible phenotypic alteration during growth under standard conditions. Apart from this specific case, forward genetics gave us no hints about the function of the individual 54 non-characterized subtilase genes. Therefore, the main objective of our work was to overcome the shortcomings of the forward genetic approach and to infer alternative experimental approaches by using an integrative biolinformatics and biological approach. Computational analyses based on transcriptional co-expression and co-response pattern revealed at least two expression networks, suggesting that functional redundancy may exist among subtilases with limited similarity. Furthermore, two hubs were identified, which may be involved in signalling or may represent higher-order regulatory factors involved in responses to environmental cues. A particular enrichment of co- regulated genes with metabolic functions was observed for four subtilases possibly representing late responsive elements of environmental stress. The kexin homologs show stronger associations with genes of transcriptional regulation context. Based on the analyses presented here and in accordance with previously characterized subtilases, we propose three main functions of subtilases: involvement in (i) control of development, (ii) protein turnover, and (iii) action as downstream components of signalling cascades}, language = {en} }