TY - JOUR A1 - Torjek, Otto A1 - Witucka-Wall, Hanna A1 - Meyer, Rhonda C. A1 - von Korff, Maria A1 - Kusterer, Barbara A1 - Rautengarten, Carsten A1 - Altmann, Thomas T1 - 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 JF - Theoretical and applied genetics N2 - 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. Y1 - 2006 U6 - https://doi.org/10.1007/s00122-006-0402-3 SN - 0040-5752 VL - 113 SP - 1551 EP - 1561 PB - Springer CY - Berlin ER - TY - GEN A1 - Andorf, Sandra A1 - Gärtner, Tanja A1 - Steinfath, Matthias A1 - Witucka-Wall, Hanna A1 - Altmann, Thomas A1 - Repsilber, Dirk T1 - Towards systems biology of heterosis BT - a hypothesis about molecular network structure applied for the Arabidopsis metabolome T2 - Postprints der Universität Potsdam : Mathematisch-Naturwissenschaftliche Reihe N2 - We propose a network structure-based model for heterosis, and investigate it relying on metabolite profiles from Arabidopsis. A simple feed-forward two-layer network model (the Steinbuch matrix) is used in our conceptual approach. It allows for directly relating structural network properties with biological function. Interpreting heterosis as increased adaptability, our model predicts that the biological networks involved show increasing connectivity of regulatory interactions. A detailed analysis of metabolite profile data reveals that the increasing-connectivity prediction is true for graphical Gaussian models in our data from early development. This mirrors properties of observed heterotic Arabidopsis phenotypes. Furthermore, the model predicts a limit for increasing hybrid vigor with increasing heterozygosity—a known phenomenon in the literature. T3 - Zweitveröffentlichungen der Universität Potsdam : Mathematisch-Naturwissenschaftliche Reihe - 949 KW - partial correlation KW - biological network KW - metabolite profile KW - molecular network KW - significant edge Y1 - 2020 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:kobv:517-opus4-436274 SN - 1866-8372 IS - 949 ER - TY - JOUR A1 - Sulpice, Ronan A1 - Pyl, Eva-Theresa A1 - Ishihara, Hirofumi A1 - Trenkamp, Sandra A1 - Steinfath, Matthias A1 - Witucka-Wall, Hanna A1 - Gibon, Yves A1 - Usadel, Björn A1 - Poree, Fabien A1 - Piques, Maria Conceicao A1 - von Korff, Maria A1 - Steinhauser, Marie Caroline A1 - Keurentjes, Joost J. B. A1 - Guenther, Manuela A1 - Hoehne, Melanie A1 - Selbig, Joachim A1 - Fernie, Alisdair R. A1 - Altmann, Thomas A1 - Stitt, Mark T1 - Starch as a major integrator in the regulation of plant growth N2 - 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. Y1 - 2009 UR - http://www.pnas.org/ U6 - https://doi.org/10.1073/pnas.0903478106 SN - 0027-8424 ER - TY - JOUR A1 - Childs, Liam H. A1 - Witucka-Wall, Hanna A1 - Guenther, Torsten A1 - Sulpice, Ronan A1 - Korff, Maria V. A1 - Stitt, Mark A1 - Walther, Dirk A1 - Schmid, Karl J. A1 - Altmann, Thomas T1 - Single feature polymorphism (SFP)-based selective sweep identification and association mapping of growth- related metabolic traits in Arabidopsis thaliana N2 - 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. Y1 - 2010 UR - http://www.biomedcentral.com/1471-2164/ U6 - https://doi.org/10.1186/1471-2164-11-188 SN - 1471-2164 ER - TY - JOUR A1 - Meyer, Rhonda C. A1 - Witucka-Wall, Hanna A1 - Becher, Martina A1 - Blacha, Anna Maria A1 - Boudichevskaia, Anastassia A1 - Dörmann, Peter A1 - Fiehn, Oliver A1 - Friedel, Svetlana A1 - von Korff, Maria A1 - Lisec, Jan A1 - Melzer, Michael A1 - Repsilber, Dirk A1 - Schmidt, Renate A1 - Scholz, Matthias A1 - Selbig, Joachim A1 - Willmitzer, Lothar A1 - Altmann, Thomas T1 - Heterosis manifestation during early Arabidopsis seedling development is characterized by intermediate gene expression and enhanced metabolic activity in the hybrids JF - The plant journal N2 - 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. KW - heterosis KW - seedlings KW - metabolite profiling KW - transcript profiling KW - morphological analysis KW - Arabidopsis thaliana KW - biomass Y1 - 2012 U6 - https://doi.org/10.1111/j.1365-313X.2012.05021.x SN - 0960-7412 VL - 71 IS - 4 SP - 669 EP - 683 PB - Wiley-Blackwell CY - Hoboken ER -