TY - GEN A1 - Steinfath, Matthias A1 - Gärtner, Tanja A1 - Lisec, Jan A1 - Meyer, Rhonda C. A1 - Altmann, Thomas A1 - Willmitzer, Lothar A1 - Selbig, Joachim T1 - Prediction of hybrid biomass in Arabidopsis thaliana by selected parental SNP and metabolic markers T2 - Zweitveröffentlichungen der Universität Potsdam : Mathematisch-Naturwissenschaftliche Reihe N2 - 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. T3 - Zweitveröffentlichungen der Universität Potsdam : Mathematisch-Naturwissenschaftliche Reihe - 1324 KW - Quantitative Trait Locus KW - feature selection KW - Partial Little Square KW - recombinant inbred line KW - Quantitative Trait Locus analysis Y1 - 2009 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:kobv:517-opus4-431115 SN - 1866-8372 IS - 1324 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 - TY - JOUR A1 - Andorf, Sandra A1 - Meyer, Rhonda C. A1 - Selbig, Joachim A1 - Altmann, Thomas A1 - Repsilber, Dirk T1 - Integration of a systems biological network analysis and QTL results for biomass heterosis in arabidopsis thaliana JF - PLoS one N2 - 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. Y1 - 2012 U6 - https://doi.org/10.1371/journal.pone.0049951 SN - 1932-6203 VL - 7 IS - 11 PB - PLoS CY - San Fransisco ER - TY - JOUR A1 - Altmann, Thomas A1 - Törjek, Otto A1 - Berger, Dieter A1 - Meyer, Rhonda C. A1 - Müssig, Carsten A1 - Schmidt, K. J. A1 - Sorensen, T. R. A1 - Weisshaar, Bernd A1 - Olds-Mitchell, T. T1 - Establishment of a high-efficiency SNP-based framework marker set for Arabidopsis Y1 - 2003 ER - TY - JOUR A1 - Meyer, Rhonda C. A1 - Törjék, Otto A1 - Becher, Monika A1 - Altmann, Thomas T1 - Heterosis of biomass production in Arabidopsis : Establishment during early development N2 - 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 Y1 - 2004 ER - TY - JOUR A1 - Meyer, Rhonda C. A1 - Müssig, Carsten A1 - Altmann, Thomas T1 - Genetic Diversity : Creation of novel genetic variants of arabidopsis Y1 - 2004 SN - 3-00-011587-0 ER - TY - GEN A1 - Gärtner, Tanja A1 - Steinfath, Matthias A1 - Andorf, Sandra A1 - Lisec, Jan A1 - Meyer, Rhonda C. A1 - Altmann, Thomas A1 - Willmitzer, Lothar A1 - Selbig, Joachim T1 - Improved heterosis prediction by combining information on DNA- and metabolic markers N2 - Background: Hybrids represent a cornerstone in the success story of breeding programs. The fundamental principle underlying this success is the phenomenon of hybrid vigour, or heterosis. It describes an advantage of the offspring as compared to the two parental lines with respect to parameters such as growth and resistance against abiotic or biotic stress. Dominance, overdominance or epistasis based models are commonly used explanations. Conclusion/Significance: The heterosis level is clearly a function of the combination of the parents used for offspring production. This results in a major challenge for plant breeders, as usually several thousand combinations of parents have to be tested for identifying the best combinations. Thus, any approach to reliably predict heterosis levels based on properties of the parental lines would be highly beneficial for plant breeding. Methodology/Principal Findings: Recently, genetic data have been used to predict heterosis. Here we show that a combination of parental genetic and metabolic markers, identified via feature selection and minimum-description-length based regression methods, significantly improves the prediction of biomass heterosis in resulting offspring. These findings will help furthering our understanding of the molecular basis of heterosis, revealing, for instance, the presence of nonlinear genotype-phenotype relationships. In addition, we describe a possible approach for accelerated selection in plant breeding. T3 - Zweitveröffentlichungen der Universität Potsdam : Mathematisch-Naturwissenschaftliche Reihe - paper 142 Y1 - 2009 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:kobv:517-opus-45132 ER -