Shu H.,Zurich Basel Plant Science Center |
Gruissem W.,Zurich Basel Plant Science Center |
Gruissem W.,University of Zurich |
Hennig L.,Zurich Basel Plant Science Center |
And 2 more authors.
Plant Physiology | Year: 2013
DNA accessibility is an important layer of regulation of DNA-dependent processes. Methods that measure DNA accessibility at local and genome-wide scales have facilitated a rapid increase in the knowledge of chromatin architecture in animal and yeast systems. In contrast, much less is known about chromatin organization in plants. We developed a robust DNase I-polymerase chain reaction (PCR) protocol for the model plant Arabidopsis (Arabidopsis thaliana). DNA accessibility is probed by digesting nuclei with a gradient of DNase I followed by locus-specific PCR. The reduction in PCR product formation along the gradient of increasing DNase I concentrations is used to determine the accessibility of the chromatin DNA. We explain a strategy to calculate the decay constant of such signal reduction as a function of increasing DNase I concentration. This allows describing DNA accessibility using a single variable: the decay constant. We also used the protocol together with AGRONOMICS1 DNA tiling microarrays to establish genome-wide DNase I sensitivity landscapes. © 2013 American Society of Plant Biologists. All Rights Reserved.
Theodoridis S.,University of Zurich |
Theodoridis S.,Zurich Basel Plant Science Center |
Randin C.,University of Basel |
Randin C.,Zurich Basel Plant Science Center |
And 6 more authors.
Journal of Biogeography | Year: 2013
Aim: It is hypothesized that the ecological niches of polyploids should be both distinct and broader than those of diploids - characteristics that might have allowed the successful colonization of open habitats by polyploids during the Pleistocene glacial cycles. Here, we test these hypotheses by quantifying and comparing the ecological niches and niche breadths of a group of European primroses. Location: Europe. Methods: We gathered georeferenced data of four related species in Primula sect. Aleuritia at different ploidy levels (diploid, tetraploid, hexaploid and octoploid) and used seven bioclimatic variables to quantify niche overlap between species by applying a series of univariate and multivariate analyses combined with modelling techniques. We also employed permutation-based tests to evaluate niche similarity between the four species. Niche breadth for each species was evaluated both in the multivariate environmental space and in geographical space. Results: The four species differed significantly from each other in mono-dimensional comparisons of climatological variables and occupied distinct habitats in the multi-dimensional environmental space. The majority of the permutation-based tests either indicated that the four species differed significantly in their habitat preferences and ecological niches or did not support significant niche similarity. Furthermore, our results revealed narrower niche breadths and geographical ranges in species of P. sect. Aleuritia at higher ploidy levels. Main conclusions: The detected ecological differentiation between the four species of P. sect. Aleuritia at different ploidy levels is consistent with the hypothesis that polyploids occupy distinct ecological niches that differ from those of their diploid relative. Contrary to expectations, we find that polyploid species of P. sect. Aleuritia occupy narrower environmental and geographical spaces than their diploid relative. These results on the ecological niches of closely related polyploid and diploid species highlight factors that potentially contribute to the evolution and distribution of polyploid species. © 2013 Blackwell Publishing Ltd.
Wuest S.E.,Zurich Basel Plant Science Center |
Philipp M.A.,Zurich Basel Plant Science Center |
Guthorl D.,Zurich Basel Plant Science Center |
Schmid B.,Zurich Basel Plant Science Center |
Grossniklaus U.,Zurich Basel Plant Science Center
Plant Physiology | Year: 2016
Correlative control (influence of one organ over another organ) of seeds over maternal growth is one of the most obvious phenotypic expressions of the trade-off between growth and reproduction. However, the underlying molecular mechanisms are largely unknown. Here, we characterize the physiological and molecular effects of correlative inhibition by seeds on Arabidopsis (Arabidopsis thaliana) inflorescences, i.e. global proliferative arrest (GPA) during which all maternal growth ceases upon the production of a given number of seeds. We observed transcriptional responses to growth- and branching-inhibitory hormones, and low mitotic activity in meristems upon GPA, but found that meristems retain their identity and proliferative potential. In shoot tissues, we detected the induction of stress- and senescence-related gene expression upon fruit production and GPA, and a drop in chlorophyll levels, suggestive of altered source-sink relationships between vegetative shoot and reproductive tissues. Levels of shoot reactive oxygen species, however, strongly decreased upon GPA, a phenomenon that is associated with bud dormancy in some perennials. Indeed, gene expression changes in arrested apical inflorescences after fruit removal resembled changes observed in axillary buds following release from apical dominance. This suggests that GPA represents a form of bud dormancy, and that dominance is gradually transferred from growing inflorescences to maturing seeds, allowing offspring control over maternal resources, simultaneously restricting offspring number. This would provide a mechanistic explanation for the constraint between offspring quality and quantity. © 2016 American Society of Plant Biologists. All rights reserved.