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Plant J. 2017 Oct;92(1):31-42. doi: 10.1111/tpj.13631. Epub 2017 Aug 11.

A 3D digital atlas of the Nicotiana tabacum root tip and its use to investigate changes in the root apical meristem induced by the Agrobacterium 6b oncogene.

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Institute of Biology II, University of Freiburg, 79104, Freiburg, Germany.
Institute of Computer Science, University of Freiburg, 79110, Freiburg, Germany.
BIOSS Centre for Biological Signalling Studies, University of Freiburg, 79104, Freiburg, Germany.
Centre for Biological Systems Analysis (ZBSA), University of Freiburg, 79104, Freiburg, Germany.
Department of Molecular Mechanisms of Phenotypic Plasticity, Institut de Biologie Moléculaire des Plantes, Rue du Général Zimmer 12, 67084, Strasbourg, France.


Using the intrinsic Root Coordinate System (iRoCS) Toolbox, a digital atlas at cellular resolution has been constructed for Nicotiana tabacum roots. Mitotic cells and cells labeled for DNA replication with 5-ethynyl-2'-deoxyuridine (EdU) were mapped. The results demonstrate that iRoCS analysis can be applied to roots that are thicker than those of Arabidopsis thaliana without histological sectioning. A three-dimensional (3-D) analysis of the root tip showed that tobacco roots undergo several irregular periclinal and tangential divisions. Irrespective of cell type, rapid cell elongation starts at the same distance from the quiescent center, however, boundaries between cell proliferation and transition domains are cell-type specific. The data support the existence of a transition domain in tobacco roots. Cell endoreduplication starts in the transition domain and continues into the elongation zone. The tobacco root map was subsequently used to analyse root organization changes caused by the inducible expression of the Agrobacterium 6b oncogene. In tobacco roots that express the 6b gene, the root apical meristem was shorter and radial cell growth was reduced, but the mitotic and DNA replication indexes were not affected. The epidermis of 6b-expressing roots produced less files and underwent abnormal periclinal divisions. The periclinal division leading to mature endodermis and cortex3 cell files was delayed. These findings define additional targets for future studies on the mode of action of the Agrobacterium 6b oncogene.


3D digital root atlas; 6b oncogene; Nicotiana tabacum; cell cycle events; root development

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