Pipeline for imaging and automated analysis
Reference:
Deja-Muylle A., Parizot B., Motte H., Beeckman T.,(2020), Exploiting natural variation in root system architecture via genome-wide association studies, Journal of Experimental Botany, Volume 71, Issue 8, 2379–2389.
https://doi.org/10.1093/jxb/eraa029
In vivo imaging of root growth and gene expression
Reference:
Xuan W, Band LR, Kumpf R.P., Van Damme D., Parizot B., De Rop G., Opdenacker D., Möller B.K., Skorzinski N., Njo M.F., De Rybel B., Audenaert D., Nowack M.K., Beeckman T.(2016), Cyclic programmed cell death stimulates hormone signaling and root development in Arabidopsis, Science, Jan 22;351(6271):384-7.
Root growth in hydroponic systems
Rhizotron
Reference:
Kerstens M. et al, (2021), Nature and Nurture: Genotype-Dependent Differential Responses of Root Architecture to Agar and Soil Environments, Genes, 12(7), 1028.
https://doi.org/10.3390/genes12071028
Microtomy of Roots
Reference:
Beeckman T., Viane R., (2009), Embedding Thin Plant Specimens for Oriented Sectioning, Biotechnic & Histochemistry, Volume 75, 2000 - Issue 1, 23-26.
https://doi.org/10.3109/10520290009047981
Lateral Root Inducible system (LRIS)
Average pericycle activation for NPA-NPA system:
In the LRIS, seedlings are germinated on N-1-naphthylphthalamic acid (NPA), a known auxin transport inhibitor and after 72hours transferred to a medium containing the synthetic auxin 1-Naphthaleneacetic acid (NAA).
The first hours are characterized by a wave of auxin response going through the pericycle starting close to the root apical meristem and proceeding in shootward direction. This first wave of auxin response is followed later by second wave of cell cycle activity again progressing from root tip towards the hypocotyl.
LRIS at the cellular level
A. Longitudinal section of a 3 days old root grown on media containing the auxin transport inhibitor NPA. Blue stained cells represent the pericycle.
B. Similar as in A. but after transfer for 6 hours on media containing the synthetic auxin NAA: pericycle cells are repolarized with the nuclei (red) and cytoplasm (blue) of neighboring cells contracted towards the common cell walls.
C. Schematic overview of the cellular changes in the protoxylem pole pericycle during the LRIS. Soon after transfer to auxin nuclei (yellow) move from a central to a polar position. Note that nuclei of 2 neighboring cells move in opposite directions. At later hours asymmetric cell divisions take place resulting in the formation of lateral root initiation sites or stage 1 lateral root primordia (composed of 1 cell layer of anticlinal divided cells).
Reference:
Himanen K., Boucheron E., Vanneste S., de Almeida Engler J., Inzé D., Beeckman T., (2002). Auxin-mediated cell cycle activation during early lateral root initiation., Plant Cell, Oct;14(10):2339-51.
https://doi.org/10.1105/tpc.004960
Himanen K., Vuylsteke M., Vanneste .S, Vercruysse S., Boucheron E., Alard .P, Chriqui D., Van Montagu M., Inzé D., Beeckman T., (2004). Transcript profiling of early lateral root initiation., Proc Natl Acad Sci U S A, 101(14):5146-51.
https://doi.org/10.1073/pnas.0308702101 Epub 2004 Mar 29.
Crombez H., Roberts I., Vangheluwe N., et al, (2016), Lateral root inducible system in Arabidopsis and maize, JOVE-JOURNAL OF VISUALIZED EXPERIMENTS, DOI: 10.3791/53481-v.
https://www.jove.com/v/53481/lateral-root-inducible-system-in-arabidopsis-and-maize
Motte H., Parizot B., Xuan W., Chen Q., Maere S., Bensmihen S., Beeckman T., (2023), Interspecies co-expression analysis of lateral root development using inducible systems in rice, Medicago, and Arabidopsis, Plant J. Nov;116(4):1052-1063.
DOI: 10.1111/tpj.16481 Epub 2023 Oct 4.