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In animals and plants, stem-cell niches are local microenvironments that are tightly regulated to preserve their unique identity while communicating with adjacent cells that will give rise to specialized cell types. In the primary root of Arabidopsis thaliana, two transcription factors, BRAVO and WOX5, among others, are expressed in the stem-cell niche. Intriguingly, BRAVO, a repressor of quiescent center divisions, confines its own gene expression to the stem-cell niche, as evidenced in a bravo mutant background. Here, we propose through mathematical modeling that BRAVO confines its own expression domain to the stem-cell niche by attenuating a WOX5-dependent diffusible activator of BRAVO. This negative feedback drives WOX5 activity to be spatially restricted as well. The results show that WOX5 diffusion and sequestration by binding to BRAVO are sufficient to drive the experimentally observed confined BRAVO expression at the stem-cell niche. We propose that the attenuation of a diffusible activator can be a general mechanism acting at other stem-cell niches to spatially confine genetic activity to a small region while maintaining signaling within them and with the surrounding cells., This work was supported by the Ministerio de Ciencia e Innovación (MCIN), Agencia Estatal de Investigación (AEI) and European Regional Development Fund (Fondo Europeo de Desarrollo Regional, FEDER) program ‘Una manera de hacer Europa’ MCIN/AEI/10.13039/501100011033/FEDER (PGC2018-101896-B-I00 to M.I.); Ministerio de Ciencia e Innovación, Agencia Estatal de Investigación and European Social Fund (Fondo Social Europeo, FSE) program ‘El FSE invierte en tu futuro’ (BES-2016-078218 to J.M.); Ministerio de Ciencia e Innovación (MCIN), Agencia Estatal de Investigación (AEI) and European Regional Development Fund (ERDF) (BIO2016-78955 to A.I.C.-D.); the European Research Council (ERC) Consolidator Grant (ERC-2015-CoG–683163 to A.I.C.-D.); Generalitat de Catalunya (M.I. and J.M. in Grup de Recerca Consolidat 2017 SGR 1061; FI-DGR 2016FI-B 00472, also funded by FSE, to N.B.); and the Ministerio de Educación, Cultura y Deporte (FPU15/02822 to I.B.-P.).

Stem cell niches are local microenvironments that preserve their unique identity while communicating with adjacent tissues. In the primary root of Arabidopsis thaliana, the stem cell niche comprises the expression of two transcription factors, BRAVO and WOX5, among others. Intriguingly, these proteins confine their own gene expression to the niche, as evidenced in each mutant background. Here we propose through mathematical modeling that BRAVO confines its own expression domain to the stem cell niche by attenuating its WOX5-dependent diffusible activator. This negative feedback drives WOX5 action to be spatially restricted as well. The results show that WOX5 diffusion and sequestration by binding to BRAVO is sufficient to drive realistic confined BRAVO expression at the stem cell niche. We propose that attenuation of a diffusible activator can be a general mechanism to confine genetic activity to a small region while at the same time maintain signaling within it and with the surrounding cells.

Understanding stem cell regulatory circuits is the next challenge in plant biology, as these cells are essential for tissue growth and organ regeneration in response to stress. In the Arabidopsis primary root apex, stem cell-specific transcription factors BRAVO and WOX5 co-localize in the quiescent centre (QC) cells, where they commonly repress cell division so that these cells can act as a reservoir to replenish surrounding stem cells, yet their molecular connection remains unknown. Genetic and biochemical analysis indicates that BRAVO and WOX5 form a transcription factor complex that modulates gene expression in the QC cells to preserve overall root growth and architecture. Furthermore, by using mathematical modelling we establish that BRAVO uses the WOX5/BRAVO complex to promote WOX5 activity in the stem cells. Our results unveil the importance of transcriptional regulatory circuits in plant stem cell development., A.I.C-D. is a recipient of a BIO2016-78955 grant from the Spanish Ministry of Economy and Competitiveness and a European Research Council, ERC Consolidator Grant (ERC-2015-CoG – 683163). I.B-P. is funded by the FPU15/02822 grant from the Spanish Ministry of Education, Culture and Sport; N.B. by the FI-DGR 2016FI_B 00472 grant from the AGAUR, Generalitat de Catalunya; and A.P-R. by the SEV-2015-0533 from the Severo Ochoa Programme for Centers of Excellence in R&D. M.I. and J.M. acknowledge support from the Spanish Ministry of Economy and Competitiveness and FEDER (EU) through grant FIS2015-66503-C3-3-P, from Ministerio de Ciencia, Innovación y Universidades / Agencia Estatal de Investigación / Fondo Europeo de Desarrollo Regional, Unión Europea through grant PGC2018-101896-B-I00 and from the Generalitat de Catalunya through Grup de Recerca Consolidat 2014 SGR 878 and 2017 SGR 1061. J.M. is funded by the Spanish Ministry of Education through BES-2016-078218. Y.S. and R.C.D. were funded by the Deutsche Forschungsgesellschaft (DFG) (grant STA12/12 1-1). A.I.C.-D.–A.C. collaboration was funded by the European Regional Development Funds and Marie Curie IRSES Project DEANN (PIRSES-GA-2013-612583). CRAG is funded by “Severo Ochoa Programme” from Centers of Excellence in R&D 2016-2019 (SEV-2015-485 0533).

The automatic measurement of external physical traits (i.e. phenotyping) of plant organs, such as root length –which is highly correlated with plant viability– is one of the current bottlenecks in academic and agricultural research. Although many root length measurement software tools are available to the community, plant scientists often find their usability is limited, the measurements they provide are not accurate enough or they are too limited to specific image characteristics. In response to that, this work describes MyROOT 2.0, an automatic software tool jointly developed by plant scientists and computer vision engineers to create a high throughput root length measurement tool that reduces user intervention to a minimum. Using Arabidopsis thaliana seedlings grown on agar plates as a case study, MyROOT 2.0 is capable of detecting the root regions of interest in a fully automatic manner with an accuracy of 98%. Furthermore, this work also presents previously unreported experiments to evaluate several constituting modules of MyROOT 2.0, such as the ability to determine image scale automatically with subpixel accuracy, or the influence of training the hypocotyl detector using wildtype or mutant samples. Finally, when compared to state-of-the-art root length measurement software tools, MyROOT 2.0 achieves the highest root detection rate, obtaining measurements which are four times more accurate than its competitors. This makes MyROOT 2.0 an attractive tool for high throughput root phenotyping., A.I.C-D. is a recipient of a BIO2016-78955 grants from the Spanish Ministry of Economy and Competitiveness and a European Research Council, ERC Consolidator Grant (ERC-2015-CoG - 683163). I.B-P. is funded by the FPU15/02822 grant from the Spanish Ministry of Education, Culture and Sport. D.B-E. is contracted with the BIO2016-78955 grant in the A.I.C-D laboratory. CRAG is funded by “Severo Ochoa Programme” from Centers of Excellence in R&D 2016–2019 (SEV-2015-485 0533).

Brassinosteroids (BRs) are steroid hormones that are essential for plant growth and development. These hormones control the division, elongation and differentiation of various cell types throughout the entire plant life cycle. Our current understanding of the BR signaling pathway has mostly been obtained from studies using Arabidopsis thaliana as a model. In this context, the membrane steroid receptor BRI1 (BRASSINOSTEROID INSENSITIVE 1) binds directly to the BR ligand, triggering a signal cascade in the cytoplasm that leads to the transcription of BR-responsive genes that drive cellular growth. However, recent studies of the primary root have revealed distinct BR signaling pathways in different cell types and have highlighted cell-specific roles for BR signaling in controlling adaptation to stress. In this Review, we summarize our current knowledge of the spatiotemporal control of BR action in plant growth and development, focusing on BR functions in primary root development and growth, in stem cell self-renewal and death, and in plant adaption to environmental stress., A.P.-R. is recipient of a PhD fellowship from the “Severo Ochoa Programme for Centers of Excellence in R&D” 2016-2019 from the Ministerio de Ciencia e Innovación (SEV-2015-0533). A.G. is a recipient of a post-doctoral fellowship from the “Severo Ochoa Programme for Centers of Excellence in R&D” 2016-2019 from the Ministerio de Ciencia e Innovación (SEV-2015-0533). I.B.-P. is funded by a grant from the Ministerio de Educación, Cultura y Deporte (FPU15/02822). N.B. is funded by a grant from the Agència de Gestió d'Ajuts Universitaris i de Recerca, Generalitat de Catalunya (FI-DGR 2016FI_B 00472). M.I. acknowledges support from the Ministerio de Economía y Competitividad (Spain) and FEDER (European Regional Development Fund of the European Union) (FIS2015-66503-C3-3-P) and from the Generalitat de Catalunya through Grup de Recerca Consolidat (2017 SGR 1061). A.I.C.-D. is recipient of a grant from the Ministerio de Economía y Competitividad (BIO2013-43873) and of an ERC Consolidator Grant from the European Research Council (ERC-2015-CoG – 683163).

Root analysis is essential for both academic and agricultural research. Despite the great advances in root phenotyping and imaging however, calculating root length is still performed manually and involves considerable amounts of labor and time. To overcome these limitations, we have developed MyROOT, a novel software for the semi-automatic quantification of root growth of seedlings growing directly in agar plates. Our method automatically determines the scale from the image of the plate, and subsequently measures the root length of the individual plants. To this aim, MyROOT combines a bottom-up root tracking approach with a hypocotyl detection algorithm. At the same time as providing accurate root measurements, MyROOT also significantly minimizes the user intervention required during the process. Using Arabidopsis, we tested MyROOT with seedlings from different growth stages. Upon comparing the data obtained using this software with that of manual root measurements, we found that there are no significant differences (t-test, p-value < 0.05). Thus, MyROOT will be of great aid to the plant science community by permitting high-throughput root length measurements while saving on both labor and time.

Brassinosteroid (BR) hormones are important regulators of plant growth and development. Recent studies revealed the cell-specific role of BRs in vascular and stem cell development by the action of cell-specific BR receptor complexes and downstream signaling components in Arabidopsis thaliana. Despite the importance of spatiotemporal regulation of hormone signaling in the control of plant vascular development, the mechanisms that confer cellular specificity to BR receptors within the vascular cells are not yet understood. The present work shows that BRI1-like receptor genes 1 and 3 (BRL1 and BRL3) are differently regulated by BRs. By using promoter deletion constructs of BRL1 and BRL3 fused to GFP/GUS (green fluorescent protein/β-glucuronidase) reporters in Arabidopsis, analysis of their cell-specific expression and regulation by BRs in the root apex has been carried out. We found that BRL3 expression is finely modulated by BRs in different root cell types, whereas the location of BRL1 appears to be independent of this hormone. Physiological and genetic analysis show a BR-dependent expression of BRL3 in the root meristem. In particular, BRL3 expression requires active BES1, a central transcriptional effector within the BRI1 pathway. ChIP analysis showed that BES1 directly binds to the BRRE present in the BRL3 promoter region, modulating its transcription in different subsets of cells of the root apex. Overall our study reveals the existence of a cell-specific negative feedback loop from BRI1-mediated BES1 transcription factor to BRL3 in phloem cells, while contributing to a general understanding of the spatial control of steroid signaling in plant development., RL was funded by the FWF Erwin Schrödinger Stipendum from Austria (J 3019-B16), and JES-H was supported by the Department of Innovation, Universities and Enterprise of the Generalitat de Catalunya, the European Social Fund FI Fellowship (AGAUR: FI-2006, Resolució EDU/3600/2006; FI-2008, Resolució IUE/2658/2007, and BE-DGR2010) in the Laboratory of AC-D. We acknowledge financial support from the Spanish Ministry of Economy and Competitiveness, through the ‘Severo Ochoa Programme for Centres of Excellence in R&D’ 2016–2019 (SEV‐2015‐0533). AIC-D is a recipient of a BIO2013-43873 grant from the Spanish Ministry of Economy and Competitiveness an European Research Council, ERC Consolidator Grant (ERC-2015-CoG – 683163).

Resumen del póster presentado al Congreso 'At the Forefront of Plant Research', celebrado en Barcelona (España) del 6 al 8 de mayo de 2019., Root analysis is essential for both academic and agricultural research. Despite the great advances in root phenotyping and imaging, calculating root length is still performed manually and involves considerable amounts of labor and time. To overcome these limitations, we have developed MyROOT, a software for the semi-automatic quantification of root growth of seedlings growing directly in agar plates. Our method automatically determines the scale from the image of the plate, and subsequently measures the root length of the individual plants. To this aim, MyROOT combines a bottom-up root tracking approach with a hypocotyl detection algorithm. At the same time as providing accurate root measurements, MyROOT also significantly minimizes the user intervention required during the process. Using Arabidopsis, we tested MyROOT with seedlings from different growth stages and experimental conditions. Upon comparing the data obtained using this software with that of manual root measurements, we found a high correlation between both methods (R2 = 0.997). When compared to previous developed softwares with similar features (BRAT and EZ-Rhizo), MyROOT offers an improved accuracy in root length measurements. Thus, MyROOT will be of great aid to the plant science community by permitting high-throughput root length measurements while saving on both labor and time.