1
|
Swartz LG, Liu S, Dahlquist D, Kramer ST, Walter ES, McInturf SA, Bucksch A, Mendoza-Cózatl DG. OPEN leaf: an open-source cloud-based phenotyping system for tracking dynamic changes at leaf-specific resolution in Arabidopsis. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2023; 116:1600-1616. [PMID: 37733751 DOI: 10.1111/tpj.16449] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/24/2022] [Accepted: 08/16/2023] [Indexed: 09/23/2023]
Abstract
The first draft of the Arabidopsis genome was released more than 20 years ago and despite intensive molecular research, more than 30% of Arabidopsis genes remained uncharacterized or without an assigned function. This is in part due to gene redundancy within gene families or the essential nature of genes, where their deletion results in lethality (i.e., the dark genome). High-throughput plant phenotyping (HTPP) offers an automated and unbiased approach to characterize subtle or transient phenotypes resulting from gene redundancy or inducible gene silencing; however, access to commercial HTPP platforms remains limited. Here we describe the design and implementation of OPEN leaf, an open-source phenotyping system with cloud connectivity and remote bilateral communication to facilitate data collection, sharing and processing. OPEN leaf, coupled with our SMART imaging processing pipeline was able to consistently document and quantify dynamic changes at the whole rosette level and leaf-specific resolution when plants experienced changes in nutrient availability. Our data also demonstrate that VIS sensors remain underutilized and can be used in high-throughput screens to identify and characterize previously unidentified phenotypes in a leaf-specific time-dependent manner. Moreover, the modular and open-source design of OPEN leaf allows seamless integration of additional sensors based on users and experimental needs.
Collapse
Affiliation(s)
- Landon G Swartz
- Department of Electrical Engineering and Computer Science, University of Missouri, 411 S 6th St., Columbia, Missouri, 65201, USA
- Division of Plant Science and Technology, C.S. Bond Life Sciences Center, University of Missouri, 1201 Rollins St., Columbia, Missouri, 65211, USA
| | - Suxing Liu
- School of Plant Sciences, University of Arizona, 1140 E South Campus, Tucson, Arizona, 85721, USA
| | - Drew Dahlquist
- Department of Electrical Engineering and Computer Science, University of Missouri, 411 S 6th St., Columbia, Missouri, 65201, USA
| | - Skyler T Kramer
- MU Institute of Data Science and Informatics, C.S. Bond Life Sciences Center, University of Missouri, 1201 Rollinst St., Columbia, Missouri, 65211, USA
| | - Emily S Walter
- Division of Plant Science and Technology, C.S. Bond Life Sciences Center, University of Missouri, 1201 Rollins St., Columbia, Missouri, 65211, USA
| | - Samuel A McInturf
- Division of Plant Science and Technology, C.S. Bond Life Sciences Center, University of Missouri, 1201 Rollins St., Columbia, Missouri, 65211, USA
| | - Alexander Bucksch
- School of Plant Sciences, University of Arizona, 1140 E South Campus, Tucson, Arizona, 85721, USA
| | - David G Mendoza-Cózatl
- Department of Electrical Engineering and Computer Science, University of Missouri, 411 S 6th St., Columbia, Missouri, 65201, USA
- Division of Plant Science and Technology, C.S. Bond Life Sciences Center, University of Missouri, 1201 Rollins St., Columbia, Missouri, 65211, USA
| |
Collapse
|
2
|
Blanco-Touriñán N, Torres-Martínez HH, Augstein F, Champeyroux C, von der Mark C, Carlsbecker A, Dubrovsky JG, Rodriguez-Villalón A. The primary root procambium contributes to lateral root formation through its impact on xylem connection. Curr Biol 2023; 33:1716-1727.e3. [PMID: 37071995 DOI: 10.1016/j.cub.2023.03.061] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2022] [Revised: 02/21/2023] [Accepted: 03/21/2023] [Indexed: 04/20/2023]
Abstract
The postembryonic formation of lateral roots (LRs) starts in internal root tissue, the pericycle. An important question of LR development is how the connection of the primary root vasculature with that of the emerging LR is established and whether the pericycle and/or other cell types direct this process. Here, using clonal analysis and time-lapse experiments, we show that both the procambium and pericycle of the primary root (PR) affect the LR vascular connectivity in a coordinated manner. We show that during LR formation, procambial derivates switch their identity and become precursors of xylem cells. These cells, together with the pericycle-origin xylem, participate in the formation of what we call a "xylem bridge" (XB), which establishes the xylem connection between the PR and the nascent LR. If the parental protoxylem cell fails to differentiate, XB is still sometimes formed but via a connection with metaxylem cells, highlighting that this process has some plasticity. Using mutant analyses, we show that the early specification of XB cells is determined by CLASS III HOMEODOMAIN-LEUCINE ZIPPER (HD-ZIP III) transcription factors (TFs). Subsequent XB cell differentiation is marked by the deposition of secondary cell walls (SCWs) in spiral and reticulate/scalariform patterns, which is dependent on the VASCULAR-RELATED NAC-DOMAIN (VND) TFs. XB elements were also observed in Solanum lycopersicum, suggesting that this mechanism may be more widely conserved in plants. Together, our results suggest that plants maintain vascular procambium activity, which safeguards the functionality of newly established lateral organs by assuring the continuity of the xylem strands throughout the root system.
Collapse
Affiliation(s)
- Noel Blanco-Touriñán
- Department of Biology, Swiss Federal Institute of Technology (ETH) Zurich, 8092 Zurich, Switzerland.
| | - Héctor H Torres-Martínez
- Departamento de Biología Molecular de Plantas, Instituto de Biotecnología, Universidad Nacional Autónoma de México, Av. Universidad, 2001, Cuernavaca 62250, Mexico
| | - Frauke Augstein
- Department of Organismal Biology, Physiological Botany, Linnean Centre for Plant Biology, Uppsala University, Ullsv. 24E, 756 51 Uppsala, Sweden
| | - Chloé Champeyroux
- Department of Biology, Swiss Federal Institute of Technology (ETH) Zurich, 8092 Zurich, Switzerland
| | - Claudia von der Mark
- Department of Biology, Swiss Federal Institute of Technology (ETH) Zurich, 8092 Zurich, Switzerland
| | - Annelie Carlsbecker
- Department of Organismal Biology, Physiological Botany, Linnean Centre for Plant Biology, Uppsala University, Ullsv. 24E, 756 51 Uppsala, Sweden
| | - Joseph G Dubrovsky
- Departamento de Biología Molecular de Plantas, Instituto de Biotecnología, Universidad Nacional Autónoma de México, Av. Universidad, 2001, Cuernavaca 62250, Mexico.
| | - Antia Rodriguez-Villalón
- Department of Biology, Swiss Federal Institute of Technology (ETH) Zurich, 8092 Zurich, Switzerland.
| |
Collapse
|
3
|
García-Gómez ML, Reyes-Hernández BJ, Sahoo DP, Napsucialy-Mendivil S, Quintana-Armas AX, Pedroza-García JA, Shishkova S, Torres-Martínez HH, Pacheco-Escobedo MA, Dubrovsky JG. A mutation in THREONINE SYNTHASE 1 uncouples proliferation and transition domains of the root apical meristem: experimental evidence and in silico proposed mechanism. Development 2022; 149:278438. [PMID: 36278862 PMCID: PMC9796171 DOI: 10.1242/dev.200899] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2022] [Accepted: 10/10/2022] [Indexed: 11/11/2022]
Abstract
A continuum from stem to transit-amplifying to a differentiated cell state is a common theme in multicellular organisms. In the plant root apical meristem (RAM), transit-amplifying cells are organized into two domains: cells from the proliferation domain (PD) are displaced to the transition domain (TD), suggesting that both domains are necessarily coupled. Here, we show that in the Arabidopsis thaliana mto2-2 mutant, in which threonine (Thr) synthesis is affected, the RAM lacks the PD. Through a combination of cell length profile analysis, mathematical modeling and molecular markers, we establish that the PD and TD can be uncoupled. Remarkably, although the RAM of mto2-2 is represented solely by the TD, the known factors of RAM maintenance and auxin signaling are expressed in the mutant. Mathematical modeling predicts that the stem cell niche depends on Thr metabolism and that, when disturbed, the normal continuum of cell states becomes aborted.
Collapse
Affiliation(s)
- Monica L. García-Gómez
- Departamento de Biología Molecular de Plantas, Instituto de Biotecnología, Universidad Nacional Autónoma de México (UNAM), Av. Universidad, 2001, Cuernavaca 62250, Mexico
| | - Blanca J. Reyes-Hernández
- Departamento de Biología Molecular de Plantas, Instituto de Biotecnología, Universidad Nacional Autónoma de México (UNAM), Av. Universidad, 2001, Cuernavaca 62250, Mexico
| | - Debee P. Sahoo
- Departamento de Biología Molecular de Plantas, Instituto de Biotecnología, Universidad Nacional Autónoma de México (UNAM), Av. Universidad, 2001, Cuernavaca 62250, Mexico
| | - Selene Napsucialy-Mendivil
- Departamento de Biología Molecular de Plantas, Instituto de Biotecnología, Universidad Nacional Autónoma de México (UNAM), Av. Universidad, 2001, Cuernavaca 62250, Mexico
| | - Aranza X. Quintana-Armas
- Departamento de Biología Molecular de Plantas, Instituto de Biotecnología, Universidad Nacional Autónoma de México (UNAM), Av. Universidad, 2001, Cuernavaca 62250, Mexico
| | - José A. Pedroza-García
- Departamento de Biología Molecular de Plantas, Instituto de Biotecnología, Universidad Nacional Autónoma de México (UNAM), Av. Universidad, 2001, Cuernavaca 62250, Mexico
| | - Svetlana Shishkova
- Departamento de Biología Molecular de Plantas, Instituto de Biotecnología, Universidad Nacional Autónoma de México (UNAM), Av. Universidad, 2001, Cuernavaca 62250, Mexico
| | - Héctor H. Torres-Martínez
- Departamento de Biología Molecular de Plantas, Instituto de Biotecnología, Universidad Nacional Autónoma de México (UNAM), Av. Universidad, 2001, Cuernavaca 62250, Mexico
| | - Mario A. Pacheco-Escobedo
- Facultad de Ciencias de la Salud, Universidad Tecnológica de México – UNITEC MÉXICO – Campus Atizapán, Av. Calacoaya 7, Atizapán de Zaragoza, Estado de México, 52970, Mexico
| | - Joseph G. Dubrovsky
- Departamento de Biología Molecular de Plantas, Instituto de Biotecnología, Universidad Nacional Autónoma de México (UNAM), Av. Universidad, 2001, Cuernavaca 62250, Mexico,Author for correspondence ()
| |
Collapse
|
4
|
Birnbaum KD, Otegui MS, Bailey-Serres J, Rhee SY. The Plant Cell Atlas: focusing new technologies on the kingdom that nourishes the planet. PLANT PHYSIOLOGY 2022; 188:675-679. [PMID: 34935969 PMCID: PMC8825275 DOI: 10.1093/plphys/kiab584] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/01/2021] [Accepted: 12/03/2021] [Indexed: 06/14/2023]
Affiliation(s)
- Kenneth D Birnbaum
- Department of Biology, Center for Genomics and Systems Biology, New York University, New York, New York 10003, USA
| | - Marisa S Otegui
- Department of Botany, Center for Quantitative Cell Imaging, University of Wisconsin–Madison, Madison, Wisconsin 53706, USA
| | - Julia Bailey-Serres
- Department of Botany and Plant Sciences, Center for Plant Cell Biology, University of California, Riverside, California 92521, USA Plant Ecophysiology, Department of Biology, Utrecht University, 3584 CH, Utrecht, The Netherlands
| | - Seung Y Rhee
- Department of Plant Biology, Carnegie Institution for Science, 260 Panama Street, Stanford, California 94305, USA
| |
Collapse
|