High‐throughput profiling and analysis of plant responses over time to abiotic stress
Abstract
Abstract Sorghum ( Sorghum bicolor (L.) Moench) is a rapidly growing, high‐biomass crop prized for abiotic stress tolerance. However, measuring genotype‐by‐environment (G x E) interactions remains a progress bottleneck. We subjected a panel of 30 genetically diverse sorghum genotypes to a spectrum of nitrogen deprivation and measured responses using high‐throughput phenotyping technology followed by ionomic profiling. Responses were quantified using shape (16 measurable outputs), color (hue and intensity), and ionome (18 elements). We measured the speed at which specific genotypes respond to environmental conditions, in terms of both biomass and color changes, and identified individual genotypes that perform most favorably. With this analysis, we present a novel approach to quantifying color‐based stress indicators over time. Additionally, ionomic profiling was conducted as an independent, low‐cost, and high‐throughput option for characterizing G x E, identifying the elements most affected by either genotype or treatment and suggesting signaling that occurs in response to the environment. This entire dataset and associated scripts are made available through an open‐access, user‐friendly, web‐based interface. In summary, this work provides analysis tools for visualizing and quantifying plant abiotic stress responses over time. These methods can be deployed as a time‐efficient method of dissecting the genetic mechanisms used bymore »
- Authors:
-
- Donald Danforth Plant Science Center Saint Louis MO USA
- Department of Agronomy and Horticulture and Center for Plant Science Innovation University of Nebraska–Lincoln Lincoln NE USA
- Donald Danforth Plant Science Center Saint Louis MO USA, USDA‐ARS Saint Louis MO USA
- Publication Date:
- Research Org.:
- Donald Danforth Plant Science Center, St. Louis, MO (United States); Univ. of Nebraska, Lincoln, NE (United States)
- Sponsoring Org.:
- USDOE Office of Science (SC); USDA
- OSTI Identifier:
- 1406154
- Alternate Identifier(s):
- OSTI ID: 1406156; OSTI ID: 1904496
- Grant/Contract Number:
- DE‐SC0014395; DESC0008769; SC0008769; SC0014395
- Resource Type:
- Published Article
- Journal Name:
- Plant Direct
- Additional Journal Information:
- Journal Name: Plant Direct Journal Volume: 1 Journal Issue: 4; Journal ID: ISSN 2475-4455
- Publisher:
- Wiley Blackwell (John Wiley & Sons)
- Country of Publication:
- United Kingdom
- Language:
- English
- Subject:
- 59 BASIC BIOLOGICAL SCIENCES; plant sciences; abiotic stress; computational modeling; image analysis; ionomics; large-scale biology; nitrogen stress
Citation Formats
Veley, Kira M., Berry, Jeffrey C., Fentress, Sarah J., Schachtman, Daniel P., Baxter, Ivan, and Bart, Rebecca. High‐throughput profiling and analysis of plant responses over time to abiotic stress. United Kingdom: N. p., 2017.
Web. doi:10.1002/pld3.23.
Veley, Kira M., Berry, Jeffrey C., Fentress, Sarah J., Schachtman, Daniel P., Baxter, Ivan, & Bart, Rebecca. High‐throughput profiling and analysis of plant responses over time to abiotic stress. United Kingdom. https://doi.org/10.1002/pld3.23
Veley, Kira M., Berry, Jeffrey C., Fentress, Sarah J., Schachtman, Daniel P., Baxter, Ivan, and Bart, Rebecca. Wed .
"High‐throughput profiling and analysis of plant responses over time to abiotic stress". United Kingdom. https://doi.org/10.1002/pld3.23.
@article{osti_1406154,
title = {High‐throughput profiling and analysis of plant responses over time to abiotic stress},
author = {Veley, Kira M. and Berry, Jeffrey C. and Fentress, Sarah J. and Schachtman, Daniel P. and Baxter, Ivan and Bart, Rebecca},
abstractNote = {Abstract Sorghum ( Sorghum bicolor (L.) Moench) is a rapidly growing, high‐biomass crop prized for abiotic stress tolerance. However, measuring genotype‐by‐environment (G x E) interactions remains a progress bottleneck. We subjected a panel of 30 genetically diverse sorghum genotypes to a spectrum of nitrogen deprivation and measured responses using high‐throughput phenotyping technology followed by ionomic profiling. Responses were quantified using shape (16 measurable outputs), color (hue and intensity), and ionome (18 elements). We measured the speed at which specific genotypes respond to environmental conditions, in terms of both biomass and color changes, and identified individual genotypes that perform most favorably. With this analysis, we present a novel approach to quantifying color‐based stress indicators over time. Additionally, ionomic profiling was conducted as an independent, low‐cost, and high‐throughput option for characterizing G x E, identifying the elements most affected by either genotype or treatment and suggesting signaling that occurs in response to the environment. This entire dataset and associated scripts are made available through an open‐access, user‐friendly, web‐based interface. In summary, this work provides analysis tools for visualizing and quantifying plant abiotic stress responses over time. These methods can be deployed as a time‐efficient method of dissecting the genetic mechanisms used by sorghum to respond to the environment to accelerate crop improvement.},
doi = {10.1002/pld3.23},
journal = {Plant Direct},
number = 4,
volume = 1,
place = {United Kingdom},
year = {Wed Oct 25 00:00:00 EDT 2017},
month = {Wed Oct 25 00:00:00 EDT 2017}
}
https://doi.org/10.1002/pld3.23
Web of Science
Works referenced in this record:
Utilization of a high-throughput shoot imaging system to examine the dynamic phenotypic responses of a C4 cereal crop plant to nitrogen and water deficiency over time
journal, February 2015
- Neilson, E. H.; Edwards, A. M.; Blomstedt, C. K.
- Journal of Experimental Botany, Vol. 66, Issue 7
Nitrogen control of developmental phase transitions in Arabidopsis thaliana
journal, August 2014
- Vidal, E. A.; Moyano, T. C.; Canales, J.
- Journal of Experimental Botany, Vol. 65, Issue 19
Future Scenarios for Plant Phenotyping
journal, April 2013
- Fiorani, Fabio; Schurr, Ulrich
- Annual Review of Plant Biology, Vol. 64, Issue 1
The Sorghum bicolor genome and the diversification of grasses
journal, January 2009
- Paterson, Andrew H.; Bowers, John E.; Bruggmann, Rémy
- Nature, Vol. 457, Issue 7229
Plant chlorophyll fluorescence: active and passive measurements at canopy and leaf scales with different nitrogen treatments
journal, October 2015
- Cendrero-Mateo, M. Pilar; Moran, M. Susan; Papuga, Shirley A.
- Journal of Experimental Botany, Vol. 67, Issue 1
Root morphology and seed and leaf ionomic traits in a Brassica napus L. diversity panel show wide phenotypic variation and are characteristic of crop habit
journal, October 2016
- Thomas, C. L.; Alcock, T. D.; Graham, N. S.
- BMC Plant Biology, Vol. 16, Issue 1
Differentiation of Seed, Sugar, and Biomass-Producing Genotypes in Saccharinae Species
book, July 2012
- Murray, Seth C.
- Genomics of the Saccharinae
The Interaction of Genotype and Environment Determines Variation in the Maize Kernel Ionome
journal, October 2016
- Asaro, Alexandra; Ziegler, Gregory; Ziyomo, Cathrine
- G3: Genes|Genomes|Genetics, Vol. 6, Issue 12
A Versatile Phenotyping System and Analytics Platform Reveals Diverse Temporal Responses to Water Availability in Setaria
journal, October 2015
- Fahlgren, Noah; Feldman, Maximilian; Gehan, Malia A.
- Molecular Plant, Vol. 8, Issue 10
Solutions for a cultivated planet
journal, October 2011
- Foley, Jonathan A.; Ramankutty, Navin; Brauman, Kate A.
- Nature, Vol. 478, Issue 7369
Physiological adaptations for nitrogen use efficiency in sorghum
book, January 2002
- Maranville, Jerry W.; Madhavan, S.
- Food Security in Nutrient-Stressed Environments: Exploiting Plants’ Genetic Capabilities
Plant Nitrogen Acquisition Under Low Availability: Regulation of Uptake and Root Architecture
journal, March 2016
- Kiba, Takatoshi; Krapp, Anne
- Plant and Cell Physiology, Vol. 57, Issue 4
Prioritizing Climate Change Adaptation Needs for Food Security in 2030
journal, February 2008
- Lobell, D. B.; Burke, M. B.; Tebaldi, C.
- Science, Vol. 319, Issue 5863
The quest for tolerant varieties: the importance of integrating “omics” techniques to phenotyping
journal, July 2015
- Zivy, Michel; Wienkoop, Stefanie; Renaut, Jenny
- Frontiers in Plant Science, Vol. 6
Genome-Wide Association Studies Identify Heavy Metal ATPase3 as the Primary Determinant of Natural Variation in Leaf Cadmium in Arabidopsis thaliana
journal, September 2012
- Chao, Dai-Yin; Silva, Adriano; Baxter, Ivan
- PLoS Genetics, Vol. 8, Issue 9
The Theoretical Limit to Plant Productivity
journal, August 2014
- DeLucia, Evan H.; Gomez-Casanovas, Nuria; Greenberg, Jonathan A.
- Environmental Science & Technology, Vol. 48, Issue 16
A Genomic Resource for the Development, Improvement, and Exploitation of Sorghum for Bioenergy
journal, June 2016
- Brenton, Zachary W.; Cooper, Elizabeth A.; Myers, Mathew T.
- Genetics, Vol. 204, Issue 1
The leaf ionome as a multivariable system to detect a plant's physiological status
journal, August 2008
- Baxter, I. R.; Vitek, O.; Lahner, B.
- Proceedings of the National Academy of Sciences, Vol. 105, Issue 33
Genetic Enhancement of Sorghum for Biomass Utilization
book, January 2012
- Vermerris, Wilfred; Saballos, Ana
- Genomics of the Saccharinae
The Identification of Multiple Outliers
journal, September 1993
- Davies, Laurie; Gather, Ursula
- Journal of the American Statistical Association, Vol. 88, Issue 423
Measuring leaf chlorophyll concentration from its color: A way in monitoring environment change to plantations
conference, January 2013
- Shibghatallah, Muhammad Abdul Hakim; Khotimah, Siti Nurul; Suhandono, Sony
- PADJADJARAN INTERNATIONAL PHYSICS SYMPOSIUM 2013 (PIPS-2013): Contribution of Physics on Environmental and Energy Conservations, AIP Conference Proceedings
The nitrogen-potassium intersection: membranes, metabolism, and mechanism: The N-K intersection
journal, January 2016
- Coskun, Devrim; Britto, Dev T.; Kronzucker, Herbert J.
- Plant, Cell & Environment, Vol. 40, Issue 10
Drought Tolerance and Water Use of Cereal Crops: A Focus on Sorghum as a Food Security Crop in Sub-Saharan Africa
journal, November 2016
- Hadebe, S. T.; Modi, A. T.; Mabhaudhi, T.
- Journal of Agronomy and Crop Science, Vol. 203, Issue 3
Genome-environment associations in sorghum landraces predict adaptive traits
journal, July 2015
- Lasky, Jesse R.; Upadhyaya, Hari D.; Ramu, Punna
- Science Advances, Vol. 1, Issue 6
Response-based selection of barley cultivars and legume species for complementarity: Root morphology and exudation in relation to nutrient source
journal, February 2017
- Giles, Courtney D.; Brown, Lawrie K.; Adu, Michael O.
- Plant Science, Vol. 255
Comparison of the Effects of a Localised Supply of Phosphate, Nitrate, Ammonium and Potassium on the Growth of the Seminal root System, and the Shoot, in Barley
journal, November 1975
- Drew, M. C.
- New Phytologist, Vol. 75, Issue 3
Genetic Regulation by NLA and MicroRNA827 for Maintaining Nitrate-Dependent Phosphate Homeostasis in Arabidopsis
journal, March 2011
- Kant, Surya; Peng, Mingsheng; Rothstein, Steven J.
- PLoS Genetics, Vol. 7, Issue 3
From association to prediction: statistical methods for the dissection and selection of complex traits in plants
journal, April 2015
- Lipka, Alexander E.; Kandianis, Catherine B.; Hudson, Matthew E.
- Current Opinion in Plant Biology, Vol. 24
Relationship between leaf optical properties, chlorophyll fluorescence and pigment changes in senescing Acer saccharum leaves
journal, February 2016
- Junker, Laura Verena; Ensminger, Ingo
- Tree Physiology, Vol. 36, Issue 6
Genome sequence of Pseudomonas parafulva CRS01-1, an antagonistic bacterium isolated from rice field
journal, July 2015
- Liu, Qunen; Zhang, Yingxin; Yu, Ning
- Journal of Biotechnology, Vol. 206
Where Have All the Crop Phenotypes Gone?
journal, June 2013
- Zamir, Dani
- PLoS Biology, Vol. 11, Issue 6
NITROGEN LIMITATION ADAPTATION, a Target of MicroRNA827, Mediates Degradation of Plasma Membrane–Localized Phosphate Transporters to Maintain Phosphate Homeostasis in Arabidopsis
journal, October 2013
- Lin, Wei-Yi; Huang, Teng-Kuei; Chiou, Tzyy-Jen
- The Plant Cell, Vol. 25, Issue 10
Population genomic and genome-wide association studies of agroclimatic traits in sorghum
journal, December 2012
- Morris, G. P.; Ramu, P.; Deshpande, S. P.
- Proceedings of the National Academy of Sciences, Vol. 110, Issue 2
Assessment of Chlorophyll Content Based on Image Color Analysis, Comparison with SPAD-502
conference, December 2010
- Hu, Hao; Liu, He-qin; Zhang, Hao
- 2010 2nd International Conference on Information Engineering and Computer Science (ICIECS)
Chlorophyll a fluorescence, under half of the adaptive growth-irradiance, for high-throughput sensing of leaf-water deficit in Arabidopsis thaliana accessions
journal, November 2016
- Mishra, Kumud B.; Mishra, Anamika; Novotná, Kateřina
- Plant Methods, Vol. 12, Issue 1
Rising atmospheric carbon dioxide concentration and the future of C 4 crops for food and fuel
journal, February 2009
- Leakey, Andrew D. B.
- Proceedings of the Royal Society B: Biological Sciences, Vol. 276, Issue 1666
Identification of differentially expressed genes between sorghum genotypes with contrasting nitrogen stress tolerance by genome-wide transcriptional profiling
journal, January 2014
- Gelli, Malleswari; Duo, Yongchao; Konda, Anji
- BMC Genomics, Vol. 15, Issue 1
Plant Responses to Multiple Environmental Factors
journal, January 1987
- Chapin, F. Stuart; Bloom, Arnold J.; Field, Christopher B.
- BioScience, Vol. 37, Issue 1
Ionomic Screening of Field-Grown Soybean Identifies Mutants with Altered Seed Elemental Composition
journal, January 2013
- Ziegler, Greg; Terauchi, Aimee; Becker, Anthony
- The Plant Genome, Vol. 6, Issue 2
Nitrate and ammonium uptake for single-and mixed-species communities grown at elevated CO2
journal, January 1996
- Jackson, R. B.; Reynolds, H. L.
- Oecologia, Vol. 105, Issue 1
Localized application of NH4 +-N plus P at the seedling and later growth stages enhances nutrient uptake and maize yield by inducing lateral root proliferation
journal, April 2013
- Ma, Qinghua; Zhang, Fusuo; Rengel, Zed
- Plant and Soil, Vol. 372, Issue 1-2
Molecular and Developmental Biology of Inorganic Nitrogen Nutrition
journal, January 2002
- Crawford, Nigel M.; Forde, Brian G.
- The Arabidopsis Book, Vol. 1
Integration of Experiments across Diverse Environments Identifies the Genetic Determinants of Variation in Sorghum bicolor Seed Element Composition
journal, February 2016
- Shakoor, Nadia; Ziegler, Greg; Dilkes, Brian P.
- Plant Physiology, Vol. 170, Issue 4
Validation of QTL mapping and transcriptome profiling for identification of candidate genes associated with nitrogen stress tolerance in sorghum
journal, July 2017
- Gelli, Malleswari; Konda, Anji Reddy; Liu, Kan
- BMC Plant Biology, Vol. 17, Issue 1
A global view of genetic diversity in cultivated sorghums using a core collection
journal, February 2006
- Deu, M.; Rattunde, F.; Chantereau, J.
- Genome, Vol. 49, Issue 2
Finding Our Way through Phenotypes
journal, January 2015
- Deans, Andrew R.; Lewis, Suzanna E.; Huala, Eva
- PLoS Biology, Vol. 13, Issue 1
Estimating rice chlorophyll content and leaf nitrogen concentration with a digital still color camera under natural light
journal, January 2014
- Wang, Yuan; Wang, Dejian; Shi, Peihua
- Plant Methods, Vol. 10, Issue 1
Elemental Profiles Reflect Plant Adaptations to the Environment
journal, June 2012
- Baxter, Ivan; Dilkes, Brian P.
- Science, Vol. 336, Issue 6089
Phenomics – technologies to relieve the phenotyping bottleneck
journal, December 2011
- Furbank, Robert T.; Tester, Mark
- Trends in Plant Science, Vol. 16, Issue 12
Field high-throughput phenotyping: the new crop breeding frontier
journal, January 2014
- Araus, José Luis; Cairns, Jill E.
- Trends in Plant Science, Vol. 19, Issue 1