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Kim D, Guadagno CR, Ewers BE, Mackay DS. Combining PSII photochemistry and hydraulics improves predictions of photosynthesis and water use from mild to lethal drought. PLANT, CELL & ENVIRONMENT 2024; 47:1255-1268. [PMID: 38178610 DOI: 10.1111/pce.14806] [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: 02/04/2023] [Revised: 12/10/2023] [Accepted: 12/20/2023] [Indexed: 01/06/2024]
Abstract
Rising temperatures and increases in drought negatively impact the efficiency and sustainability of both agricultural and forest ecosystems. Although hydraulic limitations on photosynthesis have been extensively studied, a solid understanding of the links between whole plant hydraulics and photosynthetic processes at the cellular level under changing environmental conditions is still missing, hampering our predictive power for plant mortality. Here, we examined plant hydraulic traits and CO2 assimilation rate under progressive water limitation by implementing Photosystem II (PSII) dynamics with a whole plant process model (TREES). The photosynthetic responses to plant water status were parameterized based on measurements of chlorophyll a fluorescence, gas exchange and water potential for Brassica rapa (R500) grown in a greenhouse under fully watered to lethal drought conditions. The updated model significantly improved predictions of photosynthesis, stomatal conductance and leaf water potential. TREES with PSII knowledge predicted a larger hydraulic safety margin and a decrease in percent loss of conductivity. TREES predicted a slower decrease in leaf water potential, which agreed with measurements. Our results highlight the pressing need for incorporating PSII drought photochemistry into current process models to capture cross-scale plant water dynamics from cell to whole plant level.
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Affiliation(s)
- Dohyoung Kim
- Department of Geography, State University of New York at Buffalo, Buffalo, New York, USA
| | | | - Brent E Ewers
- Department of Botany, University of Wyoming, Laramie, Wyoming, USA
| | - D Scott Mackay
- Department of Geography, State University of New York at Buffalo, Buffalo, New York, USA
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Susmitha P, Kumar P, Yadav P, Sahoo S, Kaur G, Pandey MK, Singh V, Tseng TM, Gangurde SS. Genome-wide association study as a powerful tool for dissecting competitive traits in legumes. FRONTIERS IN PLANT SCIENCE 2023; 14:1123631. [PMID: 37645459 PMCID: PMC10461012 DOI: 10.3389/fpls.2023.1123631] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/14/2022] [Accepted: 06/08/2023] [Indexed: 08/31/2023]
Abstract
Legumes are extremely valuable because of their high protein content and several other nutritional components. The major challenge lies in maintaining the quantity and quality of protein and other nutritional compounds in view of climate change conditions. The global need for plant-based proteins has increased the demand for seeds with a high protein content that includes essential amino acids. Genome-wide association studies (GWAS) have evolved as a standard approach in agricultural genetics for examining such intricate characters. Recent development in machine learning methods shows promising applications for dimensionality reduction, which is a major challenge in GWAS. With the advancement in biotechnology, sequencing, and bioinformatics tools, estimation of linkage disequilibrium (LD) based associations between a genome-wide collection of single-nucleotide polymorphisms (SNPs) and desired phenotypic traits has become accessible. The markers from GWAS could be utilized for genomic selection (GS) to predict superior lines by calculating genomic estimated breeding values (GEBVs). For prediction accuracy, an assortment of statistical models could be utilized, such as ridge regression best linear unbiased prediction (rrBLUP), genomic best linear unbiased predictor (gBLUP), Bayesian, and random forest (RF). Both naturally diverse germplasm panels and family-based breeding populations can be used for association mapping based on the nature of the breeding system (inbred or outbred) in the plant species. MAGIC, MCILs, RIAILs, NAM, and ROAM are being used for association mapping in several crops. Several modifications of NAM, such as doubled haploid NAM (DH-NAM), backcross NAM (BC-NAM), and advanced backcross NAM (AB-NAM), have also been used in crops like rice, wheat, maize, barley mustard, etc. for reliable marker-trait associations (MTAs), phenotyping accuracy is equally important as genotyping. Highthroughput genotyping, phenomics, and computational techniques have advanced during the past few years, making it possible to explore such enormous datasets. Each population has unique virtues and flaws at the genomics and phenomics levels, which will be covered in more detail in this review study. The current investigation includes utilizing elite breeding lines as association mapping population, optimizing the choice of GWAS selection, population size, and hurdles in phenotyping, and statistical methods which will analyze competitive traits in legume breeding.
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Affiliation(s)
- Pusarla Susmitha
- Regional Agricultural Research Station, Acharya N.G. Ranga Agricultural University, Andhra Pradesh, India
| | - Pawan Kumar
- Department of Genetics and Plant Breeding, College of Agriculture, Chaudhary Charan Singh (CCS) Haryana Agricultural University, Hisar, India
| | - Pankaj Yadav
- Department of Bioscience and Bioengineering, Indian Institute of Technology, Rajasthan, India
| | - Smrutishree Sahoo
- Department of Genetics and Plant Breeding, School of Agriculture, Gandhi Institute of Engineering and Technology (GIET) University, Odisha, India
| | - Gurleen Kaur
- Horticultural Sciences Department, University of Florida, Gainesville, FL, United States
| | - Manish K. Pandey
- Department of Genomics, Prebreeding and Bioinformatics, International Crops Research Institute for the Semi-Arid Tropics, Hyderabad, India
| | - Varsha Singh
- Department of Plant and Soil Sciences, Mississippi State University, Starkville, MS, United States
| | - Te Ming Tseng
- Department of Plant and Soil Sciences, Mississippi State University, Starkville, MS, United States
| | - Sunil S. Gangurde
- Department of Plant Pathology, University of Georgia, Tifton, GA, United States
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Lauterberg M, Tschiersch H, Papa R, Bitocchi E, Neumann K. Engaging Precision Phenotyping to Scrutinize Vegetative Drought Tolerance and Recovery in Chickpea Plant Genetic Resources. PLANTS (BASEL, SWITZERLAND) 2023; 12:2866. [PMID: 37571019 PMCID: PMC10421427 DOI: 10.3390/plants12152866] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/01/2023] [Revised: 07/24/2023] [Accepted: 07/28/2023] [Indexed: 08/13/2023]
Abstract
Precise and high-throughput phenotyping (HTP) of vegetative drought tolerance in chickpea plant genetic resources (PGR) would enable improved screening for genotypes with low relative loss of biomass formation and reliable physiological performance. It could also provide a basis to further decipher the quantitative trait drought tolerance and recovery and gain a better understanding of the underlying mechanisms. In the context of climate change and novel nutritional trends, legumes and chickpea in particular are becoming increasingly important because of their high protein content and adaptation to low-input conditions. The PGR of legumes represent a valuable source of genetic diversity that can be used for breeding. However, the limited use of germplasm is partly due to a lack of available characterization data. The development of HTP systems offers a perspective for the analysis of dynamic plant traits such as abiotic stress tolerance and can support the identification of suitable genetic resources with a potential breeding value. Sixty chickpea accessions were evaluated on an HTP system under contrasting water regimes to precisely evaluate growth, physiological traits, and recovery under optimal conditions in comparison to drought stress at the vegetative stage. In addition to traits such as Estimated Biovolume (EB), Plant Height (PH), and several color-related traits over more than forty days, photosynthesis was examined by chlorophyll fluorescence measurements on relevant days prior to, during, and after drought stress. With high data quality, a wide phenotypic diversity for adaptation, tolerance, and recovery to drought was recorded in the chickpea PGR panel. In addition to a loss of EB between 72% and 82% after 21 days of drought, photosynthetic capacity decreased by 16-28%. Color-related traits can be used as indicators of different drought stress stages, as they show the progression of stress.
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Affiliation(s)
- Madita Lauterberg
- Leibniz Institute of Plant Genetics and Crop Plant Research (IPK), 06466 Gatersleben, Germany; (M.L.)
| | - Henning Tschiersch
- Leibniz Institute of Plant Genetics and Crop Plant Research (IPK), 06466 Gatersleben, Germany; (M.L.)
| | - Roberto Papa
- Department of Agricultural, Food and Environmental Sciences, Università Politecnica delle Marche, 60131 Ancona, Italy
| | - Elena Bitocchi
- Department of Agricultural, Food and Environmental Sciences, Università Politecnica delle Marche, 60131 Ancona, Italy
| | - Kerstin Neumann
- Leibniz Institute of Plant Genetics and Crop Plant Research (IPK), 06466 Gatersleben, Germany; (M.L.)
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Thrash T, Lee H, Baker RL. A low-cost high-throughput phenotyping system for automatically quantifying foliar area and greenness. APPLICATIONS IN PLANT SCIENCES 2022; 10:e11502. [PMID: 36518945 PMCID: PMC9742822 DOI: 10.1002/aps3.11502] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 11/30/2021] [Accepted: 06/01/2022] [Indexed: 06/17/2023]
Abstract
PREMISE With modern advances in genetic sequencing technology, plant phenotyping has become a substantial bottleneck in crop improvement programs. Traditionally, researchers have manually measured phenotypic traits to help determine genotype-phenotype relationships, but manual measurements can be time consuming and expensive. Recently, automated phenotyping systems have increased the spatial and temporal density of measurements, but most of these systems are extremely expensive and require specialized expertise. In the present paper, we develop and validate a low-cost, scalable, high-throughput phenotyping (HTP) system for automating the measurement of foliar area and greenness. METHODS During a greenhouse experiment on the effects of abiotic stress on Brassica rapa, we collected images of hundreds of plants every hour for over a month with a system that cost approximately US$1000. RESULTS In comparison with manually acquired images, this HTP system was able to produce similar estimates of foliar area and greenness, developmental trends, and treatment effects. Foliar area was correlated between the two image sets, but greenness was not. DISCUSSION These findings highlight the potential of HTP systems built from low-cost hardware and freely available software. Future work can use this system to investigate genotype-environment interactions and the genetic loci underlying morphological changes resulting from abiotic stress.
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Affiliation(s)
- Tyler Thrash
- Department of BiologyMiami University212 Pearson Hall, OxfordOhio45056USA
- Graduate Program in BiologySaint Louis University301 Macelwane HallSt. LouisMissouri63103USA
| | - Hansol Lee
- Department of BiologyMiami University212 Pearson Hall, OxfordOhio45056USA
- Graduate Program in Ecology, Evolution, and Environmental BiologyMiami University212 Pearson HallOxfordOhio45056USA
| | - Robert L. Baker
- Department of BiologyMiami University212 Pearson Hall, OxfordOhio45056USA
- Inventory and Monitoring DivisionNational Park Service1201 Oakridge Drive, Suite 150Fort CollinsColorado80525USA
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Amitrano C, Junker A, D'Agostino N, De Pascale S, De Micco V. Integration of high-throughput phenotyping with anatomical traits of leaves to help understanding lettuce acclimation to a changing environment. PLANTA 2022; 256:68. [PMID: 36053378 PMCID: PMC9439985 DOI: 10.1007/s00425-022-03984-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 01/10/2022] [Accepted: 08/25/2022] [Indexed: 06/15/2023]
Abstract
MAIN CONCLUSION The combination of image-based phenotyping with in-depth anatomical analysis allows for a thorough investigation of plant physiological plasticity in acclimation, which is driven by environmental conditions and mediated by anatomical traits. Understanding the ability of plants to respond to fluctuations in environmental conditions is critical to addressing climate change and unlocking the agricultural potential of crops both indoor and in the field. Recent studies have revealed that the degree of eco-physiological acclimation depends on leaf anatomical traits, which show stress-induced alterations during organogenesis. Indeed, it is still a matter of debate whether plant anatomy is the bottleneck for optimal plant physiology or vice versa. Here, we cultivated 'Salanova' lettuces in a phenotyping chamber under two different vapor pressure deficits (VPDs; low, high) and watering levels (well-watered, low-watered); then, plants underwent short-term changes in VPD. We aimed to combine high-throughput phenotyping with leaf anatomical analysis to evaluate their capability in detecting the early stress signals in lettuces and to highlight the different degrees of plants' eco-physiological acclimation to the change in VPD, as influenced by anatomical traits. The results demonstrate that well-watered plants under low VPD developed a morpho-anatomical structure in terms of mesophyll organization, stomatal and vein density, which more efficiently guided the acclimation to sudden changes in environmental conditions and which was not detected by image-based phenotyping alone. Therefore, we emphasized the need to complement high-throughput phenotyping with anatomical trait analysis to unveil crop acclimation mechanisms and predict possible physiological behaviors after sudden environmental fluctuations due to climate changes.
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Affiliation(s)
- Chiara Amitrano
- Department of Agricultural Sciences, University of Naples Federico II, Portici, NA, Italy.
| | - Astrid Junker
- Leibniz Institute of Plant Genetics and Crop Plant Research, OT Gatersleben, Corrensstr. 3, 06466, Seeland, Germany
| | - Nunzio D'Agostino
- Department of Agricultural Sciences, University of Naples Federico II, Portici, NA, Italy
| | - Stefania De Pascale
- Department of Agricultural Sciences, University of Naples Federico II, Portici, NA, Italy
| | - Veronica De Micco
- Department of Agricultural Sciences, University of Naples Federico II, Portici, NA, Italy
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Pabuayon ICM, Pabuayon ILB, Singh RK, Ritchie GL, de los Reyes BG. Applicability of hyperspectral imaging during salinity stress in rice for tracking Na+ and K+ levels in planta. PLoS One 2022; 17:e0270931. [PMID: 35797400 PMCID: PMC9262187 DOI: 10.1371/journal.pone.0270931] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/21/2022] [Accepted: 06/21/2022] [Indexed: 11/19/2022] Open
Abstract
The ratio of Na+ and K+ is an important determinant of the magnitude of Na+ toxicity and osmotic stress in plant cells. Traditional analytical approaches involve destructive tissue sampling and chemical analysis, where real-time observation of spatio-temporal experiments across genetic or breeding populations is unrealistic. Such an approach can also be very inaccurate and prone to erroneous biological interpretation. Analysis by Hyperspectral Imaging (HSI) is an emerging non-destructive alternative for tracking plant nutrient status in a time-course with higher accuracy and reduced cost for chemical analysis. In this study, the feasibility and predictive power of HSI-based approach for spatio-temporal tracking of Na+ and K+ levels in tissue samples was explored using a panel recombinant inbred line (RIL) of rice (Oryza sativa L.; salt-sensitive IR29 x salt-tolerant Pokkali) with differential activities of the Na+ exclusion mechanism conferred by the SalTol QTL. In this panel of RILs the spectrum of salinity tolerance was represented by FL499 (super-sensitive), FL454 (sensitive), FL478 (tolerant), and FL510 (super-tolerant). Whole-plant image processing pipeline was optimized to generate HSI spectra during salinity stress at EC = 9 dS m-1. Spectral data was used to create models for Na+ and K+ prediction by partial least squares regression (PLSR). Three datasets, i.e., mean image pixel spectra, smoothened version of mean image pixel spectra, and wavelength bands, with wide differences in intensity between control and salinity facilitated the prediction models with high R2. The smoothened and filtered datasets showed significant improvements over the mean image pixel dataset. However, model prediction was not fully consistent with the empirical data. While the outcome of modeling-based prediction showed a great potential for improving the throughput capacity for salinity stress phenotyping, additional technical refinements including tissue-specific measurements is necessary to maximize the accuracy of prediction models.
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Affiliation(s)
| | | | | | - Glen L. Ritchie
- Department of Plant and Soil Sciences, Texas Tech University, Lubbock, Texas, United States of America
| | - Benildo G. de los Reyes
- Department of Plant and Soil Sciences, Texas Tech University, Lubbock, Texas, United States of America
- * E-mail:
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Response of Population Canopy Color Gradation Skewed Distribution Parameters of the RGB Model to Micrometeorology Environment in Begonia Fimbristipula Hance. ATMOSPHERE 2022. [DOI: 10.3390/atmos13060890] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/01/2023]
Abstract
The high quality and efficient production of greenhouse vegetation depend on micrometeorology environmental adjusting such as system warming and illumination supplement. In order to improve the quantity, quality, and efficiency of greenhouse vegetation, it is necessary to figure out the relationship between the crop growth conditions and environmental meteorological factors, which could give constructive suggestions for precise control of the greenhouse environment and reduce the running costs. The parameters from the color information of the plant canopy reflect the internal physiological conditions, thus, the RGB model has been widely used in the color analysis of digital pictures of leaves. We take photographs of Begonia Fimbristipula Hance (BFH) growing in the greenhouse at a fixed time every day and measure the meteorological factors. The results showed that the color scale for the single leaf, single plant, and the populated canopy of the BFH photographs all have skewed cumulative distribution histograms. The color gradation skewness-distribution (CGSD) parameters of the RGB model were increased from 4 to 20 after the skewness analysis, which greatly expanded the canopy leaf color information and could simultaneously describe the depth and distribution characteristics of the canopy color. The 20 CGSD parameters were sensitive to the micrometeorology factors, especially to the radiation and temperature accumulation. The multiple regression models of mean, median, mode, and kurtosis parameters to microclimate factors were established, and the spatial models of skewness parameters were optimized. The models can well explain the response of canopy color to microclimate factors and can be used to monitor the variation of plant canopy color under different micrometeorology.
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Suárez JC, Urban MO, Contreras AT, Grajales MÁ, Cajiao C, Beebe SE, Rao IM. Adaptation of Interspecific Mesoamerican Common Bean Lines to Acid Soils and High Temperature in the Amazon Region of Colombia. PLANTS (BASEL, SWITZERLAND) 2021; 10:2412. [PMID: 34834775 PMCID: PMC8623317 DOI: 10.3390/plants10112412] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 10/01/2021] [Revised: 10/26/2021] [Accepted: 10/26/2021] [Indexed: 06/13/2023]
Abstract
Knowledge of the physiological basis for improved genetic adaptation of common bean (Phaseolus vulgaris L.) lines to acid soils and high temperature conditions in the Amazon region of Colombia is limited. In this study, we evaluated the differences among 41 common bean lines in energy use, leaf cooling, photosynthate partitioning to pod formation and grain filling, and grain yield over two seasons under acid soil and high temperature stress in the Amazon region of Colombia. Common bean lines evaluated included medium and large seeded interspecific lines of Mesoamerican and Andean gene pools with different levels of adaptation to abiotic stress conditions and some lines are improved for iron and zinc (biofortified) concentration in seeds. We found three bean lines (GGR 147, SMG 21 and SMG 12) that were superior in their photosynthetic response, leaf cooling, photosynthate partitioning ability to pod formation and grain filling, resulting in grain yields exceeding 1900 kg ha-1 under acid soil and high temperature stress conditions. The superior photosynthetic performance was attributed to the efficient use of absorbed energy on the electron level in thylakoids, which is mainly oriented to a higher quantum yield of PSII (ΦII), lower energy dissipation in the form of heat (ΦNPQ), high linear electron flow (LEF) and high fraction of PSI centers in open state (PSIopen). We speculate that these photosynthetic and photosynthate partitioning responses of superior bean lines are part of the genetic adaptation to acidic soils and high temperature stress conditions. Among the evaluated bean lines, three lines (GGR 147, SMG 21 and SMG 12) combined the desirable attributes for genetic improvement of stress tolerance and biofortification. These lines can serve as parents to further improve traits (energy use efficiency and multiple stress resistance) that are important for bean production in the Amazon region.
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Affiliation(s)
- Juan Carlos Suárez
- Programa de Ingeniería Agroecológica, Facultad de Ingeniería, Universidad de la Amazonia, Florencia 180002, Colombia;
- Programa de Maestría en Sistemas Sostenibles de Producción, Facultad de Ingeniería, Universidad de la Amazonia, Florencia 180002, Colombia
- Centro de Investigaciones Amazónicas CIMAZ Macagual César Augusto Estrada González, Grupo de Investi-gaciones Agroecosistemas y Conservación en Bosques Amazónicos-GAIA, Florencia 180002, Colombia
| | - Milan O. Urban
- International Center for Tropical Agriculture (CIAT), Km 17 Recta Cali-Palmira, Cali 763537, Colombia; (M.O.U.); (M.Á.G.); (C.C.); (S.E.B.); (I.M.R.)
| | - Amara Tatiana Contreras
- Programa de Ingeniería Agroecológica, Facultad de Ingeniería, Universidad de la Amazonia, Florencia 180002, Colombia;
- Programa de Maestría en Sistemas Sostenibles de Producción, Facultad de Ingeniería, Universidad de la Amazonia, Florencia 180002, Colombia
| | - Miguel Ángel Grajales
- International Center for Tropical Agriculture (CIAT), Km 17 Recta Cali-Palmira, Cali 763537, Colombia; (M.O.U.); (M.Á.G.); (C.C.); (S.E.B.); (I.M.R.)
| | - Cesar Cajiao
- International Center for Tropical Agriculture (CIAT), Km 17 Recta Cali-Palmira, Cali 763537, Colombia; (M.O.U.); (M.Á.G.); (C.C.); (S.E.B.); (I.M.R.)
| | - Stephen E. Beebe
- International Center for Tropical Agriculture (CIAT), Km 17 Recta Cali-Palmira, Cali 763537, Colombia; (M.O.U.); (M.Á.G.); (C.C.); (S.E.B.); (I.M.R.)
| | - Idupulapati M. Rao
- International Center for Tropical Agriculture (CIAT), Km 17 Recta Cali-Palmira, Cali 763537, Colombia; (M.O.U.); (M.Á.G.); (C.C.); (S.E.B.); (I.M.R.)
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Singh D, Chaudhary P, Taunk J, Singh CK, Singh D, Tomar RSS, Aski M, Konjengbam NS, Raje RS, Singh S, Sengar RS, Yadav RK, Pal M. Fab Advances in Fabaceae for Abiotic Stress Resilience: From 'Omics' to Artificial Intelligence. Int J Mol Sci 2021; 22:10535. [PMID: 34638885 PMCID: PMC8509049 DOI: 10.3390/ijms221910535] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/04/2021] [Revised: 09/17/2021] [Accepted: 09/23/2021] [Indexed: 11/16/2022] Open
Abstract
Legumes are a better source of proteins and are richer in diverse micronutrients over the nutritional profile of widely consumed cereals. However, when exposed to a diverse range of abiotic stresses, their overall productivity and quality are hugely impacted. Our limited understanding of genetic determinants and novel variants associated with the abiotic stress response in food legume crops restricts its amelioration. Therefore, it is imperative to understand different molecular approaches in food legume crops that can be utilized in crop improvement programs to minimize the economic loss. 'Omics'-based molecular breeding provides better opportunities over conventional breeding for diversifying the natural germplasm together with improving yield and quality parameters. Due to molecular advancements, the technique is now equipped with novel 'omics' approaches such as ionomics, epigenomics, fluxomics, RNomics, glycomics, glycoproteomics, phosphoproteomics, lipidomics, regulomics, and secretomics. Pan-omics-which utilizes the molecular bases of the stress response to identify genes (genomics), mRNAs (transcriptomics), proteins (proteomics), and biomolecules (metabolomics) associated with stress regulation-has been widely used for abiotic stress amelioration in food legume crops. Integration of pan-omics with novel omics approaches will fast-track legume breeding programs. Moreover, artificial intelligence (AI)-based algorithms can be utilized for simulating crop yield under changing environments, which can help in predicting the genetic gain beforehand. Application of machine learning (ML) in quantitative trait loci (QTL) mining will further help in determining the genetic determinants of abiotic stress tolerance in pulses.
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Affiliation(s)
- Dharmendra Singh
- Division of Genetics, ICAR-Indian Agricultural Research Institute, New Delhi 110012, India
| | - Priya Chaudhary
- Division of Genetics, ICAR-Indian Agricultural Research Institute, New Delhi 110012, India
| | - Jyoti Taunk
- Division of Plant Physiology, ICAR-Indian Agricultural Research Institute, New Delhi 110012, India
| | - Chandan Kumar Singh
- Division of Genetics, ICAR-Indian Agricultural Research Institute, New Delhi 110012, India
| | - Deepti Singh
- Department of Botany, Meerut College, Meerut 250001, India
| | - Ram Sewak Singh Tomar
- College of Horticulture and Forestry, Rani Lakshmi Bai Central Agricultural University, Jhansi 284003, India
| | - Muraleedhar Aski
- Division of Genetics, ICAR-Indian Agricultural Research Institute, New Delhi 110012, India
| | - Noren Singh Konjengbam
- College of Post Graduate Studies in Agricultural Sciences, Central Agricultural University, Imphal 793103, India
| | - Ranjeet Sharan Raje
- Division of Genetics, ICAR-Indian Agricultural Research Institute, New Delhi 110012, India
| | - Sanjay Singh
- ICAR- National Institute of Plant Biotechnology, LBS Centre, Pusa Campus, New Delhi 110012, India
| | - Rakesh Singh Sengar
- College of Biotechnology, Sardar Vallabh Bhai Patel Agricultural University, Meerut 250001, India
| | - Rajendra Kumar Yadav
- Department of Genetics and Plant Breeding, Chandra Shekhar Azad University of Agriculture and Technology, Kanpur 208002, India
| | - Madan Pal
- Division of Plant Physiology, ICAR-Indian Agricultural Research Institute, New Delhi 110012, India
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Zendonadi Dos Santos N, Piepho HP, Condorelli GE, Licieri Groli E, Newcomb M, Ward R, Tuberosa R, Maccaferri M, Fiorani F, Rascher U, Muller O. High-throughput field phenotyping reveals genetic variation in photosynthetic traits in durum wheat under drought. PLANT, CELL & ENVIRONMENT 2021; 44:2858-2878. [PMID: 34189744 DOI: 10.1111/pce.14136] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/17/2020] [Revised: 04/14/2021] [Accepted: 06/13/2021] [Indexed: 06/13/2023]
Abstract
Chlorophyll fluorescence (ChlF) is a powerful non-invasive technique for probing photosynthesis. Although proposed as a method for drought tolerance screening, ChlF has not yet been fully adopted in physiological breeding, mainly due to limitations in high-throughput field phenotyping capabilities. The light-induced fluorescence transient (LIFT) sensor has recently been shown to reliably provide active ChlF data for rapid and remote characterisation of plant photosynthetic performance. We used the LIFT sensor to quantify photosynthesis traits across time in a large panel of durum wheat genotypes subjected to a progressive drought in replicated field trials over two growing seasons. The photosynthetic performance was measured at the canopy level by means of the operating efficiency of Photosystem II ( Fq'/Fm' ) and the kinetics of electron transport measured by reoxidation rates ( Fr1' and Fr2' ). Short- and long-term changes in ChlF traits were found in response to soil water availability and due to interactions with weather fluctuations. In mild drought, Fq'/Fm' and Fr2' were little affected, while Fr1' was consistently accelerated in water-limited compared to well-watered plants, increasingly so with rising vapour pressure deficit. This high-throughput approach allowed assessment of the native genetic diversity in ChlF traits while considering the diurnal dynamics of photosynthesis.
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Affiliation(s)
| | - Hans-Peter Piepho
- Biostatistics Unit, Institute of Crop Science, University of Hohenheim, Stuttgart, Germany
| | | | - Eder Licieri Groli
- Department of Agricultural and Food Sciences, University of Bologna, Bologna, Italy
| | - Maria Newcomb
- Maricopa Agricultural Center, University of Arizona, Maricopa, Arizona, USA
| | - Richard Ward
- Maricopa Agricultural Center, University of Arizona, Maricopa, Arizona, USA
| | - Roberto Tuberosa
- Department of Agricultural and Food Sciences, University of Bologna, Bologna, Italy
| | - Marco Maccaferri
- Department of Agricultural and Food Sciences, University of Bologna, Bologna, Italy
| | - Fabio Fiorani
- Institute of Bio- and Geosciences, IBG-2: Plant Sciences, Forschungszentrum Jülich GmbH, Jülich, Germany
| | - Uwe Rascher
- Institute of Bio- and Geosciences, IBG-2: Plant Sciences, Forschungszentrum Jülich GmbH, Jülich, Germany
| | - Onno Muller
- Institute of Bio- and Geosciences, IBG-2: Plant Sciences, Forschungszentrum Jülich GmbH, Jülich, Germany
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Dodig D, Božinović S, Nikolić A, Zorić M, Vančetović J, Ignjatović-Micić D, Delić N, Weigelt-Fischer K, Altmann T, Junker A. Dynamics of Maize Vegetative Growth and Drought Adaptability Using Image-Based Phenotyping Under Controlled Conditions. FRONTIERS IN PLANT SCIENCE 2021; 12:652116. [PMID: 34046050 PMCID: PMC8146906 DOI: 10.3389/fpls.2021.652116] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 01/11/2021] [Accepted: 03/15/2021] [Indexed: 06/12/2023]
Abstract
Changes in climate are likely to have a negative impact on water availability and soil fertility in many maize-growing agricultural areas. The development of high-throughput phenotyping platforms provides a new prospect for dissecting the dynamic complex plant traits such as abiotic stress tolerance into simple components. The growth phenotypes of 20 maize (Zea mays L.) inbred lines were monitored in a non-invasive way under control, nitrogen, and water limitation as well as under combined nitrogen and water stress using an automated phenotyping system in greenhouse conditions. Thirteen biomass-related and morphophysiological traits were extracted from RGB images acquired at 33 time points covering developmental stages from leaf count 5 at the first imaging date to leaf count 10-13 at the final harvest. For these traits, genetic differences were identified and dynamic developmental trends during different maize growth stages were analyzed. The difference between control and water stress was detectable 3-10 days after the beginning of stress depending on the genotype, while the effect of limited nitrogen supply only induced subtle phenotypic effects. Phenotypic traits showed different response dynamics as well as multiple and changing interaction patterns with stress progression. The estimated biovolume, leaf area index, and color ratios were found to be stress-responsive at different stages of drought stress progression and thereby represent valuable reference indicators in the selection of drought-adaptive genotypes. Furthermore, genotypes could be grouped according to two typical growth dynamic patterns in water stress treatments by c-means clustering analysis. Inbred lines with high drought adaptability across time and development were identified and could serve as a basis for designing novel genotypes with desired, stage-specific growth phenotypes under water stress through pyramiding. Drought recovery potential may play an equal role as drought tolerance in plant drought adaptation.
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Affiliation(s)
- Dejan Dodig
- Department for Research and Development, Maize Research Institute Zemun Polje, Belgrade-Zemun, Serbia
| | - Sofija Božinović
- Department for Research and Development, Maize Research Institute Zemun Polje, Belgrade-Zemun, Serbia
| | - Ana Nikolić
- Department for Research and Development, Maize Research Institute Zemun Polje, Belgrade-Zemun, Serbia
| | - Miroslav Zorić
- Department for Maize, Institute for Field and Vegetable Crops, Novi Sad, Serbia
| | - Jelena Vančetović
- Department for Research and Development, Maize Research Institute Zemun Polje, Belgrade-Zemun, Serbia
| | - Dragana Ignjatović-Micić
- Department for Research and Development, Maize Research Institute Zemun Polje, Belgrade-Zemun, Serbia
| | - Nenad Delić
- Department for Research and Development, Maize Research Institute Zemun Polje, Belgrade-Zemun, Serbia
| | - Kathleen Weigelt-Fischer
- Department of Molecular Genetics, Leibniz Institute of Plant Genetics and Crop Plant Research, Gatersleben, Germany
| | - Thomas Altmann
- Department of Molecular Genetics, Leibniz Institute of Plant Genetics and Crop Plant Research, Gatersleben, Germany
| | - Astrid Junker
- Department of Molecular Genetics, Leibniz Institute of Plant Genetics and Crop Plant Research, Gatersleben, Germany
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12
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Matallana-Ramirez LP, Whetten RW, Sanchez GM, Payn KG. Breeding for Climate Change Resilience: A Case Study of Loblolly Pine ( Pinus taeda L.) in North America. FRONTIERS IN PLANT SCIENCE 2021; 12:606908. [PMID: 33995428 PMCID: PMC8119900 DOI: 10.3389/fpls.2021.606908] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/16/2020] [Accepted: 04/08/2021] [Indexed: 05/25/2023]
Abstract
Earth's atmosphere is warming and the effects of climate change are becoming evident. A key observation is that both the average levels and the variability of temperature and precipitation are changing. Information and data from new technologies are developing in parallel to provide multidisciplinary opportunities to address and overcome the consequences of these changes in forest ecosystems. Changes in temperature and water availability impose multidimensional environmental constraints that trigger changes from the molecular to the forest stand level. These can represent a threat for the normal development of the tree from early seedling recruitment to adulthood both through direct mortality, and by increasing susceptibility to pathogens, insect attack, and fire damage. This review summarizes the strengths and shortcomings of previous work in the areas of genetic variation related to cold and drought stress in forest species with particular emphasis on loblolly pine (Pinus taeda L.), the most-planted tree species in North America. We describe and discuss the implementation of management and breeding strategies to increase resilience and adaptation, and discuss how new technologies in the areas of engineering and genomics are shaping the future of phenotype-genotype studies. Lessons learned from the study of species important in intensively-managed forest ecosystems may also prove to be of value in helping less-intensively managed forest ecosystems adapt to climate change, thereby increasing the sustainability and resilience of forestlands for the future.
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Affiliation(s)
- Lilian P. Matallana-Ramirez
- Department of Forestry and Environmental Resources, North Carolina State University, Raleigh, Raleigh, NC, United States
| | - Ross W. Whetten
- Department of Forestry and Environmental Resources, North Carolina State University, Raleigh, Raleigh, NC, United States
| | - Georgina M. Sanchez
- Center for Geospatial Analytics, North Carolina State University, Raleigh, Raleigh, NC, United States
| | - Kitt G. Payn
- Department of Forestry and Environmental Resources, North Carolina State University, Raleigh, Raleigh, NC, United States
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13
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Pandey AK, Rubiales D, Wang Y, Fang P, Sun T, Liu N, Xu P. Omics resources and omics-enabled approaches for achieving high productivity and improved quality in pea (Pisum sativum L.). TAG. THEORETICAL AND APPLIED GENETICS. THEORETISCHE UND ANGEWANDTE GENETIK 2021; 134:755-776. [PMID: 33433637 DOI: 10.1007/s00122-020-03751-5] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/06/2020] [Accepted: 12/10/2020] [Indexed: 05/09/2023]
Abstract
Pea (Pisum sativum L.), a cool-season legume crop grown in more than 85 countries, is the second most important grain legume and one of the major green vegetables in the world. While pea was historically studied as the genetic model leading to the discovery of the laws of genetics, pea research has lagged behind that of other major legumes in the genomics era, due to its large and complex genome. The evolving climate change and growing population have posed grand challenges to the objective of feeding the world, making it essential to invest research efforts to develop multi-omics resources and advanced breeding tools to support fast and continuous development of improved pea varieties. Recently, the pea researchers have achieved key milestones in omics and molecular breeding. The present review provides an overview of the recent important progress including the development of genetic resource databases, high-throughput genotyping assays, reference genome, genes/QTLs responsible for important traits, transcriptomic, proteomic, and phenomic atlases of various tissues under different conditions. These multi-faceted resources have enabled the successful implementation of various markers for monitoring early-generation populations as in marker-assisted backcrossing breeding programs. The emerging new breeding approaches such as CRISPR, speed breeding, and genomic selection are starting to change the paradigm of pea breeding. Collectively, the rich omics resources and omics-enable breeding approaches will enhance genetic gain in pea breeding and accelerate the release of novel pea varieties to meet the elevating demands on productivity and quality.
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Affiliation(s)
- Arun K Pandey
- College of Life Sciences, China Jiliang University, Hangzhou, 310018, China
| | - Diego Rubiales
- Institute for Sustainable Agriculture, CSIC, 14004, Córdoba, Spain
| | - Yonggang Wang
- College of Life Sciences, China Jiliang University, Hangzhou, 310018, China
| | - Pingping Fang
- College of Life Sciences, China Jiliang University, Hangzhou, 310018, China
| | - Ting Sun
- College of Life Sciences, China Jiliang University, Hangzhou, 310018, China
| | - Na Liu
- Institute of Vegetables, Zhejiang Academy of Agricultural Sciences, Hangzhou, 310021, China
| | - Pei Xu
- College of Life Sciences, China Jiliang University, Hangzhou, 310018, China.
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14
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Meyer RC, Weigelt-Fischer K, Knoch D, Heuermann M, Zhao Y, Altmann T. Temporal dynamics of QTL effects on vegetative growth in Arabidopsis thaliana. JOURNAL OF EXPERIMENTAL BOTANY 2021; 72:476-490. [PMID: 33080013 DOI: 10.1093/jxb/eraa490] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/11/2020] [Accepted: 10/19/2020] [Indexed: 06/11/2023]
Abstract
We assessed early vegetative growth in a population of 382 accessions of Arabidopsis thaliana using automated non-invasive high-throughput phenotyping. All accessions were imaged daily from 7 d to 18 d after sowing in three independent experiments and genotyped using the Affymetrix 250k SNP array. Projected leaf area (PLA) was derived from image analysis and used to calculate relative growth rates (RGRs). In addition, initial seed size was determined. The generated datasets were used jointly for a genome-wide association study that identified 238 marker-trait associations (MTAs) individually explaining up to 8% of the total phenotypic variation. Co-localization of MTAs occurred at 33 genomic positions. At 21 of these positions, sequential co-localization of MTAs for 2-9 consecutive days was observed. The detected MTAs for PLA and RGR could be grouped according to their temporal expression patterns, emphasizing that temporal variation of MTA action can be observed even during the vegetative growth phase, a period of continuous formation and enlargement of seemingly similar rosette leaves. This indicates that causal genes may be differentially expressed in successive periods. Analyses of the temporal dynamics of biological processes are needed to gain important insight into the molecular mechanisms of growth-controlling processes in plants.
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Affiliation(s)
- Rhonda C Meyer
- Leibniz Institute of Plant Genetics and Crop Plant Research (IPK), Department of Molecular Genetics, Research Group Heterosis, OT Gatersleben, Corrensstraße, Seeland, Germany
| | - Kathleen Weigelt-Fischer
- Leibniz Institute of Plant Genetics and Crop Plant Research (IPK), Department of Molecular Genetics, Research Group Heterosis, OT Gatersleben, Corrensstraße, Seeland, Germany
| | - Dominic Knoch
- Leibniz Institute of Plant Genetics and Crop Plant Research (IPK), Department of Molecular Genetics, Research Group Heterosis, OT Gatersleben, Corrensstraße, Seeland, Germany
| | - Marc Heuermann
- Leibniz Institute of Plant Genetics and Crop Plant Research (IPK), Department of Molecular Genetics, Research Group Heterosis, OT Gatersleben, Corrensstraße, Seeland, Germany
| | - Yusheng Zhao
- Leibniz Institute of Plant Genetics and Crop Plant Research (IPK), Department of Breeding Research, Research Group Quantitative Genetics, OT Gatersleben, Corrensstraße, Seeland, Germany
| | - Thomas Altmann
- Leibniz Institute of Plant Genetics and Crop Plant Research (IPK), Department of Molecular Genetics, Research Group Heterosis, OT Gatersleben, Corrensstraße, Seeland, Germany
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15
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Colmer J, O'Neill CM, Wells R, Bostrom A, Reynolds D, Websdale D, Shiralagi G, Lu W, Lou Q, Le Cornu T, Ball J, Renema J, Flores Andaluz G, Benjamins R, Penfield S, Zhou J. SeedGerm: a cost-effective phenotyping platform for automated seed imaging and machine-learning based phenotypic analysis of crop seed germination. THE NEW PHYTOLOGIST 2020; 228:778-793. [PMID: 32533857 DOI: 10.1111/nph.16736] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/22/2020] [Accepted: 05/25/2020] [Indexed: 05/26/2023]
Abstract
Efficient seed germination and establishment are important traits for field and glasshouse crops. Large-scale germination experiments are laborious and prone to observer errors, leading to the necessity for automated methods. We experimented with five crop species, including tomato, pepper, Brassica, barley, and maize, and concluded an approach for large-scale germination scoring. Here, we present the SeedGerm system, which combines cost-effective hardware and open-source software for seed germination experiments, automated seed imaging, and machine-learning based phenotypic analysis. The software can process multiple image series simultaneously and produce reliable analysis of germination- and establishment-related traits, in both comma-separated values (CSV) and processed images (PNG) formats. In this article, we describe the hardware and software design in detail. We also demonstrate that SeedGerm could match specialists' scoring of radicle emergence. Germination curves were produced based on seed-level germination timing and rates rather than a fitted curve. In particular, by scoring germination across a diverse panel of Brassica napus varieties, SeedGerm implicates a gene important in abscisic acid (ABA) signalling in seeds. We compared SeedGerm with existing methods and concluded that it could have wide utilities in large-scale seed phenotyping and testing, for both research and routine seed technology applications.
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Affiliation(s)
- Joshua Colmer
- Engineering biology, Earlham Institute, Norwich Research Park, Norwich, NR4 7UZ, UK
| | - Carmel M O'Neill
- Crop Genetics, John Innes Centre, Norwich Research Park, Norwich, NR4 7UH, UK
| | - Rachel Wells
- Crop Genetics, John Innes Centre, Norwich Research Park, Norwich, NR4 7UH, UK
| | - Aaron Bostrom
- Engineering biology, Earlham Institute, Norwich Research Park, Norwich, NR4 7UZ, UK
| | - Daniel Reynolds
- Engineering biology, Earlham Institute, Norwich Research Park, Norwich, NR4 7UZ, UK
| | - Danny Websdale
- Engineering biology, Earlham Institute, Norwich Research Park, Norwich, NR4 7UZ, UK
| | - Gagan Shiralagi
- Crop Genetics, John Innes Centre, Norwich Research Park, Norwich, NR4 7UH, UK
| | - Wei Lu
- College of Engineering, Nanjing Agricultural University, Nanjing, Jiangsu, 210095, China
| | - Qiaojun Lou
- Shanghai Agrobiological Gene Center, Shanghai Academy of Agricultural Sciences, Shanghai, 201106, China
| | - Thomas Le Cornu
- Engineering biology, Earlham Institute, Norwich Research Park, Norwich, NR4 7UZ, UK
| | - Joshua Ball
- Engineering biology, Earlham Institute, Norwich Research Park, Norwich, NR4 7UZ, UK
| | - Jim Renema
- Syngenta Seeds BV, Enkhuizen, 1601 BK, the Netherlands
| | | | | | - Steven Penfield
- Crop Genetics, John Innes Centre, Norwich Research Park, Norwich, NR4 7UH, UK
| | - Ji Zhou
- State Key Laboratory of Crop Genetics & Germplasm Enhancement, Plant Phenomics Research Center, Jiangsu Collaborative Innovation Center for Modern Crop Production co-sponsored by Province and Ministry, Nanjing Agricultural University, Nanjing, 210095, China
- Cambridge Crop Research, National Institute of Agricultural Botany, Cambridge, CB3 0LE, UK
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16
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Detection of Grapevine Leafroll-Associated Virus 1 and 3 in White and Red Grapevine Cultivars Using Hyperspectral Imaging. REMOTE SENSING 2020. [DOI: 10.3390/rs12101693] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Abstract
Grapevine leafroll disease (GLD) is considered one of the most widespread grapevine virus diseases, causing severe economic losses worldwide. To date, six grapevine leafroll-associated viruses (GLRaVs) are known as causal agents of the disease, of which GLRaV-1 and -3 induce the strongest symptoms. Due to the lack of efficient curative treatments in the vineyard, identification of infected plants and subsequent uprooting is crucial to reduce the spread of this disease. Ground-based hyperspectral imaging (400–2500 nm) was used in this study in order to identify white and red grapevine plants infected with GLRaV-1 or -3. Disease detection models have been successfully developed for greenhouse plants discriminating symptomatic, asymptomatic, and healthy plants. Furthermore, field tests conducted over three consecutive years showed high detection rates for symptomatic white and red cultivars, respectively. The most important detection wavelengths were used to simulate a multispectral system that achieved classification accuracies comparable to the hyperspectral approach. Although differentiation of asymptomatic and healthy field-grown grapevines showed promising results further investigations are needed to improve classification accuracy. Symptoms caused by GLRaV-1 and -3 could be differentiated.
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17
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Anandan A, Mahender A, Sah RP, Bose LK, Subudhi H, Meher J, Reddy JN, Ali J. Non-destructive phenotyping for early seedling vigor in direct-seeded rice. PLANT METHODS 2020; 16:127. [PMID: 32973913 PMCID: PMC7507283 DOI: 10.1186/s13007-020-00666-6] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/06/2019] [Accepted: 09/04/2020] [Indexed: 05/17/2023]
Abstract
BACKGROUND Early seedling vigor is an essential trait of direct-seeded rice. It helps the seedlings to compete with weeds for water and nutrient availability, and contributes to better seedling establishment during the initial phase of crop growth. Seedling vigor is a complex trait, and phenotyping by a destructive method limits the improvement of this trait through traditional breeding. Hence, a non-invasive, rapid, and precise image-based phenotyping technique is developed to increase the possibility to improve early seedling vigor through breeding in rice and other field crops. RESULTS To establish and assess the methodology using free-source software, early seedling vigor was estimated from images captured with a digital SLR camera in a non-destructive way. Here, the legitimacy and strength of the method have been proved through screening seven diverse rice cultivars varying for early seedling vigor. In the regression analysis, whole-plant area (WPA) estimated by destructive-flatbed scanner (WPAs) and non-destructive imaging (WPAi) approaches was strongly related (R2 > 83%) and suggested that WPAi can be adapted in place of destructive methods to estimate seedling vigor. In addition, this study has identified a set of new geometric traits (convex hull and top view area) for screening breeding lines for early seedling vigor in rice, which decreased the time by 80% and halved the cost of labor in data observation. CONCLUSIONS The method demonstrated here is affordable and easy to establish as a phenotypic platform. It is suitable for most glasshouses/net houses for characterizing genotypes to understand the plasticity of shoots under a given environment at the seedling stage. The methodology explained in this experiment has been proven to be practical and suggested as a technique for researchers involved in direct-seeded rice. Consequently, it will help in the simultaneous screening of genotypes in large numbers, the identification of donors, and in gaining information on the genetic basis of the trait to design a breeding program for direct-seeded rice.
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Affiliation(s)
- Annamalai Anandan
- Crop Improvement Division, Indian Council of Agricultural Research-National Rice Research Institute (ICAR-NRRI), Cuttack, Odisha 753006 India
| | - Anumalla Mahender
- Rice Breeding Platform, International Rice Research Institute (IRRI), Los Baños, Laguna, 4031 Philippines
| | - Rameswar Prasad Sah
- Crop Improvement Division, Indian Council of Agricultural Research-National Rice Research Institute (ICAR-NRRI), Cuttack, Odisha 753006 India
| | - Lotan Kumar Bose
- Crop Improvement Division, Indian Council of Agricultural Research-National Rice Research Institute (ICAR-NRRI), Cuttack, Odisha 753006 India
| | - Hatanath Subudhi
- Crop Improvement Division, Indian Council of Agricultural Research-National Rice Research Institute (ICAR-NRRI), Cuttack, Odisha 753006 India
| | - Jitendra Meher
- Crop Improvement Division, Indian Council of Agricultural Research-National Rice Research Institute (ICAR-NRRI), Cuttack, Odisha 753006 India
| | - Janga Nagi Reddy
- Crop Improvement Division, Indian Council of Agricultural Research-National Rice Research Institute (ICAR-NRRI), Cuttack, Odisha 753006 India
| | - Jauhar Ali
- Rice Breeding Platform, International Rice Research Institute (IRRI), Los Baños, Laguna, 4031 Philippines
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Tantray AY, Bashir SS, Ahmad A. Low nitrogen stress regulates chlorophyll fluorescence in coordination with photosynthesis and Rubisco efficiency of rice. PHYSIOLOGY AND MOLECULAR BIOLOGY OF PLANTS : AN INTERNATIONAL JOURNAL OF FUNCTIONAL PLANT BIOLOGY 2020; 26:83-94. [PMID: 32158122 PMCID: PMC7036394 DOI: 10.1007/s12298-019-00721-0] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/06/2019] [Revised: 08/04/2019] [Accepted: 10/10/2019] [Indexed: 05/26/2023]
Abstract
Nitrogen (N) is the basis of plant growth and development and, is considered as one of the priming agents to elevate a range of stresses. Plants use solar radiations through photosynthesis, which amasses the assimilatory components of crop yield to meet the global demand for food. Nitrogen is the main regulator in the allocation of photosynthetic apparatus which changes of the photosynthesis (Pn) and quantum yield (Fv/Fm) of the plant. In the present study, dynamics of the photosynthetic establishment, N-dependent relation with chlorophyll fluorescence attributes and Rubisco efficacy was evaluated in low-N tolerant (cv. CR Dhan 311) and low-N sensitive (cv. Rasi) rice cultivars under low-N and optimum-N conditions. There was a decrease in the stored leaf N under low-N condition, resulting in the decreased Pn and Fv/Fm efficiency of the plants through depletion in the activity and content of Rubisco. The Pn and Fv/Fm followed the parallel trend of leaf N content during low-N condition along with depletion of intercellular CO2 concentration and overall conductance under low-N condition. Photosynthetic saturation curve cleared abrupt decrease of effective quantum yield in the low-N sensitive rice cultivar than the low-N tolerant rice. Also, the rapid light curve highlighted the unacclimated regulation of photochemical and non-photochemical quenching in the low-N condition. The low-N sensitive rice cultivar triumphed non-photochemical quenching, whereas the low-N tolerant rice cultivar rose gradually during the light curve. Our study suggested that the quantum yield is the key limitation for photosynthesis in low-N condition. Regulation of Rubisco, photochemical and non-photochemical quenching may help plants to grow under low-N level.
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Affiliation(s)
- Aadil Yousuf Tantray
- Department of Botany, Aligarh Muslim University, Aligarh, Uttar Pradesh 202002 India
| | | | - Altaf Ahmad
- Department of Botany, Aligarh Muslim University, Aligarh, Uttar Pradesh 202002 India
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Dodig D, Božinović S, Nikolić A, Zorić M, Vančetović J, Ignjatović-Micić D, Delić N, Weigelt-Fischer K, Junker A, Altmann T. Image-Derived Traits Related to Mid-Season Growth Performance of Maize Under Nitrogen and Water Stress. FRONTIERS IN PLANT SCIENCE 2019; 10:814. [PMID: 31297124 PMCID: PMC6607059 DOI: 10.3389/fpls.2019.00814] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 10/31/2018] [Accepted: 06/06/2019] [Indexed: 06/09/2023]
Abstract
Phenotypic measurements under controlled cultivation conditions are essential to gain a mechanistic understanding of plant responses to environmental impacts and thus for knowledge-based improvement of their performance under natural field conditions. Twenty maize inbred lines (ILs) were phenotyped in response to two levels of water and nitrogen supply (control and stress) and combined nitrogen and water deficit. Over a course of 5 weeks (from about 4-leaf stage to the beginning of the reproductive stage), maize phenology and growth were monitored by using a high-throughput phenotyping platform for daily acquisition of images in different spectral ranges. The focus of the present study is on the measurements taken at the time of maximum water stress (for traits that reflect plant physiological properties) and at the end of the experiment (for traits that reflect plant architectural and biomass-related traits). Twenty-five phenotypic traits extracted from the digital image data that support biological interpretation of plant growth were selected for their predictive value for mid-season shoot biomass accumulation. Measured fresh and dry weights after harvest were used to calculate various indices (water-use efficiency, physiological nitrogen-use efficiency, specific plant weight) and to establish correlations with image-derived phenotypic features. Also, score indices based on dry weight were used to identify contrasting ILs in terms of productivity and tolerance to stress, and their means for image-derived and manually measured traits were compared. Color-related traits appear to be indicative of plant performance and photosystem II operating efficiency might be an importance physiological parameter of biomass accumulation, particularly under severe stress conditions. Also, genotypes showing greater leaf area may be better adapted to abiotic stress conditions.
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Affiliation(s)
- Dejan Dodig
- Department for Research and Development, Maize Research Institute Zemun Polje, Belgrade, Serbia
| | - Sofija Božinović
- Department for Research and Development, Maize Research Institute Zemun Polje, Belgrade, Serbia
| | - Ana Nikolić
- Department for Research and Development, Maize Research Institute Zemun Polje, Belgrade, Serbia
| | - Miroslav Zorić
- Department for Maize, Institute of Field and Vegetable Crops, Novi Sad, Serbia
| | - Jelena Vančetović
- Department for Research and Development, Maize Research Institute Zemun Polje, Belgrade, Serbia
| | | | - Nenad Delić
- Department for Research and Development, Maize Research Institute Zemun Polje, Belgrade, Serbia
| | - Kathleen Weigelt-Fischer
- Department of Molecular Genetics, Leibniz Institute of Plant Genetics and Crop Plant Research (IPK), Gatersleben, Germany
| | - Astrid Junker
- Department of Molecular Genetics, Leibniz Institute of Plant Genetics and Crop Plant Research (IPK), Gatersleben, Germany
| | - Thomas Altmann
- Department of Molecular Genetics, Leibniz Institute of Plant Genetics and Crop Plant Research (IPK), Gatersleben, Germany
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20
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Mir RR, Reynolds M, Pinto F, Khan MA, Bhat MA. High-throughput phenotyping for crop improvement in the genomics era. PLANT SCIENCE : AN INTERNATIONAL JOURNAL OF EXPERIMENTAL PLANT BIOLOGY 2019; 282:60-72. [PMID: 31003612 DOI: 10.1016/j.plantsci.2019.01.007] [Citation(s) in RCA: 92] [Impact Index Per Article: 18.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/18/2018] [Revised: 12/10/2018] [Accepted: 01/09/2019] [Indexed: 05/24/2023]
Abstract
Tremendous progress has been made with continually expanding genomics technologies to unravel and understand crop genomes. However, the impact of genomics data on crop improvement is still far from satisfactory, in large part due to a lack of effective phenotypic data; our capacity to collect useful high quality phenotypic data lags behind the current capacity to generate high-throughput genomics data. Thus, the research bottleneck in plant sciences is shifting from genotyping to phenotyping. This article review the current status of efforts made in the last decade to systematically collect phenotypic data to alleviate this 'phenomics bottlenecks' by recording trait data through sophisticated non-invasive imaging, spectroscopy, image analysis, robotics, high-performance computing facilities and phenomics databases. These modern phenomics platforms and tools aim to record data on traits like plant development, architecture, plant photosynthesis, growth or biomass productivity, on hundreds to thousands of plants in a single day, as a phenomics revolution. It is believed that this revolution will provide plant scientists with the knowledge and tools necessary for unlocking information coded in plant genomes. Efforts have been also made to present the advances made in the last 10 years in phenomics platforms and their use in generating phenotypic data on different traits in several major crops including rice, wheat, barley, and maize. The article also highlights the need for phenomics databases and phenotypic data sharing for crop improvement. The phenomics data generated has been used to identify genes/QTL through QTL mapping, association mapping and genome-wide association studies (GWAS) for genomics-assisted breeding (GAB) for crop improvement.
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Affiliation(s)
- Reyazul Rouf Mir
- Division of Genetics & Plant Breeding, Faculty of Agriculture (FoA), Sher-e-Kashmir University of Agricultural Sciences and Technology of Kashmir (SKUAST-K), Wadura Campus, Sopore-193201, Kashmir, India.
| | - Mathew Reynolds
- Global Wheat Program, International Maize and Wheat Improvement Centre (CIMMYT), Mexico, D.F., Mexico
| | - Francisco Pinto
- Global Wheat Program, International Maize and Wheat Improvement Centre (CIMMYT), Mexico, D.F., Mexico
| | - Mohd Anwar Khan
- Division of Genetics & Plant Breeding, Faculty of Agriculture (FoA), Sher-e-Kashmir University of Agricultural Sciences and Technology of Kashmir (SKUAST-K), Wadura Campus, Sopore-193201, Kashmir, India
| | - Mohd Ashraf Bhat
- Division of Genetics & Plant Breeding, Faculty of Agriculture (FoA), Sher-e-Kashmir University of Agricultural Sciences and Technology of Kashmir (SKUAST-K), Wadura Campus, Sopore-193201, Kashmir, India
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Abstract
Agricultural scientists face the dual challenge of breeding input-responsive, widely adoptable and climate-resilient varieties of crop plants and developing such varieties at a faster pace. Integrating the gains of genomics with modern-day phenomics will lead to increased breeding efficiency which in turn offers great promise to develop such varieties rapidly. Plant phenotyping techniques have impressively evolved during the last two decades. The low-cost, automated and semi-automated methods for data acquisition, storage and analysis are now available which allow precise quantitative analysis of plant structure and function; and genetic dissection of complex traits. Appropriate plant types can now be quickly developed that respond favorably to low input and resource-limited environments and address the challenges of subsistence agriculture. The present review focuses on the need of systematic, rapid, minimal invasive and low-cost plant phenotyping. It also discusses its evolution to modern day high throughput phenotyping (HTP), traits amenable to HTP, integration of HTP with genomics and the scope of utilizing these tools for crop improvement.
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Reynolds D, Ball J, Bauer A, Davey R, Griffiths S, Zhou J. CropSight: a scalable and open-source information management system for distributed plant phenotyping and IoT-based crop management. Gigascience 2019; 8:giz009. [PMID: 30715329 PMCID: PMC6423370 DOI: 10.1093/gigascience/giz009] [Citation(s) in RCA: 33] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/23/2018] [Revised: 12/18/2018] [Accepted: 01/15/2019] [Indexed: 12/14/2022] Open
Abstract
BACKGROUND High-quality plant phenotyping and climate data lay the foundation for phenotypic analysis and genotype-environment interaction, providing important evidence not only for plant scientists to understand the dynamics between crop performance, genotypes, and environmental factors but also for agronomists and farmers to closely monitor crops in fluctuating agricultural conditions. With the rise of Internet of Things technologies (IoT) in recent years, many IoT-based remote sensing devices have been applied to plant phenotyping and crop monitoring, which are generating terabytes of biological datasets every day. However, it is still technically challenging to calibrate, annotate, and aggregate the big data effectively, especially when they were produced in multiple locations and at different scales. FINDINGS CropSight is a PHP Hypertext Pre-processor and structured query language-based server platform that provides automated data collation, storage, and information management through distributed IoT sensors and phenotyping workstations. It provides a two-component solution to monitor biological experiments through networked sensing devices, with interfaces specifically designed for distributed plant phenotyping and centralized data management. Data transfer and annotation are accomplished automatically through an hypertext transfer protocol-accessible RESTful API installed on both device side and server side of the CropSight system, which synchronize daily representative crop growth images for visual-based crop assessment and hourly microclimate readings for GxE studies. CropSight also supports the comparison of historical and ongoing crop performance while different experiments are being conducted. CONCLUSIONS As a scalable and open-source information management system, CropSight can be used to maintain and collate important crop performance and microclimate datasets captured by IoT sensors and distributed phenotyping installations. It provides near real-time environmental and crop growth monitoring in addition to historical and current experiment comparison through an integrated cloud-ready server system. Accessible both locally in the field through smart devices and remotely in an office using a personal computer, CropSight has been applied to field experiments of bread wheat prebreeding since 2016 and speed breeding since 2017. We believe that the CropSight system could have a significant impact on scalable plant phenotyping and IoT-style crop management to enable smart agricultural practices in the near future.
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Affiliation(s)
- Daniel Reynolds
- Engineering Biology, Earlham Institute, Norwich Research Park, Colney Lane, Norwich, NR4 7UZ, UK
| | - Joshua Ball
- Engineering Biology, Earlham Institute, Norwich Research Park, Colney Lane, Norwich, NR4 7UZ, UK
| | - Alan Bauer
- Engineering Biology, Earlham Institute, Norwich Research Park, Colney Lane, Norwich, NR4 7UZ, UK
- Plant Phenomics Research Center, China-UK Plant Phenomics Research Centre, Nanjing Agricultural University, No 1, Weigang, Nanjing, Jiangsu Province, China, 210095
| | - Robert Davey
- Engineering Biology, Earlham Institute, Norwich Research Park, Colney Lane, Norwich, NR4 7UZ, UK
| | - Simon Griffiths
- Crop Genetics, John Innes Centre, Norwich Research Park, Colney Lane, Norwich, NR4 7UH, UK
| | - Ji Zhou
- Engineering Biology, Earlham Institute, Norwich Research Park, Colney Lane, Norwich, NR4 7UZ, UK
- Plant Phenomics Research Center, China-UK Plant Phenomics Research Centre, Nanjing Agricultural University, No 1, Weigang, Nanjing, Jiangsu Province, China, 210095
- University of East Anglia, Norwich Research Park, Norwich, NT4 7TJ, UK
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Janečková H, Husičková A, Lazár D, Ferretti U, Pospíšil P, Špundová M. Exogenous application of cytokinin during dark senescence eliminates the acceleration of photosystem II impairment caused by chlorophyll b deficiency in barley. PLANT PHYSIOLOGY AND BIOCHEMISTRY : PPB 2019; 136:43-51. [PMID: 30639921 DOI: 10.1016/j.plaphy.2019.01.005] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/21/2018] [Revised: 12/19/2018] [Accepted: 01/03/2019] [Indexed: 05/01/2023]
Abstract
Recent studies have shown that chlorophyll (Chl) b has an important role in the regulation of leaf senescence. However, there is only limited information about senescence of plants lacking Chl b and senescence-induced decrease in photosystem II (PSII) and photosystem I (PSI) function has not even been investigated in such plants. We have studied senescence-induced changes in photosynthetic pigment content and PSII and PSI activities in detached leaves of Chl b-deficient barley mutant, chlorina f2f2 (clo). After 4 days in the dark, the senescence-induced decrease in PSI activity was smaller in clo compared to WT leaves. On the contrary, the senescence-induced impairment in PSII function (estimated from Chl fluorescence parameters) was much more pronounced in clo leaves, even though the relative decrease in Chl content was similar to wild type (WT) leaves (Hordeum vulgare L., cv. Bonus). The stronger impairment of PSII function seems to be related to more pronounced damage of reaction centers of PSII. Interestingly, exogenously applied plant hormone cytokinin 6-benzylaminopurine (BA) was able to maintain PSII function in the dark senescing clo leaves to a similar extent as in WT. Thus, considering the fact that without BA the senescence-induced decrease in PSII photochemistry in clo was more pronounced than in WT, the relative protective effect of BA was higher in Chl b-deficient mutant than in WT.
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Affiliation(s)
- Helena Janečková
- Centre of the Region Haná for Biotechnological and Agricultural Research, Department of Biophysics, Faculty of Science, Palacký University, Šlechtitelů 241/27, Olomouc, 783 71, Czech Republic
| | - Alexandra Husičková
- Centre of the Region Haná for Biotechnological and Agricultural Research, Department of Biophysics, Faculty of Science, Palacký University, Šlechtitelů 241/27, Olomouc, 783 71, Czech Republic
| | - Dušan Lazár
- Centre of the Region Haná for Biotechnological and Agricultural Research, Department of Biophysics, Faculty of Science, Palacký University, Šlechtitelů 241/27, Olomouc, 783 71, Czech Republic
| | - Ursula Ferretti
- Centre of the Region Haná for Biotechnological and Agricultural Research, Department of Biophysics, Faculty of Science, Palacký University, Šlechtitelů 241/27, Olomouc, 783 71, Czech Republic
| | - Pavel Pospíšil
- Centre of the Region Haná for Biotechnological and Agricultural Research, Department of Biophysics, Faculty of Science, Palacký University, Šlechtitelů 241/27, Olomouc, 783 71, Czech Republic
| | - Martina Špundová
- Centre of the Region Haná for Biotechnological and Agricultural Research, Department of Biophysics, Faculty of Science, Palacký University, Šlechtitelů 241/27, Olomouc, 783 71, Czech Republic.
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24
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Mishra KB, Mishra A, Kubásek J, Urban O, Heyer AG. Low temperature induced modulation of photosynthetic induction in non-acclimated and cold-acclimated Arabidopsis thaliana: chlorophyll a fluorescence and gas-exchange measurements. PHOTOSYNTHESIS RESEARCH 2019; 139:123-143. [PMID: 30306531 DOI: 10.1007/s11120-018-0588-7] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/26/2018] [Accepted: 09/24/2018] [Indexed: 05/23/2023]
Abstract
Cold acclimation modifies the photosynthetic machinery and enables plants to survive at sub-zero temperatures, whereas in warm habitats, many species suffer even at non-freezing temperatures. We have measured chlorophyll a fluorescence (ChlF) and CO2 assimilation to investigate the effects of cold acclimation, and of low temperatures, on a cold-sensitive Arabidopsis thaliana accession C24. Upon excitation with low intensity (40 µmol photons m- 2 s- 1) ~ 620 nm light, slow (minute range) ChlF transients, at ~ 22 °C, showed two waves in the SMT phase (S, semi steady-state; M, maximum; T, terminal steady-state), whereas CO2 assimilation showed a linear increase with time. Low-temperature treatment (down to - 1.5 °C) strongly modulated the SMT phase and stimulated a peak in the CO2 assimilation induction curve. We show that the SMT phase, at ~ 22 °C, was abolished when measured under high actinic irradiance, or when 3-(3, 4-dichlorophenyl)-1, 1- dimethylurea (DCMU, an inhibitor of electron flow) or methyl viologen (MV, a Photosystem I (PSI) electron acceptor) was added to the system. Our data suggest that stimulation of the SMT wave, at low temperatures, has multiple reasons, which may include changes in both photochemical and biochemical reactions leading to modulations in non-photochemical quenching (NPQ) of the excited state of Chl, "state transitions," as well as changes in the rate of cyclic electron flow through PSI. Further, we suggest that cold acclimation, in accession C24, promotes "state transition" and protects photosystems by preventing high excitation pressure during low-temperature exposure.
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Affiliation(s)
- Kumud B Mishra
- Global Change Research Institute, Czech Academy of Sciences, Bělidla 986/4a, 603 00, Brno, Czech Republic.
- Department of Experimental Biology, Masaryk University, Kamenice 5, 625 00, Brno, Czech Republic.
| | - Anamika Mishra
- Global Change Research Institute, Czech Academy of Sciences, Bělidla 986/4a, 603 00, Brno, Czech Republic
| | - Jiří Kubásek
- Global Change Research Institute, Czech Academy of Sciences, Bělidla 986/4a, 603 00, Brno, Czech Republic
| | - Otmar Urban
- Global Change Research Institute, Czech Academy of Sciences, Bělidla 986/4a, 603 00, Brno, Czech Republic
| | - Arnd G Heyer
- Department of Plant Biotechnology, Institute of Biomaterials and Biomolecular Systems, University of Stuttgart, Pfaffenwaldring 57, 70567, Stuttgart, Germany
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25
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Paul K, Sorrentino M, Lucini L, Rouphael Y, Cardarelli M, Bonini P, Miras Moreno MB, Reynaud H, Canaguier R, Trtílek M, Panzarová K, Colla G. A Combined Phenotypic and Metabolomic Approach for Elucidating the Biostimulant Action of a Plant-Derived Protein Hydrolysate on Tomato Grown Under Limited Water Availability. FRONTIERS IN PLANT SCIENCE 2019; 10:493. [PMID: 31130970 PMCID: PMC6509618 DOI: 10.3389/fpls.2019.00493] [Citation(s) in RCA: 48] [Impact Index Per Article: 9.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/28/2019] [Accepted: 04/01/2019] [Indexed: 05/22/2023]
Abstract
Plant-derived protein hydrolysates (PHs) are an important category of biostimulants able to increase plant growth and crop yield especially under environmental stress conditions. PHs can be applied as foliar spray or soil drench. Foliar spray is generally applied to achieve a relatively short-term response, whereas soil drench is used when a long-term effect is desired. The aim of the study was to elucidate the biostimulant action of PH application method (foliar spray or substrate drench) on morpho-physiological traits and metabolic profile of tomato grown under limited water availability. An untreated control was also included. A high-throughput image-based phenotyping (HTP) approach was used to non-destructively monitor the crop response under limited water availability (40% of container capacity) in a controlled environment. Moreover, metabolic profile of leaves was determined at the end of the trial. Dry biomass of shoots at the end of the trial was significantly correlated with number of green pixels (R 2 = 0.90) and projected shoot area, respectively. Both drench and foliar treatments had a positive impact on the digital biomass compared to control while the photosynthetic performance of the plants was slightly influenced by treatments. Overall drench application under limited water availability more positively influenced biomass accumulation and metabolic profile than foliar application. Significantly higher transpiration use efficiency was observed with PH-drench applications indicating better stomatal conductance. The mass-spectrometry based metabolomic analysis allowed the identification of distinct biochemical signatures in PH-treated plants. Metabolomic changes involved a wide and organized range of biochemical processes that included, among others, phytohormones (notably a decrease in cytokinins and an accumulation of salicylates) and lipids (including membrane lipids, sterols, and terpenes). From a general perspective, treated tomato plants exhibited an improved tolerance to reactive oxygen species (ROS)-mediated oxidative imbalance. Such capability to cope with oxidative stress might have resulted from a coordinated action of signaling compounds (salicylic acid and hydroxycinnamic amides), radical scavengers such as carotenoids and prenyl quinones, as well as a reduced biosynthesis of tetrapyrrole coproporphyrins.
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Affiliation(s)
- Kenny Paul
- Photon Systems Instruments, spol. s.r.o., Drásov, Czechia
| | | | - Luigi Lucini
- Department for Sustainable Food Process, Research Centre for Nutrigenomics and Proteomics, Università Cattolica del Sacro Cuore, Piacenza, Italy
| | - Youssef Rouphael
- Department of Agricultural Sciences, University of Naples Federico II, Portici, Italy
| | - Mariateresa Cardarelli
- Consiglio per la Ricerca in Agricoltura e l’Analisi dell’Economia Agraria, Centro di Ricerca Orticoltura e Florovivaismo, Pontecagnano Faiano, Italy
| | | | - Maria Begoña Miras Moreno
- Department for Sustainable Food Process, Research Centre for Nutrigenomics and Proteomics, Università Cattolica del Sacro Cuore, Piacenza, Italy
| | | | | | - Martin Trtílek
- Photon Systems Instruments, spol. s.r.o., Drásov, Czechia
| | - Klára Panzarová
- Photon Systems Instruments, spol. s.r.o., Drásov, Czechia
- *Correspondence: Klára Panzarová, Giuseppe Colla,
| | - Giuseppe Colla
- Department of Agriculture and Forest Sciences, Tuscia University, Viterbo, Italy
- Arcadia Srl, Rivoli Veronese, Italy
- *Correspondence: Klára Panzarová, Giuseppe Colla,
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26
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Nguyen GN, Norton SL, Rosewarne GM, James LE, Slater AT. Automated phenotyping for early vigour of field pea seedlings in controlled environment by colour imaging technology. PLoS One 2018; 13:e0207788. [PMID: 30452470 PMCID: PMC6242686 DOI: 10.1371/journal.pone.0207788] [Citation(s) in RCA: 20] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/03/2018] [Accepted: 11/06/2018] [Indexed: 02/06/2023] Open
Abstract
Early vigour of seedlings is a beneficial trait of field pea (Pisum sativum L.) that contributes to weed control, water use efficiency and is likely to contribute to yield under certain environments. Although breeding is considered the most effective approach to improve early vigour of field pea, the absence of a robust and high-throughput phenotyping tool to dissect this complex trait is currently a major obstacle of genetic improvement programs to address this issue. To develop this tool, separate trials on 44 genetically diverse field pea genotypes were conducted in the automated plant phenotyping platform of Plant Phenomics Victoria, Horsham and in the field, respectively. High correlation between estimated plant parameters derived from the automated phenotyping platform and important early vigour traits such as shoot biomass, leaf area and plant height indicated that the derived plant parameters can be used to predict vigour traits in field pea seedlings. Plant growth analysis demonstrated that the "broken-stick" model fitted well with the growth pattern of all field pea genotypes and can be used to determine the linear growth phase. Further analysis suggested that the estimated plant parameters collected at the linear growth phase can effectively differentiate early vigour across field pea genotypes. High correlation between normalised difference vegetation indices captured from the field trial and estimated shoot biomass and top-view area confirmed the consistent performance of early vigour field pea genotypes under controlled and field environments. Overall, our results demonstrated that this robust screening tool is highly applicable and will enable breeding programs to rapidly identify early vigour traits and utilise germplasm to contribute to the genetic improvement of field peas.
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Affiliation(s)
- Giao N. Nguyen
- Australian Grains Genebank, Agriculture Victoria, Grains Innovation Park, Horsham, Victoria, Australia
| | - Sally L. Norton
- Australian Grains Genebank, Agriculture Victoria, Grains Innovation Park, Horsham, Victoria, Australia
| | - Garry M. Rosewarne
- Agriculture Victoria, Grains Innovation Park, Horsham, Victoria, Australia
| | - Laura E. James
- Agriculture Victoria, Grains Innovation Park, Horsham, Victoria, Australia
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27
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Kenchanmane Raju SK, Barnes AC, Schnable JC, Roston RL. Low-temperature tolerance in land plants: Are transcript and membrane responses conserved? PLANT SCIENCE : AN INTERNATIONAL JOURNAL OF EXPERIMENTAL PLANT BIOLOGY 2018; 276:73-86. [PMID: 30348330 DOI: 10.1016/j.plantsci.2018.08.002] [Citation(s) in RCA: 42] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/23/2018] [Revised: 08/01/2018] [Accepted: 08/02/2018] [Indexed: 05/20/2023]
Abstract
Plants' tolerance of low temperatures is an economically and ecologically important limitation on geographic distributions and growing seasons. Tolerance for low temperatures varies significantly across different plant species, and different mechanisms likely act in different species. In order to survive low-temperature stress, plant membranes must maintain their fluidity in increasingly cold and oxidative cellular environments. The responses of different species to low-temperature stress include changes to the types and desaturation levels of membrane lipids, though the precise lipids affected tend to vary by species. Regulation of membrane dynamics and other low-temperature tolerance factors are controlled by both transcriptional and post-transcriptional mechanisms. Here, we review low-temperature induced changes in both membrane lipid composition and gene transcription across multiple related plant species with differing degrees of low-temperature tolerance. We attempt to define a core set of changes for transcripts and lipids across species and treatment variations. Some responses appear to be consistent across all species for which data are available, while many others appear likely to be species or family-specific. Potential rationales are presented, including variance in testing, reporting and the importance of considering the level of stress perceived by the plant.
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Affiliation(s)
- Sunil Kumar Kenchanmane Raju
- Center for Plant Science Innovation, University of Nebraska-Lincoln, Lincoln, Nebraska, 68588, USA; Department of Agronomy and Horticulture, University of Nebraska-Lincoln, Lincoln, Nebraska, 68588, USA
| | - Allison C Barnes
- Center for Plant Science Innovation, University of Nebraska-Lincoln, Lincoln, Nebraska, 68588, USA; Department of Biochemistry, University of Nebraska-Lincoln, Lincoln, Nebraska, 68588, USA
| | - James C Schnable
- Center for Plant Science Innovation, University of Nebraska-Lincoln, Lincoln, Nebraska, 68588, USA; Department of Agronomy and Horticulture, University of Nebraska-Lincoln, Lincoln, Nebraska, 68588, USA
| | - Rebecca L Roston
- Center for Plant Science Innovation, University of Nebraska-Lincoln, Lincoln, Nebraska, 68588, USA; Department of Biochemistry, University of Nebraska-Lincoln, Lincoln, Nebraska, 68588, USA.
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28
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Abdelrahman M, Jogaiah S, Burritt DJ, Tran LSP. Legume genetic resources and transcriptome dynamics under abiotic stress conditions. PLANT, CELL & ENVIRONMENT 2018; 41:1972-1983. [PMID: 29314055 DOI: 10.1111/pce.13123] [Citation(s) in RCA: 40] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/19/2017] [Revised: 12/08/2017] [Accepted: 12/08/2017] [Indexed: 05/04/2023]
Abstract
Grain legumes are an important source of nutrition and income for billions of consumers and farmers around the world. However, the low productivity of new legume varieties, due to the limited genetic diversity available for legume breeding programmes and poor policymaker support, combined with an increasingly unpredictable global climate is resulting in a large gap between current yields and the increasing demand for legumes as food. Hence, there is a need for novel approaches to develop new high-yielding legume cultivars that are able to cope with a range of environmental stressors. Next-generation technologies are providing the tools that could enable the more rapid and cost-effective genomic and transcriptomic studies for most major crops, allowing the identification of key functional and regulatory genes involved in abiotic stress resistance. In this review, we provide an overview of the recent achievements regarding abiotic stress resistance in a wide range of legume crops and highlight the transcriptomic and miRNA approaches that have been used. In addition, we critically evaluate the availability and importance of legume genetic resources with desirable abiotic stress resistance traits.
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Affiliation(s)
- Mostafa Abdelrahman
- Laboratory of Genomic Reproductive Biology, Graduate School of Life Sciences, Tohoku University, 2-1-1 Katahira, Aoba-ku, Sendai, 980-8577, Japan
- Botany Department, Faculty of Science, Aswan University, Aswan, 81528, Egypt
| | - Sudisha Jogaiah
- Plant Healthcare and Diagnostic Center, Department of Studies in Biotechnology and Microbiology, Karnatak University, Dharwad, 580 003, India
| | - David J Burritt
- Department of Botany, University of Otago, P.O. Box 56, Dunedin, New Zealand
| | - Lam-Son Phan Tran
- Plant Stress Research Group & Faculty of Applied Sciences, Ton Duc Thang University, Ho Chi Minh City, Vietnam
- Signaling Pathway Research Unit, RIKEN Center for Sustainable Resource Science, Yokohama, Japan
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29
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Yao J, Sun D, Cen H, Xu H, Weng H, Yuan F, He Y. Phenotyping of Arabidopsis Drought Stress Response Using Kinetic Chlorophyll Fluorescence and Multicolor Fluorescence Imaging. FRONTIERS IN PLANT SCIENCE 2018; 9:603. [PMID: 29868063 PMCID: PMC5958224 DOI: 10.3389/fpls.2018.00603] [Citation(s) in RCA: 33] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/28/2018] [Accepted: 04/16/2018] [Indexed: 05/21/2023]
Abstract
Plant responses to drought stress are complex due to various mechanisms of drought avoidance and tolerance to maintain growth. Traditional plant phenotyping methods are labor-intensive, time-consuming, and subjective. Plant phenotyping by integrating kinetic chlorophyll fluorescence with multicolor fluorescence imaging can acquire plant morphological, physiological, and pathological traits related to photosynthesis as well as its secondary metabolites, which will provide a new means to promote the progress of breeding for drought tolerant accessions and gain economic benefit for global agriculture production. Combination of kinetic chlorophyll fluorescence and multicolor fluorescence imaging proved to be efficient for the early detection of drought stress responses in the Arabidopsis ecotype Col-0 and one of its most affected mutants called reduced hyperosmolality-induced [Ca2+]i increase 1. Kinetic chlorophyll fluorescence curves were useful for understanding the drought tolerance mechanism of Arabidopsis. Conventional fluorescence parameters provided qualitative information related to drought stress responses in different genotypes, and the corresponding images showed spatial heterogeneities of drought stress responses within the leaf and the canopy levels. Fluorescence parameters selected by sequential forward selection presented high correlations with physiological traits but not morphological traits. The optimal fluorescence traits combined with the support vector machine resulted in good classification accuracies of 93.3 and 99.1% for classifying the control plants from the drought-stressed ones with 3 and 7 days treatments, respectively. The results demonstrated that the combination of kinetic chlorophyll fluorescence and multicolor fluorescence imaging with the machine learning technique was capable of providing comprehensive information of drought stress effects on the photosynthesis and the secondary metabolisms. It is a promising phenotyping technique that allows early detection of plant drought stress.
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Affiliation(s)
- Jieni Yao
- College of Biosystems Engineering and Food Science, Zhejiang University, Hangzhou, China
- Key Laboratory of Spectroscopy Sensing, Ministry of Agriculture, Hangzhou, China
| | - Dawei Sun
- College of Biosystems Engineering and Food Science, Zhejiang University, Hangzhou, China
- Key Laboratory of Spectroscopy Sensing, Ministry of Agriculture, Hangzhou, China
| | - Haiyan Cen
- College of Biosystems Engineering and Food Science, Zhejiang University, Hangzhou, China
- Key Laboratory of Spectroscopy Sensing, Ministry of Agriculture, Hangzhou, China
| | - Haixia Xu
- College of Biosystems Engineering and Food Science, Zhejiang University, Hangzhou, China
- Key Laboratory of Spectroscopy Sensing, Ministry of Agriculture, Hangzhou, China
| | - Haiyong Weng
- College of Biosystems Engineering and Food Science, Zhejiang University, Hangzhou, China
- Key Laboratory of Spectroscopy Sensing, Ministry of Agriculture, Hangzhou, China
| | - Fang Yuan
- Center for Plant Environmental Sensing, College of Life and Environmental Sciences, Hangzhou Normal University, Hangzhou, China
| | - Yong He
- College of Biosystems Engineering and Food Science, Zhejiang University, Hangzhou, China
- Key Laboratory of Spectroscopy Sensing, Ministry of Agriculture, Hangzhou, China
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30
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Affordable Imaging Lab for Noninvasive Analysis of Biomass and Early Vigour in Cereal Crops. BIOMED RESEARCH INTERNATIONAL 2018; 2018:5713158. [PMID: 29850536 PMCID: PMC5933035 DOI: 10.1155/2018/5713158] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 10/21/2017] [Revised: 02/18/2018] [Accepted: 03/07/2018] [Indexed: 12/04/2022]
Abstract
Plant phenotyping by imaging allows automated analysis of plants for various morphological and physiological traits. In this work, we developed a low-cost RGB imaging phenotyping lab (LCP lab) for low-throughput imaging and analysis using affordable imaging equipment and freely available software. LCP lab comprising RGB imaging and analysis pipeline is set up and demonstrated with early vigour analysis in wheat. Using this lab, a few hundred pots can be photographed in a day and the pots are tracked with QR codes. The software pipeline for both imaging and analysis is built from freely available software. The LCP lab was evaluated for early vigour analysis of five wheat cultivars. A high coefficient of determination (R2 0.94) was obtained between the dry weight and the projected leaf area of 20-day-old wheat plants and R2 of 0.9 for the relative growth rate between 10 and 20 days of plant growth. Detailed description for setting up such a lab is provided together with custom scripts built for imaging and analysis. The LCP lab is an affordable alternative for analysis of cereal crops when access to a high-throughput phenotyping facility is unavailable or when the experiments require growing plants in highly controlled climate chambers. The protocols described in this work are useful for building affordable imaging system for small-scale research projects and for education.
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31
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Denaeghel HER, Van Laere K, Leus L, Lootens P, Van Huylenbroeck J, Van Labeke MC. The Variable Effect of Polyploidization on the Phenotype in Escallonia. FRONTIERS IN PLANT SCIENCE 2018; 9:354. [PMID: 29616065 PMCID: PMC5869194 DOI: 10.3389/fpls.2018.00354] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/03/2018] [Accepted: 03/02/2018] [Indexed: 05/22/2023]
Abstract
To induce new variation within the Escallonia genus, chromosome doubling was performed in E. rubra, E. rosea, and E. illinita, three important species within this genus of mainly evergreen woody ornamental species. Obtained tetraploids and diploid controls were analyzed for rooting capacity, leaf and flower characteristics, and plant architecture using image analysis and cold tolerance. In the present study, a breeders' collection of 23 accessions was characterized cytogenetically and described morphologically. All analyzed species and cultivars were diploid (2n = 2x = 24), with exception of E. pendula, a tetraploid. Today, breeding in Escallonia is limited to lucky finds in seedling populations and few efforts in interspecific hybridization. Three selected Escallonia species underwent an in vitro chromosome doubling with both oryzalin and trifluralin applied as either a continuous or shock treatment. The treatments successfully induced polyploids in all three species. Image analysis revealed that tetraploid E. rosea had decreased shoot length (from 3.8 to 1.3 cm), higher circularity and more dense growth habit compared to diploids. No significant changes in cold tolerance were seen. Tetraploid E. illinita did not differ in shoot length, but an increased outgrowth of axillary buds on the main axis led to denser plants. For tetraploid E. rubra, an increase in plant height (from 4.9 to 5.5 cm) was observed together with a large decrease in circularity and density due to a more polar outgrowth of branches on the main axis. E. rubra tetraploids bore larger flowers than diploids and had an increased cold tolerance (from -7.7 to -11.8°C). Leaf width and area of tetraploids increased for both E. illinita and E. rubra, while a decrease was seen in E. rosea genotypes. For all three species, the rooting capacity of the tetraploids did not differ from the diploids. We conclude that the effect of polyploidization on Escallonia was highly variable and species dependent.
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Affiliation(s)
- Hanne E. R. Denaeghel
- Applied Genetics and Breeding, Plant Sciences Unit, Flanders Research Institute for Agriculture, Fisheries and Food, Melle, Belgium
- Department of Plant Production, Faculty of Bioscience Engineering, Ghent University, Ghent, Belgium
| | - Katrijn Van Laere
- Applied Genetics and Breeding, Plant Sciences Unit, Flanders Research Institute for Agriculture, Fisheries and Food, Melle, Belgium
| | - Leen Leus
- Applied Genetics and Breeding, Plant Sciences Unit, Flanders Research Institute for Agriculture, Fisheries and Food, Melle, Belgium
| | - Peter Lootens
- Applied Genetics and Breeding, Plant Sciences Unit, Flanders Research Institute for Agriculture, Fisheries and Food, Melle, Belgium
| | - Johan Van Huylenbroeck
- Applied Genetics and Breeding, Plant Sciences Unit, Flanders Research Institute for Agriculture, Fisheries and Food, Melle, Belgium
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Rühle T, Reiter B, Leister D. Chlorophyll Fluorescence Video Imaging: A Versatile Tool for Identifying Factors Related to Photosynthesis. FRONTIERS IN PLANT SCIENCE 2018; 9:55. [PMID: 29472935 PMCID: PMC5810273 DOI: 10.3389/fpls.2018.00055] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/26/2017] [Accepted: 01/10/2018] [Indexed: 05/12/2023]
Abstract
Measurements of chlorophyll fluorescence provide an elegant and non-invasive means of probing the dynamics of photosynthesis. Advances in video imaging of chlorophyll fluorescence have now made it possible to study photosynthesis at all levels from individual cells to entire crop populations. Since the technology delivers quantitative data, is easily scaled up and can be readily combined with other approaches, it has become a powerful phenotyping tool for the identification of factors relevant to photosynthesis. Here, we review genetic chlorophyll fluorescence-based screens of libraries of Arabidopsis and Chlamydomonas mutants, discuss its application to high-throughput phenotyping in quantitative genetics and highlight potential future developments.
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Affiliation(s)
- Thilo Rühle
- Plant Molecular Biology, Department of Biology, Ludwig Maximilian University of Munich, Munich, Germany
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Joly-Lopez Z, Forczek E, Vello E, Hoen DR, Tomita A, Bureau TE. Abiotic Stress Phenotypes Are Associated with Conserved Genes Derived from Transposable Elements. FRONTIERS IN PLANT SCIENCE 2017; 8:2027. [PMID: 29250089 PMCID: PMC5715367 DOI: 10.3389/fpls.2017.02027] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/04/2017] [Accepted: 11/14/2017] [Indexed: 05/08/2023]
Abstract
Plant phenomics offers unique opportunities to accelerate our understanding of gene function and plant response to different environments, and may be particularly useful for studying previously uncharacterized genes. One important type of poorly characterized genes is those derived from transposable elements (TEs), which have departed from a mobility-driven lifestyle to attain new adaptive roles for the host (exapted TEs). We used phenomics approaches, coupled with reverse genetics, to analyze T-DNA insertion mutants of both previously reported and novel protein-coding exapted TEs in the model plant Arabidopsis thaliana. We show that mutations in most of these exapted TEs result in phenotypes, particularly when challenged by abiotic stress. We built statistical multi-dimensional phenotypic profiles and compared them to wild-type and known stress responsive mutant lines for each particular stress condition. We found that these exapted TEs may play roles in responses to phosphate limitation, tolerance to high salt concentration, freezing temperatures, and arsenic toxicity. These results not only experimentally validate a large set of putative functional exapted TEs recently discovered through computational analysis, but also uncover additional novel phenotypes for previously well-characterized exapted TEs in A. thaliana.
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De Diego N, Fürst T, Humplík JF, Ugena L, Podlešáková K, Spíchal L. An Automated Method for High-Throughput Screening of Arabidopsis Rosette Growth in Multi-Well Plates and Its Validation in Stress Conditions. FRONTIERS IN PLANT SCIENCE 2017; 8:1702. [PMID: 29046681 PMCID: PMC5632805 DOI: 10.3389/fpls.2017.01702] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/28/2017] [Accepted: 09/19/2017] [Indexed: 05/02/2023]
Abstract
High-throughput plant phenotyping platforms provide new possibilities for automated, fast scoring of several plant growth and development traits, followed over time using non-invasive sensors. Using Arabidopsis as a model offers important advantages for high-throughput screening with the opportunity to extrapolate the results obtained to other crops of commercial interest. In this study we describe the development of a highly reproducible high-throughput Arabidopsis in vitro bioassay established using our OloPhen platform, suitable for analysis of rosette growth in multi-well plates. This method was successfully validated on example of multivariate analysis of Arabidopsis rosette growth in different salt concentrations and the interaction with varying nutritional composition of the growth medium. Several traits such as changes in the rosette area, relative growth rate, survival rate and homogeneity of the population are scored using fully automated RGB imaging and subsequent image analysis. The assay can be used for fast screening of the biological activity of chemical libraries, phenotypes of transgenic or recombinant inbred lines, or to search for potential quantitative trait loci. It is especially valuable for selecting genotypes or growth conditions that improve plant stress tolerance.
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Affiliation(s)
- Nuria De Diego
- Department of Chemical Biology and Genetics, Centre of the Region Haná for Biotechnological and Agricultural Research, Faculty of Science, Palacký University, Olomouc, Czechia
| | - Tomáš Fürst
- Department of Chemical Biology and Genetics, Centre of the Region Haná for Biotechnological and Agricultural Research, Faculty of Science, Palacký University, Olomouc, Czechia
| | - Jan F. Humplík
- Department of Chemical Biology and Genetics, Centre of the Region Haná for Biotechnological and Agricultural Research, Faculty of Science, Palacký University, Olomouc, Czechia
- Laboratory of Growth Regulators, Centre of the Region Haná for Biotechnological and Agricultural Research, Institute of Experimental Botany, Czech Academy of Sciences, Olomouc, Czechia
| | - Lydia Ugena
- Department of Chemical Biology and Genetics, Centre of the Region Haná for Biotechnological and Agricultural Research, Faculty of Science, Palacký University, Olomouc, Czechia
| | - Kateřina Podlešáková
- Department of Chemical Biology and Genetics, Centre of the Region Haná for Biotechnological and Agricultural Research, Faculty of Science, Palacký University, Olomouc, Czechia
| | - Lukáš Spíchal
- Department of Chemical Biology and Genetics, Centre of the Region Haná for Biotechnological and Agricultural Research, Faculty of Science, Palacký University, Olomouc, Czechia
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Guadagno CR, Ewers BE, Speckman HN, Aston TL, Huhn BJ, DeVore SB, Ladwig JT, Strawn RN, Weinig C. Dead or Alive? Using Membrane Failure and Chlorophyll a Fluorescence to Predict Plant Mortality from Drought. PLANT PHYSIOLOGY 2017; 175:223-234. [PMID: 28710130 PMCID: PMC5580738 DOI: 10.1104/pp.16.00581] [Citation(s) in RCA: 44] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/13/2016] [Accepted: 07/11/2017] [Indexed: 05/02/2023]
Abstract
Climate models predict widespread increases in both drought intensity and duration in the next decades. Although water deficiency is a significant determinant of plant survival, limited understanding of plant responses to extreme drought impedes forecasts of both forest and crop productivity under increasing aridity. Drought induces a suite of physiological responses; however, we lack an accurate mechanistic description of plant response to lethal drought that would improve predictive understanding of mortality under altered climate conditions. Here, proxies for leaf cellular damage, chlorophyll a fluorescence, and electrolyte leakage were directly associated with failure to recover from drought upon rewatering in Brassicarapa (genotype R500) and thus define the exact timing of drought-induced death. We validated our results using a second genotype (imb211) that differs substantially in life history traits. Our study demonstrates that whereas changes in carbon dynamics and water transport are critical indicators of drought stress, they can be unrelated to visible metrics of mortality, i.e. lack of meristematic activity and regrowth. In contrast, membrane failure at the cellular scale is the most proximate cause of death. This hypothesis was corroborated in two gymnosperms (Picea engelmannii and Pinus contorta) that experienced lethal water stress in the field and in laboratory conditions. We suggest that measurement of chlorophyll a fluorescence can be used to operationally define plant death arising from drought, and improved plant characterization can enhance surface model predictions of drought mortality and its consequences to ecosystem services at a global scale.
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Affiliation(s)
| | - Brent E Ewers
- Botany Department, University of Wyoming, Laramie, Wyoming 82071
- Program in Ecology, University of Wyoming, Laramie, Wyoming 82071
| | - Heather N Speckman
- Botany Department, University of Wyoming, Laramie, Wyoming 82071
- Program in Ecology, University of Wyoming, Laramie, Wyoming 82071
| | - Timothy Llewellyn Aston
- Botany Department, University of Wyoming, Laramie, Wyoming 82071
- Program in Ecology, University of Wyoming, Laramie, Wyoming 82071
| | - Bridger J Huhn
- Botany Department, University of Wyoming, Laramie, Wyoming 82071
| | - Stanley B DeVore
- Botany Department, University of Wyoming, Laramie, Wyoming 82071
| | - Joshua T Ladwig
- Botany Department, University of Wyoming, Laramie, Wyoming 82071
| | - Rachel N Strawn
- Botany Department, University of Wyoming, Laramie, Wyoming 82071
| | - Cynthia Weinig
- Botany Department, University of Wyoming, Laramie, Wyoming 82071
- Program in Ecology, University of Wyoming, Laramie, Wyoming 82071
- Department of Molecular Biology, University of Wyoming, Laramie, Wyoming 82071
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Tschiersch H, Junker A, Meyer RC, Altmann T. Establishment of integrated protocols for automated high throughput kinetic chlorophyll fluorescence analyses. PLANT METHODS 2017; 13:54. [PMID: 28690669 PMCID: PMC5496596 DOI: 10.1186/s13007-017-0204-4] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/16/2017] [Accepted: 06/30/2017] [Indexed: 05/24/2023]
Abstract
BACKGROUND Automated plant phenotyping has been established as a powerful new tool in studying plant growth, development and response to various types of biotic or abiotic stressors. Respective facilities mainly apply non-invasive imaging based methods, which enable the continuous quantification of the dynamics of plant growth and physiology during developmental progression. However, especially for plants of larger size, integrative, automated and high throughput measurements of complex physiological parameters such as photosystem II efficiency determined through kinetic chlorophyll fluorescence analysis remain a challenge. RESULTS We present the technical installations and the establishment of experimental procedures that allow the integrated high throughput imaging of all commonly determined PSII parameters for small and large plants using kinetic chlorophyll fluorescence imaging systems (FluorCam, PSI) integrated into automated phenotyping facilities (Scanalyzer, LemnaTec). Besides determination of the maximum PSII efficiency, we focused on implementation of high throughput amenable protocols recording PSII operating efficiency (ΦPSII). Using the presented setup, this parameter is shown to be reproducibly measured in differently sized plants despite the corresponding variation in distance between plants and light source that caused small differences in incident light intensity. Values of ΦPSII obtained with the automated chlorophyll fluorescence imaging setup correlated very well with conventionally determined data using a spot-measuring chlorophyll fluorometer. The established high throughput operating protocols enable the screening of up to 1080 small and 184 large plants per hour, respectively. The application of the implemented high throughput protocols is demonstrated in screening experiments performed with large Arabidopsis and maize populations assessing natural variation in PSII efficiency. CONCLUSIONS The incorporation of imaging systems suitable for kinetic chlorophyll fluorescence analysis leads to a substantial extension of the feature spectrum to be assessed in the presented high throughput automated plant phenotyping platforms, thus enabling the simultaneous assessment of plant architectural and biomass-related traits and their relations to physiological features such as PSII operating efficiency. The implemented high throughput protocols are applicable to a broad spectrum of model and crop plants of different sizes (up to 1.80 m height) and architectures. The deeper understanding of the relation of plant architecture, biomass formation and photosynthetic efficiency has a great potential with respect to crop and yield improvement strategies.
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Affiliation(s)
- Henning Tschiersch
- Leibniz Institute of Plant Genetics and Crop Plant Research (IPK) Gatersleben, Corrensstr. 3, 06466 Seeland, OT Gatersleben, Germany
| | - Astrid Junker
- Leibniz Institute of Plant Genetics and Crop Plant Research (IPK) Gatersleben, Corrensstr. 3, 06466 Seeland, OT Gatersleben, Germany
| | - Rhonda C. Meyer
- Leibniz Institute of Plant Genetics and Crop Plant Research (IPK) Gatersleben, Corrensstr. 3, 06466 Seeland, OT Gatersleben, Germany
| | - Thomas Altmann
- Leibniz Institute of Plant Genetics and Crop Plant Research (IPK) Gatersleben, Corrensstr. 3, 06466 Seeland, OT Gatersleben, Germany
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Jiménez JDLC, Cardoso JA, Leiva LF, Gil J, Forero MG, Worthington ML, Miles JW, Rao IM. Non-destructive Phenotyping to Identify Brachiaria Hybrids Tolerant to Waterlogging Stress under Field Conditions. FRONTIERS IN PLANT SCIENCE 2017; 8:167. [PMID: 28243249 PMCID: PMC5303708 DOI: 10.3389/fpls.2017.00167] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/28/2016] [Accepted: 01/26/2017] [Indexed: 05/10/2023]
Abstract
Brachiaria grasses are sown in tropical regions around the world, especially in the Neotropics, to improve livestock production. Waterlogging is a major constraint to the productivity and persistence of Brachiaria grasses during the rainy season. While some Brachiaria cultivars are moderately tolerant to seasonal waterlogging, none of the commercial cultivars combines superior yield potential and nutritional quality with a high level of waterlogging tolerance. The Brachiaria breeding program at the International Center for Tropical Agriculture, has been using recurrent selection for the past two decades to combine forage yield with resistance to biotic and abiotic stress factors. The main objective of this study was to test the suitability of normalized difference vegetation index (NDVI) and image-based phenotyping as non-destructive approaches to identify Brachiaria hybrids tolerant to waterlogging stress under field conditions. Nineteen promising hybrid selections from the breeding program and three commercial checks were evaluated for their tolerance to waterlogging under field conditions. The waterlogging treatment was imposed by applying and maintaining water to 3 cm above soil surface. Plant performance was determined non-destructively using proximal sensing and image-based phenotyping and also destructively via harvesting for comparison. Image analysis of projected green and dead areas, NDVI and shoot biomass were positively correlated (r ≥ 0.8). Our results indicate that image analysis and NDVI can serve as non-destructive screening approaches for the identification of Brachiaria hybrids tolerant to waterlogging stress.
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Affiliation(s)
- Juan de la Cruz Jiménez
- School of Plant Biology, The University of Western Australia, CrawleyWA, Australia
- International Center for Tropical AgricultureCali, Colombia
| | | | - Luisa F. Leiva
- Semillero de Investigación LÚN, Grupo D+TEC, Universidad de IbaguéIbagué, Colombia
| | - Juanita Gil
- International Center for Tropical AgricultureCali, Colombia
| | - Manuel G. Forero
- Semillero de Investigación LÚN, Grupo D+TEC, Universidad de IbaguéIbagué, Colombia
| | - Margaret L. Worthington
- International Center for Tropical AgricultureCali, Colombia
- Department of Horticulture, University of Arkansas, FayettevilleAR, USA
| | - John W. Miles
- International Center for Tropical AgricultureCali, Colombia
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Trends and Challenges in Pesticide Resistance Detection. TRENDS IN PLANT SCIENCE 2016; 21:834-853. [PMID: 27475253 DOI: 10.1016/j.tplants.2016.06.006] [Citation(s) in RCA: 52] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/12/2016] [Revised: 06/15/2016] [Accepted: 06/18/2016] [Indexed: 06/06/2023]
Abstract
Pesticide resistance is a crucial factor to be considered when developing strategies for the minimal use of pesticides while maintaining pesticide efficacy. This goal requires monitoring the emergence and development of resistance to pesticides in crop pests. To this end, various methods for resistance diagnosis have been developed for different groups of pests. This review provides an overview of biological, biochemical, and molecular methods that are currently used to detect and quantify pesticide resistance. The agronomic, technical, and economic advantages and drawbacks of each method are considered. Emerging technologies are also described, with their associated challenges and their potential for the detection of resistance mechanisms likely to be selected by current and future plant protection methods.
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