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Abidi A, Soltani A, Zeinali E. Identifying plant traits to increase wheat yield under irrigated conditions. Heliyon 2024; 10:e31734. [PMID: 38845892 PMCID: PMC11154629 DOI: 10.1016/j.heliyon.2024.e31734] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2023] [Revised: 05/21/2024] [Accepted: 05/21/2024] [Indexed: 06/09/2024] Open
Abstract
Crop models have frequently been used to identify desired plant traits for rainfed wheat (Triticum aestivum L.). However, efforts to apply these models to irrigated wheat grown under non-limiting water and nitrogen conditions have been rare. Using simulation models to identify plant traits that impact yield can facilitate more targeted cultivar improvement and reduce time and cost. In this study, the SSM-iCrop model was employed to identify effective plant traits for increasing the yield of irrigated wheat in four distinct environments in Iran. A comprehensive range of traits related to phenology, leaf area development, dry matter production, and yield formation, which exhibited reported genetic variation, were tested. The impact of these traits on yield showed slight variation across different environmental zones due to genetic × environment interaction. However, across all environments, modifying current cultivars to increase radiation use efficiency (RUE) resulted in a 19 % increase in yield, accelerating leaf area development led to a 10 %-15 % increase, lengthening the grain filling period resulted in a 14 % increase, and extending the vegetative period led to a 6 % increase. These improvements were all statistically significant. Considering that longer duration cultivars may disrupt cropping systems and the need to develop simple methods for targeting and phenotyping RUE, faster leaf area development was found as the most promising option to increase irrigated wheat yield under optimal water and nitrogen management within a short time frame. It should be noted that cultivars with modified traits needed higher water and nitrogen inputs to support increased yields. These findings can be applied to select desirable key traits for targeted breeding and expedite the production of high-yielding cultivars of irrigated wheat in various environmental zones. The potential for further improvement through combined traits requires further investigation.
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Affiliation(s)
- Arezoo Abidi
- Department of Agronomy, Gorgan University of Agricultural Sciences and Natural Resources, Gorgan, 4918943464, Iran
| | - Afshin Soltani
- Department of Agronomy, Gorgan University of Agricultural Sciences and Natural Resources, Gorgan, 4918943464, Iran
| | - Ebrahim Zeinali
- Department of Agronomy, Gorgan University of Agricultural Sciences and Natural Resources, Gorgan, 4918943464, Iran
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Jadhav Y, Thakur NR, Ingle KP, Ceasar SA. The role of phenomics and genomics in delineating the genetic basis of complex traits in millets. PHYSIOLOGIA PLANTARUM 2024; 176:e14349. [PMID: 38783512 DOI: 10.1111/ppl.14349] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/12/2024] [Revised: 04/22/2024] [Accepted: 04/26/2024] [Indexed: 05/25/2024]
Abstract
Millets, comprising a diverse group of small-seeded grains, have emerged as vital crops with immense nutritional, environmental, and economic significance. The comprehension of complex traits in millets, influenced by multifaceted genetic determinants, presents a compelling challenge and opportunity in agricultural research. This review delves into the transformative roles of phenomics and genomics in deciphering these intricate genetic architectures. On the phenomics front, high-throughput platforms generate rich datasets on plant morphology, physiology, and performance in diverse environments. This data, coupled with field trials and controlled conditions, helps to interpret how the environment interacts with genetics. Genomics provides the underlying blueprint for these complex traits. Genome sequencing and genotyping technologies have illuminated the millet genome landscape, revealing diverse gene pools and evolutionary relationships. Additionally, different omics approaches unveil the intricate information of gene expression, protein function, and metabolite accumulation driving phenotypic expression. This multi-omics approach is crucial for identifying candidate genes and unfolding the intricate pathways governing complex traits. The review highlights the synergy between phenomics and genomics. Genomically informed phenotyping targets specific traits, reducing the breeding size and cost. Conversely, phenomics identifies promising germplasm for genomic analysis, prioritizing variants with superior performance. This dynamic interplay accelerates breeding programs and facilitates the development of climate-smart, nutrient-rich millet varieties and hybrids. In conclusion, this review emphasizes the crucial roles of phenomics and genomics in unlocking the genetic enigma of millets.
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Affiliation(s)
- Yashoda Jadhav
- International Crops Research Institutes for the Semi-Arid Tropics, Patancheru, TS, India
| | - Niranjan Ravindra Thakur
- International Crops Research Institutes for the Semi-Arid Tropics, Patancheru, TS, India
- Vasantrao Naik Marathwada Agricultural University, Parbhani, MS, India
| | | | - Stanislaus Antony Ceasar
- Division of Plant Molecular Biology and Biotechnology, Department of Biosciences, Rajagiri College of Social Sciences, Kochi, KL, India
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Raymundo R, Mclean G, Sexton-Bowser S, Lipka AE, Morris GP. Crop modeling suggests limited transpiration would increase yield of sorghum across drought-prone regions of the United States. FRONTIERS IN PLANT SCIENCE 2024; 14:1283339. [PMID: 38348164 PMCID: PMC10859530 DOI: 10.3389/fpls.2023.1283339] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 08/25/2023] [Accepted: 12/21/2023] [Indexed: 02/15/2024]
Abstract
Breeding sorghum to withstand droughts is pivotal to secure crop production in regions vulnerable to water scarcity. Limited transpiration (LT) restricts water demand at high vapor pressure deficit, saving water for use in critical periods later in the growing season. Here we evaluated the hypothesis that LT would increase sorghum grain yield in the United States. We used a process-based crop model, APSIM, which simulates interactions of genotype, environment, and management (G × E × M). In this study, the G component includes the LT trait (GT) and maturity group (GM), the EW component entails water deficit patterns, and the MP component represents different planting dates. Simulations were conducted over 33 years (1986-2018) for representative locations across the US sorghum belt (Kansas, Texas, and Colorado) for three planting dates and maturity groups. The interaction of GT x EW indicated a higher impact of LT sorghum on grain for late drought (LD), mid-season drought (MD), and early drought (ED, 8%), than on well-watered (WW) environments (4%). Thus, significant impacts of LT can be achieved in western regions of the sorghum belt. The lack of interaction of GT × GM × MP suggested that an LT sorghum would increase yield by around 8% across maturity groups and planting dates. Otherwise, the interaction GM × MP revealed that specific combinations are better suited across geographical regions. Overall, the findings suggest that breeding for LT would increase sorghum yield in the drought-prone areas of the US without tradeoffs.
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Affiliation(s)
- Rubí Raymundo
- Department of Soil and Crop Science, Colorado State University, Fort Collins, CO, United States
| | - Greg Mclean
- Center for Crop Science, Queensland Alliance for Agriculture and Food Innovation, The University of Queensland, Brisbane, QLD, Australia
| | - Sarah Sexton-Bowser
- Department of Agronomy, Kansas State University, Manhattan, KS, United States
| | - Alexander E. Lipka
- Department of Crop Sciences, University of Illinois, Urbana, IL, United States
| | - Geoffrey P. Morris
- Department of Soil and Crop Science, Colorado State University, Fort Collins, CO, United States
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Bazhenov M, Litvinov D, Karlov G, Divashuk M. Evaluation of phosphate rock as the only source of phosphorus for the growth of tall and semi-dwarf durum wheat and rye plants using digital phenotyping. PeerJ 2023; 11:e15972. [PMID: 37663276 PMCID: PMC10473039 DOI: 10.7717/peerj.15972] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2023] [Accepted: 08/06/2023] [Indexed: 09/05/2023] Open
Abstract
Background Phosphorus nutrition is important for obtaining high yields of crop plants. However, wheat plants are known to be almost incapable of taking up phosphorus from insoluble phosphate sources, and reduced height genes are supposed to decrease this ability further. Methods We performed a pot experiment using Triticum durum Desf. tall spring variety LD222, its near-isogenic semidwarf line carrying Rht17 (Reduced height 17) gene, and winter rye (Secale cereale L.) variety Chulpan. The individual plants were grown in quartz sand. The phosphorus was provided either as phosphate rock powder mixed with sand, or as monopotassium phosphate solution (normal nutrition control) or was not supplemented at all (no-phosphorus control). Other nutrients were provided in soluble form. During experiment the plants were assessed using the TraitFinder (Phenospex Ltd., Heerlen, Netherlands) digital phenotyping system for a standard set of parameters. Double scan with 90 degrees turns of pots around vertical axis vs. single scan were compared for accuracy of phenotyping. Results The phenotyping showed that at least 20 days of growth after seedling emergence were necessary to get stable differences between genotypes. After this initial period, phenotyping confirmed poor ability of wheat to grow on substrate with phosphate rock as the only source of phosphorus compared to rye; however, Rht17 did not cause an additional reduction in growth parameters other than plant height under this variant of substrate. The agreement between digital phenotyping and conventionally measured traits was at previously reported level for grasses (R2 = 0.85 and 0.88 for digital biomass and 3D leaf area vs. conventionally measured biomass and leaf area, single scan). Among vegetation indices, only the normalized differential vegetation index (NDVI) and the green leaf index (GLI) showed significant correlations with manually measured traits, including the percentage of dead leaves area. The double scan improved phenotyping accuracy, but not substantially.
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Affiliation(s)
- Mikhail Bazhenov
- Laboratory of Applied Genomics and Crop Breeding, All-Russia Research Institute of Agricultural Biotechnology, Moscow, Russia
| | - Dmitry Litvinov
- Kurchatov Genomics Center-ARRIAB, All-Russia Research Institute of Agricultural Biotechnology, Moscow, Russia
| | - Gennady Karlov
- Laboratory of Applied Genomics and Crop Breeding, All-Russia Research Institute of Agricultural Biotechnology, Moscow, Russia
| | - Mikhail Divashuk
- Laboratory of Applied Genomics and Crop Breeding, All-Russia Research Institute of Agricultural Biotechnology, Moscow, Russia
- Kurchatov Genomics Center-ARRIAB, All-Russia Research Institute of Agricultural Biotechnology, Moscow, Russia
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Poorter H, Hummel GM, Nagel KA, Fiorani F, von Gillhaussen P, Virnich O, Schurr U, Postma JA, van de Zedde R, Wiese-Klinkenberg A. Pitfalls and potential of high-throughput plant phenotyping platforms. FRONTIERS IN PLANT SCIENCE 2023; 14:1233794. [PMID: 37680357 PMCID: PMC10481964 DOI: 10.3389/fpls.2023.1233794] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/02/2023] [Accepted: 08/01/2023] [Indexed: 09/09/2023]
Abstract
Automated high-throughput plant phenotyping (HTPP) enables non-invasive, fast and standardized evaluations of a large number of plants for size, development, and certain physiological variables. Many research groups recognize the potential of HTPP and have made significant investments in HTPP infrastructure, or are considering doing so. To make optimal use of limited resources, it is important to plan and use these facilities prudently and to interpret the results carefully. Here we present a number of points that users should consider before purchasing, building or utilizing such equipment. They relate to (1) the financial and time investment for acquisition, operation, and maintenance, (2) the constraints associated with such machines in terms of flexibility and growth conditions, (3) the pros and cons of frequent non-destructive measurements, (4) the level of information provided by proxy traits, and (5) the utilization of calibration curves. Using data from an Arabidopsis experiment, we demonstrate how diurnal changes in leaf angle can impact plant size estimates from top-view cameras, causing deviations of more than 20% over the day. Growth analysis data from another rosette species showed that there was a curvilinear relationship between total and projected leaf area. Neglecting this curvilinearity resulted in linear calibration curves that, although having a high r2 (> 0.92), also exhibited large relative errors. Another important consideration we discussed is the frequency at which calibration curves need to be generated and whether different treatments, seasons, or genotypes require distinct calibration curves. In conclusion, HTPP systems have become a valuable addition to the toolbox of plant biologists, provided that these systems are tailored to the research questions of interest, and users are aware of both the possible pitfalls and potential involved.
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Affiliation(s)
- Hendrik Poorter
- Plant Sciences (IBG-2), Forschungszentrum Jülich GmbH, Jülich, Germany
- Department of Natural Sciences, Macquarie University, North Ryde, NSW, Australia
| | | | - Kerstin A. Nagel
- Plant Sciences (IBG-2), Forschungszentrum Jülich GmbH, Jülich, Germany
| | - Fabio Fiorani
- Plant Sciences (IBG-2), Forschungszentrum Jülich GmbH, Jülich, Germany
| | | | - Olivia Virnich
- Plant Sciences (IBG-2), Forschungszentrum Jülich GmbH, Jülich, Germany
| | - Ulrich Schurr
- Plant Sciences (IBG-2), Forschungszentrum Jülich GmbH, Jülich, Germany
| | | | - Rick van de Zedde
- Plant Sciences Group, Wageningen University & Research, Wageningen, Netherlands
| | - Anika Wiese-Klinkenberg
- Plant Sciences (IBG-2), Forschungszentrum Jülich GmbH, Jülich, Germany
- Bioinformatics (IBG-4), Forschungszentrum Jülich GmbH, Jülich, Germany
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Javornik T, Carović-Stanko K, Gunjača J, Vidak M, Lazarević B. Monitoring Drought Stress in Common Bean Using Chlorophyll Fluorescence and Multispectral Imaging. PLANTS (BASEL, SWITZERLAND) 2023; 12:1386. [PMID: 36987074 PMCID: PMC10059887 DOI: 10.3390/plants12061386] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 02/16/2023] [Revised: 03/17/2023] [Accepted: 03/18/2023] [Indexed: 06/19/2023]
Abstract
Drought is a significant constraint in bean production. In this study, we used high-throughput phenotyping methods (chlorophyll fluorescence imaging, multispectral imaging, 3D multispectral scanning) to monitor the development of drought-induced morphological and physiological symptoms at an early stage of development of the common bean. This study aimed to select the plant phenotypic traits which were most sensitive to drought. Plants were grown in an irrigated control (C) and under three drought treatments: D70, D50, and D30 (irrigated with 70, 50, and 30 mL distilled water, respectively). Measurements were performed on five consecutive days, starting on the first day after the onset of treatments (1 DAT-5 DAT), with an additional measurement taken on the eighth day (8 DAT) after the onset of treatments. Earliest detected changes were found at 3 DAT when compared to the control. D30 caused a decrease in leaf area index (of 40%), total leaf area (28%), reflectance in specific green (13%), saturation (9%), and green leaf index (9%), and an increase in the anthocyanin index (23%) and reflectance in blue (7%). The selected phenotypic traits could be used to monitor drought stress and to screen for tolerant genotypes in breeding programs.
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Affiliation(s)
- Tomislav Javornik
- Centre of Excellence for Biodiversity and Molecular Plant Breeding (CoE CroP-BioDiv), Svetošimunska cesta 25, HR-10000 Zagreb, Croatia
- Department of Seed Science and Technology, Faculty of Agriculture, University of Zagreb, Svetošimunska cesta 25, HR-10000 Zagreb, Croatia
| | - Klaudija Carović-Stanko
- Centre of Excellence for Biodiversity and Molecular Plant Breeding (CoE CroP-BioDiv), Svetošimunska cesta 25, HR-10000 Zagreb, Croatia
- Department of Seed Science and Technology, Faculty of Agriculture, University of Zagreb, Svetošimunska cesta 25, HR-10000 Zagreb, Croatia
| | - Jerko Gunjača
- Centre of Excellence for Biodiversity and Molecular Plant Breeding (CoE CroP-BioDiv), Svetošimunska cesta 25, HR-10000 Zagreb, Croatia
- Department of Plant Breeding, Genetics and Biometrics, Faculty of Agriculture, University of Zagreb, Svetošimunska cesta 25, HR-10000 Zagreb, Croatia
| | - Monika Vidak
- Centre of Excellence for Biodiversity and Molecular Plant Breeding (CoE CroP-BioDiv), Svetošimunska cesta 25, HR-10000 Zagreb, Croatia
- Department of Seed Science and Technology, Faculty of Agriculture, University of Zagreb, Svetošimunska cesta 25, HR-10000 Zagreb, Croatia
| | - Boris Lazarević
- Centre of Excellence for Biodiversity and Molecular Plant Breeding (CoE CroP-BioDiv), Svetošimunska cesta 25, HR-10000 Zagreb, Croatia
- Department of Plant Nutrition, Faculty of Agriculture, University of Zagreb, Svetošimunska cesta 25, HR-10000 Zagreb, Croatia
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Cooper M, Messina CD. Breeding crops for drought-affected environments and improved climate resilience. THE PLANT CELL 2023; 35:162-186. [PMID: 36370076 PMCID: PMC9806606 DOI: 10.1093/plcell/koac321] [Citation(s) in RCA: 10] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/14/2022] [Accepted: 11/01/2022] [Indexed: 05/12/2023]
Abstract
Breeding climate-resilient crops with improved levels of abiotic and biotic stress resistance as a response to climate change presents both opportunities and challenges. Applying the framework of the "breeder's equation," which is used to predict the response to selection for a breeding program cycle, we review methodologies and strategies that have been used to successfully breed crops with improved levels of drought resistance, where the target population of environments (TPEs) is a spatially and temporally heterogeneous mixture of drought-affected and favorable (water-sufficient) environments. Long-term improvement of temperate maize for the US corn belt is used as a case study and compared with progress for other crops and geographies. Integration of trait information across scales, from genomes to ecosystems, is needed to accurately predict yield outcomes for genotypes within the current and future TPEs. This will require transdisciplinary teams to explore, identify, and exploit novel opportunities to accelerate breeding program outcomes; both improved germplasm resources and improved products (cultivars, hybrids, clones, and populations) that outperform and replace the products in use by farmers, in combination with modified agronomic management strategies suited to their local environments.
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Affiliation(s)
| | - Carlos D Messina
- Horticultural Sciences Department, University of Florida, Gainesville, Florida 32611, USA
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Barmukh R, Roorkiwal M, Dixit GP, Bajaj P, Kholova J, Smith MR, Chitikineni A, Bharadwaj C, Sreeman SM, Rathore A, Tripathi S, Yasin M, Vijayakumar AG, Rao Sagurthi S, Siddique KHM, Varshney RK. Characterization of 'QTL-hotspot' introgression lines reveals physiological mechanisms and candidate genes associated with drought adaptation in chickpea. JOURNAL OF EXPERIMENTAL BOTANY 2022; 73:7255-7272. [PMID: 36006832 PMCID: PMC9730794 DOI: 10.1093/jxb/erac348] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/11/2022] [Accepted: 08/24/2022] [Indexed: 05/16/2023]
Abstract
'QTL-hotspot' is a genomic region on linkage group 04 (CaLG04) in chickpea (Cicer arietinum) that harbours major-effect quantitative trait loci (QTLs) for multiple drought-adaptive traits, and it therefore represents a promising target for improving drought adaptation. To investigate the mechanisms underpinning the positive effects of 'QTL-hotspot' on seed yield under drought, we introgressed this region from the ICC 4958 genotype into five elite chickpea cultivars. The resulting introgression lines (ILs) and their parents were evaluated in multi-location field trials and semi-controlled conditions. The results showed that the 'QTL-hotspot' region improved seed yield under rainfed conditions by increasing seed weight, reducing the time to flowering, regulating traits related to canopy growth and early vigour, and enhancing transpiration efficiency. Whole-genome sequencing data analysis of the ILs and parents revealed four genes underlying the 'QTL-hotspot' region associated with drought adaptation. We validated diagnostic KASP markers closely linked to these genes using the ILs and their parents for future deployment in chickpea breeding programs. The CaTIFY4b-H2 haplotype of a potential candidate gene CaTIFY4b was identified as the superior haplotype for 100-seed weight. The candidate genes and superior haplotypes identified in this study have the potential to serve as direct targets for genetic manipulation and selection for chickpea improvement.
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Affiliation(s)
- Rutwik Barmukh
- Centre of Excellence in Genomics and Systems Biology, International Crops Research Institute for the Semi-Arid Tropics (ICRISAT), Hyderabad, India
- Department of Genetics, Osmania University, Hyderabad, India
| | | | - Girish P Dixit
- ICAR - Indian Institute of Pulses Research (IIPR), Kanpur, India
| | - Prasad Bajaj
- Centre of Excellence in Genomics and Systems Biology, International Crops Research Institute for the Semi-Arid Tropics (ICRISAT), Hyderabad, India
| | - Jana Kholova
- Crops Physiology & Modeling, International Crops Research Institute for the Semi-Arid Tropics (ICRISAT), Hyderabad, India
- Department of Information Technologies, Faculty of Economics and Management, Czech University of Life Sciences Prague, Kamýcká 129, Prague, Czech Republic
| | - Millicent R Smith
- Centre of Excellence in Genomics and Systems Biology, International Crops Research Institute for the Semi-Arid Tropics (ICRISAT), Hyderabad, India
- Queensland Alliance for Agriculture and Food Innovation, The University of Queensland, Australia
| | - Annapurna Chitikineni
- Centre of Excellence in Genomics and Systems Biology, International Crops Research Institute for the Semi-Arid Tropics (ICRISAT), Hyderabad, India
| | - Chellapilla Bharadwaj
- The UWA Institute of Agriculture, The University of Western Australia, Perth, Western Australia, Australia
- ICAR - Indian Agricultural Research Institute (IARI), Delhi, India
| | - Sheshshayee M Sreeman
- Department of Crop Physiology, University of Agricultural Sciences, Bengaluru, India
| | - Abhishek Rathore
- Centre of Excellence in Genomics and Systems Biology, International Crops Research Institute for the Semi-Arid Tropics (ICRISAT), Hyderabad, India
| | | | - Mohammad Yasin
- RAK College of Agriculture, Rajmata Vijayaraje Scindia Krishi Vishwa Vidyalaya, Gwalior, India
| | | | | | - Kadambot H M Siddique
- The UWA Institute of Agriculture, The University of Western Australia, Perth, Western Australia, Australia
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Affortit P, Effa-Effa B, Ndoye MS, Moukouanga D, Luchaire N, Cabrera-Bosquet L, Perálvarez M, Pilloni R, Welcker C, Champion A, Gantet P, Diedhiou AG, Manneh B, Aroca R, Vadez V, Laplaze L, Cubry P, Grondin A. Physiological and genetic control of transpiration efficiency in African rice, Oryza glaberrima Steud. JOURNAL OF EXPERIMENTAL BOTANY 2022; 73:5279-5293. [PMID: 35429274 DOI: 10.1093/jxb/erac156] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/28/2021] [Accepted: 04/13/2022] [Indexed: 06/14/2023]
Abstract
Improving crop water use efficiency, the amount of carbon assimilated as biomass per unit of water used by a plant, is of major importance as water for agriculture becomes scarcer. In rice, the genetic bases of transpiration efficiency, the derivation of water use efficiency at the whole-plant scale, and its putative component trait transpiration restriction under high evaporative demand remain unknown. These traits were measured in 2019 in a panel of 147 African rice (Oryza glaberrima) genotypes known to be potential sources of tolerance genes to biotic and abiotic stresses. Our results reveal that higher transpiration efficiency is associated with transpiration restriction in African rice. Detailed measurements in a subset of highly contrasted genotypes in terms of biomass accumulation and transpiration confirmed these associations and suggested that root to shoot ratio played an important role in transpiration restriction. Genome wide association studies identified marker-trait associations for transpiration response to evaporative demand, transpiration efficiency, and its residuals, with links to genes involved in water transport and cell wall patterning. Our data suggest that root-shoot partitioning is an important component of transpiration restriction that has a positive effect on transpiration efficiency in African rice. Both traits are heritable and define targets for breeding rice with improved water use strategies.
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Affiliation(s)
- Pablo Affortit
- DIADE, Université de Montpellier, IRD, CIRAD, Montpellier, France
| | - Branly Effa-Effa
- DIADE, Université de Montpellier, IRD, CIRAD, Montpellier, France
- CENAREST, Libreville, Gabon
| | - Mame Sokhatil Ndoye
- DIADE, Université de Montpellier, IRD, CIRAD, Montpellier, France
- CERAAS, Thiès, Senegal
| | | | - Nathalie Luchaire
- LEPSE, Université de Montpellier, INRAE, Institut Agro, Montpellier, France
| | | | | | - Raphaël Pilloni
- DIADE, Université de Montpellier, IRD, CIRAD, Montpellier, France
| | - Claude Welcker
- LEPSE, Université de Montpellier, INRAE, Institut Agro, Montpellier, France
| | - Antony Champion
- DIADE, Université de Montpellier, IRD, CIRAD, Montpellier, France
| | - Pascal Gantet
- DIADE, Université de Montpellier, IRD, CIRAD, Montpellier, France
| | | | | | | | - Vincent Vadez
- DIADE, Université de Montpellier, IRD, CIRAD, Montpellier, France
- CERAAS, Thiès, Senegal
- LMI LAPSE, Dakar, Senegal
- ICRISAT, Patancheru, India
| | - Laurent Laplaze
- DIADE, Université de Montpellier, IRD, CIRAD, Montpellier, France
- LMI LAPSE, Dakar, Senegal
| | - Philippe Cubry
- DIADE, Université de Montpellier, IRD, CIRAD, Montpellier, France
| | - Alexandre Grondin
- DIADE, Université de Montpellier, IRD, CIRAD, Montpellier, France
- CERAAS, Thiès, Senegal
- LMI LAPSE, Dakar, Senegal
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10
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Li J, Xie T, Chen Y, Zhang Y, Wang C, Jiang Z, Yang W, Zhou G, Guo L, Zhang J. High-throughput unmanned aerial vehicle-based phenotyping provides insights into the dynamic process and genetic basis of rapeseed waterlogging response in the field. JOURNAL OF EXPERIMENTAL BOTANY 2022; 73:5264-5278. [PMID: 35641129 DOI: 10.1093/jxb/erac242] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/27/2022] [Accepted: 05/28/2022] [Indexed: 06/15/2023]
Abstract
Waterlogging severely affects the growth, development, and yield of crops. Accurate high-throughput phenotyping is important for exploring the dynamic crop waterlogging response in the field, and the genetic basis of waterlogging tolerance. In this study, a multi-model remote sensing phenotyping platform based on an unmanned aerial vehicle (UAV) was used to assess the genetic response of rapeseed (Brassica napus) to waterlogging, by measuring morphological traits and spectral indices over 2 years. The dynamic responses of the morphological and spectral traits indicated that the rapeseed waterlogging response was severe before the middle stage within 18 d after recovery, but it subsequently decreased partly. Genome-wide association studies identified 289 and 333 loci associated with waterlogging tolerance in 2 years. Next, 25 loci with at least nine associations with waterlogging-related traits were defined as highly reliable loci, and 13 loci were simultaneously identified by waterlogging tolerance coefficients of morphological traits, spectral indices, and common factors. Forty candidate genes were predicted in the regions of 13 overlapping loci. Our study provides insights into the understanding of the dynamic process and genetic basis of rapeseed waterlogging response in the field by a high-throughput UAV phenotyping platform. The highly reliable loci identified in this study are valuable for breeding waterlogging-tolerant rapeseed cultivars.
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Affiliation(s)
- Jijun Li
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, China
- Hubei Hongshan Laboratory, Wuhan, China
| | - Tianjin Xie
- Macro Agriculture Research Institute, College of Resource and Environment, Huazhong Agricultural University, Wuhan, China
| | - Yahui Chen
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, China
- Hubei Hongshan Laboratory, Wuhan, China
| | - Yuting Zhang
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, China
- Hubei Hongshan Laboratory, Wuhan, China
| | - Chufeng Wang
- Macro Agriculture Research Institute, College of Resource and Environment, Huazhong Agricultural University, Wuhan, China
| | - Zhao Jiang
- Macro Agriculture Research Institute, College of Resource and Environment, Huazhong Agricultural University, Wuhan, China
| | - Wanneng Yang
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, China
- Hubei Hongshan Laboratory, Wuhan, China
| | - Guangsheng Zhou
- College of Plant Science and Technology, Huazhong Agricultural University, Wuhan, China
| | - Liang Guo
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, China
- Hubei Hongshan Laboratory, Wuhan, China
| | - Jian Zhang
- Macro Agriculture Research Institute, College of Resource and Environment, Huazhong Agricultural University, Wuhan, China
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Barmukh R, Roorkiwal M, Garg V, Khan AW, German L, Jaganathan D, Chitikineni A, Kholova J, Kudapa H, Sivasakthi K, Samineni S, Kale SM, Gaur PM, Sagurthi SR, Benitez‐Alfonso Y, Varshney RK. Genetic variation in CaTIFY4b contributes to drought adaptation in chickpea. PLANT BIOTECHNOLOGY JOURNAL 2022; 20:1701-1715. [PMID: 35534989 PMCID: PMC9398337 DOI: 10.1111/pbi.13840] [Citation(s) in RCA: 13] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/17/2021] [Accepted: 04/28/2022] [Indexed: 05/26/2023]
Abstract
Chickpea production is vulnerable to drought stress. Identifying the genetic components underlying drought adaptation is crucial for enhancing chickpea productivity. Here, we present the fine mapping and characterization of 'QTL-hotspot', a genomic region controlling chickpea growth with positive consequences on crop production under drought. We report that a non-synonymous substitution in the transcription factor CaTIFY4b regulates seed weight and organ size in chickpea. Ectopic expression of CaTIFY4b in Medicago truncatula enhances root growth under water deficit. Our results suggest that allelic variation in 'QTL-hotspot' improves pre-anthesis water use, transpiration efficiency, root architecture and canopy development, enabling high-yield performance under terminal drought conditions. Gene expression analysis indicated that CaTIFY4b may regulate organ size under water deficit by modulating the expression of GRF-INTERACTING FACTOR1 (GIF1), a transcriptional co-activator of Growth-Regulating Factors. Taken together, our study offers new insights into the role of CaTIFY4b and on diverse physiological and molecular mechanisms underpinning chickpea growth and production under specific drought scenarios.
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Affiliation(s)
- Rutwik Barmukh
- Centre of Excellence in Genomics and Systems BiologyInternational Crops Research Institute for the Semi‐Arid Tropics (ICRISAT)HyderabadIndia
- Department of GeneticsOsmania UniversityHyderabadIndia
| | - Manish Roorkiwal
- Centre of Excellence in Genomics and Systems BiologyInternational Crops Research Institute for the Semi‐Arid Tropics (ICRISAT)HyderabadIndia
- Khalifa Center for Genetic Engineering and BiotechnologyUnited Arab Emirates UniversityAl‐AinUnited Arab Emirates
- The UWA Institute of AgricultureThe University of Western AustraliaPerthWestern AustraliaAustralia
| | - Vanika Garg
- Centre of Excellence in Genomics and Systems BiologyInternational Crops Research Institute for the Semi‐Arid Tropics (ICRISAT)HyderabadIndia
| | - Aamir W. Khan
- Centre of Excellence in Genomics and Systems BiologyInternational Crops Research Institute for the Semi‐Arid Tropics (ICRISAT)HyderabadIndia
| | - Liam German
- Centre for Plant ScienceSchool of BiologyUniversity of LeedsLeedsUK
| | - Deepa Jaganathan
- Centre of Excellence in Genomics and Systems BiologyInternational Crops Research Institute for the Semi‐Arid Tropics (ICRISAT)HyderabadIndia
| | - Annapurna Chitikineni
- Centre of Excellence in Genomics and Systems BiologyInternational Crops Research Institute for the Semi‐Arid Tropics (ICRISAT)HyderabadIndia
| | - Jana Kholova
- Crop Physiology and ModellingInternational Crops Research Institute for the Semi‐Arid Tropics (ICRISAT)HyderabadIndia
| | - Himabindu Kudapa
- Centre of Excellence in Genomics and Systems BiologyInternational Crops Research Institute for the Semi‐Arid Tropics (ICRISAT)HyderabadIndia
| | - Kaliamoorthy Sivasakthi
- Crop Physiology and ModellingInternational Crops Research Institute for the Semi‐Arid Tropics (ICRISAT)HyderabadIndia
| | - Srinivasan Samineni
- Crop BreedingInternational Crops Research Institute for the Semi‐Arid Tropics (ICRISAT)HyderabadIndia
| | - Sandip M. Kale
- Centre of Excellence in Genomics and Systems BiologyInternational Crops Research Institute for the Semi‐Arid Tropics (ICRISAT)HyderabadIndia
| | - Pooran M. Gaur
- The UWA Institute of AgricultureThe University of Western AustraliaPerthWestern AustraliaAustralia
- Crop BreedingInternational Crops Research Institute for the Semi‐Arid Tropics (ICRISAT)HyderabadIndia
| | | | | | - Rajeev K. Varshney
- Centre of Excellence in Genomics and Systems BiologyInternational Crops Research Institute for the Semi‐Arid Tropics (ICRISAT)HyderabadIndia
- The UWA Institute of AgricultureThe University of Western AustraliaPerthWestern AustraliaAustralia
- Murdoch’s Centre for Crop & Food InnovationState Agricultural Biotechnology CentreFood Futures InstituteMurdoch UniversityMurdochWestern AustraliaAustralia
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12
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Srivastava RK, Yadav OP, Kaliamoorthy S, Gupta SK, Serba DD, Choudhary S, Govindaraj M, Kholová J, Murugesan T, Satyavathi CT, Gumma MK, Singh RB, Bollam S, Gupta R, Varshney RK. Breeding Drought-Tolerant Pearl Millet Using Conventional and Genomic Approaches: Achievements and Prospects. FRONTIERS IN PLANT SCIENCE 2022; 13:781524. [PMID: 35463391 PMCID: PMC9021881 DOI: 10.3389/fpls.2022.781524] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/22/2021] [Accepted: 02/11/2022] [Indexed: 06/03/2023]
Abstract
Pearl millet [Pennisetum glaucum (L.) R. Br.] is a C4 crop cultivated for its grain and stover in crop-livestock-based rain-fed farming systems of tropics and subtropics in the Indian subcontinent and sub-Saharan Africa. The intensity of drought is predicted to further exacerbate because of looming climate change, necessitating greater focus on pearl millet breeding for drought tolerance. The nature of drought in different target populations of pearl millet-growing environments (TPEs) is highly variable in its timing, intensity, and duration. Pearl millet response to drought in various growth stages has been studied comprehensively. Dissection of drought tolerance physiology and phenology has helped in understanding the yield formation process under drought conditions. The overall understanding of TPEs and differential sensitivity of various growth stages to water stress helped to identify target traits for manipulation through breeding for drought tolerance. Recent advancement in high-throughput phenotyping platforms has made it more realistic to screen large populations/germplasm for drought-adaptive traits. The role of adapted germplasm has been emphasized for drought breeding, as the measured performance under drought stress is largely an outcome of adaptation to stress environments. Hybridization of adapted landraces with selected elite genetic material has been stated to amalgamate adaptation and productivity. Substantial progress has been made in the development of genomic resources that have been used to explore genetic diversity, linkage mapping (QTLs), marker-trait association (MTA), and genomic selection (GS) in pearl millet. High-throughput genotyping (HTPG) platforms are now available at a low cost, offering enormous opportunities to apply markers assisted selection (MAS) in conventional breeding programs targeting drought tolerance. Next-generation sequencing (NGS) technology, micro-environmental modeling, and pearl millet whole genome re-sequence information covering circa 1,000 wild and cultivated accessions have helped to greater understand germplasm, genomes, candidate genes, and markers. Their application in molecular breeding would lead to the development of high-yielding and drought-tolerant pearl millet cultivars. This review examines how the strategic use of genetic resources, modern genomics, molecular biology, and shuttle breeding can further enhance the development and delivery of drought-tolerant cultivars.
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Affiliation(s)
- Rakesh K. Srivastava
- International Crops Research Institute for the Semi-Arid Tropics (ICRISAT), Patancheru, India
| | - O. P. Yadav
- Indian Council of Agricultural Research-Central Arid Zone Research Institute, Jodhpur, India
| | - Sivasakthi Kaliamoorthy
- International Crops Research Institute for the Semi-Arid Tropics (ICRISAT), Patancheru, India
| | - S. K. Gupta
- International Crops Research Institute for the Semi-Arid Tropics (ICRISAT), Patancheru, India
| | - Desalegn D. Serba
- United States Department of Agriculture-Agriculture Research Service (ARS), U.S. Arid Land Agricultural Research Center, Maricopa, AZ, United States
| | - Sunita Choudhary
- International Crops Research Institute for the Semi-Arid Tropics (ICRISAT), Patancheru, India
| | - Mahalingam Govindaraj
- International Crops Research Institute for the Semi-Arid Tropics (ICRISAT), Patancheru, India
| | - Jana Kholová
- International Crops Research Institute for the Semi-Arid Tropics (ICRISAT), Patancheru, India
| | - Tharanya Murugesan
- International Crops Research Institute for the Semi-Arid Tropics (ICRISAT), Patancheru, India
| | - C. Tara Satyavathi
- Indian Council of Agricultural Research – All India Coordinated Research Project on Pearl Millet, Jodhpur, India
| | - Murali Krishna Gumma
- International Crops Research Institute for the Semi-Arid Tropics (ICRISAT), Patancheru, India
| | - Ram B. Singh
- International Crops Research Institute for the Semi-Arid Tropics (ICRISAT), Patancheru, India
| | - Srikanth Bollam
- International Crops Research Institute for the Semi-Arid Tropics (ICRISAT), Patancheru, India
| | - Rajeev Gupta
- United States Department of Agriculture-Agriculture Research Service (ARS), Edward T. Schafer Agricultural Research Center, Fargo, ND, United States
| | - Rajeev K. Varshney
- International Crops Research Institute for the Semi-Arid Tropics (ICRISAT), Patancheru, India
- State Agricultural Biotechnology Centre, Centre for Crop & Food Innovation, Food Futures Institute, Murdoch University, Murdoch, WA, Australia
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13
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Sun Z, Li Q, Jin S, Song Y, Xu S, Wang X, Cai J, Zhou Q, Ge Y, Zhang R, Zang J, Jiang D. Simultaneous Prediction of Wheat Yield and Grain Protein Content Using Multitask Deep Learning from Time-Series Proximal Sensing. PLANT PHENOMICS 2022; 2022:9757948. [PMID: 35441150 PMCID: PMC8988204 DOI: 10.34133/2022/9757948] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 12/17/2021] [Accepted: 03/07/2022] [Indexed: 01/14/2023]
Abstract
Wheat yield and grain protein content (GPC) are two main optimization targets for breeding and cultivation. Remote sensing provides nondestructive and early predictions of yield and GPC, respectively. However, whether it is possible to simultaneously predict yield and GPC in one model and the accuracy and influencing factors are still unclear. In this study, we made a systematic comparison of different deep learning models in terms of data fusion, time-series feature extraction, and multitask learning. The results showed that time-series data fusion significantly improved yield and GPC prediction accuracy with R2 values of 0.817 and 0.809. Multitask learning achieved simultaneous prediction of yield and GPC with comparable accuracy to the single-task model. We further proposed a two-to-two model that combines data fusion (two kinds of data sources for input) and multitask learning (two outputs) and compared different feature extraction layers, including RNN (recurrent neural network), LSTM (long short-term memory), CNN (convolutional neural network), and attention module. The two-to-two model with the attention module achieved the best prediction accuracy for yield (R2 = 0.833) and GPC (R2 = 0.846). The temporal distribution of feature importance was visualized based on the attention feature values. Although the temporal patterns of structural traits and spectral traits were inconsistent, the overall importance of both structural traits and spectral traits at the postanthesis stage was more important than that at the preanthesis stage. This study provides new insights into the simultaneous prediction of yield and GPC using deep learning from time-series proximal sensing, which may contribute to the accurate and efficient predictions of agricultural production.
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Affiliation(s)
- Zhuangzhuang Sun
- Plant Phenomics Research Centre, Academy for Advanced Interdisciplinary Studies, Regional Technique Innovation Center for Wheat Production, Ministry of Agriculture, Key Laboratory of Crop Physiology and Ecology in Southern China, Ministry of Agriculture, Collaborative Innovation Centre for Modern Crop Production Co-Sponsored by Province and Ministry, Nanjing Agricultural University, Nanjing 210095, China
| | - Qing Li
- Plant Phenomics Research Centre, Academy for Advanced Interdisciplinary Studies, Regional Technique Innovation Center for Wheat Production, Ministry of Agriculture, Key Laboratory of Crop Physiology and Ecology in Southern China, Ministry of Agriculture, Collaborative Innovation Centre for Modern Crop Production Co-Sponsored by Province and Ministry, Nanjing Agricultural University, Nanjing 210095, China
| | - Shichao Jin
- Plant Phenomics Research Centre, Academy for Advanced Interdisciplinary Studies, Regional Technique Innovation Center for Wheat Production, Ministry of Agriculture, Key Laboratory of Crop Physiology and Ecology in Southern China, Ministry of Agriculture, Collaborative Innovation Centre for Modern Crop Production Co-Sponsored by Province and Ministry, Nanjing Agricultural University, Nanjing 210095, China
- Jiangsu Provincial Key Laboratory of Geographic Information Science and Technology, International Institute for Earth System Sciences, Nanjing University, Nanjing, Jiangsu 210023, China
| | - Yunlin Song
- Plant Phenomics Research Centre, Academy for Advanced Interdisciplinary Studies, Regional Technique Innovation Center for Wheat Production, Ministry of Agriculture, Key Laboratory of Crop Physiology and Ecology in Southern China, Ministry of Agriculture, Collaborative Innovation Centre for Modern Crop Production Co-Sponsored by Province and Ministry, Nanjing Agricultural University, Nanjing 210095, China
| | - Shan Xu
- Plant Phenomics Research Centre, Academy for Advanced Interdisciplinary Studies, Regional Technique Innovation Center for Wheat Production, Ministry of Agriculture, Key Laboratory of Crop Physiology and Ecology in Southern China, Ministry of Agriculture, Collaborative Innovation Centre for Modern Crop Production Co-Sponsored by Province and Ministry, Nanjing Agricultural University, Nanjing 210095, China
| | - Xiao Wang
- Plant Phenomics Research Centre, Academy for Advanced Interdisciplinary Studies, Regional Technique Innovation Center for Wheat Production, Ministry of Agriculture, Key Laboratory of Crop Physiology and Ecology in Southern China, Ministry of Agriculture, Collaborative Innovation Centre for Modern Crop Production Co-Sponsored by Province and Ministry, Nanjing Agricultural University, Nanjing 210095, China
| | - Jian Cai
- Plant Phenomics Research Centre, Academy for Advanced Interdisciplinary Studies, Regional Technique Innovation Center for Wheat Production, Ministry of Agriculture, Key Laboratory of Crop Physiology and Ecology in Southern China, Ministry of Agriculture, Collaborative Innovation Centre for Modern Crop Production Co-Sponsored by Province and Ministry, Nanjing Agricultural University, Nanjing 210095, China
| | - Qin Zhou
- Plant Phenomics Research Centre, Academy for Advanced Interdisciplinary Studies, Regional Technique Innovation Center for Wheat Production, Ministry of Agriculture, Key Laboratory of Crop Physiology and Ecology in Southern China, Ministry of Agriculture, Collaborative Innovation Centre for Modern Crop Production Co-Sponsored by Province and Ministry, Nanjing Agricultural University, Nanjing 210095, China
| | - Yan Ge
- Plant Phenomics Research Centre, Academy for Advanced Interdisciplinary Studies, Regional Technique Innovation Center for Wheat Production, Ministry of Agriculture, Key Laboratory of Crop Physiology and Ecology in Southern China, Ministry of Agriculture, Collaborative Innovation Centre for Modern Crop Production Co-Sponsored by Province and Ministry, Nanjing Agricultural University, Nanjing 210095, China
| | - Ruinan Zhang
- Plant Phenomics Research Centre, Academy for Advanced Interdisciplinary Studies, Regional Technique Innovation Center for Wheat Production, Ministry of Agriculture, Key Laboratory of Crop Physiology and Ecology in Southern China, Ministry of Agriculture, Collaborative Innovation Centre for Modern Crop Production Co-Sponsored by Province and Ministry, Nanjing Agricultural University, Nanjing 210095, China
| | - Jingrong Zang
- Plant Phenomics Research Centre, Academy for Advanced Interdisciplinary Studies, Regional Technique Innovation Center for Wheat Production, Ministry of Agriculture, Key Laboratory of Crop Physiology and Ecology in Southern China, Ministry of Agriculture, Collaborative Innovation Centre for Modern Crop Production Co-Sponsored by Province and Ministry, Nanjing Agricultural University, Nanjing 210095, China
| | - Dong Jiang
- Plant Phenomics Research Centre, Academy for Advanced Interdisciplinary Studies, Regional Technique Innovation Center for Wheat Production, Ministry of Agriculture, Key Laboratory of Crop Physiology and Ecology in Southern China, Ministry of Agriculture, Collaborative Innovation Centre for Modern Crop Production Co-Sponsored by Province and Ministry, Nanjing Agricultural University, Nanjing 210095, China
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14
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Lube V, Noyan MA, Przybysz A, Salama K, Blilou I. MultipleXLab: A high-throughput portable live-imaging root phenotyping platform using deep learning and computer vision. PLANT METHODS 2022; 18:38. [PMID: 35346267 PMCID: PMC8958799 DOI: 10.1186/s13007-022-00864-4] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 11/05/2021] [Accepted: 02/24/2022] [Indexed: 06/14/2023]
Abstract
BACKGROUND Profiling the plant root architecture is vital for selecting resilient crops that can efficiently take up water and nutrients. The high-performance imaging tools available to study root-growth dynamics with the optimal resolution are costly and stationary. In addition, performing nondestructive high-throughput phenotyping to extract the structural and morphological features of roots remains challenging. RESULTS We developed the MultipleXLab: a modular, mobile, and cost-effective setup to tackle these limitations. The system can continuously monitor thousands of seeds from germination to root development based on a conventional camera attached to a motorized multiaxis-rotational stage and custom-built 3D-printed plate holder with integrated light-emitting diode lighting. We also developed an image segmentation model based on deep learning that allows the users to analyze the data automatically. We tested the MultipleXLab to monitor seed germination and root growth of Arabidopsis developmental, cell cycle, and auxin transport mutants non-invasively at high-throughput and showed that the system provides robust data and allows precise evaluation of germination index and hourly growth rate between mutants. CONCLUSION MultipleXLab provides a flexible and user-friendly root phenotyping platform that is an attractive mobile alternative to high-end imaging platforms and stationary growth chambers. It can be used in numerous applications by plant biologists, the seed industry, crop scientists, and breeding companies.
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Affiliation(s)
- Vinicius Lube
- Laboratory of Plant Cell and Developmental Biology (LPCDB), Biological and Environmental Sciences and Engineering (BESE), King Abdullah University of Science and Technology (KAUST), Thuwal, 23955-6900, Saudi Arabia
| | | | - Alexander Przybysz
- Sensors Lab, Advanced Membranes and Porous Materials Center (AMPMC), Computer, Electrical and Mathematical Science and Engineering (CEMSE), KAUST, Thuwal, Saudi Arabia
| | - Khaled Salama
- Sensors Lab, Advanced Membranes and Porous Materials Center (AMPMC), Computer, Electrical and Mathematical Science and Engineering (CEMSE), KAUST, Thuwal, Saudi Arabia
| | - Ikram Blilou
- Laboratory of Plant Cell and Developmental Biology (LPCDB), Biological and Environmental Sciences and Engineering (BESE), King Abdullah University of Science and Technology (KAUST), Thuwal, 23955-6900, Saudi Arabia.
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15
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Tanabata T, Kodama K, Hashiguchi T, Inomata D, Tanaka H, Isobe S. Development of a plant conveyance system using an AGV and a self-designed plant-handling device: A case study of DIY plant phenotyping. BREEDING SCIENCE 2022; 72:85-95. [PMID: 36045895 PMCID: PMC8987848 DOI: 10.1270/jsbbs.21070] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 08/31/2021] [Accepted: 01/19/2022] [Indexed: 06/15/2023]
Abstract
Plant phenotyping technology has been actively developed in recent years, but the introduction of these technologies into the field of agronomic research has not progressed as expected, in part due to the need for flexibility and low cost. "DIY" (Do It Yourself) methodologies are an efficient way to overcome such obstacles. Devices with modular functionality are critical to DIY experimentation, allowing researchers flexibility of design. In this study, we developed a plant conveyance system using a commercial AGV (Automated Guided Vehicle) as a case study of DIY plant phenotyping. The convey module consists of two devices, a running device and a plant-handling device. The running device was developed based on a commercial AGV Kit. The plant-handling device, plant stands, and pot attachments were originally designed and fabricated by us and our associates. Software was also developed for connecting the devices and operating the system. The run route was set with magnetic tape, which can be easily changed or rerouted. Our plant delivery system was developed with low cost and having high flexibility, as a unit that can contribute to others' DIY' plant research efforts as well as our own. It is expected that the developed devices will contribute to diverse phenotype observations of plants in the greenhouse as well as to other important functions in plant breeding and agricultural production.
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Affiliation(s)
- Takanari Tanabata
- Department of Frontier Research and Development, Kazusa DNA Research Institute, 2-6-7 Kazusa-kamatari, Kisarazu, Chiba 292-0818, Japan
| | - Kunihiro Kodama
- Department of Frontier Research and Development, Kazusa DNA Research Institute, 2-6-7 Kazusa-kamatari, Kisarazu, Chiba 292-0818, Japan
| | - Takuyu Hashiguchi
- Faculty of Agriculture, University of Miyazaki, 1-1 Gakuenkibanadai-Nishi, Miyazaki 889-2192, Japan
| | | | - Hidenori Tanaka
- Interdisciplinary Graduate School of Agriculture and Engineering, University of Miyazaki, 1-1 Gakuenkibanadai-Nishi, Miyazaki 889-2192, Japan
| | - Sachiko Isobe
- Department of Frontier Research and Development, Kazusa DNA Research Institute, 2-6-7 Kazusa-kamatari, Kisarazu, Chiba 292-0818, Japan
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16
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Li R, Su X, Zhou R, Zhang Y, Wang T. Molecular mechanism of mulberry response to drought stress revealed by complementary transcriptomic and iTRAQ analyses. BMC PLANT BIOLOGY 2022; 22:36. [PMID: 35039015 PMCID: PMC8762937 DOI: 10.1186/s12870-021-03410-x] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 07/02/2021] [Accepted: 12/20/2021] [Indexed: 06/14/2023]
Abstract
BACKGROUND The use of mulberry leaves has long been limited to raising silkworms, but with the continuous improvement of mulberry (Morus alba) resource development and utilization, various mulberry leaf extension products have emerged. However, the fresh leaves of mulberry trees have a specific window of time for picking and are susceptible to adverse factors, such as drought stress. Therefore, exploring the molecular mechanism by which mulberry trees resist drought stress and clarifying the regulatory network of the mulberry drought response is the focus of the current work. RESULTS In this study, natural and drought-treated mulberry grafted seedlings were used for transcriptomic and proteomic analyses (CK vs. DS9), aiming to clarify the molecular mechanism of the mulberry drought stress response. Through transcriptome and proteome sequencing, we identified 9889 DEGs and 1893 DEPs enriched in stress-responsive GO functional categories, such as signal transducer activity, antioxidant activity, and transcription regulator activity. KEGG enrichment analysis showed that a large number of codifferentially expressed genes were enriched in flavonoid biosynthesis pathways, hormone signalling pathways, lignin metabolism and other pathways. Through subsequent cooperation analysis, we identified 818 codifferentially expressed genes in the CK vs. DS9 comparison group, including peroxidase (POD), superoxide dismutase (SOD), aldehyde dehydrogenase (ALDHs), glutathione s-transferase (GST) and other genes closely related to the stress response. In addition, we determined that the mulberry gene MaWRKYIII8 (XP_010104968.1) underwent drought- and abscisic acid (ABA)-induced expression, indicating that it may play an important role in the mulberry response to drought stress. CONCLUSIONS Our research shows that mulberry can activate proline and ABA biosynthesis pathways and produce a large amount of proline and ABA, which improves the drought resistance of mulberry. MaWRKYIII8 was up-regulated and induced by drought and exogenous ABA, indicating that MaWRKYIII8 may be involved in the mulberry response to drought stress. These studies will help us to analyse the molecular mechanism underlying mulberry drought tolerance and provide important gene information and a theoretical basis for improving mulberry drought tolerance through molecular breeding in the future.
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Affiliation(s)
- Ruixue Li
- Sericultural Research Institute, Anhui Academy of Agricultural Sciences, Hefei, Anhui, China
| | - Xueqiang Su
- Sericultural Research Institute, Anhui Academy of Agricultural Sciences, Hefei, Anhui, China
| | - Rong Zhou
- Sericultural Research Institute, Anhui Academy of Agricultural Sciences, Hefei, Anhui, China
| | - Yuping Zhang
- Sericultural Research Institute, Anhui Academy of Agricultural Sciences, Hefei, Anhui, China
| | - Taichu Wang
- Sericultural Research Institute, Anhui Academy of Agricultural Sciences, Hefei, Anhui, China.
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17
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Burridge JD, Grondin A, Vadez V. Optimizing Crop Water Use for Drought and Climate Change Adaptation Requires a Multi-Scale Approach. FRONTIERS IN PLANT SCIENCE 2022; 13:824720. [PMID: 35574091 PMCID: PMC9100818 DOI: 10.3389/fpls.2022.824720] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/29/2021] [Accepted: 04/11/2022] [Indexed: 05/09/2023]
Abstract
Selection criteria that co-optimize water use efficiency and yield are needed to promote plant productivity in increasingly challenging and variable drought scenarios, particularly dryland cereals in the semi-arid tropics. Optimizing water use efficiency and yield fundamentally involves transpiration dynamics, where restriction of maximum transpiration rate helps to avoid early crop failure, while maximizing grain filling. Transpiration restriction can be regulated by multiple mechanisms and involves cross-organ coordination. This coordination involves complex feedbacks and feedforwards over time scales ranging from minutes to weeks, and from spatial scales ranging from cell membrane to crop canopy. Aquaporins have direct effect but various compensation and coordination pathways involve phenology, relative root and shoot growth, shoot architecture, root length distribution profile, as well as other architectural and anatomical aspects of plant form and function. We propose gravimetric phenotyping as an integrative, cross-scale solution to understand the dynamic, interwoven, and context-dependent coordination of transpiration regulation. The most fruitful breeding strategy is likely to be that which maintains focus on the phene of interest, namely, daily and season level transpiration dynamics. This direct selection approach is more precise than yield-based selection but sufficiently integrative to capture attenuating and complementary factors.
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Affiliation(s)
- James D. Burridge
- DIADE Group, Cereal Root Systems, Institute de Recherche pour le Développement/Université de Montpellier, Montpellier, France
- *Correspondence: James D. Burridge,
| | - Alexandre Grondin
- DIADE Group, Cereal Root Systems, Institute de Recherche pour le Développement/Université de Montpellier, Montpellier, France
- Adaptation des Plantes et Microorganismes Associés aux Stress Environnementaux, Laboratoire Mixte International, Dakar, Senegal
- Centre d’Étude Régional pour l’Amélioration de l’Adaptation à la Sécheresse, Thiès, Senegal
| | - Vincent Vadez
- DIADE Group, Cereal Root Systems, Institute de Recherche pour le Développement/Université de Montpellier, Montpellier, France
- Adaptation des Plantes et Microorganismes Associés aux Stress Environnementaux, Laboratoire Mixte International, Dakar, Senegal
- Centre d’Étude Régional pour l’Amélioration de l’Adaptation à la Sécheresse, Thiès, Senegal
- International Crops Research Institute for Semi-Arid Tropics (ICRISAT), Patancheru, India
- Vincent Vadez,
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18
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Langstroff A, Heuermann MC, Stahl A, Junker A. Opportunities and limits of controlled-environment plant phenotyping for climate response traits. TAG. THEORETICAL AND APPLIED GENETICS. THEORETISCHE UND ANGEWANDTE GENETIK 2022; 135:1-16. [PMID: 34302493 PMCID: PMC8741719 DOI: 10.1007/s00122-021-03892-1] [Citation(s) in RCA: 16] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/19/2020] [Accepted: 06/17/2021] [Indexed: 05/19/2023]
Abstract
Rising temperatures and changing precipitation patterns will affect agricultural production substantially, exposing crops to extended and more intense periods of stress. Therefore, breeding of varieties adapted to the constantly changing conditions is pivotal to enable a quantitatively and qualitatively adequate crop production despite the negative effects of climate change. As it is not yet possible to select for adaptation to future climate scenarios in the field, simulations of future conditions in controlled-environment (CE) phenotyping facilities contribute to the understanding of the plant response to special stress conditions and help breeders to select ideal genotypes which cope with future conditions. CE phenotyping facilities enable the collection of traits that are not easy to measure under field conditions and the assessment of a plant's phenotype under repeatable, clearly defined environmental conditions using automated, non-invasive, high-throughput methods. However, extrapolation and translation of results obtained under controlled environments to field environments is ambiguous. This review outlines the opportunities and challenges of phenotyping approaches under controlled environments complementary to conventional field trials. It gives an overview on general principles and introduces existing phenotyping facilities that take up the challenge of obtaining reliable and robust phenotypic data on climate response traits to support breeding of climate-adapted crops.
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Affiliation(s)
- Anna Langstroff
- Department of Plant Breeding, IFZ Research Centre for Biosystems, Land Use and Nutrition, Justus Liebig University Giessen, Heinrich Buff-Ring 26, 35392, Giessen, Germany
| | - Marc C Heuermann
- Leibniz Institute of Plant Genetics and Crop Plant Research (IPK) Gatersleben, Corrensstr. 3, OT Gatersleben, 06466, Seeland, Germany
| | - Andreas Stahl
- Department of Plant Breeding, IFZ Research Centre for Biosystems, Land Use and Nutrition, Justus Liebig University Giessen, Heinrich Buff-Ring 26, 35392, Giessen, Germany
- Institute for Resistance Research and Stress Tolerance, Federal Research Centre for Cultivated Plants, Julius Kühn-Institut (JKI), Erwin-Baur-Strasse 27, 06484, Quedlinburg, Germany
| | - Astrid Junker
- Leibniz Institute of Plant Genetics and Crop Plant Research (IPK) Gatersleben, Corrensstr. 3, OT Gatersleben, 06466, Seeland, Germany.
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19
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Kartal S, Choudhary S, Masner J, Kholová J, Stočes M, Gattu P, Schwartz S, Kissel E. Machine Learning-Based Plant Detection Algorithms to Automate Counting Tasks Using 3D Canopy Scans. SENSORS (BASEL, SWITZERLAND) 2021; 21:8022. [PMID: 34884027 PMCID: PMC8659963 DOI: 10.3390/s21238022] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 09/30/2021] [Revised: 10/29/2021] [Accepted: 11/05/2021] [Indexed: 11/22/2022]
Abstract
This study tested whether machine learning (ML) methods can effectively separate individual plants from complex 3D canopy laser scans as a prerequisite to analyzing particular plant features. For this, we scanned mung bean and chickpea crops with PlantEye (R) laser scanners. Firstly, we segmented the crop canopies from the background in 3D space using the Region Growing Segmentation algorithm. Then, Convolutional Neural Network (CNN) based ML algorithms were fine-tuned for plant counting. Application of the CNN-based (Convolutional Neural Network) processing architecture was possible only after we reduced the dimensionality of the data to 2D. This allowed for the identification of individual plants and their counting with an accuracy of 93.18% and 92.87% for mung bean and chickpea plants, respectively. These steps were connected to the phenotyping pipeline, which can now replace manual counting operations that are inefficient, costly, and error-prone. The use of CNN in this study was innovatively solved with dimensionality reduction, addition of height information as color, and consequent application of a 2D CNN-based approach. We found there to be a wide gap in the use of ML on 3D information. This gap will have to be addressed, especially for more complex plant feature extractions, which we intend to implement through further research.
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Affiliation(s)
- Serkan Kartal
- Department of Computer Engineering, Faculty of Engineering, Cukurova University, Adana 01330, Turkey;
| | - Sunita Choudhary
- System Analysis for Climate Smart Agriculture (SACSA), ISD, International Crops Research Institute for the Semi-Arid Tropics, Patancheru 5023204, Telangana, India; (S.C.); (J.K.)
| | - Jan Masner
- Department of Information Technologies, Faculty of Economics and Management, Czech University of Life Sciences Prague, Kamýcká 129, 165 00 Prague, Czech Republic;
| | - Jana Kholová
- System Analysis for Climate Smart Agriculture (SACSA), ISD, International Crops Research Institute for the Semi-Arid Tropics, Patancheru 5023204, Telangana, India; (S.C.); (J.K.)
| | - Michal Stočes
- Department of Information Technologies, Faculty of Economics and Management, Czech University of Life Sciences Prague, Kamýcká 129, 165 00 Prague, Czech Republic;
| | - Priyanka Gattu
- Department of Electrical Engineering, Indian Institute of Technology Hyderabad, Sangareddy 502285, Telangana, India;
| | - Stefan Schwartz
- Phenospex B. V., Jan Campertstraat 11, 6416 SG Heerlen, The Netherlands; (S.S.); (E.K.)
| | - Ewaut Kissel
- Phenospex B. V., Jan Campertstraat 11, 6416 SG Heerlen, The Netherlands; (S.S.); (E.K.)
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20
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Zhu Y, Sun G, Ding G, Zhou J, Wen M, Jin S, Zhao Q, Colmer J, Ding Y, Ober ES, Zhou J. Large-scale field phenotyping using backpack LiDAR and CropQuant-3D to measure structural variation in wheat. PLANT PHYSIOLOGY 2021; 187:716-738. [PMID: 34608970 PMCID: PMC8491082 DOI: 10.1093/plphys/kiab324] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/19/2021] [Accepted: 06/22/2021] [Indexed: 05/12/2023]
Abstract
Plant phenomics bridges the gap between traits of agricultural importance and genomic information. Limitations of current field-based phenotyping solutions include mobility, affordability, throughput, accuracy, scalability, and the ability to analyze big data collected. Here, we present a large-scale phenotyping solution that combines a commercial backpack Light Detection and Ranging (LiDAR) device and our analytic software, CropQuant-3D, which have been applied jointly to phenotype wheat (Triticum aestivum) and associated 3D trait analysis. The use of LiDAR can acquire millions of 3D points to represent spatial features of crops, and CropQuant-3D can extract meaningful traits from large, complex point clouds. In a case study examining the response of wheat varieties to three different levels of nitrogen fertilization in field experiments, the combined solution differentiated significant genotype and treatment effects on crop growth and structural variation in the canopy, with strong correlations with manual measurements. Hence, we demonstrate that this system could consistently perform 3D trait analysis at a larger scale and more quickly than heretofore possible and addresses challenges in mobility, throughput, and scalability. To ensure our work could reach non-expert users, we developed an open-source graphical user interface for CropQuant-3D. We, therefore, believe that the combined system is easy-to-use and could be used as a reliable research tool in multi-location phenotyping for both crop research and breeding. Furthermore, together with the fast maturity of LiDAR technologies, the system has the potential for further development in accuracy and affordability, contributing to the resolution of the phenotyping bottleneck and exploiting available genomic resources more effectively.
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Affiliation(s)
- Yulei Zhu
- State Key Laboratory of Crop Genetics and Germplasm Enhancement, College of Engineering, College of Agriculture, Plant Phenomics Research Center, Academy for Advanced Interdisciplinary Studies, Jiangsu Collaborative Innovation Center for Modern Crop Production Co-sponsored by Province and Ministry, Nanjing Agricultural University, Nanjing 210095, China
| | - Gang Sun
- State Key Laboratory of Crop Genetics and Germplasm Enhancement, College of Engineering, College of Agriculture, Plant Phenomics Research Center, Academy for Advanced Interdisciplinary Studies, Jiangsu Collaborative Innovation Center for Modern Crop Production Co-sponsored by Province and Ministry, Nanjing Agricultural University, Nanjing 210095, China
| | - Guohui Ding
- State Key Laboratory of Crop Genetics and Germplasm Enhancement, College of Engineering, College of Agriculture, Plant Phenomics Research Center, Academy for Advanced Interdisciplinary Studies, Jiangsu Collaborative Innovation Center for Modern Crop Production Co-sponsored by Province and Ministry, Nanjing Agricultural University, Nanjing 210095, China
| | - Jie Zhou
- State Key Laboratory of Crop Genetics and Germplasm Enhancement, College of Engineering, College of Agriculture, Plant Phenomics Research Center, Academy for Advanced Interdisciplinary Studies, Jiangsu Collaborative Innovation Center for Modern Crop Production Co-sponsored by Province and Ministry, Nanjing Agricultural University, Nanjing 210095, China
| | - Mingxing Wen
- State Key Laboratory of Crop Genetics and Germplasm Enhancement, College of Engineering, College of Agriculture, Plant Phenomics Research Center, Academy for Advanced Interdisciplinary Studies, Jiangsu Collaborative Innovation Center for Modern Crop Production Co-sponsored by Province and Ministry, Nanjing Agricultural University, Nanjing 210095, China
- Zhenjiang Institute of Agricultural Science in Hill Area of Jiangsu Province, Jurong 212400, China
| | - Shichao Jin
- State Key Laboratory of Crop Genetics and Germplasm Enhancement, College of Engineering, College of Agriculture, Plant Phenomics Research Center, Academy for Advanced Interdisciplinary Studies, Jiangsu Collaborative Innovation Center for Modern Crop Production Co-sponsored by Province and Ministry, Nanjing Agricultural University, Nanjing 210095, China
| | - Qiang Zhao
- National Center for Gene Research, CAS Center for Excellence in Molecular Plant Sciences, Chinese Academy of Sciences, Shanghai 200233, China
| | - Joshua Colmer
- Earlham Institute, Norwich Research Park, Norwich NR4 7UH, UK
| | - Yanfeng Ding
- State Key Laboratory of Crop Genetics and Germplasm Enhancement, College of Engineering, College of Agriculture, Plant Phenomics Research Center, Academy for Advanced Interdisciplinary Studies, Jiangsu Collaborative Innovation Center for Modern Crop Production Co-sponsored by Province and Ministry, Nanjing Agricultural University, Nanjing 210095, China
| | - Eric S. Ober
- Cambridge Crop Research, National Institute of Agricultural Botany (NIAB), Cambridge CB3 0LE, UK
| | - Ji Zhou
- State Key Laboratory of Crop Genetics and Germplasm Enhancement, College of Engineering, College of Agriculture, Plant Phenomics Research Center, Academy for Advanced Interdisciplinary Studies, 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 (NIAB), Cambridge CB3 0LE, UK
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21
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Danilevicz MF, Bayer PE, Nestor BJ, Bennamoun M, Edwards D. Resources for image-based high-throughput phenotyping in crops and data sharing challenges. PLANT PHYSIOLOGY 2021; 187:699-715. [PMID: 34608963 PMCID: PMC8561249 DOI: 10.1093/plphys/kiab301] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/04/2020] [Accepted: 05/26/2021] [Indexed: 05/06/2023]
Abstract
High-throughput phenotyping (HTP) platforms are capable of monitoring the phenotypic variation of plants through multiple types of sensors, such as red green and blue (RGB) cameras, hyperspectral sensors, and computed tomography, which can be associated with environmental and genotypic data. Because of the wide range of information provided, HTP datasets represent a valuable asset to characterize crop phenotypes. As HTP becomes widely employed with more tools and data being released, it is important that researchers are aware of these resources and how they can be applied to accelerate crop improvement. Researchers may exploit these datasets either for phenotype comparison or employ them as a benchmark to assess tool performance and to support the development of tools that are better at generalizing between different crops and environments. In this review, we describe the use of image-based HTP for yield prediction, root phenotyping, development of climate-resilient crops, detecting pathogen and pest infestation, and quantitative trait measurement. We emphasize the need for researchers to share phenotypic data, and offer a comprehensive list of available datasets to assist crop breeders and tool developers to leverage these resources in order to accelerate crop breeding.
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Affiliation(s)
- Monica F. Danilevicz
- School of Biological Sciences and Institute of Agriculture, University of Western Australia, Perth, Western Australia 6009, Australia
| | - Philipp E. Bayer
- School of Biological Sciences and Institute of Agriculture, University of Western Australia, Perth, Western Australia 6009, Australia
| | - Benjamin J. Nestor
- School of Biological Sciences and Institute of Agriculture, University of Western Australia, Perth, Western Australia 6009, Australia
| | - Mohammed Bennamoun
- Department of Computer Science and Software Engineering, University of Western Australia, Perth, Western Australia 6009, Australia
| | - David Edwards
- School of Biological Sciences and Institute of Agriculture, University of Western Australia, Perth, Western Australia 6009, Australia
- Author for communication:
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22
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Jiang Z, Tu H, Bai B, Yang C, Zhao B, Guo Z, Liu Q, Zhao H, Yang W, Xiong L, Zhang J. Combining UAV-RGB high-throughput field phenotyping and genome-wide association study to reveal genetic variation of rice germplasms in dynamic response to drought stress. THE NEW PHYTOLOGIST 2021; 232:440-455. [PMID: 34165797 DOI: 10.1111/nph.17580] [Citation(s) in RCA: 18] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/09/2021] [Accepted: 06/17/2021] [Indexed: 05/24/2023]
Abstract
Accurate and high-throughput phenotyping of the dynamic response of a large rice population to drought stress in the field is a bottleneck for genetic dissection and breeding of drought resistance. Here, high-efficiency and high-frequent image acquisition by an unmanned aerial vehicle (UAV) was utilized to quantify the dynamic drought response of a rice population under field conditions. Deep convolutional neural networks (DCNNs) and canopy height models were applied to extract highly correlated phenotypic traits including UAV-based leaf-rolling score (LRS_uav), plant water content (PWC_uav) and a new composite trait, drought resistance index by UAV (DRI_uav). The DCNNs achieved high accuracy (correlation coefficient R = 0.84 for modeling set and R = 0.86 for test set) to replace manual leaf-rolling rating. PWC_uav values were precisely estimated (correlation coefficient R = 0.88) and DRI_uav was modeled to monitor the drought resistance of rice accessions dynamically and comprehensively. A total of 111 significantly associated loci were detected by genome-wide association study for the three dynamic traits, and 30.6% of them were not detected in previous mapping studies using nondynamic drought response traits. Unmanned aerial vehicle and deep learning are confirmed effective phenotyping techniques for more complete genetic dissection of rice dynamic responses to drought and exploration of valuable alleles for drought resistance improvement.
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Affiliation(s)
- Zhao Jiang
- Macro Agriculture Research Institute, College of Resource and Environment, Huazhong Agricultural University, Wuhan, 430070, China
| | - Haifu Tu
- National Key Laboratory of Crop Genetic Improvement and National Center of Plant Gene Research (Wuhan), Hubei Hongshan Laboratory, Huazhong Agricultural University, Wuhan, 430070, China
| | - Baowei Bai
- National Key Laboratory of Crop Genetic Improvement and National Center of Plant Gene Research (Wuhan), Hubei Hongshan Laboratory, Huazhong Agricultural University, Wuhan, 430070, China
| | - Chenghai Yang
- Aerial Application Technology Research Unit, USDA-Agricultural Research Service, College Station, TX, 77845, USA
| | - Biquan Zhao
- School of Natural Resources, University of Nebraska-Lincoln, Lincoln, NE, 68583-0988, USA
- Department of Biological Systems Engineering, University of Nebraska-Lincoln, Lincoln, NE, 68583-0726, USA
| | - Ziyue Guo
- Macro Agriculture Research Institute, College of Resource and Environment, Huazhong Agricultural University, Wuhan, 430070, China
| | - Qian Liu
- National Key Laboratory of Crop Genetic Improvement and National Center of Plant Gene Research (Wuhan), Hubei Hongshan Laboratory, Huazhong Agricultural University, Wuhan, 430070, China
| | - Hu Zhao
- National Key Laboratory of Crop Genetic Improvement and National Center of Plant Gene Research (Wuhan), Hubei Hongshan Laboratory, Huazhong Agricultural University, Wuhan, 430070, China
| | - Wanneng Yang
- National Key Laboratory of Crop Genetic Improvement and National Center of Plant Gene Research (Wuhan), Hubei Hongshan Laboratory, Huazhong Agricultural University, Wuhan, 430070, China
| | - Lizhong Xiong
- National Key Laboratory of Crop Genetic Improvement and National Center of Plant Gene Research (Wuhan), Hubei Hongshan Laboratory, Huazhong Agricultural University, Wuhan, 430070, China
| | - Jian Zhang
- Macro Agriculture Research Institute, College of Resource and Environment, Huazhong Agricultural University, Wuhan, 430070, China
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23
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Kholová J, Urban MO, Cock J, Arcos J, Arnaud E, Aytekin D, Azevedo V, Barnes AP, Ceccarelli S, Chavarriaga P, Cobb JN, Connor D, Cooper M, Craufurd P, Debouck D, Fungo R, Grando S, Hammer GL, Jara CE, Messina C, Mosquera G, Nchanji E, Ng EH, Prager S, Sankaran S, Selvaraj M, Tardieu F, Thornton P, Valdes-Gutierrez SP, van Etten J, Wenzl P, Xu Y. In pursuit of a better world: crop improvement and the CGIAR. JOURNAL OF EXPERIMENTAL BOTANY 2021; 72:5158-5179. [PMID: 34021317 PMCID: PMC8272562 DOI: 10.1093/jxb/erab226] [Citation(s) in RCA: 17] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/17/2020] [Accepted: 05/20/2021] [Indexed: 05/10/2023]
Abstract
The CGIAR crop improvement (CI) programs, unlike commercial CI programs, which are mainly geared to profit though meeting farmers' needs, are charged with meeting multiple objectives with target populations that include both farmers and the community at large. We compiled the opinions from >30 experts in the private and public sector on key strategies, methodologies, and activities that could the help CGIAR meet the challenges of providing farmers with improved varieties while simultaneously meeting the goals of: (i) nutrition, health, and food security; (ii) poverty reduction, livelihoods, and jobs; (iii) gender equality, youth, and inclusion; (iv) climate adaptation and mitigation; and (v) environmental health and biodiversity. We review the crop improvement processes starting with crop choice, moving through to breeding objectives, production of potential new varieties, selection, and finally adoption by farmers. The importance of multidisciplinary teams working towards common objectives is stressed as a key factor to success. The role of the distinct disciplines, actors, and their interactions throughout the process from crop choice through to adoption by farmers is discussed and illustrated.
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Affiliation(s)
- Jana Kholová
- International Crops Research Institute for the Semi-Arid Tropics, Hyderabad-502324, India
| | - Milan Oldřich Urban
- International Center for Tropical Agriculture, Km 17 Recta Cali-Palmira, CP 763537, A.A. 12 6713, Cali, Colombia
| | - James Cock
- International Center for Tropical Agriculture, Km 17 Recta Cali-Palmira, CP 763537, A.A. 12 6713, Cali, Colombia
| | - Jairo Arcos
- HarvestPlus, Km 17 Recta Cali-Palmira, CP 763537, A.A. 12 6713, Cali, Colombia
| | - Elizabeth Arnaud
- Bioversity International, Parc scientifique Agropolis II, 1990 Boulevard de la Lironde, 34397 Montpellier, France
| | | | - Vania Azevedo
- International Crops Research Institute for the Semi-Arid Tropics, Hyderabad-502324, India
| | | | | | - Paul Chavarriaga
- International Center for Tropical Agriculture, Km 17 Recta Cali-Palmira, CP 763537, A.A. 12 6713, Cali, Colombia
| | | | - David Connor
- Department of Agriculture and Food, The University of Melbourne, Australia
| | - Mark Cooper
- Queensland Alliance for Agriculture and Food Innovation, The University of Queensland, Brisbane, Qld 4072, Australia
| | - Peter Craufurd
- CIMMYT, 1st floor, National Plant Breeding and Genetics Centre, NARC Research Station, Khumaltor, Lalitpur, PO Box 5186, Kathmandu, Nepal
| | - Daniel Debouck
- International Center for Tropical Agriculture, Km 17 Recta Cali-Palmira, CP 763537, A.A. 12 6713, Cali, Colombia
| | - Robert Fungo
- International Center for Tropical Agriculture, PO Box 6247, Kampala, Uganda
- School of Food Technology, Nutrition & Bio-Engineering, Makerere University, PO Box, 7062, Kampala, Uganda
| | - Stefania Grando
- Independent Consultant, Corso Mazzini 256, 63100 Ascoli Piceno, Italy
| | - Graeme L Hammer
- Queensland Alliance for Agriculture and Food Innovation, The University of Queensland, Brisbane, Qld 4072, Australia
| | - Carlos E Jara
- Independent Consultant, Hacienda Real, Torre 2, CP 760033, Cali, Colombia
| | - Charlie Messina
- Corteva Agriscience, 7200 62nd Avenue, Johnston, IA 50131, USA
| | - Gloria Mosquera
- International Center for Tropical Agriculture, Km 17 Recta Cali-Palmira, CP 763537, A.A. 12 6713, Cali, Colombia
| | - Eileen Nchanji
- International Center for Tropical Agriculture, African hub, Box 823-00621, Nairobi, Kenya
| | - Eng Hwa Ng
- International Maize and Wheat Improvement Center (CIMMYT); México-Veracruz, El Batán Km. 45, 56237, Mexico
| | - Steven Prager
- International Center for Tropical Agriculture, Km 17 Recta Cali-Palmira, CP 763537, A.A. 12 6713, Cali, Colombia
| | - Sindhujan Sankaran
- Department of Biological Systems Engineering, Washington State University, 1935 E. Grimes Way, PO Box 646120, Pullman, WA 99164, USA
| | - Michael Selvaraj
- International Center for Tropical Agriculture, Km 17 Recta Cali-Palmira, CP 763537, A.A. 12 6713, Cali, Colombia
| | - François Tardieu
- INRA Centre de Montpellier, Montpellier, Languedoc-Roussillon, France
| | - Philip Thornton
- CGIAR Research Program on Climate Change, Agriculture 37 and Food Security (CCAFS), International Livestock Research Institute (ILRI), Nairobi, Kenya
| | - Sandra P Valdes-Gutierrez
- International Center for Tropical Agriculture, Km 17 Recta Cali-Palmira, CP 763537, A.A. 12 6713, Cali, Colombia
| | - Jacob van Etten
- Bioversity International, Parc scientifique Agropolis II, 1990 Boulevard de la Lironde, 34397 Montpellier, France
| | - Peter Wenzl
- International Center for Tropical Agriculture, Km 17 Recta Cali-Palmira, CP 763537, A.A. 12 6713, Cali, Colombia
| | - Yunbi Xu
- Institute of Crop Science, Chinese Academy of Agricultural Sciences, Beijing 100081, China
- International Maize and Wheat Improvement Center (CIMMYT), El Batan Texcoco 56130, Mexico
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24
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Kholová J, Urban MO, Cock J, Arcos J, Arnaud E, Aytekin D, Azevedo V, Barnes AP, Ceccarelli S, Chavarriaga P, Cobb JN, Connor D, Cooper M, Craufurd P, Debouck D, Fungo R, Grando S, Hammer GL, Jara CE, Messina C, Mosquera G, Nchanji E, Ng EH, Prager S, Sankaran S, Selvaraj M, Tardieu F, Thornton P, Valdes-Gutierrez SP, van Etten J, Wenzl P, Xu Y. In pursuit of a better world: crop improvement and the CGIAR. JOURNAL OF EXPERIMENTAL BOTANY 2021. [PMID: 34021317 DOI: 10.5281/zenodo.4638248] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Subscribe] [Scholar Register] [Indexed: 05/11/2023]
Abstract
The CGIAR crop improvement (CI) programs, unlike commercial CI programs, which are mainly geared to profit though meeting farmers' needs, are charged with meeting multiple objectives with target populations that include both farmers and the community at large. We compiled the opinions from >30 experts in the private and public sector on key strategies, methodologies, and activities that could the help CGIAR meet the challenges of providing farmers with improved varieties while simultaneously meeting the goals of: (i) nutrition, health, and food security; (ii) poverty reduction, livelihoods, and jobs; (iii) gender equality, youth, and inclusion; (iv) climate adaptation and mitigation; and (v) environmental health and biodiversity. We review the crop improvement processes starting with crop choice, moving through to breeding objectives, production of potential new varieties, selection, and finally adoption by farmers. The importance of multidisciplinary teams working towards common objectives is stressed as a key factor to success. The role of the distinct disciplines, actors, and their interactions throughout the process from crop choice through to adoption by farmers is discussed and illustrated.
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Affiliation(s)
- Jana Kholová
- International Crops Research Institute for the Semi-Arid Tropics, Hyderabad-502324, India
| | - Milan Oldřich Urban
- International Center for Tropical Agriculture, Km 17 Recta Cali-Palmira, CP 763537, A.A. 12 6713, Cali, Colombia
| | - James Cock
- International Center for Tropical Agriculture, Km 17 Recta Cali-Palmira, CP 763537, A.A. 12 6713, Cali, Colombia
| | - Jairo Arcos
- HarvestPlus, Km 17 Recta Cali-Palmira, CP 763537, A.A. 12 6713, Cali, Colombia
| | - Elizabeth Arnaud
- Bioversity International, Parc scientifique Agropolis II, 1990 Boulevard de la Lironde, 34397 Montpellier, France
| | | | - Vania Azevedo
- International Crops Research Institute for the Semi-Arid Tropics, Hyderabad-502324, India
| | | | | | - Paul Chavarriaga
- International Center for Tropical Agriculture, Km 17 Recta Cali-Palmira, CP 763537, A.A. 12 6713, Cali, Colombia
| | | | - David Connor
- Department of Agriculture and Food, The University of Melbourne, Australia
| | - Mark Cooper
- Queensland Alliance for Agriculture and Food Innovation, The University of Queensland, Brisbane, Qld 4072, Australia
| | - Peter Craufurd
- CIMMYT, 1st floor, National Plant Breeding and Genetics Centre, NARC Research Station, Khumaltor, Lalitpur, PO Box 5186, Kathmandu, Nepal
| | - Daniel Debouck
- International Center for Tropical Agriculture, Km 17 Recta Cali-Palmira, CP 763537, A.A. 12 6713, Cali, Colombia
| | - Robert Fungo
- International Center for Tropical Agriculture, PO Box 6247, Kampala, Uganda
- School of Food Technology, Nutrition & Bio-Engineering, Makerere University, PO Box, 7062, Kampala, Uganda
| | - Stefania Grando
- Independent Consultant, Corso Mazzini 256, 63100 Ascoli Piceno, Italy
| | - Graeme L Hammer
- Queensland Alliance for Agriculture and Food Innovation, The University of Queensland, Brisbane, Qld 4072, Australia
| | - Carlos E Jara
- Independent Consultant, Hacienda Real, Torre 2, CP 760033, Cali, Colombia
| | - Charlie Messina
- Corteva Agriscience, 7200 62nd Avenue, Johnston, IA 50131, USA
| | - Gloria Mosquera
- International Center for Tropical Agriculture, Km 17 Recta Cali-Palmira, CP 763537, A.A. 12 6713, Cali, Colombia
| | - Eileen Nchanji
- International Center for Tropical Agriculture, African hub, Box 823-00621, Nairobi, Kenya
| | - Eng Hwa Ng
- International Maize and Wheat Improvement Center (CIMMYT); México-Veracruz, El Batán Km. 45, 56237, Mexico
| | - Steven Prager
- International Center for Tropical Agriculture, Km 17 Recta Cali-Palmira, CP 763537, A.A. 12 6713, Cali, Colombia
| | - Sindhujan Sankaran
- Department of Biological Systems Engineering, Washington State University, 1935 E. Grimes Way, PO Box 646120, Pullman, WA 99164, USA
| | - Michael Selvaraj
- International Center for Tropical Agriculture, Km 17 Recta Cali-Palmira, CP 763537, A.A. 12 6713, Cali, Colombia
| | - François Tardieu
- INRA Centre de Montpellier, Montpellier, Languedoc-Roussillon, France
| | - Philip Thornton
- CGIAR Research Program on Climate Change, Agriculture 37 and Food Security (CCAFS), International Livestock Research Institute (ILRI), Nairobi, Kenya
| | - Sandra P Valdes-Gutierrez
- International Center for Tropical Agriculture, Km 17 Recta Cali-Palmira, CP 763537, A.A. 12 6713, Cali, Colombia
| | - Jacob van Etten
- Bioversity International, Parc scientifique Agropolis II, 1990 Boulevard de la Lironde, 34397 Montpellier, France
| | - Peter Wenzl
- International Center for Tropical Agriculture, Km 17 Recta Cali-Palmira, CP 763537, A.A. 12 6713, Cali, Colombia
| | - Yunbi Xu
- Institute of Crop Science, Chinese Academy of Agricultural Sciences, Beijing 100081, China
- International Maize and Wheat Improvement Center (CIMMYT), El Batan Texcoco 56130, Mexico
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25
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Pandey AK, Jiang L, Moshelion M, Gosa SC, Sun T, Lin Q, Wu R, Xu P. Functional physiological phenotyping with functional mapping: A general framework to bridge the phenotype-genotype gap in plant physiology. iScience 2021; 24:102846. [PMID: 34381971 PMCID: PMC8333144 DOI: 10.1016/j.isci.2021.102846] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2020] [Revised: 05/27/2021] [Accepted: 07/09/2021] [Indexed: 11/19/2022] Open
Abstract
The recent years have witnessed the emergence of high-throughput phenotyping techniques. In particular, these techniques can characterize a comprehensive landscape of physiological traits of plants responding to dynamic changes in the environment. These innovations, along with the next-generation genomic technologies, have brought plant science into the big-data era. However, a general framework that links multifaceted physiological traits to DNA variants is still lacking. Here, we developed a general framework that integrates functional physiological phenotyping (FPP) with functional mapping (FM). This integration, implemented with high-dimensional statistical reasoning, can aid in our understanding of how genotype is translated toward phenotype. As a demonstration of method, we implemented the transpiration and soil-plant-atmosphere measurements of a tomato introgression line population into the FPP-FM framework, facilitating the identification of quantitative trait loci (QTLs) that mediate the spatiotemporal change of transpiration rate and the test of how these QTLs control, through their interaction networks, phenotypic plasticity under drought stress.
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Affiliation(s)
- Arun K. Pandey
- College of Life Sciences, China Jiliang University, Hangzhou 310018, China
| | - Libo Jiang
- Center for Computational Biology, College of Biological Sciences and Technology, Beijing Forestry University, Beijing 100080, China
| | - Menachem Moshelion
- The Robert H. Smith Institute of Plant Sciences and Genetics in Agriculture, The Robert H. Smith Faculty of Agriculture, Food and Environment, The Hebrew University of Jerusalem, Rehovot 76100, Israel
- Corresponding author
| | - Sanbon Chaka Gosa
- The Robert H. Smith Institute of Plant Sciences and Genetics in Agriculture, The Robert H. Smith Faculty of Agriculture, Food and Environment, The Hebrew University of Jerusalem, Rehovot 76100, Israel
| | - Ting Sun
- College of Life Sciences, China Jiliang University, Hangzhou 310018, China
| | - Qin Lin
- Biozeron Biotechnology Co., Ltd, Shanghai 201800, China
| | - Rongling Wu
- Center for Statistical Genetics, Departments of Public Health Sciences and Statistics, The Pennsylvania State University, Hershey, PA 17033, USA
- Corresponding author
| | - Pei Xu
- College of Life Sciences, China Jiliang University, Hangzhou 310018, China
- Corresponding author
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Development of a Raspberry Pi-Based Sensor System for Automated In-Field Monitoring to Support Crop Breeding Programs. INVENTIONS 2021. [DOI: 10.3390/inventions6020042] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
Sensor applications for plant phenotyping can advance and strengthen crop breeding programs. One of the powerful sensing options is the automated sensor system, which can be customized and applied for plant science research. The system can provide high spatial and temporal resolution data to delineate crop interaction with weather changes in a diverse environment. Such a system can be integrated with the internet to enable the internet of things (IoT)-based sensor system development for real-time crop monitoring and management. In this study, the Raspberry Pi-based sensor (imaging) system was fabricated and integrated with a microclimate sensor to evaluate crop growth in a spring wheat breeding trial for automated phenotyping applications. Such an in-field sensor system will increase the reproducibility of measurements and improve the selection efficiency by investigating dynamic crop responses as well as identifying key growth stages (e.g., heading), assisting in the development of high-performing crop varieties. In the low-cost system developed here-in, a Raspberry Pi computer and multiple cameras (RGB and multispectral) were the main components. The system was programmed to automatically capture and manage the crop image data at user-defined time points throughout the season. The acquired images were suitable for extracting quantifiable plant traits, and the images were automatically processed through a Python script (an open-source programming language) to extract vegetation indices, representing crop growth and overall health. Ongoing efforts are conducted towards integrating the sensor system for real-time data monitoring via the internet that will allow plant breeders to monitor multiple trials for timely crop management and decision making.
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Yadav OP, Gupta SK, Govindaraj M, Sharma R, Varshney RK, Srivastava RK, Rathore A, Mahala RS. Genetic Gains in Pearl Millet in India: Insights Into Historic Breeding Strategies and Future Perspective. FRONTIERS IN PLANT SCIENCE 2021; 12:645038. [PMID: 33859663 DOI: 10.3389/fpls.2021.64503] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Subscribe] [Scholar Register] [Received: 12/22/2020] [Accepted: 02/19/2021] [Indexed: 05/27/2023]
Abstract
Pearl millet (Pennisetum glaucum R. Br.) is an important staple and nutritious food crop in the semiarid and arid ecologies of South Asia (SA) and Sub-Saharan Africa (SSA). In view of climate change, depleting water resources, and widespread malnutrition, there is a need to accelerate the rate of genetic gains in pearl millet productivity. This review discusses past strategies and future approaches to accelerate genetic gains to meet future demand. Pearl millet breeding in India has historically evolved very comprehensively from open-pollinated varieties development to hybrid breeding. Availability of stable cytoplasmic male sterility system with adequate restorers and strategic use of genetic resources from India and SSA laid the strong foundation of hybrid breeding. Genetic and cytoplasmic diversification of hybrid parental lines, periodic replacement of hybrids, and breeding disease-resistant and stress-tolerant cultivars have been areas of very high priority. As a result, an annual yield increase of 4% has been realized in the last three decades. There is considerable scope to further accelerate the efforts on hybrid breeding for drought-prone areas in SA and SSA. Heterotic grouping of hybrid parental lines is essential to sustain long-term genetic gains. Time is now ripe for mainstreaming of the nutritional traits improvement in pearl millet breeding programs. New opportunities are emerging to improve the efficiency and precision of breeding. Development and application of high-throughput genomic tools, speed breeding, and precision phenotyping protocols need to be intensified to exploit a huge wealth of native genetic variation available in pearl millet to accelerate the genetic gains.
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Affiliation(s)
| | - S K Gupta
- International Crops Research Institute for the Semi-Arid Tropics (ICRISAT), Patancheru, India
| | - Mahalingam Govindaraj
- International Crops Research Institute for the Semi-Arid Tropics (ICRISAT), Patancheru, India
| | - Rajan Sharma
- International Crops Research Institute for the Semi-Arid Tropics (ICRISAT), Patancheru, India
| | - Rajeev K Varshney
- International Crops Research Institute for the Semi-Arid Tropics (ICRISAT), Patancheru, India
- State Agricultural Biotechnology Centre, Centre for Crop and Food Innovation, Food Futures Institute, Murdoch University, Murdoch, WA, Australia
| | - Rakesh K Srivastava
- International Crops Research Institute for the Semi-Arid Tropics (ICRISAT), Patancheru, India
| | - A Rathore
- International Crops Research Institute for the Semi-Arid Tropics (ICRISAT), Patancheru, India
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Lazarević B, Šatović Z, Nimac A, Vidak M, Gunjača J, Politeo O, Carović-Stanko K. Application of Phenotyping Methods in Detection of Drought and Salinity Stress in Basil ( Ocimum basilicum L.). FRONTIERS IN PLANT SCIENCE 2021; 12:629441. [PMID: 33679843 PMCID: PMC7929983 DOI: 10.3389/fpls.2021.629441] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/14/2020] [Accepted: 01/25/2021] [Indexed: 05/27/2023]
Abstract
Basil is one of the most widespread aromatic and medicinal plants, which is often grown in drought- and salinity-prone regions. Often co-occurrence of drought and salinity stresses in agroecosystems and similarities of symptoms which they cause on plants complicates the differentiation among them. Development of automated phenotyping techniques with integrative and simultaneous quantification of multiple morphological and physiological traits enables early detection and quantification of different stresses on a whole plant basis. In this study, we have used different phenotyping techniques including chlorophyll fluorescence imaging, multispectral imaging, and 3D multispectral scanning, aiming to quantify changes in basil phenotypic traits under early and prolonged drought and salinity stress and to determine traits which could differentiate among drought and salinity stressed basil plants. Ocimum basilicum "Genovese" was grown in a growth chamber under well-watered control [45-50% volumetric water content (VWC)], moderate salinity stress (100 mM NaCl), severe salinity stress (200 mM NaCl), moderate drought stress (25-30% VWC), and severe drought stress (15-20% VWC). Phenotypic traits were measured for 3 weeks in 7-day intervals. Automated phenotyping techniques were able to detect basil responses to early and prolonged salinity and drought stress. In addition, several phenotypic traits were able to differentiate among salinity and drought. At early stages, low anthocyanin index (ARI), chlorophyll index (CHI), and hue (HUE2 D ), and higher reflectance in red (R Red ), reflectance in green (R Green ), and leaf inclination (LINC) indicated drought stress. At later stress stages, maximum fluorescence (F m ), HUE2 D , normalized difference vegetation index (NDVI), and LINC contribute the most to the differentiation among drought and non-stressed as well as among drought and salinity stressed plants. ARI and electron transport rate (ETR) were best for differentiation of salinity stressed plants from non-stressed plants both at early and prolonged stress.
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Affiliation(s)
- Boris Lazarević
- Department of Plant Nutrition, Faculty of Agriculture, University of Zagreb, Zagreb, Croatia
- Centre of Excellence for Biodiversity and Molecular Plant Breeding (CroP-BioDiv), Faculty of Agriculture, University of Zagreb, Zagreb, Croatia
| | - Zlatko Šatović
- Centre of Excellence for Biodiversity and Molecular Plant Breeding (CroP-BioDiv), Faculty of Agriculture, University of Zagreb, Zagreb, Croatia
- Department of Seed Science and Technology, Faculty of Agriculture, University of Zagreb, Zagreb, Croatia
| | - Ana Nimac
- Centre of Excellence for Biodiversity and Molecular Plant Breeding (CroP-BioDiv), Faculty of Agriculture, University of Zagreb, Zagreb, Croatia
| | - Monika Vidak
- Centre of Excellence for Biodiversity and Molecular Plant Breeding (CroP-BioDiv), Faculty of Agriculture, University of Zagreb, Zagreb, Croatia
| | - Jerko Gunjača
- Centre of Excellence for Biodiversity and Molecular Plant Breeding (CroP-BioDiv), Faculty of Agriculture, University of Zagreb, Zagreb, Croatia
- Department of Plant Breeding, Genetics and Biometrics, Faculty of Agriculture, University of Zagreb, Zagreb, Croatia
| | - Olivera Politeo
- Department of Biochemistry, Faculty of Chemistry and Technology, University of Split, Split, Croatia
| | - Klaudija Carović-Stanko
- Centre of Excellence for Biodiversity and Molecular Plant Breeding (CroP-BioDiv), Faculty of Agriculture, University of Zagreb, Zagreb, Croatia
- Department of Seed Science and Technology, Faculty of Agriculture, University of Zagreb, Zagreb, Croatia
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Li D, Quan C, Song Z, Li X, Yu G, Li C, Muhammad A. High-Throughput Plant Phenotyping Platform (HT3P) as a Novel Tool for Estimating Agronomic Traits From the Lab to the Field. Front Bioeng Biotechnol 2021; 8:623705. [PMID: 33520974 PMCID: PMC7838587 DOI: 10.3389/fbioe.2020.623705] [Citation(s) in RCA: 25] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2020] [Accepted: 12/15/2020] [Indexed: 11/13/2022] Open
Abstract
Food scarcity, population growth, and global climate change have propelled crop yield growth driven by high-throughput phenotyping into the era of big data. However, access to large-scale phenotypic data has now become a critical barrier that phenomics urgently must overcome. Fortunately, the high-throughput plant phenotyping platform (HT3P), employing advanced sensors and data collection systems, can take full advantage of non-destructive and high-throughput methods to monitor, quantify, and evaluate specific phenotypes for large-scale agricultural experiments, and it can effectively perform phenotypic tasks that traditional phenotyping could not do. In this way, HT3Ps are novel and powerful tools, for which various commercial, customized, and even self-developed ones have been recently introduced in rising numbers. Here, we review these HT3Ps in nearly 7 years from greenhouses and growth chambers to the field, and from ground-based proximal phenotyping to aerial large-scale remote sensing. Platform configurations, novelties, operating modes, current developments, as well the strengths and weaknesses of diverse types of HT3Ps are thoroughly and clearly described. Then, miscellaneous combinations of HT3Ps for comparative validation and comprehensive analysis are systematically present, for the first time. Finally, we consider current phenotypic challenges and provide fresh perspectives on future development trends of HT3Ps. This review aims to provide ideas, thoughts, and insights for the optimal selection, exploitation, and utilization of HT3Ps, and thereby pave the way to break through current phenotyping bottlenecks in botany.
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Affiliation(s)
- Daoliang Li
- National Innovation Center for Digital Fishery, China Agricultural University, Beijing, China
- Beijing Engineering and Technology Research Centre for Internet of Things in Agriculture, China Agricultural University, Beijing, China
- China-EU Center for Information and Communication Technologies in Agriculture, China Agriculture University, Beijing, China
- Key Laboratory of Agriculture Information Acquisition Technology, Ministry of Agriculture, China Agricultural University, Beijing, China
- College of Information and Electrical Engineering, China Agricultural University, Beijing, China
| | - Chaoqun Quan
- National Innovation Center for Digital Fishery, China Agricultural University, Beijing, China
- Beijing Engineering and Technology Research Centre for Internet of Things in Agriculture, China Agricultural University, Beijing, China
- China-EU Center for Information and Communication Technologies in Agriculture, China Agriculture University, Beijing, China
- Key Laboratory of Agriculture Information Acquisition Technology, Ministry of Agriculture, China Agricultural University, Beijing, China
- College of Information and Electrical Engineering, China Agricultural University, Beijing, China
| | - Zhaoyang Song
- National Innovation Center for Digital Fishery, China Agricultural University, Beijing, China
- Beijing Engineering and Technology Research Centre for Internet of Things in Agriculture, China Agricultural University, Beijing, China
- China-EU Center for Information and Communication Technologies in Agriculture, China Agriculture University, Beijing, China
- Key Laboratory of Agriculture Information Acquisition Technology, Ministry of Agriculture, China Agricultural University, Beijing, China
- College of Information and Electrical Engineering, China Agricultural University, Beijing, China
| | - Xiang Li
- Department of Psychology, College of Education, Hubei University, Wuhan, China
| | - Guanghui Yu
- National Innovation Center for Digital Fishery, China Agricultural University, Beijing, China
- Beijing Engineering and Technology Research Centre for Internet of Things in Agriculture, China Agricultural University, Beijing, China
- China-EU Center for Information and Communication Technologies in Agriculture, China Agriculture University, Beijing, China
- Key Laboratory of Agriculture Information Acquisition Technology, Ministry of Agriculture, China Agricultural University, Beijing, China
- College of Information and Electrical Engineering, China Agricultural University, Beijing, China
| | - Cheng Li
- National Innovation Center for Digital Fishery, China Agricultural University, Beijing, China
- Beijing Engineering and Technology Research Centre for Internet of Things in Agriculture, China Agricultural University, Beijing, China
- China-EU Center for Information and Communication Technologies in Agriculture, China Agriculture University, Beijing, China
- Key Laboratory of Agriculture Information Acquisition Technology, Ministry of Agriculture, China Agricultural University, Beijing, China
- College of Information and Electrical Engineering, China Agricultural University, Beijing, China
| | - Akhter Muhammad
- National Innovation Center for Digital Fishery, China Agricultural University, Beijing, China
- College of Information and Electrical Engineering, China Agricultural University, Beijing, China
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Yadav OP, Gupta SK, Govindaraj M, Sharma R, Varshney RK, Srivastava RK, Rathore A, Mahala RS. Genetic Gains in Pearl Millet in India: Insights Into Historic Breeding Strategies and Future Perspective. FRONTIERS IN PLANT SCIENCE 2021; 12:645038. [PMID: 33859663 PMCID: PMC8042313 DOI: 10.3389/fpls.2021.645038] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/22/2020] [Accepted: 02/19/2021] [Indexed: 05/09/2023]
Abstract
Pearl millet (Pennisetum glaucum R. Br.) is an important staple and nutritious food crop in the semiarid and arid ecologies of South Asia (SA) and Sub-Saharan Africa (SSA). In view of climate change, depleting water resources, and widespread malnutrition, there is a need to accelerate the rate of genetic gains in pearl millet productivity. This review discusses past strategies and future approaches to accelerate genetic gains to meet future demand. Pearl millet breeding in India has historically evolved very comprehensively from open-pollinated varieties development to hybrid breeding. Availability of stable cytoplasmic male sterility system with adequate restorers and strategic use of genetic resources from India and SSA laid the strong foundation of hybrid breeding. Genetic and cytoplasmic diversification of hybrid parental lines, periodic replacement of hybrids, and breeding disease-resistant and stress-tolerant cultivars have been areas of very high priority. As a result, an annual yield increase of 4% has been realized in the last three decades. There is considerable scope to further accelerate the efforts on hybrid breeding for drought-prone areas in SA and SSA. Heterotic grouping of hybrid parental lines is essential to sustain long-term genetic gains. Time is now ripe for mainstreaming of the nutritional traits improvement in pearl millet breeding programs. New opportunities are emerging to improve the efficiency and precision of breeding. Development and application of high-throughput genomic tools, speed breeding, and precision phenotyping protocols need to be intensified to exploit a huge wealth of native genetic variation available in pearl millet to accelerate the genetic gains.
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Affiliation(s)
- Om Parkash Yadav
- ICAR-Central Arid Zone Research Institute, Jodhpur, India
- *Correspondence: Om Parkash Yadav
| | - S. K. Gupta
- International Crops Research Institute for the Semi-Arid Tropics (ICRISAT), Patancheru, India
| | - Mahalingam Govindaraj
- International Crops Research Institute for the Semi-Arid Tropics (ICRISAT), Patancheru, India
| | - Rajan Sharma
- International Crops Research Institute for the Semi-Arid Tropics (ICRISAT), Patancheru, India
| | - Rajeev K. Varshney
- International Crops Research Institute for the Semi-Arid Tropics (ICRISAT), Patancheru, India
- State Agricultural Biotechnology Centre, Centre for Crop and Food Innovation, Food Futures Institute, Murdoch University, Murdoch, WA, Australia
| | - Rakesh K. Srivastava
- International Crops Research Institute for the Semi-Arid Tropics (ICRISAT), Patancheru, India
| | - A. Rathore
- International Crops Research Institute for the Semi-Arid Tropics (ICRISAT), Patancheru, India
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Kar S, Garin V, Kholová J, Vadez V, Durbha SS, Tanaka R, Iwata H, Urban MO, Adinarayana J. SpaTemHTP: A Data Analysis Pipeline for Efficient Processing and Utilization of Temporal High-Throughput Phenotyping Data. FRONTIERS IN PLANT SCIENCE 2020; 11:552509. [PMID: 33329623 PMCID: PMC7714717 DOI: 10.3389/fpls.2020.552509] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 04/16/2020] [Accepted: 10/19/2020] [Indexed: 06/12/2023]
Abstract
The rapid development of phenotyping technologies over the last years gave the opportunity to study plant development over time. The treatment of the massive amount of data collected by high-throughput phenotyping (HTP) platforms is however an important challenge for the plant science community. An important issue is to accurately estimate, over time, the genotypic component of plant phenotype. In outdoor and field-based HTP platforms, phenotype measurements can be substantially affected by data-generation inaccuracies or failures, leading to erroneous or missing data. To solve that problem, we developed an analytical pipeline composed of three modules: detection of outliers, imputation of missing values, and mixed-model genotype adjusted means computation with spatial adjustment. The pipeline was tested on three different traits (3D leaf area, projected leaf area, and plant height), in two crops (chickpea, sorghum), measured during two seasons. Using real-data analyses and simulations, we showed that the sequential application of the three pipeline steps was particularly useful to estimate smooth genotype growth curves from raw data containing a large amount of noise, a situation that is potentially frequent in data generated on outdoor HTP platforms. The procedure we propose can handle up to 50% of missing values. It is also robust to data contamination rates between 20 and 30% of the data. The pipeline was further extended to model the genotype time series data. A change-point analysis allowed the determination of growth phases and the optimal timing where genotypic differences were the largest. The estimated genotypic values were used to cluster the genotypes during the optimal growth phase. Through a two-way analysis of variance (ANOVA), clusters were found to be consistently defined throughout the growth duration. Therefore, we could show, on a wide range of scenarios, that the pipeline facilitated efficient extraction of useful information from outdoor HTP platform data. High-quality plant growth time series data is also provided to support breeding decisions. The R code of the pipeline is available at https://github.com/ICRISAT-GEMS/SpaTemHTP.
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Affiliation(s)
- Soumyashree Kar
- Centre of Studies in Resources Engineering, Indian Institute of Technology Bombay, Mumbai, India
| | - Vincent Garin
- Crop Physiology, International Crop Research Institute for Semi-Arid Tropics (ICRISAT), Hyderabad, India
| | - Jana Kholová
- Crop Physiology, International Crop Research Institute for Semi-Arid Tropics (ICRISAT), Hyderabad, India
| | - Vincent Vadez
- Crop Physiology, International Crop Research Institute for Semi-Arid Tropics (ICRISAT), Hyderabad, India
- Institut de Recherche pour le Développement (IRD) – Université de Montpellier – UMR DIADE, Montpellier, France
| | - Surya S. Durbha
- Centre of Studies in Resources Engineering, Indian Institute of Technology Bombay, Mumbai, India
| | - Ryokei Tanaka
- Laboratory of Biometrics and Bioinformatics, University of Tokyo, Tokyo, Japan
| | - Hiroyoshi Iwata
- Laboratory of Biometrics and Bioinformatics, University of Tokyo, Tokyo, Japan
| | - Milan O. Urban
- Bean Physiology - Agrobiodiversity, Alliance of Bioversity International and CIAT, Cali, Colombia
| | - J. Adinarayana
- Centre of Studies in Resources Engineering, Indian Institute of Technology Bombay, Mumbai, India
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Kar S, Tanaka R, Korbu LB, Kholová J, Iwata H, Durbha SS, Adinarayana J, Vadez V. Automated discretization of 'transpiration restriction to increasing VPD' features from outdoors high-throughput phenotyping data. PLANT METHODS 2020; 16:140. [PMID: 33072176 PMCID: PMC7565372 DOI: 10.1186/s13007-020-00680-8] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/31/2020] [Accepted: 10/05/2020] [Indexed: 05/24/2023]
Abstract
BACKGROUND Restricting transpiration under high vapor pressure deficit (VPD) is a promising water-saving trait for drought adaptation. However, it is often measured under controlled conditions and at very low throughput, unsuitable for breeding. A few high-throughput phenotyping (HTP) studies exist, and have considered only maximum transpiration rate in analyzing genotypic differences in this trait. Further, no study has precisely identified the VPD breakpoints where genotypes restrict transpiration under natural conditions. Therefore, outdoors HTP data (15 min frequency) of a chickpea population were used to automate the generation of smooth transpiration profiles, extract informative features of the transpiration response to VPD for optimal genotypic discretization, identify VPD breakpoints, and compare genotypes. RESULTS Fifteen biologically relevant features were extracted from the transpiration rate profiles derived from load cells data. Genotypes were clustered (C1, C2, C3) and 6 most important features (with heritability > 0.5) were selected using unsupervised Random Forest. All the wild relatives were found in C1, while C2 and C3 mostly comprised high TE and low TE lines, respectively. Assessment of the distinct p-value groups within each selected feature revealed highest genotypic variation for the feature representing transpiration response to high VPD condition. Sensitivity analysis on a multi-output neural network model (with R of 0.931, 0.944, 0.953 for C1, C2, C3, respectively) found C1 with the highest water saving ability, that restricted transpiration at relatively low VPD levels, 56% (i.e. 3.52 kPa) or 62% (i.e. 3.90 kPa), depending whether the influence of other environmental variables was minimum or maximum. Also, VPD appeared to have the most striking influence on the transpiration response independently of other environment variable, whereas light, temperature, and relative humidity alone had little/no effect. CONCLUSION Through this study, we present a novel approach to identifying genotypes with drought-tolerance potential, which overcomes the challenges in HTP of the water-saving trait. The six selected features served as proxy phenotypes for reliable genotypic discretization. The wild chickpeas were found to limit water-loss faster than the water-profligate cultivated ones. Such an analytic approach can be directly used for prescriptive breeding applications, applied to other traits, and help expedite maximized information extraction from HTP data.
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Affiliation(s)
- Soumyashree Kar
- Centre of Studies in Resources Engineering, Indian Institute of Technology Bombay, Mumbai, India 400076
| | - Ryokei Tanaka
- Laboratory of Biometrics and Bioinformatics, University of Tokyo, Tokyo, Japan
| | - Lijalem Balcha Korbu
- Debre Zeit Research Center, Ethiopian Institute of Agricultural Research (EIAR), Debre Zeit, Ethiopia
| | - Jana Kholová
- International Crop Research Institute for Semi-Arid Tropics, Hyderabad, India 502319
| | - Hiroyoshi Iwata
- Laboratory of Biometrics and Bioinformatics, University of Tokyo, Tokyo, Japan
| | - Surya S. Durbha
- Centre of Studies in Resources Engineering, Indian Institute of Technology Bombay, Mumbai, India 400076
| | - J. Adinarayana
- Centre of Studies in Resources Engineering, Indian Institute of Technology Bombay, Mumbai, India 400076
| | - Vincent Vadez
- International Crop Research Institute for Semi-Arid Tropics, Hyderabad, India 502319
- Institut de Recherche Pour Le Développement (IRD), Université de Montpellier—UMR DIADE, 911 Avenue Agropolis, BP 64501, 34394 Montpellier cedex 5, France
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Korwin Krukowski P, Ellenberger J, Röhlen-Schmittgen S, Schubert A, Cardinale F. Phenotyping in Arabidopsis and Crops-Are We Addressing the Same Traits? A Case Study in Tomato. Genes (Basel) 2020; 11:E1011. [PMID: 32867311 PMCID: PMC7564427 DOI: 10.3390/genes11091011] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/05/2020] [Revised: 08/21/2020] [Accepted: 08/24/2020] [Indexed: 11/18/2022] Open
Abstract
The convenient model Arabidopsis thaliana has allowed tremendous advances in plant genetics and physiology, in spite of only being a weed. It has also unveiled the main molecular networks governing, among others, abiotic stress responses. Through the use of the latest genomic tools, Arabidopsis research is nowadays being translated to agronomically interesting crop models such as tomato, but at a lagging pace. Knowledge transfer has been hindered by invariable differences in plant architecture and behaviour, as well as the divergent direct objectives of research in Arabidopsis versus crops compromise transferability. In this sense, phenotype translation is still a very complex matter. Here, we point out the challenges of "translational phenotyping" in the case study of drought stress phenotyping in Arabidopsis and tomato. After briefly defining and describing drought stress and survival strategies, we compare drought stress protocols and phenotyping techniques most commonly used in the two species, and discuss their potential to gain insights, which are truly transferable between species. This review is intended to be a starting point for discussion about translational phenotyping approaches among plant scientists, and provides a useful compendium of methods and techniques used in modern phenotyping for this specific plant pair as a case study.
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Affiliation(s)
- Paolo Korwin Krukowski
- Plant Stress Lab, Department of Agriculture, Forestry and Food Sciences DISAFA-Turin University, 10095 Grugliasco, Italy; (A.S.); (F.C.)
| | - Jan Ellenberger
- INRES Horticultural Sciences, University of Bonn, 53121 Bonn, Germany;
| | | | - Andrea Schubert
- Plant Stress Lab, Department of Agriculture, Forestry and Food Sciences DISAFA-Turin University, 10095 Grugliasco, Italy; (A.S.); (F.C.)
| | - Francesca Cardinale
- Plant Stress Lab, Department of Agriculture, Forestry and Food Sciences DISAFA-Turin University, 10095 Grugliasco, Italy; (A.S.); (F.C.)
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Banerjee BP, Joshi S, Thoday-Kennedy E, Pasam RK, Tibbits J, Hayden M, Spangenberg G, Kant S. High-throughput phenotyping using digital and hyperspectral imaging-derived biomarkers for genotypic nitrogen response. JOURNAL OF EXPERIMENTAL BOTANY 2020; 71:4604-4615. [PMID: 32185382 PMCID: PMC7382386 DOI: 10.1093/jxb/eraa143] [Citation(s) in RCA: 25] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/29/2019] [Accepted: 03/17/2020] [Indexed: 05/18/2023]
Abstract
The development of crop varieties with higher nitrogen use efficiency is crucial for sustainable crop production. Combining high-throughput genotyping and phenotyping will expedite the discovery of novel alleles for breeding crop varieties with higher nitrogen use efficiency. Digital and hyperspectral imaging techniques can efficiently evaluate the growth, biophysical, and biochemical performance of plant populations by quantifying canopy reflectance response. Here, these techniques were used to derive automated phenotyping of indicator biomarkers, biomass and chlorophyll levels, corresponding to different nitrogen levels. A detailed description of digital and hyperspectral imaging and the associated challenges and required considerations are provided, with application to delineate the nitrogen response in wheat. Computational approaches for spectrum calibration and rectification, plant area detection, and derivation of vegetation index analysis are presented. We developed a novel vegetation index with higher precision to estimate chlorophyll levels, underpinned by an image-processing algorithm that effectively removed background spectra. Digital shoot biomass and growth parameters were derived, enabling the efficient phenotyping of wheat plants at the vegetative stage, obviating the need for phenotyping until maturity. Overall, our results suggest value in the integration of high-throughput digital and spectral phenomics for rapid screening of large wheat populations for nitrogen response.
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Affiliation(s)
- Bikram P Banerjee
- Agriculture Victoria, Grains Innovation Park, Horsham, VIC, Australia
| | - Sameer Joshi
- Agriculture Victoria, Grains Innovation Park, Horsham, VIC, Australia
| | | | - Raj K Pasam
- Agriculture Victoria, AgriBio, Centre for AgriBioscience, Bundoora, VIC, Australia
| | - Josquin Tibbits
- Agriculture Victoria, AgriBio, Centre for AgriBioscience, Bundoora, VIC, Australia
| | - Matthew Hayden
- Agriculture Victoria, AgriBio, Centre for AgriBioscience, Bundoora, VIC, Australia
- School of Applied Systems Biology, La Trobe University, Bundoora, VIC, Australia
| | - German Spangenberg
- Agriculture Victoria, AgriBio, Centre for AgriBioscience, Bundoora, VIC, Australia
- School of Applied Systems Biology, La Trobe University, Bundoora, VIC, Australia
| | - Surya Kant
- Agriculture Victoria, Grains Innovation Park, Horsham, VIC, Australia
- Centre for Agricultural Innovation, School of Agriculture and Food, Faculty of Veterinary and Agricultural Sciences, The University of Melbourne, Victoria, Australia
- Correspondence:
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Vijayaraghavareddy P, Vemanna RS, Yin X, Struik PC, Makarla U, Sreeman S. Acquired Traits Contribute More to Drought Tolerance in Wheat Than in Rice. PLANT PHENOMICS (WASHINGTON, D.C.) 2020; 2020:5905371. [PMID: 33313560 PMCID: PMC7706322 DOI: 10.34133/2020/5905371] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/11/2019] [Accepted: 05/04/2020] [Indexed: 05/27/2023]
Abstract
Drought tolerance is governed by constitutive and acquired traits. Combining them has relevance for sustaining crop productivity under drought. Mild levels of stress induce specific mechanisms that protect metabolism when stress becomes severe. Here, we report a comparative assessment of "acquired drought tolerance (ADT)" traits in two rice cultivars, IR64 (drought susceptible) and Apo (tolerant), and a drought-tolerant wheat cultivar, Weebill. Young seedlings were exposed to progressive concentrations of methyl viologen (MV), a stress inducer, before transferring to a severe concentration. "Induced" seedlings showed higher tolerance and recovery growth than seedlings exposed directly to severe stress. A novel phenomic platform with an automated irrigation system was used for precisely imposing soil moisture stress to capture ADT traits during the vegetative stage. Gradual progression of drought was achieved through a software-controlled automated irrigation facility. This facility allowed the maintenance of the same level of soil moisture irrespective of differences in transpiration, and hence, this platform provided the most appropriate method to assess ADT traits. Total biomass decreased more in IR64 than in Apo. The wheat cultivar showed lower levels of damage and higher recovery growth even compared to Apo. Expression of ROS-scavenging enzymes and drought-responsive genes was significantly higher in Apo than in IR64, but differences were only marginal between Apo and Weebill. The wheat cultivar showed significantly higher stomatal conductance, carbon gain, and biomass than the rice cultivars, under drought. These differences in ADT traits between cultivars as well as between species can be utilised for improving drought tolerance in crop plants.
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Affiliation(s)
- Preethi Vijayaraghavareddy
- Department of Crop Physiology, University of Agricultural Sciences, Bengaluru, India
- Centre for Crop Systems Analysis, Department of Plant Sciences, Wageningen University & Research, PO Box 430, 6700 AK Wageningen, Netherlands
| | - Ramu S. Vemanna
- Regional Centre for Biotechnology, Faridabad, Haryana, India
| | - Xinyou Yin
- Centre for Crop Systems Analysis, Department of Plant Sciences, Wageningen University & Research, PO Box 430, 6700 AK Wageningen, Netherlands
| | - Paul C. Struik
- Centre for Crop Systems Analysis, Department of Plant Sciences, Wageningen University & Research, PO Box 430, 6700 AK Wageningen, Netherlands
| | - Udayakumar Makarla
- Department of Crop Physiology, University of Agricultural Sciences, Bengaluru, India
| | - Sheshshayee Sreeman
- Department of Crop Physiology, University of Agricultural Sciences, Bengaluru, India
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Stahl A, Wittkop B, Snowdon RJ. High-resolution digital phenotyping of water uptake and transpiration efficiency. TRENDS IN PLANT SCIENCE 2020; 25:429-433. [PMID: 32304656 DOI: 10.1016/j.tplants.2020.02.001] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/16/2019] [Revised: 01/28/2020] [Accepted: 02/04/2020] [Indexed: 05/16/2023]
Abstract
Despite innovations in phenotyping, dissecting impacts of water uptake, transpiration efficiency and harvest index on crop yield under defined drought stress scenarios remains challenging. Here, we highlight benefits of concepts enabling plant growth in extra-large containers accompanied by continuous tracking of transpiration, nondestructive plant growth monitoring, and subsequent yield evaluation.
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Affiliation(s)
- Andreas Stahl
- Department of Plant Breeding, IFZ Research Centre for Biosystems, Land Use and Nutrition, Justus Liebig University Giessen, Heinrich Buff-Ring 26, 35392 Giessen, Germany. @agrar.uni-giessen.de
| | - Benjamin Wittkop
- Department of Plant Breeding, IFZ Research Centre for Biosystems, Land Use and Nutrition, Justus Liebig University Giessen, Heinrich Buff-Ring 26, 35392 Giessen, Germany
| | - Rod J Snowdon
- Department of Plant Breeding, IFZ Research Centre for Biosystems, Land Use and Nutrition, Justus Liebig University Giessen, Heinrich Buff-Ring 26, 35392 Giessen, Germany
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Yang W, Feng H, Zhang X, Zhang J, Doonan JH, Batchelor WD, Xiong L, Yan J. Crop Phenomics and High-Throughput Phenotyping: Past Decades, Current Challenges, and Future Perspectives. MOLECULAR PLANT 2020; 13:187-214. [PMID: 31981735 DOI: 10.1016/j.molp.2020.01.008] [Citation(s) in RCA: 232] [Impact Index Per Article: 58.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/11/2019] [Revised: 01/06/2020] [Accepted: 01/10/2020] [Indexed: 05/18/2023]
Abstract
Since whole-genome sequencing of many crops has been achieved, crop functional genomics studies have stepped into the big-data and high-throughput era. However, acquisition of large-scale phenotypic data has become one of the major bottlenecks hindering crop breeding and functional genomics studies. Nevertheless, recent technological advances provide us potential solutions to relieve this bottleneck and to explore advanced methods for large-scale phenotyping data acquisition and processing in the coming years. In this article, we review the major progress on high-throughput phenotyping in controlled environments and field conditions as well as its use for post-harvest yield and quality assessment in the past decades. We then discuss the latest multi-omics research combining high-throughput phenotyping with genetic studies. Finally, we propose some conceptual challenges and provide our perspectives on how to bridge the phenotype-genotype gap. It is no doubt that accurate high-throughput phenotyping will accelerate plant genetic improvements and promote the next green revolution in crop breeding.
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Affiliation(s)
- Wanneng Yang
- National Key Laboratory of Crop Genetic Improvement and National Center of Plant Gene Research, Huazhong Agricultural University, Wuhan 430070, P.R. China.
| | - Hui Feng
- National Key Laboratory of Crop Genetic Improvement and National Center of Plant Gene Research, Huazhong Agricultural University, Wuhan 430070, P.R. China
| | - Xuehai Zhang
- National Key Laboratory of Wheat and Maize Crops Science/College of Agronomy, Henan Agricultural University, Zhengzhou 450002, P.R. China
| | - Jian Zhang
- National Key Laboratory of Crop Genetic Improvement and National Center of Plant Gene Research, Huazhong Agricultural University, Wuhan 430070, P.R. China
| | - John H Doonan
- The National Plant Phenomics Centre, Institute of Biological, Environmental and Rural Sciences, Aberystwyth University, Aberystwyth, UK
| | | | - Lizhong Xiong
- National Key Laboratory of Crop Genetic Improvement and National Center of Plant Gene Research, Huazhong Agricultural University, Wuhan 430070, P.R. China
| | - Jianbing Yan
- National Key Laboratory of Crop Genetic Improvement and National Center of Plant Gene Research, Huazhong Agricultural University, Wuhan 430070, P.R. China
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Martignago D, Rico-Medina A, Blasco-Escámez D, Fontanet-Manzaneque JB, Caño-Delgado AI. Drought Resistance by Engineering Plant Tissue-Specific Responses. FRONTIERS IN PLANT SCIENCE 2020; 10:1676. [PMID: 32038670 PMCID: PMC6987726 DOI: 10.3389/fpls.2019.01676] [Citation(s) in RCA: 49] [Impact Index Per Article: 12.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/08/2019] [Accepted: 11/28/2019] [Indexed: 05/18/2023]
Abstract
Drought is the primary cause of agricultural loss globally, and represents a major threat to food security. Currently, plant biotechnology stands as one of the most promising fields when it comes to developing crops that are able to produce high yields in water-limited conditions. From studies of Arabidopsis thaliana whole plants, the main response mechanisms to drought stress have been uncovered, and multiple drought resistance genes have already been engineered into crops. So far, most plants with enhanced drought resistance have displayed reduced crop yield, meaning that there is still a need to search for novel approaches that can uncouple drought resistance from plant growth. Our laboratory has recently shown that the receptors of brassinosteroid (BR) hormones use tissue-specific pathways to mediate different developmental responses during root growth. In Arabidopsis, we found that increasing BR receptors in the vascular plant tissues confers resistance to drought without penalizing growth, opening up an exceptional opportunity to investigate the mechanisms that confer drought resistance with cellular specificity in plants. In this review, we provide an overview of the most promising phenotypical drought traits that could be improved biotechnologically to obtain drought-tolerant cereals. In addition, we discuss how current genome editing technologies could help to identify and manipulate novel genes that might grant resistance to drought stress. In the upcoming years, we expect that sustainable solutions for enhancing crop production in water-limited environments will be identified through joint efforts.
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Affiliation(s)
| | | | | | | | - Ana I. Caño-Delgado
- Department of Molecular Genetics, Centre for Research in Agricultural Genomics (CRAG) CSIC-IRTA-UAB-UB, Barcelona, Spain
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Cousins OH, Garnett TP, Rasmussen A, Mooney SJ, Smernik RJ, Brien CJ, Cavagnaro TR. Variable water cycles have a greater impact on wheat growth and soil nitrogen response than constant watering. PLANT SCIENCE : AN INTERNATIONAL JOURNAL OF EXPERIMENTAL PLANT BIOLOGY 2020; 290:110146. [PMID: 31779906 DOI: 10.1016/j.plantsci.2019.05.009] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/25/2018] [Revised: 05/10/2019] [Accepted: 05/11/2019] [Indexed: 06/10/2023]
Abstract
Current climate change models project that water availability will become more erratic in the future. With soil nitrogen (N) supply coupled to water availability, it is important to understand the combined effects of variable water and N supply on food crop plants (above- and below-ground). Here we present a study that precisely controls soil moisture and compares stable soil moisture contents with a controlled wetting-drying cycle. Our aim was to identify how changes in soil moisture and N concentration affect shoot-root biomass, N acquisition in wheat, and soil N cycling. Using a novel gravimetric platform allowing fine-scale control of soil moisture dynamics, a 3 × 3 factorial experiment was conducted on wheat plants subjected to three rates of N application (0, 25 and 75 mg N/kg soil) and three soil moisture regimes (two uniform treatments: 23.5 and 13% gravimetric moisture content (herein referred to as Well-watered and Reduced water, respectively), and a Variable treatment which cycled between the two). Plant biomass, soil N and microbial biomass carbon were measured at three developmental stages: tillering (Harvest 1), flowering (Harvest 2), and early grain milk development (Harvest 3). Reduced water supply encouraged root growth when combined with medium and high N. Plant growth was more responsive to N than the water treatments imposed, with a 15-fold increase in biomass between the high and no added N treatment plants. Both uniform soil water treatments resulted in similar plant biomass, while the Variable water treatment resulted in less biomass overall, suggesting wheat prefers consistency whether at a Well-watered or Reduced water level. Plants did not respond well to variable soil moisture, highlighting the need to understand plant adaptation and biomass allocation with resource limitation. This is particularly relevant to developing irrigation practices, but also in the design of water availability experiments.
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Affiliation(s)
- Olivia H Cousins
- The Waite Research Institute and The School of Agriculture, Food and Wine, University of Adelaide, Waite Campus, PMB1, Glen Osmond, SA, 5064, Australia; School of Biosciences, University of Nottingham, Sutton Bonington, LE12 5RD, UK.
| | - Trevor P Garnett
- The Waite Research Institute and The School of Agriculture, Food and Wine, University of Adelaide, Waite Campus, PMB1, Glen Osmond, SA, 5064, Australia; The Plant Accelerator, University of Adelaide, Waite Campus, PMB1, Glen Osmond, SA, 5064, Australia
| | - Amanda Rasmussen
- School of Biosciences, University of Nottingham, Sutton Bonington, LE12 5RD, UK
| | - Sacha J Mooney
- School of Biosciences, University of Nottingham, Sutton Bonington, LE12 5RD, UK
| | - Ronald J Smernik
- The Waite Research Institute and The School of Agriculture, Food and Wine, University of Adelaide, Waite Campus, PMB1, Glen Osmond, SA, 5064, Australia
| | - Chris J Brien
- The Waite Research Institute and The School of Agriculture, Food and Wine, University of Adelaide, Waite Campus, PMB1, Glen Osmond, SA, 5064, Australia; The Plant Accelerator, University of Adelaide, Waite Campus, PMB1, Glen Osmond, SA, 5064, Australia
| | - Timothy R Cavagnaro
- The Waite Research Institute and The School of Agriculture, Food and Wine, University of Adelaide, Waite Campus, PMB1, Glen Osmond, SA, 5064, Australia
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Sivasakthi K, Marques E, Kalungwana N, Carrasquilla-Garcia N, Chang PL, Bergmann EM, Bueno E, Cordeiro M, Sani SGA, Udupa SM, Rather IA, Rouf Mir R, Vadez V, Vandemark GJ, Gaur PM, Cook DR, Boesch C, von Wettberg EJ, Kholova J, Penmetsa RV. Functional Dissection of the Chickpea ( Cicer arietinum L.) Stay-Green Phenotype Associated with Molecular Variation at an Ortholog of Mendel's I Gene for Cotyledon Color: Implications for Crop Production and Carotenoid Biofortification. Int J Mol Sci 2019; 20:E5562. [PMID: 31703441 PMCID: PMC6888616 DOI: 10.3390/ijms20225562] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2019] [Revised: 10/31/2019] [Accepted: 11/01/2019] [Indexed: 11/16/2022] Open
Abstract
"Stay-green" crop phenotypes have been shown to impact drought tolerance and nutritional content of several crops. We aimed to genetically describe and functionally dissect the particular stay-green phenomenon found in chickpeas with a green cotyledon color of mature dry seed and investigate its potential use for improvement of chickpea environmental adaptations and nutritional value. We examined 40 stay-green accessions and a set of 29 BC2F4-5 stay-green introgression lines using a stay-green donor parent ICC 16340 and two Indian elite cultivars (KAK2, JGK1) as recurrent parents. Genetic studies of segregating populations indicated that the green cotyledon trait is controlled by a single recessive gene that is invariantly associated with the delayed degreening (extended chlorophyll retention). We found that the chickpea ortholog of Mendel's I locus of garden pea, encoding a SGR protein as very likely to underlie the persistently green cotyledon color phenotype of chickpea. Further sequence characterization of this chickpea ortholog CaStGR1 (CaStGR1, for carietinum stay-green gene 1) revealed the presence of five different molecular variants (alleles), each of which is likely a loss-of-function of the chickpea protein (CaStGR1) involved in chlorophyll catabolism. We tested the wild type and green cotyledon lines for components of adaptations to dry environments and traits linked to agronomic performance in different experimental systems and different levels of water availability. We found that the plant processes linked to disrupted CaStGR1 gene did not functionality affect transpiration efficiency or water usage. Photosynthetic pigments in grains, including provitaminogenic carotenoids important for human nutrition, were 2-3-fold higher in the stay-green type. Agronomic performance did not appear to be correlated with the presence/absence of the stay-green allele. We conclude that allelic variation in chickpea CaStGR1 does not compromise traits linked to environmental adaptation and agronomic performance, and is a promising genetic technology for biofortification of provitaminogenic carotenoids in chickpea.
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Affiliation(s)
- Kaliamoorthy Sivasakthi
- International Crops Research Institute for the Semi-Arid Tropics (ICRISAT), Patancheru 502 324, India; (K.S.); (V.V.); (P.M.G.)
| | - Edward Marques
- Department of Plant and Soil Science, University of Vermont, and Gund Institute for the Environment, Burlington, VT 05405, USA; (E.M.); (E.B.)
| | - Ng’andwe Kalungwana
- School of Food Science and Nutrition, University of Leeds, Leeds, LS2 9JT, UK; (N.K.); (C.B.)
| | - Noelia Carrasquilla-Garcia
- Department of Plant Pathology, University of California, Davis, CA 95616, USA; (N.C.-G.); (P.L.C.); (E.M.B.); (M.C.); (D.R.C.)
| | - Peter L. Chang
- Department of Plant Pathology, University of California, Davis, CA 95616, USA; (N.C.-G.); (P.L.C.); (E.M.B.); (M.C.); (D.R.C.)
| | - Emily M. Bergmann
- Department of Plant Pathology, University of California, Davis, CA 95616, USA; (N.C.-G.); (P.L.C.); (E.M.B.); (M.C.); (D.R.C.)
| | - Erika Bueno
- Department of Plant and Soil Science, University of Vermont, and Gund Institute for the Environment, Burlington, VT 05405, USA; (E.M.); (E.B.)
| | - Matilde Cordeiro
- Department of Plant Pathology, University of California, Davis, CA 95616, USA; (N.C.-G.); (P.L.C.); (E.M.B.); (M.C.); (D.R.C.)
| | - Syed Gul A.S. Sani
- Department of Plant Pathology, University of California, Davis, CA 95616, USA; (N.C.-G.); (P.L.C.); (E.M.B.); (M.C.); (D.R.C.)
| | - Sripada M. Udupa
- International Center for Agricultural Research in the Dry Areas (ICARDA), P.O.Box 6299, Rue Hafiane Cherkaoui, 10112 Rabat, Morocco;
| | - Irshad A. Rather
- Division of Genetics & Plant Breeding, Sher-e-Kashmir University of Agricultural Sciences & Technology (SKUAST), Sopore 193 201, India; (I.A.R.); (R.R.M.)
| | - Reyazul Rouf Mir
- Division of Genetics & Plant Breeding, Sher-e-Kashmir University of Agricultural Sciences & Technology (SKUAST), Sopore 193 201, India; (I.A.R.); (R.R.M.)
| | - Vincent Vadez
- International Crops Research Institute for the Semi-Arid Tropics (ICRISAT), Patancheru 502 324, India; (K.S.); (V.V.); (P.M.G.)
| | - George J. Vandemark
- Grain Legume Genetics and Physiology Research, USDA-ARS, and, Washington State University, Pullman, WA 99164, USA;
| | - Pooran M. Gaur
- International Crops Research Institute for the Semi-Arid Tropics (ICRISAT), Patancheru 502 324, India; (K.S.); (V.V.); (P.M.G.)
| | - Douglas R. Cook
- Department of Plant Pathology, University of California, Davis, CA 95616, USA; (N.C.-G.); (P.L.C.); (E.M.B.); (M.C.); (D.R.C.)
| | - Christine Boesch
- School of Food Science and Nutrition, University of Leeds, Leeds, LS2 9JT, UK; (N.K.); (C.B.)
| | - Eric J.B. von Wettberg
- Department of Plant and Soil Science, University of Vermont, and Gund Institute for the Environment, Burlington, VT 05405, USA; (E.M.); (E.B.)
| | - Jana Kholova
- International Crops Research Institute for the Semi-Arid Tropics (ICRISAT), Patancheru 502 324, India; (K.S.); (V.V.); (P.M.G.)
| | - R. Varma Penmetsa
- Department of Plant Sciences, University of California, Davis, CA 95616, USA
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Geetika G, van Oosterom EJ, George-Jaeggli B, Mortlock MY, Deifel KS, McLean G, Hammer GL. Genotypic variation in whole-plant transpiration efficiency in sorghum only partly aligns with variation in stomatal conductance. FUNCTIONAL PLANT BIOLOGY : FPB 2019; 46:1072-1089. [PMID: 31615621 DOI: 10.1071/fp18177] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/04/2018] [Accepted: 07/01/2019] [Indexed: 05/13/2023]
Abstract
Water scarcity can limit sorghum (Sorghum bicolor (L.) Moench) production in dryland agriculture, but increased whole-plant transpiration efficiency (TEwp, biomass production per unit of water transpired) can enhance grain yield in such conditions. The objectives of this study were to quantify variation in TEwp for 27 sorghum genotypes and explore the linkages of this variation to responses of the underpinning leaf-level processes to environmental conditions. Individual plants were grown in large lysimeters in two well-watered experiments. Whole-plant transpiration per unit of green leaf area (TGLA) was monitored continuously and stomatal conductance and maximum photosynthetic capacity were measured during sunny conditions on recently expanded leaves. Leaf chlorophyll measurements of the upper five leaves of the main shoot were conducted during early grain filling. TEwp was determined at harvest. The results showed that diurnal patterns in TGLA were determined by vapour pressure deficit (VPD) and by the response of whole-plant conductance to radiation and VPD. Significant genotypic variation in the response of TGLA to VPD occurred and was related to genotypic differences in stomatal conductance. However, variation in TGLA explained only part of the variation in TEwp, with some of the residual variation explained by leaf chlorophyll readings, which were a reflection of photosynthetic capacity. Genotypes with different genetic background often differed in TEwp, TGLA and leaf chlorophyll, indicating potential differences in photosynthetic capacity among these groups. Observed differences in TEwp and its component traits can affect adaptation to drought stress.
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Affiliation(s)
- Geetika Geetika
- The University of Queensland, Queensland Alliance for Agriculture and Food Innovation, St Lucia, Qld 4072, Australia; and Corresponding author.
| | - Erik J van Oosterom
- The University of Queensland, Queensland Alliance for Agriculture and Food Innovation, St Lucia, Qld 4072, Australia
| | - Barbara George-Jaeggli
- The University of Queensland, Queensland Alliance for Agriculture and Food Innovation, Hermitage Research Facility, Warwick, Qld 4370, Australia; and Agri-Science Queensland, Department of Agriculture and Fisheries, Warwick, Qld 4370, Australia
| | - Miranda Y Mortlock
- The University of Queensland, Queensland Alliance for Agriculture and Food Innovation, St Lucia, Qld 4072, Australia
| | - Kurt S Deifel
- The University of Queensland, Queensland Alliance for Agriculture and Food Innovation, St Lucia, Qld 4072, Australia
| | - Greg McLean
- Agri-Science Queensland, Department of Agriculture and Fisheries, Toowoomba, Qld 4350, Australia
| | - Graeme L Hammer
- The University of Queensland, Queensland Alliance for Agriculture and Food Innovation, St Lucia, Qld 4072, Australia
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Paulus S. Measuring crops in 3D: using geometry for plant phenotyping. PLANT METHODS 2019; 15:103. [PMID: 31497064 PMCID: PMC6719375 DOI: 10.1186/s13007-019-0490-0] [Citation(s) in RCA: 21] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/29/2019] [Accepted: 08/27/2019] [Indexed: 05/22/2023]
Abstract
Using 3D sensing for plant phenotyping has risen within the last years. This review provides an overview on 3D traits for the demands of plant phenotyping considering different measuring techniques, derived traits and use-cases of biological applications. A comparison between a high resolution 3D measuring device and an established measuring tool, the leaf meter, is shown to categorize the possible measurement accuracy. Furthermore, different measuring techniques such as laser triangulation, structure from motion, time-of-flight, terrestrial laser scanning or structured light approaches enable the assessment of plant traits such as leaf width and length, plant size, volume and development on plant and organ level. The introduced traits were shown with respect to the measured plant types, the used measuring technique and the link to their biological use case. These were trait and growth analysis for measurements over time as well as more complex investigation on water budget, drought responses and QTL (quantitative trait loci) analysis. The used processing pipelines were generalized in a 3D point cloud processing workflow showing the single processing steps to derive plant parameters on plant level, on organ level using machine learning or over time using time series measurements. Finally the next step in plant sensing, the fusion of different sensor types namely 3D and spectral measurements is introduced by an example on sugar beet. This multi-dimensional plant model is the key to model the influence of geometry on radiometric measurements and to correct it. This publication depicts the state of the art for 3D measuring of plant traits as they were used in plant phenotyping regarding how the data is acquired, how this data is processed and what kind of traits is measured at the single plant, the miniplot, the experimental field and the open field scale. Future research will focus on highly resolved point clouds on the experimental and field scale as well as on the automated trait extraction of organ traits to track organ development at these scales.
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Affiliation(s)
- Stefan Paulus
- Institute of Sugar Beet Research, Holtenser Landstr. 77, 37079 Göttingen, Germany
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Basava RK, Hash CT, Mahendrakar MD, Kishor P. B. K, Satyavathi CT, Kumar S, Singh RB, Yadav RS, Gupta R, Srivastava RK. Discerning combining ability loci for divergent environments using chromosome segment substitution lines (CSSLs) in pearl millet. PLoS One 2019; 14:e0218916. [PMID: 31461465 PMCID: PMC6713397 DOI: 10.1371/journal.pone.0218916] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/15/2019] [Accepted: 06/13/2019] [Indexed: 11/18/2022] Open
Abstract
Pearl millet is an important crop for arid and semi-arid regions of the world. Genomic regions associated with combining ability for yield-related traits under irrigated and drought conditions are useful in heterosis breeding programs. Chromosome segment substitution lines (CSSLs) are excellent genetic resources for precise QTL mapping and identifying naturally occurring favorable alleles. In the present study, testcross hybrid populations of 85 CSSLs were evaluated for 15 grain and stover yield-related traits for summer and wet seasons under irrigated control (CN) and moisture stress (MS) conditions. General combining ability (GCA) and specific combining ability (SCA) effects of all these traits were estimated and significant marker loci linked to GCA and SCA of the traits were identified. Heritability of the traits ranged from 53-94% in CN and 63-94% in MS. A total of 40 significant GCA loci and 36 significant SCA loci were identified for 14 different traits. Five QTLs (flowering time, panicle number and panicle yield linked to Xpsmp716 on LG4, flowering time and grain number per panicle with Xpsmp2076 on LG4) simultaneously controlled both GCA and SCA, demonstrating their unique genetic basis and usefulness for hybrid breeding programs. This study for the first time demonstrated the potential of a set of CSSLs for trait mapping in pearl millet. The novel combining ability loci linked with GCA and SCA values of the traits identified in this study may be useful in pearl millet hybrid and population improvement programs using marker-assisted selection (MAS).
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Affiliation(s)
- Ramana Kumari Basava
- International Crops Research Institute for the Semi-Arid Tropics (ICRISAT), Patancheru, Hyderabad, Telangana State, India
| | - Charles Thomas Hash
- International Crops Research Institute for the Semi-Arid Tropics (ICRISAT), Patancheru, Hyderabad, Telangana State, India
| | - Mahesh D. Mahendrakar
- International Crops Research Institute for the Semi-Arid Tropics (ICRISAT), Patancheru, Hyderabad, Telangana State, India
| | | | - C. Tara Satyavathi
- All India Coordinated Research Project on Pearl Millet (AICRP-PM), Indian Council of Agricultural Research (ICAR), Mandor, Jodhpur, Rajasthan, India
| | - Sushil Kumar
- International Crops Research Institute for the Semi-Arid Tropics (ICRISAT), Patancheru, Hyderabad, Telangana State, India
- Anand Agricultural University, Anand, Gujarat, India
| | - R. B. Singh
- International Crops Research Institute for the Semi-Arid Tropics (ICRISAT), Patancheru, Hyderabad, Telangana State, India
| | - Rattan S. Yadav
- Institute of Biological, Environmental & Rural Sciences (IBERS), Aberystwyth University, Gogerddan, Wales, United Kingdom
| | - Rajeev Gupta
- International Crops Research Institute for the Semi-Arid Tropics (ICRISAT), Patancheru, Hyderabad, Telangana State, India
| | - Rakesh K. Srivastava
- International Crops Research Institute for the Semi-Arid Tropics (ICRISAT), Patancheru, Hyderabad, Telangana State, India
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Ojiewo C, Monyo E, Desmae H, Boukar O, Mukankusi‐Mugisha C, Thudi M, Pandey MK, Saxena RK, Gaur PM, Chaturvedi SK, Fikre A, Ganga Rao NPVR, SameerKumar CV, Okori P, Janila P, Rubyogo JC, Godfree C, Akpo E, Omoigui L, Nkalubo S, Fenta B, Binagwa P, Kilango M, Williams M, Mponda O, Okello D, Chichaybelu M, Miningou A, Bationo J, Sako D, Diallo S, Echekwu C, Umar ML, Oteng‐Frimpong R, Mohammed H, Varshney RK. Genomics, genetics and breeding of tropical legumes for better livelihoods of smallholder farmers. PLANT BREEDING = ZEITSCHRIFT FUR PFLANZENZUCHTUNG 2019; 138:487-499. [PMID: 31787790 PMCID: PMC6876654 DOI: 10.1111/pbr.12554] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/07/2017] [Accepted: 11/04/2017] [Indexed: 05/04/2023]
Abstract
Legumes are important components of sustainable agricultural production, food, nutrition and income systems of developing countries. In spite of their importance, legume crop production is challenged by a number of biotic (diseases and pests) and abiotic stresses (heat, frost, drought and salinity), edaphic factors (associated with soil nutrient deficits) and policy issues (where less emphasis is put on legumes compared to priority starchy staples). Significant research and development work have been done in the past decade on important grain legumes through collaborative bilateral and multilateral projects as well as the CGIAR Research Program on Grain Legumes (CRP-GL). Through these initiatives, genomic resources and genomic tools such as draft genome sequence, resequencing data, large-scale genomewide markers, dense genetic maps, quantitative trait loci (QTLs) and diagnostic markers have been developed for further use in multiple genetic and breeding applications. Also, these mega-initiatives facilitated release of a number of new varieties and also dissemination of on-the-shelf varieties to the farmers. More efforts are needed to enhance genetic gains by reducing the time required in cultivar development through integration of genomics-assisted breeding approaches and rapid generation advancement.
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Affiliation(s)
- Chris Ojiewo
- International Crops Research Institute for the Semi‐Arid Tropics (ICRISAT)NairobiKenya
| | - Emmanuel Monyo
- International Crops Research Institute for the Semi‐Arid Tropics (ICRISAT)NairobiKenya
| | | | - Ousmane Boukar
- International Institute of Tropical Agriculture (IITA)KanoNigeria
| | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | - Stanley Nkalubo
- National Agricultural Research Organization (NARO)NamulongeUganda
| | - Berhanu Fenta
- Ethiopian Institute of Agricultural Research (EIAR)MelkassaEthiopia
| | - Papias Binagwa
- Selian Agricultural Research Institute (SARI)ArushaTanzania
| | | | | | | | - David Okello
- National Semi Arid Resources Research Institute (NaSARRI)SorotiUganda
| | | | - Amos Miningou
- Environmental Institute for Agricultural Research (INERA)OuagadougouBurkina Faso
| | - Joseph Bationo
- Environmental Institute for Agricultural Research (INERA)OuagadougouBurkina Faso
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Abstract
Rice is a staple crop for half the world's population, which is expected to grow by 3 billion over the next 30 years. It is also a key model for studying the genomics of agroecosystems. This dual role places rice at the centre of an enormous challenge facing agriculture: how to leverage genomics to produce enough food to feed an expanding global population. Scientists worldwide are investigating the genetic variation among domesticated rice species and their wild relatives with the aim of identifying loci that can be exploited to breed a new generation of sustainable crops known as Green Super Rice.
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46
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Zhao C, Zhang Y, Du J, Guo X, Wen W, Gu S, Wang J, Fan J. Crop Phenomics: Current Status and Perspectives. FRONTIERS IN PLANT SCIENCE 2019; 10:714. [PMID: 31214228 PMCID: PMC6557228 DOI: 10.3389/fpls.2019.00714] [Citation(s) in RCA: 130] [Impact Index Per Article: 26.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/30/2018] [Accepted: 05/14/2019] [Indexed: 05/19/2023]
Abstract
Reliable, automatic, multifunctional, and high-throughput phenotypic technologies are increasingly considered important tools for rapid advancement of genetic gain in breeding programs. With the rapid development in high-throughput phenotyping technologies, research in this area is entering a new era called 'phenomics.' The crop phenotyping community not only needs to build a multi-domain, multi-level, and multi-scale crop phenotyping big database, but also to research technical systems for phenotypic traits identification and develop bioinformatics technologies for information extraction from the overwhelming amounts of omics data. Here, we provide an overview of crop phenomics research, focusing on two parts, from phenotypic data collection through various sensors to phenomics analysis. Finally, we discussed the challenges and prospective of crop phenomics in order to provide suggestions to develop new methods of mining genes associated with important agronomic traits, and propose new intelligent solutions for precision breeding.
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Ward B, Brien C, Oakey H, Pearson A, Negrão S, Schilling RK, Taylor J, Jarvis D, Timmins A, Roy SJ, Tester M, Berger B, van den Hengel A. High-throughput 3D modelling to dissect the genetic control of leaf elongation in barley (Hordeum vulgare). THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2019; 98:555-570. [PMID: 30604470 PMCID: PMC6850118 DOI: 10.1111/tpj.14225] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/25/2018] [Revised: 12/17/2018] [Accepted: 12/19/2018] [Indexed: 05/11/2023]
Abstract
To optimize shoot growth and structure of cereals, we need to understand the genetic components controlling initiation and elongation. While measuring total shoot growth at high throughput using 2D imaging has progressed, recovering the 3D shoot structure of small grain cereals at a large scale is still challenging. Here, we present a method for measuring defined individual leaves of cereals, such as wheat and barley, using few images. Plant shoot modelling over time was used to measure the initiation and elongation of leaves in a bi-parental barley mapping population under low and high soil salinity. We detected quantitative trait loci (QTL) related to shoot growth per se, using both simple 2D total shoot measurements and our approach of measuring individual leaves. In addition, we detected QTL specific to leaf elongation and not to total shoot size. Of particular importance was the detection of a QTL on chromosome 3H specific to the early responses of leaf elongation to salt stress, a locus that could not be detected without the computer vision tools developed in this study.
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Affiliation(s)
- Ben Ward
- Australian Center for Visual TechnologiesUniversity of AdelaideAdelaideSA5005Australia
| | - Chris Brien
- Australian Plant Phenomics FacilityThe Plant AcceleratorSchool of Agriculture Food & WineUniversity of AdelaideUrrbraeSA5064Australia
- School of Agriculture Food & Wine and Waite Research InstituteUniversity of AdelaideUrrbraeSA5064Australia
- Phenomics and Bioinformatics Research CentreSchool of Information Technology and Mathematical SciencesUniversity of South AustraliaAdelaide5001Australia
| | - Helena Oakey
- School of Agriculture Food & Wine and Waite Research InstituteUniversity of AdelaideUrrbraeSA5064Australia
| | - Allison Pearson
- School of Agriculture Food & Wine and Waite Research InstituteUniversity of AdelaideUrrbraeSA5064Australia
- ARC Centre of Excellence in Plant Energy BiologyThe University of AdelaidePMB 1, Glen OsmondAdelaideSouth Australia5064Australia
- Australian Centre for Plant Functional GenomicsPMB 1, Glen OsmondAdelaideSouth Australia5064Australia
| | - Sónia Negrão
- Division of Biological and Environmental Sciences and Engineering (BESE)King Abdullah University of Science and Technology (KAUST)Thuwal23955‐6900Saudi Arabia
| | - Rhiannon K. Schilling
- School of Agriculture Food & Wine and Waite Research InstituteUniversity of AdelaideUrrbraeSA5064Australia
- Australian Centre for Plant Functional GenomicsPMB 1, Glen OsmondAdelaideSouth Australia5064Australia
| | - Julian Taylor
- School of Agriculture Food & Wine and Waite Research InstituteUniversity of AdelaideUrrbraeSA5064Australia
| | - David Jarvis
- Division of Biological and Environmental Sciences and Engineering (BESE)King Abdullah University of Science and Technology (KAUST)Thuwal23955‐6900Saudi Arabia
| | - Andy Timmins
- School of Agriculture Food & Wine and Waite Research InstituteUniversity of AdelaideUrrbraeSA5064Australia
- Australian Centre for Plant Functional GenomicsPMB 1, Glen OsmondAdelaideSouth Australia5064Australia
| | - Stuart J. Roy
- School of Agriculture Food & Wine and Waite Research InstituteUniversity of AdelaideUrrbraeSA5064Australia
- Australian Centre for Plant Functional GenomicsPMB 1, Glen OsmondAdelaideSouth Australia5064Australia
| | - Mark Tester
- Division of Biological and Environmental Sciences and Engineering (BESE)King Abdullah University of Science and Technology (KAUST)Thuwal23955‐6900Saudi Arabia
| | - Bettina Berger
- Australian Plant Phenomics FacilityThe Plant AcceleratorSchool of Agriculture Food & WineUniversity of AdelaideUrrbraeSA5064Australia
- School of Agriculture Food & Wine and Waite Research InstituteUniversity of AdelaideUrrbraeSA5064Australia
| | - Anton van den Hengel
- Australian Center for Visual TechnologiesUniversity of AdelaideAdelaideSA5005Australia
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Reynolds D, Baret F, Welcker C, Bostrom A, Ball J, Cellini F, Lorence A, Chawade A, Khafif M, Noshita K, Mueller-Linow M, Zhou J, Tardieu F. What is cost-efficient phenotyping? Optimizing costs for different scenarios. PLANT SCIENCE : AN INTERNATIONAL JOURNAL OF EXPERIMENTAL PLANT BIOLOGY 2019; 282:14-22. [PMID: 31003607 DOI: 10.1016/j.plantsci.2018.06.015] [Citation(s) in RCA: 39] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/05/2017] [Revised: 05/17/2018] [Accepted: 06/13/2018] [Indexed: 05/22/2023]
Abstract
Progress in remote sensing and robotic technologies decreases the hardware costs of phenotyping. Here, we first review cost-effective imaging devices and environmental sensors, and present a trade-off between investment and manpower costs. We then discuss the structure of costs in various real-world scenarios. Hand-held low-cost sensors are suitable for quick and infrequent plant diagnostic measurements. In experiments for genetic or agronomic analyses, (i) major costs arise from plant handling and manpower; (ii) the total costs per plant/microplot are similar in robotized platform or field experiments with drones, hand-held or robotized ground vehicles; (iii) the cost of vehicles carrying sensors represents only 5-26% of the total costs. These conclusions depend on the context, in particular for labor cost, the quantitative demand of phenotyping and the number of days available for phenotypic measurements due to climatic constraints. Data analysis represents 10-20% of total cost if pipelines have already been developed. A trade-off exists between the initial high cost of pipeline development and labor cost of manual operations. Overall, depending on the context and objsectives, "cost-effective" phenotyping may involve either low investment ("affordable phenotyping"), or initial high investments in sensors, vehicles and pipelines that result in higher quality and lower operational costs.
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Affiliation(s)
- Daniel Reynolds
- Earlham Institute, Norwich Research Park, Norwich, NR4 7UH, UK
| | | | - Claude Welcker
- INRA Univ Montpellier, LEPSE, 2 place Viala 34060 Montpellier, France
| | - Aaron Bostrom
- Earlham Institute, Norwich Research Park, Norwich, NR4 7UH, UK
| | - Joshua Ball
- Earlham Institute, Norwich Research Park, Norwich, NR4 7UH, UK
| | - Francesco Cellini
- Agenzia Lucana di Sviluppo e di Innovazione in Agricoltura, 75010, Metaponto, MT, Italy
| | - Argelia Lorence
- Phenomics Facility, Arkansas Biosciences Institute, Arkansas State University, Jonesboro, Arkansas, USA
| | - Aakash Chawade
- Department of Plant Breeding, Swedish University of Agricultural Sciences (SLU), P.O. Box 101, 230 53 Alnarp, Sweden
| | - Mehdi Khafif
- Université de Toulouse, INRA, CNRS, LIPM Castanet-Tolosan, France
| | - Koji Noshita
- Japan Science and Technology Agency (JST), Precursory Research for Embryonic Science and Technology (PRESTO), Graduate School of Agriculture and Life Science, The University of Tokyo, Japan
| | - Mark Mueller-Linow
- Institute of Bio- and Geosciences (IBG), IBG-2: Plant Sciences, Forschungszentrum Juelich GmbH, Juelich, Germany
| | - Ji Zhou
- Earlham Institute, Norwich Research Park, Norwich, NR4 7UH, UK; Plant Phenomics Research Center, Nanjing Agricultural University, Nanjing, 210095, China.
| | - François Tardieu
- INRA Univ Montpellier, LEPSE, 2 place Viala 34060 Montpellier, France.
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49
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Roitsch T, Cabrera-Bosquet L, Fournier A, Ghamkhar K, Jiménez-Berni J, Pinto F, Ober ES. Review: New sensors and data-driven approaches-A path to next generation phenomics. PLANT SCIENCE : AN INTERNATIONAL JOURNAL OF EXPERIMENTAL PLANT BIOLOGY 2019; 282:2-10. [PMID: 31003608 PMCID: PMC6483971 DOI: 10.1016/j.plantsci.2019.01.011] [Citation(s) in RCA: 78] [Impact Index Per Article: 15.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/07/2017] [Revised: 12/15/2018] [Accepted: 01/09/2019] [Indexed: 05/19/2023]
Abstract
At the 4th International Plant Phenotyping Symposium meeting of the International Plant Phenotyping Network (IPPN) in 2016 at CIMMYT in Mexico, a workshop was convened to consider ways forward with sensors for phenotyping. The increasing number of field applications provides new challenges and requires specialised solutions. There are many traits vital to plant growth and development that demand phenotyping approaches that are still at early stages of development or elude current capabilities. Further, there is growing interest in low-cost sensor solutions, and mobile platforms that can be transported to the experiments, rather than the experiment coming to the platform. Various types of sensors are required to address diverse needs with respect to targets, precision and ease of operation and readout. Converting data into knowledge, and ensuring that those data (and the appropriate metadata) are stored in such a way that they will be sensible and available to others now and for future analysis is also vital. Here we are proposing mechanisms for "next generation phenomics" based on our learning in the past decade, current practice and discussions at the IPPN Symposium, to encourage further thinking and collaboration by plant scientists, physicists and engineering experts.
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Affiliation(s)
- Thomas Roitsch
- Department of Plant and Environmental Sciences, University of Copenhagen, Thorvaldsensvej 40, 1871 Frederiksberg C, Denmark; Department of Adaptive Biotechnologies, Global Change Research Institute, CAS, Brno, Czech Republic
| | | | - Antoine Fournier
- Arvalis, Institut du végétal, 45, voie Romaine 41240 Beauce la Romaine, France
| | - Kioumars Ghamkhar
- Forage Science, Grasslands Research Centre, AgResearch, Tennent Drive, Fitzherbert, Palmerston North 4410, New Zealand
| | - José Jiménez-Berni
- Instituto de Agricultura Sostenible, Consejo Superior de Investigaciones Cientificas (CSIC) Avenida Menéndez Pidal, Campus Alameda del Obispo, 14004 Córdoba, Spain
| | - Francisco Pinto
- Global Wheat Program, International Maize and Wheat Improvement Center (CIMMYT), El Batán, Texcoco, México C.P. 56237, Mexico
| | - Eric S Ober
- National Institute of Agricultural Botany (NIAB), Huntingdon Road, Cambridge, CB3 0LE, UK.
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50
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Leakey ADB, Ferguson JN, Pignon CP, Wu A, Jin Z, Hammer GL, Lobell DB. Water Use Efficiency as a Constraint and Target for Improving the Resilience and Productivity of C 3 and C 4 Crops. ANNUAL REVIEW OF PLANT BIOLOGY 2019; 70:781-808. [PMID: 31035829 DOI: 10.1146/annurev-arplant-042817-040305] [Citation(s) in RCA: 108] [Impact Index Per Article: 21.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/20/2023]
Abstract
The ratio of plant carbon gain to water use, known as water use efficiency (WUE), has long been recognized as a key constraint on crop production and an important target for crop improvement. WUE is a physiologically and genetically complex trait that can be defined at a range of scales. Many component traits directly influence WUE, including photosynthesis, stomatal and mesophyll conductances, and canopy structure. Interactions of carbon and water relations with diverse aspects of the environment and crop development also modulate WUE. As a consequence, enhancing WUE by breeding or biotechnology has proven challenging but not impossible. This review aims to synthesize new knowledge of WUE arising from advances in phenotyping, modeling, physiology, genetics, and molecular biology in the context of classical theoretical principles. In addition, we discuss how rising atmospheric CO2 concentration has created and will continue to create opportunities for enhancing WUE by modifying the trade-off between photosynthesis and transpiration.
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Affiliation(s)
- Andrew D B Leakey
- Department of Plant Biology, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, USA;
- Department of Crop Sciences, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, USA
- Institute for Genomic Biology, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, USA
| | - John N Ferguson
- Institute for Genomic Biology, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, USA
| | - Charles P Pignon
- Department of Plant Biology, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, USA;
| | - Alex Wu
- Centre for Crop Science and Centre of Excellence for Translational Photosynthesis, University of Queensland, St. Lucia, Queensland 4069, Australia
| | - Zhenong Jin
- Department of Earth System Science and Center for Food Security and Environment, Stanford University, Stanford, California 94305, USA
| | - Graeme L Hammer
- Centre for Crop Science and Centre of Excellence for Translational Photosynthesis, University of Queensland, St. Lucia, Queensland 4069, Australia
| | - David B Lobell
- Department of Earth System Science and Center for Food Security and Environment, Stanford University, Stanford, California 94305, USA
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