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Nguyen HA, Martre P, Collet C, Draye X, Salon C, Jeudy C, Rincent R, Muller B. Are high-throughput root phenotyping platforms suitable for informing root system architecture models with genotype-specific parameters? An evaluation based on the root model ArchiSimple and a small panel of wheat cultivars. J Exp Bot 2024; 75:2510-2526. [PMID: 38520390 DOI: 10.1093/jxb/erae009] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/26/2023] [Accepted: 03/21/2024] [Indexed: 03/25/2024]
Abstract
Given the difficulties in accessing plant roots in situ, high-throughput root phenotyping (HTRP) platforms under controlled conditions have been developed to meet the growing demand for characterizing root system architecture (RSA) for genetic analyses. However, a proper evaluation of their capacity to provide the same estimates for strictly identical root traits across platforms has never been achieved. In this study, we performed such an evaluation based on six major parameters of the RSA model ArchiSimple, using a diversity panel of 14 bread wheat cultivars in two HTRP platforms that had different growth media and non-destructive imaging systems together with a conventional set-up that had a solid growth medium and destructive sampling. Significant effects of the experimental set-up were found for all the parameters and no significant correlations across the diversity panel among the three set-ups could be detected. Differences in temperature, irradiance, and/or the medium in which the plants were growing might partly explain both the differences in the parameter values across the experiments as well as the genotype × set-up interactions. Furthermore, the values and the rankings across genotypes of only a subset of parameters were conserved between contrasting growth stages. As the parameters chosen for our analysis are root traits that have strong impacts on RSA and are close to parameters used in a majority of RSA models, our results highlight the need to carefully consider both developmental and environmental drivers in root phenomics studies.
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Affiliation(s)
- Hong Anh Nguyen
- LEPSE, Université de Montpellier, INRAE, Institut Agro Montpellier, Montpellier, France
| | - Pierre Martre
- LEPSE, Université de Montpellier, INRAE, Institut Agro Montpellier, Montpellier, France
| | - Clothilde Collet
- Earth and Life Institute, Université catholique de Louvain, Louvain-la-Neuve, Belgium
| | - Xavier Draye
- Earth and Life Institute, Université catholique de Louvain, Louvain-la-Neuve, Belgium
| | - Christophe Salon
- Agroécologie, AgroSup Dijon, INRAE, Université Bourgogne Franche-Comté, Dijon, France
| | - Christian Jeudy
- Agroécologie, AgroSup Dijon, INRAE, Université Bourgogne Franche-Comté, Dijon, France
| | - Renaud Rincent
- GDEC, Université Clermont-Auvergne, INRAE, Clermont-Ferrand, France
| | - Bertrand Muller
- LEPSE, Université de Montpellier, INRAE, Institut Agro Montpellier, Montpellier, France
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Plessis A, Ravel C, Risacher T, Duchateau N, Dardevet M, Merlino M, Torney F, Martre P. Storage protein activator controls grain protein accumulation in bread wheat in a nitrogen dependent manner. Sci Rep 2023; 13:22736. [PMID: 38123623 PMCID: PMC10733432 DOI: 10.1038/s41598-023-49139-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/12/2023] [Accepted: 12/05/2023] [Indexed: 12/23/2023] Open
Abstract
The expression of cereal grain storage protein (GSP) genes is controlled by a complex network of transcription factors (TFs). Storage protein activator (SPA) is a major TF acting in this network but its specific function in wheat (Triticum aestivum L.) remains to be determined. Here we generated an RNAi line in which expression of the three SPA homoeologs was reduced. In this line and its null segregant we analyzed GSP accumulation and expression of GSP and regulatory TF genes under two regimes of nitrogen availability. We show that down regulation of SPA decreases grain protein concentration at maturity under low but not high nitrogen supply. Under low nitrogen supply, the decrease in SPA expression also caused a reduction in the total quantity of GSP per grain and in the ratio of GSP to albumin-globulins, without significantly affecting GSP composition. The slight reduction in GSP gene expression measured in the SPA RNAi line under low nitrogen supply did not entirely account for the more significant decrease in GSP accumulation, suggesting that SPA regulates additional levels of GSP synthesis. Our results demonstrate a clear role of SPA in the regulation of grain nitrogen metabolism when nitrogen is a limiting resource.
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Affiliation(s)
- Anne Plessis
- Université Clermont Auvergne, INRAE, UMR1095 GDEC, 63000, Clermont Ferrand, France
- School of Biological and Marine Sciences, University of Plymouth, Drake Circus, Plymouth, PL4 8AA, UK
| | - Catherine Ravel
- Université Clermont Auvergne, INRAE, UMR1095 GDEC, 63000, Clermont Ferrand, France.
| | | | - Nathalie Duchateau
- Université Clermont Auvergne, INRAE, UMR1095 GDEC, 63000, Clermont Ferrand, France
| | - Mireille Dardevet
- Université Clermont Auvergne, INRAE, UMR1095 GDEC, 63000, Clermont Ferrand, France
| | - Marielle Merlino
- Université Clermont Auvergne, INRAE, UMR1095 GDEC, 63000, Clermont Ferrand, France
| | - François Torney
- Centre de Recherche, Limagrain Europe, 63 720, Chappes, France
| | - Pierre Martre
- Université Clermont Auvergne, INRAE, UMR1095 GDEC, 63000, Clermont Ferrand, France
- LEPSE, Université de Montpellier, INRAE, Institut SupAgro Montpellier, 34000, Montpellier, France
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Merlino M, Gaudin JC, Dardevet M, Martre P, Ravel C, Boudet J. Wheat DOF transcription factors TaSAD and WPBF regulate glutenin gene expression in cooperation with SPA. PLoS One 2023; 18:e0287645. [PMID: 37352279 PMCID: PMC10289392 DOI: 10.1371/journal.pone.0287645] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/16/2023] [Accepted: 06/12/2023] [Indexed: 06/25/2023] Open
Abstract
Grain storage proteins (GSPs) quantity and composition determine the end-use value of wheat flour. GSPs consists of low-molecular-weight glutenins (LMW-GS), high-molecular-weight glutenins (HMW-GS) and gliadins. GSP gene expression is controlled by a complex network of DNA-protein and protein-protein interactions, which coordinate the tissue-specific protein expression during grain development. The regulatory network has been most extensively studied in barley, particularly the two transcription factors (TFs) of the DNA binding with One Finger (DOF) family, barley Prolamin-box Binding Factor (BPBF) and Scutellum and Aleurone-expressed DOF (SAD). They activate hordein synthesis by binding to the Prolamin box, a motif in the hordein promoter. The BPBF ortholog previously identified in wheat, WPBF, has a transcriptional activity in expression of some GSP genes. Here, the wheat ortholog of SAD, named TaSAD, was identified. The binding of TaSAD to GSP gene promoter sequences in vitro and its transcriptional activity in vivo were investigated. In electrophoretic mobility shift assays, recombinant TaSAD and WPBF proteins bound to cis-motifs like those located on HMW-GS and LMW-GS gene promoters known to bind DOF TFs. We showed by transient expression assays in wheat endosperms that TaSAD and WPBF activate GSP gene expression. Moreover, co-bombardment of Storage Protein Activator (SPA) with WPBF or TaSAD had an additive effect on the expression of GSP genes, possibly through conserved cooperative protein-protein interactions.
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Affiliation(s)
- Marielle Merlino
- INRAE, Clermont Auvergne University, UMR GDEC, Clermont-Ferrand, France
| | | | - Mireille Dardevet
- INRAE, Clermont Auvergne University, UMR GDEC, Clermont-Ferrand, France
| | - Pierre Martre
- LEPSE, Univ. Montpellier, INRAE, Institut Agro Montpellier, Montpellier, France
| | - Catherine Ravel
- INRAE, Clermont Auvergne University, UMR GDEC, Clermont-Ferrand, France
| | - Julie Boudet
- INRAE, Clermont Auvergne University, UMR GDEC, Clermont-Ferrand, France
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Nóia Júnior RDS, Deswarte JC, Cohan JP, Martre P, van der Velde M, Lecerf R, Webber H, Ewert F, Ruane AC, Slafer GA, Asseng S. The extreme 2016 wheat yield failure in France. Glob Chang Biol 2023; 29:3130-3146. [PMID: 36951185 DOI: 10.1111/gcb.16662] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/15/2022] [Revised: 12/11/2022] [Accepted: 01/08/2023] [Indexed: 05/03/2023]
Abstract
France suffered, in 2016, the most extreme wheat yield decline in recent history, with some districts losing 55% yield. To attribute causes, we combined the largest coherent detailed wheat field experimental dataset with statistical and crop model techniques, climate information, and yield physiology. The 2016 yield was composed of up to 40% fewer grains that were up to 30% lighter than expected across eight research stations in France. The flowering stage was affected by prolonged cloud cover and heavy rainfall when 31% of the loss in grain yield was incurred from reduced solar radiation and 19% from floret damage. Grain filling was also affected as 26% of grain yield loss was caused by soil anoxia, 11% by fungal foliar diseases, and 10% by ear blight. Compounding climate effects caused the extreme yield decline. The likelihood of these compound factors recurring under future climate change is estimated to change with a higher frequency of extremely low wheat yields.
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Affiliation(s)
- Rogério de S Nóia Júnior
- Department of Life Science Engineering, Digital Agriculture, HEF World Agricultural Systems Center, Technical University of Munich, Freising, Germany
| | | | | | - Pierre Martre
- LEPSE, Univ Montpellier, INRAE, Institut Agro Montpellier, Montpellier, France
| | | | - Remi Lecerf
- European Commission, Joint Research Centre, Ispra, Italy
| | - Heidi Webber
- Leibniz-Centre for Agricultural Landscape Research (ZALF), Müncheberg, Germany
- Brandenburg Technical University (BTU), Cottbus, Germany
| | - Frank Ewert
- Leibniz-Centre for Agricultural Landscape Research (ZALF), Müncheberg, Germany
- Crop Science Group, INRES, University of Bonn, Bonn, Germany
| | - Alex C Ruane
- NASA Goddard Institute for Space Studies, New York, New York, USA
| | - Gustavo A Slafer
- Department of Crop and Forest Sciences, University of Lleida - AGROTECNIO Center, Lleida, Spain
- ICREA, Catalonian Institution for Research and Advanced Studies, Barcelona, Spain
| | - Senthold Asseng
- Department of Life Science Engineering, Digital Agriculture, HEF World Agricultural Systems Center, Technical University of Munich, Freising, Germany
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Martre P, Chati R, Schwarz L, Wood G, Logeay M, Grognu A, Tuech JJ, Huet E. Minimally invasive laparo-thoracoscopic Ivor-Lewis esophagectomy with semi-mechanical triangular anastomosis: Short-term outcomes of 114 consecutive patients. J Visc Surg 2023; 160:196-202. [PMID: 36333184 DOI: 10.1016/j.jviscsurg.2022.08.004] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/13/2023]
Abstract
INTRODUCTION Several surgical teams have developed so-called minimally invasive esophagectomy techniques with the intention of decreasing post-operative complications. The goal of this report is to determine the feasibility, reproducibility, morbidity and mortality of esophagectomy and intrathoracic anastomosis via thoracoscopy. METHODS This retrospective series included 114 consecutive non-selected patients who underwent Lewis Santy type esophagectomy between 2016 and 2020. The procedure was performed via abdominal laparoscopy, thoracoscopy with the patient in a supine position, without selective intubation, with intra-thoracic semi-mechanical triangular esophagogastric anastomosis. RESULTS Mean patient age was 62.8years. Conversion from laparoscopy to laparotomy was required in three patients (2.6%); no patient required conversion from thoracoscopy to thoracotomy. A semi-mechanical triangular esophagogastric anastomosis was successfully performed in all patients. Median duration of hospital stay was 16 (8-116) days. Mortality was 2.6%; 34 patients (29.8%) had major complications, 55 (48%) had a respiratory complication. The leakage rate was 12.3%; most were type I. Only 5.2% required an additional procedure. There was no mortality. CONCLUSION The analysis of this consecutive series found that this operative technique was reproducible and reliable. These results need to be confirmed by other studies. Pulmonary morbidity was high and remains the main challenge in this type of surgery.
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Affiliation(s)
- P Martre
- Digestive Surgery Department, CHU Rouen, 76031 Rouen cedex, France
| | - R Chati
- Digestive Surgery Department, CHU Rouen, 76031 Rouen cedex, France
| | - L Schwarz
- Digestive Surgery Department, CHU Rouen, 76031 Rouen cedex, France
| | - G Wood
- Digestive Surgery Department, CHU Rouen, 76031 Rouen cedex, France
| | - M Logeay
- Digestive Surgery Department, CHU Rouen, 76031 Rouen cedex, France
| | - A Grognu
- Digestive Surgery Department, CHU Rouen, 76031 Rouen cedex, France
| | - J-J Tuech
- Digestive Surgery Department, CHU Rouen, 76031 Rouen cedex, France.
| | - E Huet
- Digestive Surgery Department, CHU Rouen, 76031 Rouen cedex, France
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Fang L, Martre P, Jin K, Du X, van der Putten PEL, Yin X, Struik PC. Neglecting acclimation of photosynthesis under drought can cause significant errors in predicting leaf photosynthesis in wheat. Glob Chang Biol 2023; 29:505-521. [PMID: 36300859 PMCID: PMC10091787 DOI: 10.1111/gcb.16488] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 05/19/2022] [Revised: 09/14/2022] [Accepted: 10/04/2022] [Indexed: 06/16/2023]
Abstract
Extreme climatic events, such as heat waves, cold snaps and drought spells, related to global climate change, have become more frequent and intense in recent years. Acclimation of plant physiological processes to changes in environmental conditions is a key component of plant adaptation to climate change. We assessed the temperature response of leaf photosynthetic parameters in wheat grown under contrasting water regimes and growth temperatures (Tgrowth ). Two independent experiments were conducted under controlled conditions. In Experiment 1, two wheat genotypes were subjected to well-watered or drought-stressed treatments; in Experiment 2, the two water regimes combined with high, medium and low Tgrowth were imposed on one genotype. Parameters of a biochemical C3 -photosynthesis model were estimated at six leaf temperatures for each factor combination. Photosynthesis acclimated more to drought than to Tgrowth . Drought affected photosynthesis by lowering its optimum temperature (Topt ) and the values at Topt of light-saturated net photosynthesis, stomatal conductance, mesophyll conductance, the maximum rate of electron transport (Jmax ) and the maximum rate of carboxylation by Rubisco (Vcmax ). Topt for Vcmax was up to 40°C under well-watered conditions but 24-34°C under drought. The decrease in photosynthesis under drought varied among Tgrowth but was similar between genotypes. The temperature response of photosynthetic quantum yield under drought was partly attributed to photorespiration but more to alternative electron transport. All these changes in biochemical parameters could not be fully explained by the changed leaf nitrogen content. Further model analysis showed that both diffusional and biochemical parameters of photosynthesis and their thermal sensitivity acclimate little to Tgrowth , but acclimate considerably to drought and the combination of drought and Tgrowth . The commonly used modelling approaches, which typically consider the response of diffusional parameters, but ignore acclimation responses of biochemical parameters to drought and Tgrowth , strongly overestimate leaf photosynthesis under variable temperature and drought.
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Affiliation(s)
- Liang Fang
- Department of Plant Sciences, Centre for Crop Systems AnalysisWageningen University and ResearchWageningenThe Netherlands
| | - Pierre Martre
- LEPSEUniv Montpellier, INRAE, Institut Agro MontpellierMontpellierFrance
| | - Kaining Jin
- Department of Plant Sciences, Centre for Crop Systems AnalysisWageningen University and ResearchWageningenThe Netherlands
| | - Xinmiao Du
- Department of Plant Sciences, Centre for Crop Systems AnalysisWageningen University and ResearchWageningenThe Netherlands
| | - Peter E. L. van der Putten
- Department of Plant Sciences, Centre for Crop Systems AnalysisWageningen University and ResearchWageningenThe Netherlands
| | - Xinyou Yin
- Department of Plant Sciences, Centre for Crop Systems AnalysisWageningen University and ResearchWageningenThe Netherlands
| | - Paul C. Struik
- Department of Plant Sciences, Centre for Crop Systems AnalysisWageningen University and ResearchWageningenThe Netherlands
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7
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Nóia Júnior RDS, Ewert F, Webber H, Martre P, Hertel TW, van Ittersum MK, Asseng S. Needed global wheat stock and crop management in response to the war in Ukraine. Global Food Security 2022. [DOI: 10.1016/j.gfs.2022.100662] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/27/2022]
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Dueri S, Brown H, Asseng S, Ewert F, Webber H, George M, Craigie R, Guarin JR, Pequeno DNL, Stella T, Ahmed M, Alderman PD, Basso B, Berger AG, Mujica GB, Cammarano D, Chen Y, Dumont B, Rezaei EE, Fereres E, Ferrise R, Gaiser T, Gao Y, Garcia-Vila M, Gayler S, Hochman Z, Hoogenboom G, Kersebaum KC, Nendel C, Olesen JE, Padovan G, Palosuo T, Priesack E, Pullens JWM, Rodríguez A, Rötter RP, Ramos MR, Semenov MA, Senapati N, Siebert S, Srivastava AK, Stöckle C, Supit I, Tao F, Thorburn P, Wang E, Weber TKD, Xiao L, Zhao C, Zhao J, Zhao Z, Zhu Y, Martre P. Simulation of winter wheat response to variable sowing dates and densities in a high-yielding environment. J Exp Bot 2022; 73:5715-5729. [PMID: 35728801 PMCID: PMC9467659 DOI: 10.1093/jxb/erac221] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 11/03/2021] [Accepted: 06/21/2022] [Indexed: 06/15/2023]
Abstract
Crop multi-model ensembles (MME) have proven to be effective in increasing the accuracy of simulations in modelling experiments. However, the ability of MME to capture crop responses to changes in sowing dates and densities has not yet been investigated. These management interventions are some of the main levers for adapting cropping systems to climate change. Here, we explore the performance of a MME of 29 wheat crop models to predict the effect of changing sowing dates and rates on yield and yield components, on two sites located in a high-yielding environment in New Zealand. The experiment was conducted for 6 years and provided 50 combinations of sowing date, sowing density and growing season. We show that the MME simulates seasonal growth of wheat well under standard sowing conditions, but fails under early sowing and high sowing rates. The comparison between observed and simulated in-season fraction of intercepted photosynthetically active radiation (FIPAR) for early sown wheat shows that the MME does not capture the decrease of crop above ground biomass during winter months due to senescence. Models need to better account for tiller competition for light, nutrients, and water during vegetative growth, and early tiller senescence and tiller mortality, which are exacerbated by early sowing, high sowing densities, and warmer winter temperatures.
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Affiliation(s)
- Sibylle Dueri
- LEPSE, Univ. Montpellier, INRAE, Institut Agro Montpellier, Montpellier, France
| | - Hamish Brown
- The New Zealand Institute for Plant & Food Research Limited, Christchurch, New Zealand
| | - Senthold Asseng
- Department of Life Science Engineering, Digital Agriculture, Technical University of Munich, Freising, Germany
| | - Frank Ewert
- Institute of Crop Science and Resource Conservation INRES, University of Bonn, Bonn, Germany
- Leibniz Centre for Agricultural Landscape Research, Müncheberg, Germany
| | - Heidi Webber
- Leibniz Centre for Agricultural Landscape Research, Müncheberg, Germany
- Brandenburg University of Technology, Faculty of Environment and Natural Sciences, Cottbus, Germany
| | - Mike George
- The New Zealand Institute for Plant & Food Research Limited, Christchurch, New Zealand
| | - Rob Craigie
- Foundation for Arable Research, Templeton, New Zealand
| | - Jose Rafael Guarin
- Agricultural & Biological Engineering Department, University of Florida, Gainesville, FL, USA
- Center for Climate Systems Research, Earth Institute, Columbia University, New York, NY, USA
- NASA Goddard Institute for Space Studies, New York, NY, USA
| | - Diego N L Pequeno
- International Maize and Wheat Improvement Center (CIMMYT), Mexico DF, Mexico
| | - Tommaso Stella
- Institute of Crop Science and Resource Conservation INRES, University of Bonn, Bonn, Germany
- Leibniz Centre for Agricultural Landscape Research, Müncheberg, Germany
| | - Mukhtar Ahmed
- Department of Agronomy, Pir Mehr Ali Shah Arid Agriculture University, Rawalpindi, Pakistan
- Department of Agricultural Research for Northern Sweden, Swedish University of Agricultural Sciences Umeå, Sweden
| | - Phillip D Alderman
- Department of Plant and Soil Sciences, Oklahoma State University, Stillwater, OK, USA
| | - Bruno Basso
- Department of Earth and Environmental Sciences, Michigan State University, East Lansing, MI, USA
- W. K. Kellogg Biological Station, Michigan State University, East Lansing, MI, USA
| | - Andres G Berger
- National Institute of Agricultural Research (INIA), Colonia, Uruguay
| | - Gennady Bracho Mujica
- Tropical Plant Production and Agricultural Systems Modelling (TROPAGS), University of Göttingen, Göttingen, Germany
| | | | - Yi Chen
- Institute of Geographical Sciences and Natural Resources Research, Chinese Academy of Science, Beijing, China
| | - Benjamin Dumont
- Plant Sciences Axis – Crop Science, Gembloux Agro-Bio Tech, University of Liege, Gembloux, Belgium
| | | | - Elias Fereres
- IAS-CSIC & DAUCO, University of Cordoba, Cordoba, Spain
| | - Roberto Ferrise
- Department of Agriculture, food, environment and forestry (DAGRI), University of Florence, Florence, Italy
| | - Thomas Gaiser
- Institute of Crop Science and Resource Conservation INRES, University of Bonn, Bonn, Germany
| | - Yujing Gao
- Agricultural & Biological Engineering Department, University of Florida, Gainesville, FL, USA
| | | | - Sebastian Gayler
- Institute of Soil Science and Land Evaluation, University of Hohenheim, Stuttgart, Germany
| | - Zvi Hochman
- CSIRO Agriculture and Food, Brisbane, Queensland, Australia
| | - Gerrit Hoogenboom
- Agricultural & Biological Engineering Department, University of Florida, Gainesville, FL, USA
- Institute for Sustainable Food Systems, University of Florida, Gainesville, FL, USA
| | - Kurt C Kersebaum
- Leibniz Centre for Agricultural Landscape Research, Müncheberg, Germany
- Tropical Plant Production and Agricultural Systems Modelling (TROPAGS), University of Göttingen, Göttingen, Germany
- Global Change Research Institute, Academy of Sciences of the Czech Republic, Brno, Czech Republic
| | - Claas Nendel
- Leibniz Centre for Agricultural Landscape Research, Müncheberg, Germany
- Global Change Research Institute, Academy of Sciences of the Czech Republic, Brno, Czech Republic
- Institute of Biochemistry and Biology, University of Potsdam, Potsdam, Germany
| | - Jørgen E Olesen
- Department of Agroecology, Aarhus University, Tjele, Denmark
- Global Change Research Institute, Academy of Sciences of the Czech Republic, Brno, Czech Republic
| | - Gloria Padovan
- Department of Agriculture, food, environment and forestry (DAGRI), University of Florence, Florence, Italy
| | - Taru Palosuo
- Natural Resources Institute Finland (Luke), Helsinki, Finland
| | - Eckart Priesack
- Institute of Biochemical Plant Pathology, Helmholtz Zentrum München—German Research Center for Environmental Health, Neuherberg, Germany
| | | | - Alfredo Rodríguez
- CEIGRAM, Technical University of Madrid, Madrid, Spain
- Department of Economic Analysis and Finances, University of Castilla-La Mancha, Toledo, Spain
| | - Reimund P Rötter
- Tropical Plant Production and Agricultural Systems Modelling (TROPAGS), University of Göttingen, Göttingen, Germany
- Centre of Biodiversity and Sustainable Land Use (CBL), University of Göttingen, Göttingen, Germany
| | | | | | | | - Stefan Siebert
- Centre of Biodiversity and Sustainable Land Use (CBL), University of Göttingen, Göttingen, Germany
- Department of Crop Sciences, University of Göttingen, Göttingen, Germany
| | - Amit Kumar Srivastava
- Institute of Crop Science and Resource Conservation INRES, University of Bonn, Bonn, Germany
| | - Claudio Stöckle
- Biological Systems Engineering, Washington State University, Pullman, WA, USA
| | - Iwan Supit
- Water Systems & Global Change Group, Wageningen University, Wageningen, The Netherlands
| | - Fulu Tao
- Institute of Geographical Sciences and Natural Resources Research, Chinese Academy of Science, Beijing, China
- Natural Resources Institute Finland (Luke), Helsinki, Finland
| | - Peter Thorburn
- CSIRO Agriculture and Food, Brisbane, Queensland, Australia
| | - Enli Wang
- CSIRO Agriculture and Food, Canberra, Australian Capital Territory, Australia
| | | | - Liujun Xiao
- College of Environmental and Resource Sciences, Zhejiang University, Hangzhou, Zhejiang, China
- National Engineering and Technology Center for Information Agriculture, Key Laboratory for Crop System Analysis and Decision Making, Ministry of Agriculture, Jiangsu Key Laboratory for Information Agriculture, Jiangsu Collaborative Innovation Center for Modern Crop Production, Nanjing Agricultural University, Nanjing, China
| | - Chuang Zhao
- College of Resources and Environmental Sciences, China Agricultural University, Beijing, China
| | - Jin Zhao
- Department of Agroecology, Aarhus University, Tjele, Denmark
- College of Resources and Environmental Sciences, China Agricultural University, Beijing, China
| | - Zhigan Zhao
- CSIRO Agriculture and Food, Canberra, Australian Capital Territory, Australia
| | - Yan Zhu
- National Engineering and Technology Center for Information Agriculture, Key Laboratory for Crop System Analysis and Decision Making, Ministry of Agriculture, Jiangsu Key Laboratory for Information Agriculture, Jiangsu Collaborative Innovation Center for Modern Crop Production, Nanjing Agricultural University, Nanjing, China
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9
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Fang L, Yin X, van der Putten PEL, Martre P, Struik PC. Drought exerts a greater influence than growth temperature on the temperature response of leaf day respiration in wheat (Triticum aestivum). Plant Cell Environ 2022; 45:2062-2077. [PMID: 35357701 PMCID: PMC9324871 DOI: 10.1111/pce.14324] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/24/2021] [Revised: 03/21/2022] [Accepted: 03/26/2022] [Indexed: 05/22/2023]
Abstract
We assessed how the temperature response of leaf day respiration (Rd ) in wheat responded to contrasting water regimes and growth temperatures. In Experiment 1, well-watered and drought-stressed conditions were imposed on two genotypes; in Experiment 2, the two water regimes combined with high (HT), medium (MT) and low (LT) growth temperatures were imposed on one of the genotypes. Rd was estimated from simultaneous gas exchange and chlorophyll fluorescence measurements at six leaf temperatures (Tleaf ) for each treatment, using the Yin method for nonphotorespiratory conditions and the nonrectangular hyperbolic fitting method for photorespiratory conditions. The two genotypes responded similarly to growth and measurement conditions. Estimates of Rd for nonphotorespiratory conditions were generally higher than those for photorespiratory conditions, but their responses to Tleaf were similar. Under well-watered conditions, Rd and its sensitivity to Tleaf slightly acclimated to LT, but did not acclimate to HT. Temperature sensitivities of Rd were considerably suppressed by drought, and the suppression varied among growth temperatures. Thus, it is necessary to quantify interactions between drought and growth temperature for reliably modelling Rd under climate change. Our study also demonstrated that the Kok method, one of the currently popular methods for estimating Rd , underestimated Rd significantly.
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Affiliation(s)
- Liang Fang
- Department of Plant Sciences, Centre for Crop Systems AnalysisWageningen University & ResearchWageningenThe Netherlands
| | - Xinyou Yin
- Department of Plant Sciences, Centre for Crop Systems AnalysisWageningen University & ResearchWageningenThe Netherlands
| | - Peter E. L. van der Putten
- Department of Plant Sciences, Centre for Crop Systems AnalysisWageningen University & ResearchWageningenThe Netherlands
| | - Pierre Martre
- LEPSE, Institut Agro SupAgro, INRAE, Univ MontpellierMontpellierFrance
| | - Paul C. Struik
- Department of Plant Sciences, Centre for Crop Systems AnalysisWageningen University & ResearchWageningenThe Netherlands
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10
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Senapati N, Semenov MA, Halford NG, Hawkesford MJ, Asseng S, Cooper M, Ewert F, van Ittersum MK, Martre P, Olesen JE, Reynolds M, Rötter RP, Webber H. Global wheat production could benefit from closing the genetic yield gap. Nat Food 2022; 3:532-541. [PMID: 37117937 DOI: 10.1038/s43016-022-00540-9] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/01/2021] [Accepted: 05/20/2022] [Indexed: 04/30/2023]
Abstract
Global food security requires food production to be increased in the coming decades. The closure of any existing genetic yield gap (Yig) by genetic improvement could increase crop yield potential and global production. Here we estimated present global wheat Yig, covering all wheat-growing environments and major producers, by optimizing local wheat cultivars using the wheat model Sirius. The estimated mean global Yig was 51%, implying that global wheat production could benefit greatly from exploiting the untapped global Yig through the use of optimal cultivar designs, utilization of the vast variation available in wheat genetic resources, application of modern advanced breeding tools, and continuous improvements of crop and soil management.
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Affiliation(s)
- Nimai Senapati
- Plant Sciences Department, Rothamsted Research, Harpenden, UK.
| | | | - Nigel G Halford
- Plant Sciences Department, Rothamsted Research, Harpenden, UK
| | | | - Senthold Asseng
- TUM School of Life Sciences, Technical University of Munich, Freising, Germany
| | - Mark Cooper
- The University of Queensland, Queensland Alliance for Agriculture and Food Innovation, Centre for Crop Science, Brisbane, Queensland, Australia
| | - Frank Ewert
- Institute of Crop Science and Resource Conservation INRES, University of Bonn, Bonn, Germany
- Leibniz Centre for Agricultural Landscape Research, Müncheberg, Germany
| | | | - Pierre Martre
- LEPSE, Université Montpellier, INRAE, Institut Agro Montpellier, Montpellier, France
| | - Jørgen E Olesen
- Department of Agroecology, Aarhus University, Tjele, Denmark
| | - Matthew Reynolds
- International Maize and Wheat Improvement Center, Texcoco, Mexico
| | - Reimund P Rötter
- Tropical Plant Production & Agricultural Systems Modelling (TROPAGS), University of Göttingen, Göttingen, Germany
- Centre of Biodiversity and Sustainable Land Use (CBL), University of Göttingen, Göttingen, Germany
| | - Heidi Webber
- Institute of Crop Science and Resource Conservation INRES, University of Bonn, Bonn, Germany
- Leibniz Centre for Agricultural Landscape Research, Müncheberg, Germany
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11
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Leveau S, Parent B, Zaka S, Martre P. Sensitivities to temperature and evaporative demand in wheat relatives. J Exp Bot 2021:erab431. [PMID: 34559211 DOI: 10.1093/jxb/erab431] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/12/2021] [Indexed: 06/13/2023]
Abstract
There is potential sources of alleles and genes currently locked into wheat-related species that could be introduced into wheat breeding programs for current and future hot and dry climates. However, neither the intra- nor the inter-specific diversity of the responses of leaf growth and transpiration to temperature and evaporative demand have been investigated in a large diversity of wheat-related species. By analysing 12 groups of wheat-related sub-species, we questioned the n-dimensional structure of the genetic diversity for traits linked to plant vegetative structures and development, leaf expansion and transpiration together with their responses to "non-stressing" range of temperature and evaporative demand. In addition to provide new insight on how genome type, ploidy level, phylogeny and breeding pressure together structure this genetic diversity, this study provides new mathematical formalisms and the associated parameters of trait responses in the large genetic diversity of wheat-related species. This potentially allow crop models predicting the impact of this diversity on yield, and indicate potential sources of varietal improvement for modern wheat germplasms, through interspecific crosses.
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Affiliation(s)
- Stéphane Leveau
- LEPSE, Univ Montpellier, INRAE, Institut Agro, Montpellier, France
- ITK, Clapiers, France
| | - Boris Parent
- LEPSE, Univ Montpellier, INRAE, Institut Agro, Montpellier, France
| | | | - Pierre Martre
- LEPSE, Univ Montpellier, INRAE, Institut Agro, Montpellier, France
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12
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Liu S, Baret F, Abichou M, Manceau L, Andrieu B, Weiss M, Martre P. Importance of the description of light interception in crop growth models. Plant Physiol 2021; 186:977-997. [PMID: 33710303 PMCID: PMC8253170 DOI: 10.1093/plphys/kiab113] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/02/2020] [Accepted: 02/11/2021] [Indexed: 05/22/2023]
Abstract
Canopy light interception determines the amount of energy captured by a crop, and is thus critical to modeling crop growth and yield, and may substantially contribute to the prediction uncertainty of crop growth models (CGMs). We thus analyzed the canopy light interception models of the 26 wheat (Triticum aestivum) CGMs used by the Agricultural Model Intercomparison and Improvement Project (AgMIP). Twenty-one CGMs assume that the light extinction coefficient (K) is constant, varying from 0.37 to 0.80 depending on the model. The other models take into account the illumination conditions and assume either that all green surfaces in the canopy have the same inclination angle (θ) or that θ distribution follows a spherical distribution. These assumptions have not yet been evaluated due to a lack of experimental data. Therefore, we conducted a field experiment with five cultivars with contrasting leaf stature sown at normal and double row spacing, and analyzed θ distribution in the canopies from three-dimensional canopy reconstructions. In all the canopies, θ distribution was well represented by an ellipsoidal distribution. We thus carried out an intercomparison between the light interception models of the AgMIP-Wheat CGMs ensemble and a physically based K model with ellipsoidal leaf angle distribution and canopy clumping (KellC). Results showed that the KellC model outperformed current approaches under most illumination conditions and that the uncertainty in simulated wheat growth and final grain yield due to light models could be as high as 45%. Therefore, our results call for an overhaul of light interception models in CGMs.
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Affiliation(s)
- Shouyang Liu
- LEPSE, Univ Montpellier, INRAE, Institut Agro Montpellier, Montpellier, France
- CAPTE-EMMAH, Université d'Avignon et des Pays de Vaucluse, INRAE, Avignon, France
- PheniX, Plant Phenomics Research Centre, Nanjing Agricultural University, Nanjing, China
| | - Frédéric Baret
- CAPTE-EMMAH, Université d'Avignon et des Pays de Vaucluse, INRAE, Avignon, France
| | | | - Loïc Manceau
- LEPSE, Univ Montpellier, INRAE, Institut Agro Montpellier, Montpellier, France
| | - Bruno Andrieu
- EcoSys, INRAE, AgroParisTech, Thiverval-Grignon, France
| | - Marie Weiss
- CAPTE-EMMAH, Université d'Avignon et des Pays de Vaucluse, INRAE, Avignon, France
| | - Pierre Martre
- LEPSE, Univ Montpellier, INRAE, Institut Agro Montpellier, Montpellier, France
- Author for communication:
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13
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Barillot R, De Swaef T, Combes D, Durand JL, Escobar-Gutiérrez AJ, Martre P, Perrot C, Roy E, Frak E. Leaf elongation response to blue light is mediated by stomatal-induced variations in transpiration in Festuca arundinacea. J Exp Bot 2021; 72:2642-2656. [PMID: 33326568 DOI: 10.1093/jxb/eraa585] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/30/2020] [Accepted: 12/14/2020] [Indexed: 06/12/2023]
Abstract
Reduced blue light irradiance is known to enhance leaf elongation rate (LER) in grasses, but the mechanisms involved have not yet been elucidated. We investigated whether leaf elongation response to reduced blue light could be mediated by stomata-induced variations of plant transpiration. Two experiments were carried out on tall fescue in order to monitor LER and transpiration under reduced blue light irradiance. Additionally, LER dynamics were compared with those observed in the response to vapour pressure deficit (VPD)-induced variations of transpiration. Finally, we developed a model of water flow within a tiller to simulate the observed short-term response of LER to various transpiration regimes. LER dramatically increased in response to blue light reduction and then reached new steady states, which remained higher than the control. Reduced blue light triggered a simultaneous stomatal closure which induced an immediate decrease of leaf transpiration. The hydraulic model of leaf elongation accurately predicted the LER response to blue light and VPD, resulting from an increase in the growth-induced water potential gradient in the leaf growth zone. Our results suggest that the blue light signal is sensed by stomata of expanded leaves and transduced to the leaf growth zone through the hydraulic architecture of the tiller.
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Affiliation(s)
| | - Tom De Swaef
- Plant Sciences Unit, Institute for Agricultural and Fisheries Research (ILVO), Melle, Belgium
| | | | | | | | - Pierre Martre
- INRAE, Univ Montpellier, Montpellier SupAgro, UMR LEPSE, Montpellier, France
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14
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Manceau G, Sabbagh C, Mege D, Lakkis Z, Bege T, Tuech JJ, Benoist S, Lefèvre JH, Karoui M, Bridoux V, Venara A, Beyer‐Berjot L, Codjia T, Dazza M, Gagnat G, Hamel S, Mallet L, Martre P, Philouze G, Roussel E, Tortajada P, Dumaine AS, Heyd B, Paquette B, Brunetti F, Esposito F, Lizzi V, Michot N, Denost Q, Rullier E, Tresallet C, Tetard O, Rivier P, Fayssal E, Collard M, Moszkowicz D, Lupinacci R, Peschaud F, Etienne JC, Loge L, Bege T, Corte H, D’Annunzio E, Humeau M, Issard J, Munoz N, Abba J, Jafar Y, Lacaze L, Sage PY, Susoko L, Trilling B, Arvieux C, Mauvais F, Ulloa‐Severino B, Pitel S, Vauchaussade de Chaumont A, Badic B, Blanc B, Bert M, Rat P, Ortega‐Deballon P, Chau A, Dejeante C, Piessen G, Grégoire E, Alfarai A, Cabau M, David A, Kadoche D, Dufour F, Goin G, Goudard Y, Pauleau G, Sockeel P, Villeon B, Pautrat K, Eveno C, Abdalla S, Couchard AC, Balbo G, Mabrut JY, Bellinger J, Bertrand M, Aumont A, Duchalais E, Messière AS, Tranchart A, Cazauran JB, Pichot‐Delahaye V, Dubuisson V, Maggiori L, Panis Y, Djawad‐Boumediene B, Fuks D, Kahn X, Huart E, Catheline JM, Lailler G, Baraket O, Baque P, Diaz de Cerio JM, Mariol P, Maes B, Fernoux P, Guillem P, Chatelain E, de Saint Roman C, Fixot K, Voron T, Parc Y. Colon sparing resection versus extended colectomy for left-sided obstructing colon cancer with caecal ischaemia or perforation: a nationwide study from the French Surgical Association. Colorectal Dis 2020; 22:1304-1313. [PMID: 32368856 DOI: 10.1111/codi.15111] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/14/2020] [Accepted: 04/02/2020] [Indexed: 02/08/2023]
Abstract
AIM It is not known whether patients with obstructive left colon cancer (OLCC) with caecal ischaemia or diastatic perforation (defined as a blowout of the caecal wall related to colonic overdistension) should undergo a (sub)total colectomy (STC) or an ileo-caecal resection with double-barrelled ileo-colostomy. We aimed to compare the results of these two strategies. METHOD From 2000 to 2015, 1220 patients with OLCC underwent surgery by clinicians who were members of the French Surgical Association. Of these cases, 201 (16%) were found to have caecal ischaemia or diastatic perforation intra-operatively: 174 patients (87%) underwent a STC (extended colectomy group) and 27 (13%) an ileo-caecal resection with double-end stoma (colon-sparing group). Outcomes were compared retrospectively. RESULTS In the extended colectomy group, 95 patients (55%) had primary anastomosis and 79 (45%) had a STC with an end ileostomy. In the colon-sparing group, 10 patients (37%) had simultaneous resection of their primary tumour with segmental colectomy and an anastomosis which was protected by a double-barrelled ileo-colostomy. The demographic data for the two groups were comparable. Median operative time was longer in the STC group (P = 0.0044). There was a decrease in postoperative mortality (7% vs 12%, P = 0.75) and overall morbidity (56% vs 67%, P = 0.37) including surgical (30% vs 40%, P = 0.29) and severe complications (17% vs 27%, P = 0.29) in the colon-sparing group, although these differences did not reach statistical significance. Cumulative morbidity included all surgical stages and the rate of permanent stoma was 66% and 37%, respectively, with no significant difference between the two groups. Overall survival and disease-free survival were similar between the two groups. CONCLUSION The colon-sparing strategy may represent a valid and safe alternative to STC in OLCC patients with caecal ischaemia or diastatic perforation.
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Affiliation(s)
- G Manceau
- Department of Digestive Surgery, Assistance Publique-Hôpitaux de Paris, Pitié Salpêtrière University Hospital, Sorbonne Université, Paris, France
| | - C Sabbagh
- Department of Digestive Surgery, Amiens University Hospital, Amiens, France
| | - D Mege
- Department of Digestive Surgery, Assistance Publique-Hôpitaux de Marseille, Timone University Hospital, Marseille, France
| | - Z Lakkis
- Department of Digestive Surgery, Besançon University Hospital, Besançon, France
| | - T Bege
- Department of Digestive Surgery, Assistance Publique Hôpitaux de Marseille, North University Hospital, Marseille, France
| | - J J Tuech
- Department of Digestive Surgery, Charles Nicolle University Hospital, Rouen, France
| | - S Benoist
- Department of Digestive Surgery, Assistance Publique-Hôpitaux de Paris, Bicêtre University Hospital, Université Paris-Sud, Le Kremlin Bicêtre, France
| | - J H Lefèvre
- Department of Digestive Surgery, Assistance Publique-Hôpitaux de Paris, Saint-Antoine University Hospital, Sorbonne Université, Paris, France
| | - M Karoui
- Department of Digestive Surgery, Assistance Publique-Hôpitaux de Paris, Pitié Salpêtrière University Hospital, Sorbonne Université, Paris, France
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15
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Bonnot T, Martre P, Hatte V, Dardevet M, Leroy P, Bénard C, Falagán N, Martin-Magniette ML, Deborde C, Moing A, Gibon Y, Pailloux M, Bancel E, Ravel C. Omics Data Reveal Putative Regulators of Einkorn Grain Protein Composition under Sulfur Deficiency. Plant Physiol 2020; 183:501-516. [PMID: 32295821 PMCID: PMC7271774 DOI: 10.1104/pp.19.00842] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/26/2019] [Accepted: 03/27/2020] [Indexed: 05/06/2023]
Abstract
Understanding the molecular mechanisms controlling the accumulation of grain storage proteins in response to nitrogen (N) and sulfur (S) nutrition is essential to improve cereal grain nutritional and functional properties. Here, we studied the grain transcriptome and metabolome responses to postanthesis N and S supply for the diploid wheat einkorn (Triticum monococcum). During grain filling, 848 transcripts and 24 metabolites were differentially accumulated in response to N and S availability. The accumulation of total free amino acids per grain and the expression levels of 241 genes showed significant modifications during most of the grain filling period and were upregulated in response to S deficiency. Among them, 24 transcripts strongly responded to S deficiency and were identified in coexpression network analyses as potential coordinators of the grain response to N and S supply. Sulfate transporters and genes involved in sulfate and Met metabolism were upregulated, suggesting regulation of the pool of free amino acids and of the grain N-to-S ratio. Several genes highlighted in this study might limit the impact of S deficiency on the accumulation of grain storage proteins.
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Affiliation(s)
- Titouan Bonnot
- Genetics Diversity and Ecophysiology of Cereals, Institut National de l'Agriculture, de l'Alimentation et de l'Environnement (INRAE), Université Clermont-Auvergne, 63000 Clermont-Ferrand, France
| | - Pierre Martre
- Genetics Diversity and Ecophysiology of Cereals, Institut National de l'Agriculture, de l'Alimentation et de l'Environnement (INRAE), Université Clermont-Auvergne, 63000 Clermont-Ferrand, France
| | - Victor Hatte
- Genetics Diversity and Ecophysiology of Cereals, Institut National de l'Agriculture, de l'Alimentation et de l'Environnement (INRAE), Université Clermont-Auvergne, 63000 Clermont-Ferrand, France
| | - Mireille Dardevet
- Genetics Diversity and Ecophysiology of Cereals, Institut National de l'Agriculture, de l'Alimentation et de l'Environnement (INRAE), Université Clermont-Auvergne, 63000 Clermont-Ferrand, France
| | - Philippe Leroy
- Genetics Diversity and Ecophysiology of Cereals, Institut National de l'Agriculture, de l'Alimentation et de l'Environnement (INRAE), Université Clermont-Auvergne, 63000 Clermont-Ferrand, France
| | - Camille Bénard
- Biologie du Fruit et Pathologie, INRAE, Université de Bordeaux, Plateforme Métabolome Bordeaux, MetaboHUB-PHENOME, 33140 Villenave d'Ornon, France
| | - Natalia Falagán
- Biologie du Fruit et Pathologie, INRAE, Université de Bordeaux, Plateforme Métabolome Bordeaux, MetaboHUB-PHENOME, 33140 Villenave d'Ornon, France
| | - Marie-Laure Martin-Magniette
- L'Institut des Sciences des Plantes (IPS2), CNRS, INRAE, Université Paris-Sud, Université Evry, Université Paris-Saclay, 91400 Orsay, France
- Mathématiques et informatique appliqués (MIA)-Paris, AgroParisTech, INRAE, Université Paris-Saclay, 75231 Paris, France
| | - Catherine Deborde
- Biologie du Fruit et Pathologie, INRAE, Université de Bordeaux, Plateforme Métabolome Bordeaux, MetaboHUB-PHENOME, 33140 Villenave d'Ornon, France
| | - Annick Moing
- Biologie du Fruit et Pathologie, INRAE, Université de Bordeaux, Plateforme Métabolome Bordeaux, MetaboHUB-PHENOME, 33140 Villenave d'Ornon, France
| | - Yves Gibon
- Biologie du Fruit et Pathologie, INRAE, Université de Bordeaux, Plateforme Métabolome Bordeaux, MetaboHUB-PHENOME, 33140 Villenave d'Ornon, France
| | - Marie Pailloux
- Laboratoire d'Informatique, de Modélisation et d'Optimisation des Systèmes, Centre National de la Recherche Scientifique (CNRS), Université Clermont-Auvergne, 63000 Clermont-Ferrand, France
| | - Emmanuelle Bancel
- Genetics Diversity and Ecophysiology of Cereals, Institut National de l'Agriculture, de l'Alimentation et de l'Environnement (INRAE), Université Clermont-Auvergne, 63000 Clermont-Ferrand, France
| | - Catherine Ravel
- Genetics Diversity and Ecophysiology of Cereals, Institut National de l'Agriculture, de l'Alimentation et de l'Environnement (INRAE), Université Clermont-Auvergne, 63000 Clermont-Ferrand, France
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16
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Rincent R, Malosetti M, Ababaei B, Touzy G, Mini A, Bogard M, Martre P, Le Gouis J, van Eeuwijk F. Using crop growth model stress covariates and AMMI decomposition to better predict genotype-by-environment interactions. Theor Appl Genet 2019; 132:3399-3411. [PMID: 31562567 DOI: 10.1007/s00122-019-03432-y] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/23/2019] [Accepted: 09/17/2019] [Indexed: 05/20/2023]
Abstract
We propose new methods to predict genotype × environment interaction by selecting relevant environmental covariates and using an AMMI decomposition of the interaction. Farmers are asked to produce more efficiently and to reduce their inputs in the context of climate change. They have to face more and more limiting factors that can combine in numerous stress scenarios. One solution to this challenge is to develop varieties adapted to specific environmental stress scenarios. For this, plant breeders can use genomic predictions coupled with environmental characterization to identify promising combinations of genes in relation to stress covariates. One way to do it is to take into account the genetic similarity between varieties and the similarity between environments within a mixed model framework. Molecular markers and environmental covariates (EC) can be used to estimate relevant covariance matrices. In the present study, based on a multi-environment trial of 220 European elite winter bread wheat (Triticum aestivum L.) varieties phenotyped in 42 environments, we compared reference regression models potentially including ECs, and proposed alternative models to increase prediction accuracy. We showed that selecting a subset of ECs, and estimating covariance matrices using an AMMI decomposition to benefit from the information brought by the phenotypic records of the training set are promising approaches to better predict genotype-by-environment interactions (G × E). We found that using a different kinship for the main genetic effect and the G × E effect increased prediction accuracy. Our study also demonstrates that integrative stress indexes simulated by crop growth models are more efficient to capture G × E than climatic covariates.
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Affiliation(s)
- R Rincent
- INRA, UMR 1095 Génétique, Diversité et Ecophysiologie des Céréales, 5 Chemin de Beaulieu, 63100, Clermont-Ferrand, France.
- Université Blaise Pascal, UMR 1095 Génétique, Diversité et Ecophysiologie des Céréales, 63178, Aubière Cedex, France.
| | - M Malosetti
- Biometris, Wageningen University and Research Center, PO Box 100, 6700 AC, Wageningen, The Netherlands
| | - B Ababaei
- LEPSE, INRA, Montpellier SupAgro, Université Montpellier, 34060, Montpellier, France
- Native Trait Research, Limagrain Europe, 63720, Chappes, France
| | - G Touzy
- INRA, UMR 1095 Génétique, Diversité et Ecophysiologie des Céréales, 5 Chemin de Beaulieu, 63100, Clermont-Ferrand, France
- Université Blaise Pascal, UMR 1095 Génétique, Diversité et Ecophysiologie des Céréales, 63178, Aubière Cedex, France
- Arvalis Institut Du Végétal, 6 Chemin de la Côté Vieille, 31450, Baziège, France
- BIOGEMMA, Genetics and Genomics in Cereals, 63720, Chappes, France
| | - A Mini
- INRA, UMR 1095 Génétique, Diversité et Ecophysiologie des Céréales, 5 Chemin de Beaulieu, 63100, Clermont-Ferrand, France
| | - M Bogard
- Arvalis Institut Du Végétal, 6 Chemin de la Côté Vieille, 31450, Baziège, France
| | - P Martre
- LEPSE, INRA, Montpellier SupAgro, Université Montpellier, 34060, Montpellier, France
| | - J Le Gouis
- INRA, UMR 1095 Génétique, Diversité et Ecophysiologie des Céréales, 5 Chemin de Beaulieu, 63100, Clermont-Ferrand, France
- Université Blaise Pascal, UMR 1095 Génétique, Diversité et Ecophysiologie des Céréales, 63178, Aubière Cedex, France
| | - F van Eeuwijk
- Biometris, Wageningen University and Research Center, PO Box 100, 6700 AC, Wageningen, The Netherlands
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17
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Liu S, Martre P, Buis S, Abichou M, Andrieu B, Baret F. Estimation of Plant and Canopy Architectural Traits Using the Digital Plant Phenotyping Platform. Plant Physiol 2019; 181:881-890. [PMID: 31420444 PMCID: PMC6836827 DOI: 10.1104/pp.19.00554] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/08/2019] [Accepted: 08/01/2019] [Indexed: 05/19/2023]
Abstract
The extraction of desirable heritable traits for crop improvement from high-throughput phenotyping (HTP) observations remains challenging. We developed a modeling workflow named "Digital Plant Phenotyping Platform" (D3P), to access crop architectural traits from HTP observations. D3P couples the Architectural model of DEvelopment based on L-systems (ADEL) wheat (Triticum aestivum) model (ADEL-Wheat), which describes the time course of the three-dimensional architecture of wheat crops, with simulators of images acquired with HTP sensors. We demonstrated that a sequential assimilation of the green fraction derived from Red-Green-Blue images of the crop into D3P provides accurate estimates of five key parameters (phyllochron, lamina length of the first leaf, rate of elongation of leaf lamina, number of green leaves at the start of leaf senescence, and minimum number of green leaves) of the ADEL-Wheat model that drive the time course of green area index and the number of axes with more than three leaves at the end of the tillering period. However, leaf and tiller orientation and inclination characteristics were poorly estimated. D3P was also used to optimize the observational configuration. The results, obtained from in silico experiments conducted on wheat crops at several vegetative stages, showed that the accessible traits could be estimated accurately with observations made at 0° and 60° zenith view inclination with a temporal frequency of 100 °Cd (degree day). This illustrates the potential of the proposed holistic approach that integrates all the available information into a consistent system for interpretation. The potential benefits and limitations of the approach are further discussed.
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Affiliation(s)
- Shouyang Liu
- Environnement Méditerranéen et Modélisation des Agro-Hydrosystèmes (EMMAH), Institut National de la Recherche Agronomique, Unité Mixte de Recherche 1114 Domaine Saint-Paul, 84914 Avignon Cedex 9, France
- Laboratoire d'Écophysiologie des Plantes sous Stress Environnementaux (LEPSE), Université Montpellier, Institut National de la Recherche Agronomique, Montpellier SupAgro, 34060 Montpellier, France
| | - Pierre Martre
- Laboratoire d'Écophysiologie des Plantes sous Stress Environnementaux (LEPSE), Université Montpellier, Institut National de la Recherche Agronomique, Montpellier SupAgro, 34060 Montpellier, France
| | - Samuel Buis
- Environnement Méditerranéen et Modélisation des Agro-Hydrosystèmes (EMMAH), Institut National de la Recherche Agronomique, Unité Mixte de Recherche 1114 Domaine Saint-Paul, 84914 Avignon Cedex 9, France
| | - Mariem Abichou
- Institut National de la Recherche Agronomique-AgroParisTech, Unité Mixte de Recherche 1091 Environnement et Grandes Cultures, 78850 Thiverval-Grignon, France
| | - Bruno Andrieu
- Institut National de la Recherche Agronomique-AgroParisTech, Unité Mixte de Recherche 1091 Environnement et Grandes Cultures, 78850 Thiverval-Grignon, France
| | - Frédéric Baret
- Environnement Méditerranéen et Modélisation des Agro-Hydrosystèmes (EMMAH), Institut National de la Recherche Agronomique, Unité Mixte de Recherche 1114 Domaine Saint-Paul, 84914 Avignon Cedex 9, France
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Porter JR, Challinor AJ, Henriksen CB, Howden SM, Martre P, Smith P. Invited review: Intergovernmental Panel on Climate Change, agriculture, and food-A case of shifting cultivation and history. Glob Chang Biol 2019; 25:2518-2529. [PMID: 31095820 DOI: 10.1111/gcb.14700] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/06/2019] [Accepted: 04/01/2019] [Indexed: 05/23/2023]
Abstract
Since 1990, the Intergovernmental Panel on Climate Change (IPCC) has produced five Assessment Reports (ARs), in which agriculture as the production of food for humans via crops and livestock have featured in one form or another. A constructed database of the ca. 2,100 cited experiments and simulations in the five ARs was analyzed with respect to impacts on yields via crop type, region, and whether adaptation was included. Quantitative data on impacts and adaptation in livestock farming have been extremely scarce in the ARs. The main conclusions from impact and adaptation are that crop yields will decline, but that responses have large statistical variation. Mitigation assessments in the ARs have used both bottom-up and top-down methods but need better to link emissions and their mitigation with food production and security. Relevant policy options have become broader in later ARs and included more of the social and nonproduction aspects of food security. Our overall conclusion is that agriculture and food security, which are two of the most central, critical, and imminent issues in climate change, have been dealt with an unfocussed and inconsistent manner between the IPCC five ARs. This is partly a result of not only agriculture spanning two IPCC working groups but also the very strong focus on projections from computer crop simulation modeling. For the future, we suggest a need to examine interactions between themes such as crop resource use efficiencies and to include all production and nonproduction aspects of food security in future roles for integrated assessment models.
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Affiliation(s)
- John R Porter
- CIHEAM-IAMM - SupAgro - MUSE University of Montpellier, Montpellier, France
- Plant and Environmental Sciences, University of Copenhagen, Taastrup, Denmark
| | - Andrew J Challinor
- School of Earth and Environment, Institute for Climate and Atmospheric Science (ICAS), University of Leeds, Leeds, UK
| | | | - Stuart Mark Howden
- Climate Change Institute, Australian National University, Canberra, ACT, Australia
| | - Pierre Martre
- LEPSE, INRA, Montpellier SupAgro, Université Montpellier, Montpellier, France
| | - Pete Smith
- Institute of Biological and Environmental Sciences, University of Aberdeen, Aberdeen, UK
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19
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Bancel E, Bonnot T, Davanture M, Alvarez D, Zivy M, Martre P, Déjean S, Ravel C. Proteomic Data Integration Highlights Central Actors Involved in Einkorn ( Triticum monococcum ssp. monococcum) Grain Filling in Relation to Grain Storage Protein Composition. Front Plant Sci 2019; 10:832. [PMID: 31333693 PMCID: PMC6620720 DOI: 10.3389/fpls.2019.00832] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 02/15/2019] [Accepted: 06/07/2019] [Indexed: 06/10/2023]
Abstract
Albumins and globulins (AGs) of wheat endosperm represent about 20% of total grain proteins. Some of these physiologically active proteins can influence the synthesis of storage proteins (SPs) (gliadins and glutenins) and consequently, rheological properties of wheat flour and processing. To identify such AGs, data, (published by Bonnot et al., 2017) concerning abundance in 352 AGs and in the different seed SPs during grain filling and in response to different nitrogen (N) and sulfur (S) supply, were integrated with mixOmics R package. Relationships between AGs and SPs were first unraveled using the unsupervised method sparse Partial Least Square, also known as Projection to Latent Structure (sPLS). Then, data were integrated using a supervised approach taking into account the nutrition and the grain developmental stage. We used the block.splda procedure also referred to as DIABLO (Data Integration Analysis for Biomarker discovery using Latent variable approaches for Omics studies). These approaches led to the identification of discriminant and highly correlated features from the two datasets (AGs and SPs) which are not necessarily differentially expressed during seed development or in response to N or S supply. Eighteen AGs were correlated with the quantity of SPs per grain. A statistical validation of these proteins by genetic association analysis confirmed that 5 out of this AG set were robust candidate proteins able to modulate the seed SP synthesis. In conclusion, this latter result confirmed that the integrative strategy is an adequate way to reduce the number of potentially relevant AGs for further functional validation.
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Affiliation(s)
- Emmanuelle Bancel
- UMR GDEC, Institut National de la Recherche Agronomique (INRA), Université Clermont Auvergne, Clermont-Ferrand, France
- UMR1095, Genetics Diversity and Ecophysiology of Cereals, Clermont Auvergne University, Clermont-Ferrand, France
| | - Titouan Bonnot
- UMR GDEC, Institut National de la Recherche Agronomique (INRA), Université Clermont Auvergne, Clermont-Ferrand, France
- UMR1095, Genetics Diversity and Ecophysiology of Cereals, Clermont Auvergne University, Clermont-Ferrand, France
| | - Marlène Davanture
- UMR GQE, Institut National de la Recherche Agronomique (INRA), Centre National de la Recherche Scientifique (CNRS), Agro ParisTech, Université Paris-Sud – Université Paris-Saclay, Gif-sur-Yvette, France
| | - David Alvarez
- UMR GDEC, Institut National de la Recherche Agronomique (INRA), Université Clermont Auvergne, Clermont-Ferrand, France
- UMR1095, Genetics Diversity and Ecophysiology of Cereals, Clermont Auvergne University, Clermont-Ferrand, France
| | - Michel Zivy
- UMR GQE, Institut National de la Recherche Agronomique (INRA), Centre National de la Recherche Scientifique (CNRS), Agro ParisTech, Université Paris-Sud – Université Paris-Saclay, Gif-sur-Yvette, France
| | - Pierre Martre
- UMR GDEC, Institut National de la Recherche Agronomique (INRA), Université Clermont Auvergne, Clermont-Ferrand, France
- UMR1095, Genetics Diversity and Ecophysiology of Cereals, Clermont Auvergne University, Clermont-Ferrand, France
| | - Sébastien Déjean
- Institut de Mathématiques de Toulouse, UMR5219 Université de Toulouse, Centre National de la Recherche Scientifique (CNRS), Toulouse, France
| | - Catherine Ravel
- UMR GDEC, Institut National de la Recherche Agronomique (INRA), Université Clermont Auvergne, Clermont-Ferrand, France
- UMR1095, Genetics Diversity and Ecophysiology of Cereals, Clermont Auvergne University, Clermont-Ferrand, France
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20
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Manceau G, Mege D, Bridoux V, Lakkis Z, Venara A, Voron T, De Angelis N, Ouaissi M, Sielezneff I, Karoui M, Dazza M, Gagnat G, Hamel S, Mallet L, Martre P, Philouze G, Roussel E, Tortajada P, Dumaine AS, Heyd B, Paquette B, Brunetti F, Esposito F, Lizzi V, Michot N, Denost Q, Tresallet C, Tetard O, Regimbeau JM, Sabbagh C, Rivier P, Fayssal E, Collard M, Moszkowicz D, Peschaud F, Etienne JC, loge L, Beyer L, Bege T, Corte H, D'Annunzio E, Humeau M, Issard J, Munoz N, Abba J, Jafar Y, Lacaze L, Sage PY, Susoko L, Trilling B, Arvieux C, Mauvais F, Ulloa‐Severino B, Lefevre JH, Pitel S, Vauchaussade de Chaumont A, Badic B, Blanc B, Bert M, Rat P, Ortega‐Deballon P, Chau A, Dejeante C, Piessen G, Grégoire E, Alfarai A, Cabau M, David A, Kadoche D, Dufour F, Goin G, Goudard Y, Pauleau G, Sockeel P, De la Villeon B, Pautrat K, Eveno C, Brouquet A, Couchard AC, Balbo G, Mabrut JY, Bellinger J, Bertrand M, Aumont A, Duchalais E, Messière AS, Tranchart A, Cazauran JB, Pichot‐Delahaye V, Dubuisson V, Maggiori L, Djawad‐Boumediene B, Fuks D, Kahn X, Huart E, Catheline JM, Lailler G, Baraket O, Baque P, Diaz de Cerio JM, Mariol P, Maes B, Fernoux P, Guillem P, Chatelain E, de Saint Roman C, Fixot K. Thirty-day mortality after emergency surgery for obstructing colon cancer: survey and dedicated score from the French Surgical Association. Colorectal Dis 2019; 21:782-790. [PMID: 30884089 DOI: 10.1111/codi.14614] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 12/09/2018] [Accepted: 02/27/2019] [Indexed: 02/08/2023]
Abstract
AIM The aim was to define risk factors for postoperative mortality in patients undergoing emergency surgery for obstructing colon cancer (OCC) and to propose a dedicated score. METHOD From 2000 to 2015, 2325 patients were treated for OCC in French surgical centres by members of the French National Surgical Association. A multivariate analysis was performed for variables with P value ≤ 0.20 in the univariate analysis for 30-day mortality. Predictive performance was assessed by the area under the receiver operating characteristic curve. RESULTS A total of 1983 patients were included. Thirty-day postoperative mortality was 7%. Multivariate analysis found five significant independent risk factors: age ≥ 75 (P = 0.013), American Society of Anesthesiologists (ASA) score ≥ III (P = 0.027), pulmonary comorbidity (P = 0.0002), right-sided cancer (P = 0.047) and haemodynamic failure (P < 0.0001). The odds ratio for risk of postoperative death was 3.42 with one factor, 5.80 with two factors, 15.73 with three factors, 29.23 with four factors and 77.25 with five factors. The discriminating capacity in predicting 30-day postoperative mortality was 0.80. CONCLUSION Thirty-day postoperative mortality after emergency surgery for OCC is correlated with age, ASA score, pulmonary comorbidity, site of tumour and haemodynamic failure, with a specific score ranging from 0 to 5.
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Affiliation(s)
- G Manceau
- Department of Digestive Surgery, Assistance Publique Hôpitaux de Paris, Pitié Salpêtrière Hospital, Sorbonne Université, Paris, France
| | - D Mege
- Department of Digestive Surgery, Timone University Hospital, Marseille, France
| | - V Bridoux
- Department of Digestive Surgery, Charles Nicolle University Hospital, Rouen, France
| | - Z Lakkis
- Department of Digestive Surgery, Besançon University Hospital, Besançon, France
| | - A Venara
- Department of Digestive Surgery, Angers University Hospital, Angers, France
| | - T Voron
- Department of Digestive Surgery, Assistance Publique Hôpitaux de Paris, Saint Antoine Hospital, Sorbonne Université, Paris, France
| | - N De Angelis
- Department of Digestive Surgery, Assistance Publique Hôpitaux de Paris, Henri Mondor Hospital, Université Paris-Est (UEP), Créteil, France
| | - M Ouaissi
- Department of Digestive Surgery, Tours University Hospital, Tours, France
| | - I Sielezneff
- Department of Digestive Surgery, Timone University Hospital, Marseille, France
| | - M Karoui
- Department of Digestive Surgery, Assistance Publique Hôpitaux de Paris, Pitié Salpêtrière Hospital, Sorbonne Université, Paris, France
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21
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Affiliation(s)
- Bertrand Muller
- UMR LEPSE, Univ Montpellier, INRA, Montpellier SupAgro, Montpellier, France
| | - Pierre Martre
- UMR LEPSE, Univ Montpellier, INRA, Montpellier SupAgro, Montpellier, France
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22
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Baumont M, Parent B, Manceau L, Brown HE, Driever SM, Muller B, Martre P. Experimental and modeling evidence of carbon limitation of leaf appearance rate for spring and winter wheat. J Exp Bot 2019; 70:2449-2462. [PMID: 30785619 PMCID: PMC6487592 DOI: 10.1093/jxb/erz012] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/26/2018] [Accepted: 01/29/2019] [Indexed: 05/23/2023]
Abstract
Accurate predictions of the timing of physiological stages and the development rate are crucial for predicting crop performance under field conditions. Plant development is controlled by the leaf appearance rate (LAR) and our understanding of how LAR responds to environmental factors is still limited. Here, we tested the hypothesis that carbon availability may account for the effects of irradiance, photoperiod, atmospheric CO2 concentration, and ontogeny on LAR. We conducted three experiments in growth chambers to quantify and disentangle these effects for both winter and spring wheat cultivars. Variations of LAR observed between environmental scenarios were well explained by the supply/demand ratio for carbon, quantified using the photothermal quotient. We therefore developed an ecophysiological model based on the photothermal quotient that accounts for the effects of temperature, irradiance, photoperiod, and ontogeny on LAR. Comparisons of observed leaf stages and LAR with simulations from our model, from a linear thermal-time model, and from a segmented linear thermal-time model corrected for sowing date showed that our model can simulate the observed changes in LAR in the field with the lowest error. Our findings demonstrate that a hypothesis-driven approach that incorporates more physiology in specific processes of crop models can increase their predictive power under variable environments.
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Affiliation(s)
- Maeva Baumont
- LEPSE, Université Montpellier, INRA, Montpellier SupAgro, Montpellier, France
| | - Boris Parent
- LEPSE, Université Montpellier, INRA, Montpellier SupAgro, Montpellier, France
| | - Loïc Manceau
- LEPSE, Université Montpellier, INRA, Montpellier SupAgro, Montpellier, France
| | - Hamish E Brown
- The New Zealand Institute for Plant & Food Research Limited, Private Bag, Christchurch, New Zealand
| | - Steven M Driever
- Centre for Crop Systems Analysis, Department of Plant Sciences, Wageningen University, AK Wageningen, The Netherlands
| | - Bertrand Muller
- LEPSE, Université Montpellier, INRA, Montpellier SupAgro, Montpellier, France
| | - Pierre Martre
- LEPSE, Université Montpellier, INRA, Montpellier SupAgro, Montpellier, France
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23
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Liu B, Martre P, Ewert F, Porter JR, Challinor AJ, Müller C, Ruane AC, Waha K, Thorburn PJ, Aggarwal PK, Ahmed M, Balkovič J, Basso B, Biernath C, Bindi M, Cammarano D, De Sanctis G, Dumont B, Espadafor M, Eyshi Rezaei E, Ferrise R, Garcia-Vila M, Gayler S, Gao Y, Horan H, Hoogenboom G, Izaurralde RC, Jones CD, Kassie BT, Kersebaum KC, Klein C, Koehler AK, Maiorano A, Minoli S, Montesino San Martin M, Naresh Kumar S, Nendel C, O'Leary GJ, Palosuo T, Priesack E, Ripoche D, Rötter RP, Semenov MA, Stöckle C, Streck T, Supit I, Tao F, Van der Velde M, Wallach D, Wang E, Webber H, Wolf J, Xiao L, Zhang Z, Zhao Z, Zhu Y, Asseng S. Global wheat production with 1.5 and 2.0°C above pre-industrial warming. Glob Chang Biol 2019; 25:1428-1444. [PMID: 30536680 DOI: 10.1111/gcb.14542] [Citation(s) in RCA: 21] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/10/2018] [Accepted: 11/24/2018] [Indexed: 05/21/2023]
Abstract
Efforts to limit global warming to below 2°C in relation to the pre-industrial level are under way, in accordance with the 2015 Paris Agreement. However, most impact research on agriculture to date has focused on impacts of warming >2°C on mean crop yields, and many previous studies did not focus sufficiently on extreme events and yield interannual variability. Here, with the latest climate scenarios from the Half a degree Additional warming, Prognosis and Projected Impacts (HAPPI) project, we evaluated the impacts of the 2015 Paris Agreement range of global warming (1.5 and 2.0°C warming above the pre-industrial period) on global wheat production and local yield variability. A multi-crop and multi-climate model ensemble over a global network of sites developed by the Agricultural Model Intercomparison and Improvement Project (AgMIP) for Wheat was used to represent major rainfed and irrigated wheat cropping systems. Results show that projected global wheat production will change by -2.3% to 7.0% under the 1.5°C scenario and -2.4% to 10.5% under the 2.0°C scenario, compared to a baseline of 1980-2010, when considering changes in local temperature, rainfall, and global atmospheric CO2 concentration, but no changes in management or wheat cultivars. The projected impact on wheat production varies spatially; a larger increase is projected for temperate high rainfall regions than for moderate hot low rainfall and irrigated regions. Grain yields in warmer regions are more likely to be reduced than in cooler regions. Despite mostly positive impacts on global average grain yields, the frequency of extremely low yields (bottom 5 percentile of baseline distribution) and yield inter-annual variability will increase under both warming scenarios for some of the hot growing locations, including locations from the second largest global wheat producer-India, which supplies more than 14% of global wheat. The projected global impact of warming <2°C on wheat production is therefore not evenly distributed and will affect regional food security across the globe as well as food prices and trade.
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Affiliation(s)
- Bing Liu
- National Engineering and Technology Center for Information Agriculture, Key Laboratory for Crop System Analysis and Decision Making, Ministry of Agriculture, Jiangsu Key Laboratory for Information Agriculture, Jiangsu Collaborative Innovation Center for Modern Crop Production, Nanjing Agricultural University, Nanjing, China
| | - Pierre Martre
- LEPSE, Université Montpellier, INRA, Montpellier SupAgro, Montpellier, France
| | - Frank Ewert
- Institute of Crop Science and Resource Conservation INRES, University of Bonn, Bonn, Germany
- Leibniz Centre for Agricultural Landscape Research (ZALF), Müncheberg, Germany
| | - John R Porter
- Plant & Environment Sciences, University Copenhagen, Taastrup, Denmark
- Lincoln University, Lincoln, New Zealand
- Montpellier SupAgro, INRA, CIHEAM-IAMM, CIRAD, University Montpellier, Montpellier, France
| | - Andy J Challinor
- Institute for Climate and Atmospheric Science, School of Earth and Environment, University of Leeds, Leeds, UK
- CGIAR-ESSP Program on Climate Change, Agriculture and Food Security, International Centre for Tropical Agriculture (CIAT), Cali, Colombia
| | - Christoph Müller
- Potsdam Institute for Climate Impact Research, Member of the Leibniz Association, Potsdam, Germany
| | - Alex C Ruane
- NASA Goddard Institute for Space Studies, New York, New York
| | | | | | - Pramod K Aggarwal
- CGIAR Research Program on Climate Change, Agriculture and Food Security, BISA-CIMMYT, New Delhi, India
| | - Mukhtar Ahmed
- Biological Systems Engineering, Washington State University, Pullman, Washington
- Department of agronomy, Pir Mehr Ali Shah Arid Agriculture University, Rawalpindi, Pakistan
| | - Juraj Balkovič
- International Institute for Applied Systems Analysis, Ecosystem Services and Management Program, Laxenburg, Austria
- Department of Soil Science, Faculty of Natural Sciences, Comenius University in Bratislava, Bratislava, Slovakia
| | - Bruno Basso
- Department of Earth and Environmental Sciences, Michigan State University East Lansing, East Lansing, Michigan
- W.K. Kellogg Biological Station, Michigan State University, East Lansing, Michigan
| | - Christian Biernath
- Institute of Biochemical Plant Pathology, Helmholtz Zentrum München-German Research Center for Environmental Health, Neuherberg, Germany
| | - Marco Bindi
- Department of Agri-food Production and Environmental Sciences (DISPAA), University of Florence, Florence, Italy
| | | | | | - Benjamin Dumont
- Department AgroBioChem & TERRA Teaching and Research Center, Gembloux Agro-Bio Tech, University of Liege, Gembloux, Belgium
| | - Mónica Espadafor
- IAS-CSIC, Department of Agronomy, University of Cordoba, Cordoba, Spain
| | - Ehsan Eyshi Rezaei
- Institute of Crop Science and Resource Conservation INRES, University of Bonn, Bonn, Germany
- Department of Crop Sciences, University of Göttingen, Göttingen, Germany
| | - Roberto Ferrise
- Department of Agri-food Production and Environmental Sciences (DISPAA), University of Florence, Florence, Italy
| | | | - Sebastian Gayler
- Institute of Soil Science and Land Evaluation, University of Hohenheim, Stuttgart, Germany
| | - Yujing Gao
- Agricultural & Biological Engineering Department, University of Florida, Gainesville, Florida
| | - Heidi Horan
- CSIRO Agriculture and Food, Brisbane, Qld, Australia
| | - Gerrit Hoogenboom
- Agricultural & Biological Engineering Department, University of Florida, Gainesville, Florida
- Institute for Sustainable Food Systems, University of Florida, Gainesville, Florida
| | - Roberto C Izaurralde
- Department of Geographical Sciences, University of Maryland, College Park, Maryland
- Texas A&M AgriLife Research and Extension Center, Texas A&M Univ., Temple, Texas
| | - Curtis D Jones
- Department of Geographical Sciences, University of Maryland, College Park, Maryland
| | - Belay T Kassie
- Agricultural & Biological Engineering Department, University of Florida, Gainesville, Florida
| | - Kurt C Kersebaum
- Leibniz Centre for Agricultural Landscape Research (ZALF), Müncheberg, Germany
| | - Christian Klein
- Institute of Biochemical Plant Pathology, Helmholtz Zentrum München-German Research Center for Environmental Health, Neuherberg, Germany
| | - Ann-Kristin Koehler
- Institute for Climate and Atmospheric Science, School of Earth and Environment, University of Leeds, Leeds, UK
| | - Andrea Maiorano
- LEPSE, Université Montpellier, INRA, Montpellier SupAgro, Montpellier, France
- European Food Safety Authority, Parma, Italy
| | - Sara Minoli
- Potsdam Institute for Climate Impact Research, Member of the Leibniz Association, Potsdam, Germany
| | | | - Soora Naresh Kumar
- Centre for Environment Science and Climate Resilient Agriculture, Indian Agricultural Research Institute, IARI PUSA, New Delhi, India
| | - Claas Nendel
- Leibniz Centre for Agricultural Landscape Research (ZALF), Müncheberg, Germany
| | - Garry J O'Leary
- Department of Economic Development, Jobs, Transport and Resources, Grains Innovation Park, Agriculture Victoria Research, Horsham, Vic., Australia
| | - Taru Palosuo
- Natural Resources Institute Finland (Luke), Helsinki, Finland
| | - Eckart Priesack
- Institute of Biochemical Plant Pathology, Helmholtz Zentrum München-German Research Center for Environmental Health, Neuherberg, Germany
| | | | - Reimund P Rötter
- University of Göttingen, Tropical Plant Production and Agricultural Systems Modelling (TROPAGS), Göttingen, Germany
- Centre of Biodiversity and Sustainable Land Use (CBL), University of Göttingen, Göttingen, Germany
| | | | - Claudio Stöckle
- Biological Systems Engineering, Washington State University, Pullman, Washington
| | - Thilo Streck
- Institute of Soil Science and Land Evaluation, University of Hohenheim, Stuttgart, Germany
| | - Iwan Supit
- Water Systems & Global Change Group and WENR (Water & Food), Wageningen University, Wageningen, The Netherlands
| | - Fulu Tao
- Natural Resources Institute Finland (Luke), Helsinki, Finland
- Institute of Geographical Sciences and Natural Resources Research, Chinese Academy of Science, Beijing, China
| | | | | | - Enli Wang
- CSIRO Agriculture and Food, Black Mountain, ACT, Australia
| | - Heidi Webber
- Institute of Crop Science and Resource Conservation INRES, University of Bonn, Bonn, Germany
- Leibniz Centre for Agricultural Landscape Research (ZALF), Müncheberg, Germany
| | - Joost Wolf
- Plant Production Systems, Wageningen University, Wageningen, The Netherlands
| | - Liujun Xiao
- National Engineering and Technology Center for Information Agriculture, Key Laboratory for Crop System Analysis and Decision Making, Ministry of Agriculture, Jiangsu Key Laboratory for Information Agriculture, Jiangsu Collaborative Innovation Center for Modern Crop Production, Nanjing Agricultural University, Nanjing, China
- Agricultural & Biological Engineering Department, University of Florida, Gainesville, Florida
| | - Zhao Zhang
- State Key Laboratory of Earth Surface Processes and Resource Ecology, Faculty of Geographical Science, Beijing Normal University, Beijing, China
| | - Zhigan Zhao
- CSIRO Agriculture and Food, Black Mountain, ACT, Australia
- Department of Agronomy and Biotechnology, China Agricultural University, Beijing, China
| | - Yan Zhu
- National Engineering and Technology Center for Information Agriculture, Key Laboratory for Crop System Analysis and Decision Making, Ministry of Agriculture, Jiangsu Key Laboratory for Information Agriculture, Jiangsu Collaborative Innovation Center for Modern Crop Production, Nanjing Agricultural University, Nanjing, China
| | - Senthold Asseng
- Agricultural & Biological Engineering Department, University of Florida, Gainesville, Florida
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24
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Boudet J, Merlino M, Plessis A, Gaudin JC, Dardevet M, Perrochon S, Alvarez D, Risacher T, Martre P, Ravel C. The bZIP transcription factor SPA Heterodimerizing Protein represses glutenin synthesis in Triticum aestivum. Plant J 2019; 97:858-871. [PMID: 30444293 DOI: 10.1111/tpj.14163] [Citation(s) in RCA: 22] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/06/2018] [Accepted: 10/31/2018] [Indexed: 05/12/2023]
Abstract
The quality of wheat grain is mainly determined by the quantity and composition of its grain storage proteins (GSPs). Grain storage proteins consist of low- and high-molecular-weight glutenins (LMW-GS and HMW-GS, respectively) and gliadins. The synthesis of these proteins is essentially regulated at the transcriptional level and by the availability of nitrogen and sulfur. The regulation network has been extensively studied in barley where BLZ1 and BLZ2, members of the basic leucine zipper (bZIP) family, activate the synthesis of hordeins. To date, in wheat, only the ortholog of BLZ2, Storage Protein Activator (SPA), has been identified as playing a major role in the regulation of GSP synthesis. Here, the ortholog of BLZ1, named SPA Heterodimerizing Protein (SHP), was identified and its involvement in the transcriptional regulation of the genes coding for GSPs was analyzed. In gel mobility shift assays, SHP binds cis-motifs known to bind to bZIP family transcription factors in HMW-GS and LMW-GS promoters. Moreover, we showed by transient expression assays in wheat endosperm that SHP acts as a repressor of the activity of these gene promoters. This result was confirmed in transgenic lines overexpressing SHP, which were grown with low and high nitrogen supply. The phenotype of SHP-overexpressing lines showed a lower quantity of both LMW-GS and HMW-GS, while the quantity of gliadin was unchanged, whatever the nitrogen availability. Thus, the gliadin/glutenin ratio was increased, which suggests that gliadin and glutenin genes may be differently regulated.
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Affiliation(s)
- Julie Boudet
- UMR GDEC, INRA, Clermont Auvergne University, 63000, Clermont-Ferrand, France
| | - Marielle Merlino
- UMR GDEC, INRA, Clermont Auvergne University, 63000, Clermont-Ferrand, France
| | - Anne Plessis
- UMR GDEC, INRA, Clermont Auvergne University, 63000, Clermont-Ferrand, France
| | | | - Mireille Dardevet
- UMR GDEC, INRA, Clermont Auvergne University, 63000, Clermont-Ferrand, France
| | - Sibille Perrochon
- UMR GDEC, INRA, Clermont Auvergne University, 63000, Clermont-Ferrand, France
| | - David Alvarez
- UMR GDEC, INRA, Clermont Auvergne University, 63000, Clermont-Ferrand, France
| | - Thierry Risacher
- Biogemma, Centre de Recherche de Chappes, 63720, Chappes, France
| | - Pierre Martre
- UMR GDEC, INRA, Clermont Auvergne University, 63000, Clermont-Ferrand, France
| | - Catherine Ravel
- UMR GDEC, INRA, Clermont Auvergne University, 63000, Clermont-Ferrand, France
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25
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Asseng S, Martre P, Maiorano A, Rötter RP, O'Leary GJ, Fitzgerald GJ, Girousse C, Motzo R, Giunta F, Babar MA, Reynolds MP, Kheir AMS, Thorburn PJ, Waha K, Ruane AC, Aggarwal PK, Ahmed M, Balkovič J, Basso B, Biernath C, Bindi M, Cammarano D, Challinor AJ, De Sanctis G, Dumont B, Eyshi Rezaei E, Fereres E, Ferrise R, Garcia-Vila M, Gayler S, Gao Y, Horan H, Hoogenboom G, Izaurralde RC, Jabloun M, Jones CD, Kassie BT, Kersebaum KC, Klein C, Koehler AK, Liu B, Minoli S, Montesino San Martin M, Müller C, Naresh Kumar S, Nendel C, Olesen JE, Palosuo T, Porter JR, Priesack E, Ripoche D, Semenov MA, Stöckle C, Stratonovitch P, Streck T, Supit I, Tao F, Van der Velde M, Wallach D, Wang E, Webber H, Wolf J, Xiao L, Zhang Z, Zhao Z, Zhu Y, Ewert F. Climate change impact and adaptation for wheat protein. Glob Chang Biol 2019; 25:155-173. [PMID: 30549200 DOI: 10.1111/gcb.14481] [Citation(s) in RCA: 126] [Impact Index Per Article: 25.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/09/2018] [Accepted: 09/06/2018] [Indexed: 05/20/2023]
Abstract
Wheat grain protein concentration is an important determinant of wheat quality for human nutrition that is often overlooked in efforts to improve crop production. We tested and applied a 32-multi-model ensemble to simulate global wheat yield and quality in a changing climate. Potential benefits of elevated atmospheric CO2 concentration by 2050 on global wheat grain and protein yield are likely to be negated by impacts from rising temperature and changes in rainfall, but with considerable disparities between regions. Grain and protein yields are expected to be lower and more variable in most low-rainfall regions, with nitrogen availability limiting growth stimulus from elevated CO2 . Introducing genotypes adapted to warmer temperatures (and also considering changes in CO2 and rainfall) could boost global wheat yield by 7% and protein yield by 2%, but grain protein concentration would be reduced by -1.1 percentage points, representing a relative change of -8.6%. Climate change adaptations that benefit grain yield are not always positive for grain quality, putting additional pressure on global wheat production.
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Affiliation(s)
- Senthold Asseng
- Agricultural & Biological Engineering Department, University of Florida, Gainesville, Florida
| | - Pierre Martre
- LEPSE, Université Montpellier INRA, Montpellier SupAgro, Montpellier, France
| | - Andrea Maiorano
- LEPSE, Université Montpellier INRA, Montpellier SupAgro, Montpellier, France
| | - Reimund P Rötter
- Tropical Plant Production and Agricultural Systems Modelling (TROPAGS), University of Göttingen, Göttingen, Germany
- Centre of Biodiversity and Sustainable Land Use (CBL), University of Göttingen, Göttingen, Germany
| | - Garry J O'Leary
- Department of Economic Development Jobs, Transport and Resources, Grains Innovation Park, Agriculture Victoria Research, Horsham, Victoria, Australia
| | - Glenn J Fitzgerald
- Department of Economic Development, Jobs, Transport and Resources, Agriculture Victoria Research, Horsham, Victoria, Australia
- Faculty of Veterinary and Agricultural Sciences, The University of Melbourne, Creswick, Victoria, Australia
| | | | - Rosella Motzo
- Department of Agricultural Sciences, University of Sassari, Sassari, Italy
| | - Francesco Giunta
- Department of Agricultural Sciences, University of Sassari, Sassari, Italy
| | - M Ali Babar
- World Food Crops Breeding, Department of Agronomy, IFAS, University of Florida, Gainesville, Florida
| | | | - Ahmed M S Kheir
- Soils, Water and Environment Research Institute, Agricultural Research Center, Giza, Egypt
| | | | - Katharina Waha
- CSIRO Agriculture and Food, Brisbane, Queensland, Australia
| | - Alex C Ruane
- NASA Goddard Institute for Space Studies, New York, New York
| | - Pramod K Aggarwal
- CGIAR Research Program on Climate Change, Agriculture and Food Security, BISA-CIMMYT, New Delhi, India
| | - Mukhtar Ahmed
- Biological Systems Engineering, Washington State University, Pullman, Washington
- Department of Agronomy, Pir Mehr Ali Shah Arid Agriculture University, Rawalpindi, Pakistan
| | - Juraj Balkovič
- International Institute for Applied Systems Analysis, Ecosystem Services and Management Program, Laxenburg, Austria
- Department of Soil Science, Faculty of Natural Sciences, Comenius University in Bratislava, Bratislava, Slovakia
| | - Bruno Basso
- Department of Earth and Environmental Sciences, Michigan State University, East Lansing, Michigan
- W.K. Kellogg Biological Station, Michigan State University, East Lansing, Michigan
| | - Christian Biernath
- Institute of Biochemical Plant Pathology, Helmholtz Zentrum München-German Research Center for Environmental Health, Neuherberg, Germany
| | - Marco Bindi
- Department of Agri-food Production and Environmental Sciences (DISPAA), University of Florence, Florence, Italy
| | | | - Andrew J Challinor
- Institute for Climate and Atmospheric Science, School of Earth and Environment, University of Leeds, Leeds, UK
- Collaborative Research Program from CGIAR and Future Earth on Climate Change, Agriculture and Food Security (CCAFS), International Centre for Tropical Agriculture (CIAT), Cali, Colombia
| | | | - Benjamin Dumont
- Department Terra & AgroBioChem, Gembloux Agro-Bio Tech, University of Liege, Gembloux, Belgium
| | - Ehsan Eyshi Rezaei
- Institute of Crop Science and Resource Conservation INRES, University of Bonn, Bonn, Germany
- Department of Crop Sciences, University of Göttingen, Göttingen, Germany
| | | | - Roberto Ferrise
- Department of Agri-food Production and Environmental Sciences (DISPAA), University of Florence, Florence, Italy
| | | | - Sebastian Gayler
- Institute of Soil Science and Land Evaluation, University of Hohenheim, Stuttgart, Germany
| | - Yujing Gao
- Agricultural & Biological Engineering Department, University of Florida, Gainesville, Florida
| | - Heidi Horan
- CSIRO Agriculture and Food, Brisbane, Queensland, Australia
| | - Gerrit Hoogenboom
- Agricultural & Biological Engineering Department, University of Florida, Gainesville, Florida
- Institute for Sustainable Food Systems, University of Florida, Gainesville, Florida
| | - R César Izaurralde
- Department of Geographical Sciences, University of Maryland, College Park, Maryland
- Texas A&M AgriLife Research and Extension Center, Texas A&M University, Temple, Texas
| | - Mohamed Jabloun
- Department of Agroecology, Aarhus University, Tjele, Denmark
| | - Curtis D Jones
- Department of Geographical Sciences, University of Maryland, College Park, Maryland
| | - Belay T Kassie
- Agricultural & Biological Engineering Department, University of Florida, Gainesville, Florida
| | | | - Christian Klein
- Institute of Biochemical Plant Pathology, Helmholtz Zentrum München-German Research Center for Environmental Health, Neuherberg, Germany
| | - Ann-Kristin Koehler
- Institute for Climate and Atmospheric Science, School of Earth and Environment, University of Leeds, Leeds, UK
| | - Bing Liu
- Agricultural & Biological Engineering Department, University of Florida, Gainesville, Florida
- National Engineering and Technology Center for Information Agriculture, Key Laboratory for Crop System Analysis and Decision Making, Ministry of Agriculture, Jiangsu Key Laboratory for Information Agriculture, Jiangsu Collaborative Innovation Center for Modern Crop Production, Nanjing Agricultural University, Nanjing, China
| | - Sara Minoli
- Potsdam Institute for Climate Impact Research, Member of the Leibniz Association, Potsdam, Germany
| | | | - Christoph Müller
- Potsdam Institute for Climate Impact Research, Member of the Leibniz Association, Potsdam, Germany
| | - Soora Naresh Kumar
- Centre for Environment Science and Climate Resilient Agriculture, Indian Agricultural Research Institute, IARI PUSA, New Delhi, India
| | - Claas Nendel
- Leibniz Centre for Agricultural Landscape Research, Müncheberg, Germany
| | | | - Taru Palosuo
- Montpellier SupAgro, INRA, CIHEAM-IAMM, CIRAD, University Montpellier, Montpellier, France
| | - John R Porter
- Plant & Environment Sciences, University Copenhagen, Taastrup, Denmark
- Lincoln University, Lincoln, New Zealand
- Montpellier SupAgro, INRA, CIHEAM-IAMM, CIRAD, University Montpellier, Montpellier, France
| | - Eckart Priesack
- Institute of Biochemical Plant Pathology, Helmholtz Zentrum München-German Research Center for Environmental Health, Neuherberg, Germany
| | | | | | - Claudio Stöckle
- Biological Systems Engineering, Washington State University, Pullman, Washington
| | | | - Thilo Streck
- Institute of Soil Science and Land Evaluation, University of Hohenheim, Stuttgart, Germany
| | - Iwan Supit
- Water & Food and Water Systems & Global Change Group, Wageningen University, Wageningen, The Netherlands
| | - Fulu Tao
- Natural Resources Institute Finland (Luke), Helsinki, Finland
- Institute of Geographical Sciences and Natural Resources Research, Chinese Academy of Science, Beijing, China
| | | | | | - Enli Wang
- CSIRO Agriculture and Food, Canberra, Australian Capital Territory, Australia
| | - Heidi Webber
- Institute of Crop Science and Resource Conservation INRES, University of Bonn, Bonn, Germany
- Leibniz Centre for Agricultural Landscape Research, Müncheberg, Germany
| | - Joost Wolf
- Plant Production Systems, Wageningen University, Wageningen, The Netherlands
| | - Liujun Xiao
- National Engineering and Technology Center for Information Agriculture, Key Laboratory for Crop System Analysis and Decision Making, Ministry of Agriculture, Jiangsu Key Laboratory for Information Agriculture, Jiangsu Collaborative Innovation Center for Modern Crop Production, Nanjing Agricultural University, Nanjing, China
| | - Zhao Zhang
- State Key Laboratory of Earth Surface Processes and Resource Ecology, Faculty of Geographical Science, Beijing Normal University, Beijing, China
| | - Zhigan Zhao
- CSIRO Agriculture and Food, Canberra, Australian Capital Territory, Australia
- Department of Agronomy and Biotechnology, China Agricultural University, Beijing, China
| | - Yan Zhu
- National Engineering and Technology Center for Information Agriculture, Key Laboratory for Crop System Analysis and Decision Making, Ministry of Agriculture, Jiangsu Key Laboratory for Information Agriculture, Jiangsu Collaborative Innovation Center for Modern Crop Production, Nanjing Agricultural University, Nanjing, China
| | - Frank Ewert
- Institute of Crop Science and Resource Conservation INRES, University of Bonn, Bonn, Germany
- Leibniz Centre for Agricultural Landscape Research, Müncheberg, Germany
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26
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Wallach D, Martre P, Liu B, Asseng S, Ewert F, Thorburn PJ, van Ittersum M, Aggarwal PK, Ahmed M, Basso B, Biernath C, Cammarano D, Challinor AJ, De Sanctis G, Dumont B, Eyshi Rezaei E, Fereres E, Fitzgerald GJ, Gao Y, Garcia-Vila M, Gayler S, Girousse C, Hoogenboom G, Horan H, Izaurralde RC, Jones CD, Kassie BT, Kersebaum KC, Klein C, Koehler AK, Maiorano A, Minoli S, Müller C, Naresh Kumar S, Nendel C, O'Leary GJ, Palosuo T, Priesack E, Ripoche D, Rötter RP, Semenov MA, Stöckle C, Stratonovitch P, Streck T, Supit I, Tao F, Wolf J, Zhang Z. Multimodel ensembles improve predictions of crop-environment-management interactions. Glob Chang Biol 2018; 24:5072-5083. [PMID: 30055118 DOI: 10.1111/gcb.14411] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/31/2018] [Revised: 07/01/2018] [Accepted: 07/05/2018] [Indexed: 06/08/2023]
Abstract
A recent innovation in assessment of climate change impact on agricultural production has been to use crop multimodel ensembles (MMEs). These studies usually find large variability between individual models but that the ensemble mean (e-mean) and median (e-median) often seem to predict quite well. However, few studies have specifically been concerned with the predictive quality of those ensemble predictors. We ask what is the predictive quality of e-mean and e-median, and how does that depend on the ensemble characteristics. Our empirical results are based on five MME studies applied to wheat, using different data sets but the same 25 crop models. We show that the ensemble predictors have quite high skill and are better than most and sometimes all individual models for most groups of environments and most response variables. Mean squared error of e-mean decreases monotonically with the size of the ensemble if models are added at random, but has a minimum at usually 2-6 models if best-fit models are added first. Our theoretical results describe the ensemble using four parameters: average bias, model effect variance, environment effect variance, and interaction variance. We show analytically that mean squared error of prediction (MSEP) of e-mean will always be smaller than MSEP averaged over models and will be less than MSEP of the best model if squared bias is less than the interaction variance. If models are added to the ensemble at random, MSEP of e-mean will decrease as the inverse of ensemble size, with a minimum equal to squared bias plus interaction variance. This minimum value is not necessarily small, and so it is important to evaluate the predictive quality of e-mean for each target population of environments. These results provide new information on the advantages of ensemble predictors, but also show their limitations.
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Affiliation(s)
| | - Pierre Martre
- UMR LEPSE, INRA, Montpellier SupAgro, Montpellier, France
| | - Bing Liu
- National Engineering and Technology Center for Information Agriculture, Key Laboratory for Crop System Analysis and Decision Making, Ministry of Agriculture, Jiangsu Key Laboratory for Information Agriculture, Jiangsu Collaborative Innovation Center for Modern Crop Production, Nanjing Agricultural University, Nanjing, Jiangsu, China
- Agricultural and Biological Engineering Department, University of Florida, Gainesville, Florida
| | - Senthold Asseng
- Agricultural and Biological Engineering Department, University of Florida, Gainesville, Florida
| | - Frank Ewert
- Institute of Crop Science and Resource Conservation INRES, University of, Bonn, Germany
- Leibniz Centre for Agricultural Landscape Research, Müncheberg, Germany
| | - Peter J Thorburn
- CSIRO Agriculture and Food Brisbane, St Lucia, Queensland, Australia
| | - Martin van Ittersum
- Plant Production Systems Group, Wageningen University, Wageningen, The Netherlands
| | - Pramod K Aggarwal
- CGIAR Research Program on Climate Change, Agriculture and Food Security, BISA-CIMMYT, New Delhi, India
| | - Mukhtar Ahmed
- Biological Systems Engineering, Washington State University, Pullman, Washington
- Department of Agronomy, Pir Mehr Ali Shah Arid Agriculture University, Rawalpindi, Pakistan
| | - Bruno Basso
- Department of Earth and Environmental Sciences, Michigan State University, East Lansing, Michigan
- W.K. Kellogg Biological Station, Michigan State University, East Lansing, Michigan
| | - Christian Biernath
- Institute of Biochemical Plant Pathology, Helmholtz Zentrum München-German Research Center for Environmental Health, Neuherberg, Germany
| | | | - Andrew J Challinor
- Institute for Climate and Atmospheric Science, School of Earth and Environment, University of Leeds, Leeds, UK
- CGIAR-ESSP Program on Climate Change, Agriculture and Food Security, International Centre for Tropical Agriculture (CIAT), Cali, Colombia
| | | | - Benjamin Dumont
- Department Terra & AgroBioChem, Gembloux Agro-Bio Tech, University of Liege, Liege, Belgium
| | - Ehsan Eyshi Rezaei
- Institute of Crop Science and Resource Conservation INRES, University of, Bonn, Germany
- Center for Development Research (ZEF), Bonn, Germany
| | | | - Glenn J Fitzgerald
- Agriculture Victoria Research, Department of Economic Development, Jobs, Transport and Resources, Ballarat, Victoria, Australia
- Faculty of Veterinary and Agricultural Sciences, The University of Melbourne, Creswick, Victoria, Australia
| | - Y Gao
- Agricultural and Biological Engineering Department, University of Florida, Gainesville, Florida
| | | | - Sebastian Gayler
- Institute of Soil Science and Land Evaluation, University of Hohenheim, Stuttgart, Germany
| | | | - Gerrit Hoogenboom
- Agricultural and Biological Engineering Department, University of Florida, Gainesville, Florida
- Institute for Sustainable Food Systems, University of Florida, Gainesville, Florida
| | - Heidi Horan
- CSIRO Agriculture and Food Brisbane, St Lucia, Queensland, Australia
| | - Roberto C Izaurralde
- Department of Geographical Sciences, University of Maryland, College Park, Maryland
- Texas A&M AgriLife Research and Extension Center, Texas A&M University, Temple, Texas
| | - Curtis D Jones
- Texas A&M AgriLife Research and Extension Center, Texas A&M University, Temple, Texas
| | - Belay T Kassie
- Agricultural and Biological Engineering Department, University of Florida, Gainesville, Florida
| | - Kurt C Kersebaum
- Institute of Landscape Systems Analysis, Leibniz Centre for Agricultural Landscape Research, Müncheberg, Germany
| | - Christian Klein
- Institute of Biochemical Plant Pathology, Helmholtz Zentrum München-German Research Center for Environmental Health, Neuherberg, Germany
| | - Ann-Kristin Koehler
- Institute for Climate and Atmospheric Science, School of Earth and Environment, University of Leeds, Leeds, UK
| | | | - Sara Minoli
- Potsdam Institute for Climate Impact Research, Potsdam, Germany
| | | | - Soora Naresh Kumar
- Centre for Environment Science and Climate Resilient Agriculture, Indian Agricultural Research Institute, IARI PUSA, New Delhi, India
| | - Claas Nendel
- Institute of Landscape Systems Analysis, Leibniz Centre for Agricultural Landscape Research, Müncheberg, Germany
| | - Garry J O'Leary
- Grains Innovation Park, Department of Economic Development, Jobs, Transport and Resources, Agriculture Victoria Research, Horsham, Victoria, Australia
| | - Taru Palosuo
- Natural Resources Institute Finland (Luke), Helsinki, Finland
| | - Eckart Priesack
- Institute of Biochemical Plant Pathology, Helmholtz Zentrum München-German Research Center for Environmental Health, Neuherberg, Germany
| | | | - Reimund P Rötter
- Tropical Plant Production and Agricultural Systems Modelling (TROPAGS), University of Göttingen, Göttingen, Germany
- Centre of Biodiversity and Sustainable Land Use (CBL), University of Göttingen, Göttingen, Germany
| | - Mikhail A Semenov
- Computational and Systems Biology Department, Rothamsted Research, Harpenden, Herts, UK
| | - Claudio Stöckle
- Biological Systems Engineering, Washington State University, Pullman, Washington
| | - Pierre Stratonovitch
- Computational and Systems Biology Department, Rothamsted Research, Harpenden, Herts, UK
| | - Thilo Streck
- Institute of Soil Science and Land Evaluation, University of Hohenheim, Stuttgart, Germany
| | - Iwan Supit
- Water & Food and Water Systems & Global Change Group, Wageningen University, Wageningen, The Netherlands
| | - Fulu Tao
- Natural Resources Institute Finland (Luke), Helsinki, Finland
- Institute of Geographical Sciences and Natural Resources Research, Chinese Academy of Science, Beijing, China
| | - Joost Wolf
- Plant Production Systems, Wageningen University, Wageningen, The Netherlands
| | - Zhao Zhang
- State Key Laboratory of Earth Surface Processes and Resource Ecology, Faculty of Geographical Science, Beijing Normal University, Beijing, China
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27
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Webber H, Ewert F, Olesen JE, Müller C, Fronzek S, Ruane AC, Bourgault M, Martre P, Ababaei B, Bindi M, Ferrise R, Finger R, Fodor N, Gabaldón-Leal C, Gaiser T, Jabloun M, Kersebaum KC, Lizaso JI, Lorite IJ, Manceau L, Moriondo M, Nendel C, Rodríguez A, Ruiz-Ramos M, Semenov MA, Siebert S, Stella T, Stratonovitch P, Trombi G, Wallach D. Diverging importance of drought stress for maize and winter wheat in Europe. Nat Commun 2018; 9:4249. [PMID: 30315168 PMCID: PMC6185965 DOI: 10.1038/s41467-018-06525-2] [Citation(s) in RCA: 147] [Impact Index Per Article: 24.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2018] [Accepted: 09/07/2018] [Indexed: 12/22/2022] Open
Abstract
Understanding the drivers of yield levels under climate change is required to support adaptation planning and respond to changing production risks. This study uses an ensemble of crop models applied on a spatial grid to quantify the contributions of various climatic drivers to past yield variability in grain maize and winter wheat of European cropping systems (1984–2009) and drivers of climate change impacts to 2050. Results reveal that for the current genotypes and mix of irrigated and rainfed production, climate change would lead to yield losses for grain maize and gains for winter wheat. Across Europe, on average heat stress does not increase for either crop in rainfed systems, while drought stress intensifies for maize only. In low-yielding years, drought stress persists as the main driver of losses for both crops, with elevated CO2 offering no yield benefit in these years. Drivers of crop yield variability require quantification, and historical records can help in improving understanding. Here, Webber et al. report that drought stress will remain a key driver of yield losses in wheat and maize across Europe, and benefits from CO2 will be limited in low-yielding years.
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Affiliation(s)
- Heidi Webber
- Leibniz-Centre for Agricultural Landscape Research (ZALF), 15374, Müncheberg, Germany. .,Institute of Crop Science and Resources Conservation, University of Bonn, Bonn, 53115, Germany.
| | - Frank Ewert
- Leibniz-Centre for Agricultural Landscape Research (ZALF), 15374, Müncheberg, Germany.,Institute of Crop Science and Resources Conservation, University of Bonn, Bonn, 53115, Germany
| | - Jørgen E Olesen
- Department of Agroecology, Aarhus University, Tjele, 8830, Denmark
| | - Christoph Müller
- Potsdam Institute for Climate Impact Research, Member of the Leibniz Association, Potsdam, 14473, Germany
| | | | - Alex C Ruane
- National Aeronautics and Space Administration Goddard Institute for Space Studies, New York, 10025, NY, USA
| | - Maryse Bourgault
- Northern Ag Research Center, Montana State University, 3710 Assinniboine Road, Havre, MT, USA
| | - Pierre Martre
- LEPSE, Université Montpellier, INRA, Montpellier SupAgro, 34060, Montpellier, France
| | - Behnam Ababaei
- LEPSE, Université Montpellier, INRA, Montpellier SupAgro, 34060, Montpellier, France.,Native Trait Research, Limagrain Europe, 63720, Chappes, France.,Centre for Crop Science, Queensland Alliance for Agriculture and Food Innovation, University of Queensland, 4069, Toowoomba, Australia
| | - Marco Bindi
- Department of Agri-food Production and Environmental Sciences, University of Florence, P.le delle Cascine 18, 50144, Firenze, Italy
| | - Roberto Ferrise
- Department of Agri-food Production and Environmental Sciences, University of Florence, P.le delle Cascine 18, 50144, Firenze, Italy
| | - Robert Finger
- ETH Zurich, Agricultural Economics and Policy Group, Zürich, 8092, Switzerland
| | - Nándor Fodor
- Agricultural Institute, Centre for Agricultural Research, Hungarian Academy of Sciences, Martonvásár, 2462, Hungary
| | | | - Thomas Gaiser
- Institute of Crop Science and Resources Conservation, University of Bonn, Bonn, 53115, Germany
| | - Mohamed Jabloun
- School of Biosciences, University of Nottingham, Loughborough, LE12 5RD, UK
| | | | - Jon I Lizaso
- Research Centre for the Management of Agricultural and Environmental Risks (CEIGRAM), Universidad Politécnica de Madrid, Madrid, 28040, Spain
| | - Ignacio J Lorite
- IFAPA-Centro Alameda del Obispo, P.O. Box 3092, 14080, Córdoba, Spain
| | - Loic Manceau
- LEPSE, Université Montpellier, INRA, Montpellier SupAgro, 34060, Montpellier, France
| | | | - Claas Nendel
- Leibniz-Centre for Agricultural Landscape Research (ZALF), 15374, Müncheberg, Germany
| | - Alfredo Rodríguez
- Research Centre for the Management of Agricultural and Environmental Risks (CEIGRAM), Universidad Politécnica de Madrid, Madrid, 28040, Spain.,Department of Economic Analysis and Finances, Universidad de Castilla-La Mancha, 45071, Toledo, Spain
| | - Margarita Ruiz-Ramos
- Research Centre for the Management of Agricultural and Environmental Risks (CEIGRAM), Universidad Politécnica de Madrid, Madrid, 28040, Spain
| | - Mikhail A Semenov
- Department of Plant Science, Rothamsted Research, Harpenden, AL5 2JQ, UK
| | - Stefan Siebert
- Department of Crop Sciences, University of Göttingen, Göttingen, 37075, Germany
| | - Tommaso Stella
- Leibniz-Centre for Agricultural Landscape Research (ZALF), 15374, Müncheberg, Germany
| | | | - Giacomo Trombi
- Centre for Crop Science, Queensland Alliance for Agriculture and Food Innovation, University of Queensland, 4069, Toowoomba, Australia
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28
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Tao F, Rötter RP, Palosuo T, Gregorio Hernández Díaz-Ambrona C, Mínguez MI, Semenov MA, Kersebaum KC, Nendel C, Specka X, Hoffmann H, Ewert F, Dambreville A, Martre P, Rodríguez L, Ruiz-Ramos M, Gaiser T, Höhn JG, Salo T, Ferrise R, Bindi M, Cammarano D, Schulman AH. Contribution of crop model structure, parameters and climate projections to uncertainty in climate change impact assessments. Glob Chang Biol 2018; 24:1291-1307. [PMID: 29245185 DOI: 10.1111/gcb.14019] [Citation(s) in RCA: 35] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/22/2017] [Revised: 11/05/2017] [Accepted: 11/27/2017] [Indexed: 05/27/2023]
Abstract
Climate change impact assessments are plagued with uncertainties from many sources, such as climate projections or the inadequacies in structure and parameters of the impact model. Previous studies tried to account for the uncertainty from one or two of these. Here, we developed a triple-ensemble probabilistic assessment using seven crop models, multiple sets of model parameters and eight contrasting climate projections together to comprehensively account for uncertainties from these three important sources. We demonstrated the approach in assessing climate change impact on barley growth and yield at Jokioinen, Finland in the Boreal climatic zone and Lleida, Spain in the Mediterranean climatic zone, for the 2050s. We further quantified and compared the contribution of crop model structure, crop model parameters and climate projections to the total variance of ensemble output using Analysis of Variance (ANOVA). Based on the triple-ensemble probabilistic assessment, the median of simulated yield change was -4% and +16%, and the probability of decreasing yield was 63% and 31% in the 2050s, at Jokioinen and Lleida, respectively, relative to 1981-2010. The contribution of crop model structure to the total variance of ensemble output was larger than that from downscaled climate projections and model parameters. The relative contribution of crop model parameters and downscaled climate projections to the total variance of ensemble output varied greatly among the seven crop models and between the two sites. The contribution of downscaled climate projections was on average larger than that of crop model parameters. This information on the uncertainty from different sources can be quite useful for model users to decide where to put the most effort when preparing or choosing models or parameters for impact analyses. We concluded that the triple-ensemble probabilistic approach that accounts for the uncertainties from multiple important sources provide more comprehensive information for quantifying uncertainties in climate change impact assessments as compared to the conventional approaches that are deterministic or only account for the uncertainties from one or two of the uncertainty sources.
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Affiliation(s)
- Fulu Tao
- Natural Resources Institute Finland (Luke), Helsinki, Finland
| | - Reimund P Rötter
- Department of Crop Sciences, Tropical Plant Production and Agricultural Systems Modelling (TROPAGS), Georg-August-University of Göttingen, Göttingen, Germany
- Centre for Biodiversity and Sustainable Land Use (CBL), Georg-August-University of Göttingen, Göttingen, Germany
| | - Taru Palosuo
- Natural Resources Institute Finland (Luke), Helsinki, Finland
| | | | - M Inés Mínguez
- AgSystems-CEIGRAM Research Centre for Agricultural and Environmental Risk Management-Technical, University of Madrid, Madrid, Spain
| | | | - Kurt Christian Kersebaum
- Institute of Landscape Systems Analysis, Leibniz Centre for Agricultural Landscape Research, Müncheberg, Germany
| | - Claas Nendel
- Institute of Landscape Systems Analysis, Leibniz Centre for Agricultural Landscape Research, Müncheberg, Germany
| | - Xenia Specka
- Institute of Landscape Systems Analysis, Leibniz Centre for Agricultural Landscape Research, Müncheberg, Germany
| | - Holger Hoffmann
- Crop Science Group, INRES, University of Bonn, Bonn, Germany
| | - Frank Ewert
- Institute of Landscape Systems Analysis, Leibniz Centre for Agricultural Landscape Research, Müncheberg, Germany
- Crop Science Group, INRES, University of Bonn, Bonn, Germany
| | | | | | - Lucía Rodríguez
- AgSystems-CEIGRAM Research Centre for Agricultural and Environmental Risk Management-Technical, University of Madrid, Madrid, Spain
| | - Margarita Ruiz-Ramos
- AgSystems-CEIGRAM Research Centre for Agricultural and Environmental Risk Management-Technical, University of Madrid, Madrid, Spain
| | - Thomas Gaiser
- Crop Science Group, INRES, University of Bonn, Bonn, Germany
| | - Jukka G Höhn
- Natural Resources Institute Finland (Luke), Helsinki, Finland
| | - Tapio Salo
- Natural Resources Institute Finland (Luke), Helsinki, Finland
| | - Roberto Ferrise
- Department of Agri-food Production and Environmental Sciences, University of Florence, Firenze, Italy
| | - Marco Bindi
- Department of Agri-food Production and Environmental Sciences, University of Florence, Firenze, Italy
| | | | - Alan H Schulman
- Natural Resources Institute Finland (Luke), Helsinki, Finland
- Institute of Biotechnology and Viikki Plant Science Centre, University of Helsinki, Helsinki, Finland
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Martre P, Codjia T, Tuech JJ, Schwarz L. Pelvic tumor fed by the superior mesenteric artery. What is your diagnosis? GIST complicating Meckel's diverticulum. J Visc Surg 2018; 155:83-85. [PMID: 29396111 DOI: 10.1016/j.jviscsurg.2017.11.004] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
Affiliation(s)
- P Martre
- Service de chirurgie digestive, hôpital Charles-Nicolle, CHU de Rouen, 1, rue de Germont, 76000 Rouen, France
| | - T Codjia
- Service de chirurgie digestive, hôpital Charles-Nicolle, CHU de Rouen, 1, rue de Germont, 76000 Rouen, France
| | - J-J Tuech
- Service de chirurgie digestive, hôpital Charles-Nicolle, CHU de Rouen, 1, rue de Germont, 76000 Rouen, France; Centre Normand de medicine génomique et de medicine personalisée, Inserm U1245, Groupe IRON, université de Rouen, CHU de Rouen, 76000 Rouen, France
| | - L Schwarz
- Service de chirurgie digestive, hôpital Charles-Nicolle, CHU de Rouen, 1, rue de Germont, 76000 Rouen, France; Centre Normand de medicine génomique et de medicine personalisée, Inserm U1245, Groupe IRON, université de Rouen, CHU de Rouen, 76000 Rouen, France.
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Martre P, Dambreville A. A Model of Leaf Coordination to Scale-Up Leaf Expansion from the Organ to the Canopy. Plant Physiol 2018; 176:704-716. [PMID: 29142024 PMCID: PMC5761778 DOI: 10.1104/pp.17.00986] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/18/2017] [Accepted: 11/12/2017] [Indexed: 05/29/2023]
Abstract
Process-based crop growth models are popular tools with which to analyze and understand the impact of crop management, genotype-by-environment interactions, or climate change. The ability to predict leaf area development is critical to predict crop growth, particularly under conditions of limited resources. Here, we aimed at deciphering growth coordination rules between wheat (Triticum aestivum) plant organs (i.e. between leaves within a stem, between laminae and sheaths, and between the mainstem and axillary tillers) to model the dynamics of canopy development. We found a unique relationship between laminae area and leaf rank for the mainstem and its tillers, which was robust across a range of sowing dates and plant densities. Robust relationships between laminae and sheath areas also were found, highlighting the tight control of organ growth within and between phytomers. These relationships identified at the phytomer scale were used to develop a simulation model of leaf area dynamics at the canopy level that was integrated in the wheat model SiriusQuality. The model was then evaluated using several independent experiments. The model accurately predicts leaf area dynamics under different scenarios of nitrogen and water limitations. It accounted for 85%, 64%, and 73% of the variability of the surface area of leaf cohorts, total leaf area index, and total green area index, respectively. The process-based model of the dynamics of leaf area described here is a key element to quantify the value of candidate traits for use in plant breeding and to project the impact of climate change on wheat growth.
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Affiliation(s)
- Pierre Martre
- Laboratoire d'Ecophysiologie des Plantes sous Stress Environnementaux, Université Montpellier, Institut National de la Recherche Agronomique, Montpellier SupAgro, 34060 Montpellier, France
| | - Anaelle Dambreville
- Laboratoire d'Ecophysiologie des Plantes sous Stress Environnementaux, Université Montpellier, Institut National de la Recherche Agronomique, Montpellier SupAgro, 34060 Montpellier, France
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Martre P. The Hot Serial Cereal Experiment for modeling wheat response to temperature: field experiments and AgMIP-Wheat multi-model simulations. ACTA ACUST UNITED AC 2018. [DOI: 10.18174/odjar.v4i0.15830] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
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Ruane AC, Rosenzweig C, Asseng S, Boote KJ, Elliott J, Ewert F, Jones JW, Martre P, McDermid SP, Müller C, Snyder A, Thorburn PJ. An AgMIP framework for improved agricultural representation in IAMs. Environ Res Lett 2017; 12:125003. [PMID: 30881482 PMCID: PMC6417889 DOI: 10.1088/1748-9326/aa8da6] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/23/2023]
Abstract
Integrated assessment models (IAMs) hold great potential to assess how future agricultural systems will be shaped by socioeconomic development, technological innovation, and changing climate conditions. By coupling with climate and crop model emulators, IAMs have the potential to resolve important agricultural feedback loops and identify unintended consequences of socioeconomic development for agricultural systems. Here we propose a framework to develop robust representation of agricultural system responses within IAMs, linking downstream applications with model development and the coordinated evaluation of key climate responses from local to global scales. We survey the strengths and weaknesses of protocol-based assessments linked to the Agricultural Model Intercomparison and Improvement Project (AgMIP), each utilizing multiple sites and models to evaluate crop response to core climate changes including shifts in carbon dioxide concentration, temperature, and water availability, with some studies further exploring how climate responses are affected by nitrogen levels and adaptation in farm systems. Site-based studies with carefully calibrated models encompass the largest number of activities; however they are limited in their ability to capture the full range of global agricultural system diversity. Representative site networks provide more targeted response information than broadly-sampled networks, with limitations stemming from difficulties in covering the diversity of farming systems. Global gridded crop models provide comprehensive coverage, although with large challenges for calibration and quality control of inputs. Diversity in climate responses underscores that crop model emulators must distinguish between regions and farming system while recognizing model uncertainty. Finally, to bridge the gap between bottom-up and top-down approaches we recommend the deployment of a hybrid climate response system employing a representative network of sites to bias-correct comprehensive gridded simulations, opening the door to accelerated development and a broad range of applications.
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Affiliation(s)
- Alex C Ruane
- NASA Goddard Institute for Space Studies, New York, NY, USA
| | | | - Senthold Asseng
- University of Florida, Agricultural and Biological Engineering, Gainesville, FL, USA
| | - Kenneth J Boote
- University of Florida, Agricultural and Biological Engineering, Gainesville, FL, USA
| | - Joshua Elliott
- University of Chicago, Computation Institute, Chicago, IL, USA
| | - Frank Ewert
- University of Bonn, Bonn, Germany
- Leibniz Center of Agricultural landscape Research (ZALF), Muencheberg, Germany
| | - James W Jones
- University of Florida, Agricultural and Biological Engineering, Gainesville, FL, USA
- National Science Foundation, Arlington, VA, USA
| | - Pierre Martre
- UMR LEPSE, INRA, Montpellier SupAgro, Montpellier, France
| | | | | | - Abigail Snyder
- Pacific Northwest National Laboratory, College Park, MD, USA
| | - Peter J Thorburn
- Commonwealth Scientific and Industrial Research Organization, Brisbane, Australia
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Wang E, Martre P, Zhao Z, Ewert F, Maiorano A, Rötter RP, Kimball BA, Ottman MJ, Wall GW, White JW, Reynolds MP, Alderman PD, Aggarwal PK, Anothai J, Basso B, Biernath C, Cammarano D, Challinor AJ, De Sanctis G, Doltra J, Dumont B, Fereres E, Garcia-Vila M, Gayler S, Hoogenboom G, Hunt LA, Izaurralde RC, Jabloun M, Jones CD, Kersebaum KC, Koehler AK, Liu L, Müller C, Kumar SN, Nendel C, O'Leary G, Olesen JE, Palosuo T, Priesack E, Rezaei EE, Ripoche D, Ruane AC, Semenov MA, Shcherbak I, Stöckle C, Stratonovitch P, Streck T, Supit I, Tao F, Thorburn P, Waha K, Wallach D, Wang Z, Wolf J, Zhu Y, Asseng S. Author Correction: The uncertainty of crop yield projections is reduced by improved temperature response functions. Nat Plants 2017; 3:833. [PMID: 28955035 DOI: 10.1038/s41477-017-0032-6] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/07/2023]
Abstract
Nature Plants 3, 17102 (2017); published online 17 July 2017; corrected online 27 September 2017.
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Affiliation(s)
- Enli Wang
- CSIRO Agriculture and Food, Black Mountain, ACT, 2601, Australia.
| | - Pierre Martre
- UMR LEPSE, INRA, Montpellier SupAgro, 2 Place Viala, 34 060, Montpellier, France
| | - Zhigan Zhao
- CSIRO Agriculture and Food, Black Mountain, ACT, 2601, Australia
- College of Agronomy and Biotechnology, China Agricultural University, Beijing, 100193, China
| | - Frank Ewert
- Institute of Crop Science and Resource Conservation (INRES), University of Bonn, 53115, Bonn, Germany
- Institute of Landscape Systems Analysis, Leibniz Centre for Agricultural Landscape Research, 15374, Müncheberg, Germany
| | - Andrea Maiorano
- UMR LEPSE, INRA, Montpellier SupAgro, 2 Place Viala, 34 060, Montpellier, France
| | - Reimund P Rötter
- Department of Crop Sciences, University of Goettingen, Tropical Plant Production and Agricultural Systems Modelling (TROPAGS), 37077, Göttingen, Germany
- Centre of Biodiversity and Sustainable Land Use (CBL), University of Goettingen, Büsgenweg 1, 37077, Göttingen, Germany
| | - Bruce A Kimball
- USDA, Agricultural Research Service, U.S. Arid-Land Agricultural Research Center, Maricopa, AZ, 85138, USA
| | - Michael J Ottman
- The School of Plant Sciences, University of Arizona, Tucson, AZ, 85721, USA
| | - Gerard W Wall
- USDA, Agricultural Research Service, U.S. Arid-Land Agricultural Research Center, Maricopa, AZ, 85138, USA
| | - Jeffrey W White
- USDA, Agricultural Research Service, U.S. Arid-Land Agricultural Research Center, Maricopa, AZ, 85138, USA
| | - Matthew P Reynolds
- Global Wheat Program, International Maize and Wheat Improvement Center (CIMMYT) Apdo, 06600, Mexico, D.F, Mexico
| | - Phillip D Alderman
- Global Wheat Program, International Maize and Wheat Improvement Center (CIMMYT) Apdo, 06600, Mexico, D.F, Mexico
| | - Pramod K Aggarwal
- CGIAR Research Program on Climate Change, Agriculture and Food Security, Borlaug Institute for South Asia, International Maize and Wheat Improvement Center (CIMMYT), New Delhi, 110012, India
| | - Jakarat Anothai
- AgWeatherNet Program, Washington State University, Prosser, WA, 99350-8694, USA
| | - Bruno Basso
- Department of Earth and Environmental Sciences and W.K. Kellogg Biological Station, Michigan State University, East Lansing, MI, 48823, USA
| | - Christian Biernath
- Helmholtz Zentrum München - German Research Center for Environmental Health, Institute of Biochemical Plant Pathology, Neuherberg, 85764, Germany
| | - Davide Cammarano
- Agricultural and Biological Engineering Department, University of Florida, Gainesville, FL, 32611, USA
| | - Andrew J Challinor
- Institute for Climate and Atmospheric Science, School of Earth and Environment, University of Leeds, Leeds, LS29JT, UK
- CGIAR Research Program on Climate Change, Agriculture and Food Security (CCAFS), Km 17, Recta Cali-Palmira Apartado Aéreo, 6713, Cali, Colombia
| | - Giacomo De Sanctis
- GMO Unit, European Food Safety Authority (EFSA), Via Carlo Magno, 1A, 43126, Parma, Italy
| | - Jordi Doltra
- Cantabrian Agricultural Research and Training Centre (CIFA), 39600, Muriedas, Spain
| | - Benjamin Dumont
- Department of Earth and Environmental Sciences and W.K. Kellogg Biological Station, Michigan State University, East Lansing, MI, 48823, USA
| | - Elias Fereres
- Dep. Agronomia, University of Cordoba, Apartado 3048, 14080, Cordoba, Spain
- IAS-CSIC, Cordoba, 14080, Spain
| | - Margarita Garcia-Vila
- Dep. Agronomia, University of Cordoba, Apartado 3048, 14080, Cordoba, Spain
- IAS-CSIC, Cordoba, 14080, Spain
| | - Sebastian Gayler
- Institute of Soil Science and Land Evaluation, University of Hohenheim, 70599, Stuttgart, Germany
| | - Gerrit Hoogenboom
- AgWeatherNet Program, Washington State University, Prosser, WA, 99350-8694, USA
| | - Leslie A Hunt
- Department of Plant Agriculture, University of Guelph, Guelph, ON, N1G 2W1, Canada
| | - Roberto C Izaurralde
- Department of Geographical Sciences, University of Maryland, College Park, MD, 20742, USA
- Texas A&M AgriLife Research and Extension Center, Texas A&M University, Temple, TX, 76502, USA
| | - Mohamed Jabloun
- Department of Agroecology, Aarhus University, 8830, Tjele, Denmark
| | - Curtis D Jones
- Department of Geographical Sciences, University of Maryland, College Park, MD, 20742, USA
| | - Kurt C Kersebaum
- Institute of Landscape Systems Analysis, Leibniz Centre for Agricultural Landscape Research, 15374, Müncheberg, Germany
| | - Ann-Kristin Koehler
- Institute for Climate and Atmospheric Science, School of Earth and Environment, University of Leeds, Leeds, LS29JT, UK
| | - Leilei Liu
- National Engineering and Technology Center for Information Agriculture, Key Laboratory for Crop System Analysis and Decision Making, Ministry of Agriculture, Jiangsu Key Laboratory for Information Agriculture, Jiangsu Collaborative Innovation Center for Modern Crop Production, Nanjing Agricultural University, Nanjing, Jiangsu, 210095, China
| | - Christoph Müller
- Potsdam Institute for Climate Impact Research, 14473, Potsdam, Germany
| | - Soora Naresh Kumar
- Centre for Environment Science and Climate Resilient Agriculture, Indian Agricultural Research Institute, IARI PUSA, New Delhi, 110 012, India
| | - Claas Nendel
- Institute of Landscape Systems Analysis, Leibniz Centre for Agricultural Landscape Research, 15374, Müncheberg, Germany
| | - Garry O'Leary
- Department of Economic Development, Landscape & Water Sciences, Jobs, Transport and Resources, Horsham, 3400, Australia
| | - Jørgen E Olesen
- Department of Agroecology, Aarhus University, 8830, Tjele, Denmark
| | - Taru Palosuo
- Natural Resources Institute Finland (Luke), Latokartanonkaari 9, 00790, Helsinki, Finland
| | - Eckart Priesack
- Helmholtz Zentrum München - German Research Center for Environmental Health, Institute of Biochemical Plant Pathology, Neuherberg, 85764, Germany
| | - Ehsan Eyshi Rezaei
- Institute of Crop Science and Resource Conservation (INRES), University of Bonn, 53115, Bonn, Germany
| | | | - Alex C Ruane
- NASA Goddard Institute for Space Studies, New York, NY, 10025, USA
| | - Mikhail A Semenov
- Computational and Systems Biology Department, Rothamsted Research, Harpenden, Herts, AL5 2JQ, UK
| | - Iurii Shcherbak
- Department of Earth and Environmental Sciences and W.K. Kellogg Biological Station, Michigan State University, East Lansing, MI, 48823, USA
| | - Claudio Stöckle
- Biological Systems Engineering, Washington State University, Pullman, WA, 99164-6120, USA
| | - Pierre Stratonovitch
- Computational and Systems Biology Department, Rothamsted Research, Harpenden, Herts, AL5 2JQ, UK
| | - Thilo Streck
- Institute of Soil Science and Land Evaluation, University of Hohenheim, 70599, Stuttgart, Germany
| | - Iwan Supit
- PPS and WSG & CALM, Wageningen University, 6700AA, Wageningen, The Netherlands
| | - Fulu Tao
- Natural Resources Institute Finland (Luke), Latokartanonkaari 9, 00790, Helsinki, Finland
- Institute of Geographical Sciences and Natural Resources Research, Chinese Academy of Science, Beijing, 100101, China
| | - Peter Thorburn
- CSIRO Agriculture and Food, St Lucia, QLD, 4067, Australia
| | - Katharina Waha
- Potsdam Institute for Climate Impact Research, 14473, Potsdam, Germany
| | - Daniel Wallach
- INRA, UMR 1248 Agrosystèmes et développement territorial (AGIR), 31 326, Castanet-Tolosan, France
| | - Zhimin Wang
- College of Agronomy and Biotechnology, China Agricultural University, Beijing, 100193, China
| | - Joost Wolf
- PPS and WSG & CALM, Wageningen University, 6700AA, Wageningen, The Netherlands
| | - Yan Zhu
- National Engineering and Technology Center for Information Agriculture, Key Laboratory for Crop System Analysis and Decision Making, Ministry of Agriculture, Jiangsu Key Laboratory for Information Agriculture, Jiangsu Collaborative Innovation Center for Modern Crop Production, Nanjing Agricultural University, Nanjing, Jiangsu, 210095, China
| | - Senthold Asseng
- Agricultural and Biological Engineering Department, University of Florida, Gainesville, FL, 32611, USA
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Bonnot T, Bancel E, Alvarez D, Davanture M, Boudet J, Pailloux M, Zivy M, Ravel C, Martre P. Grain subproteome responses to nitrogen and sulfur supply in diploid wheat Triticum monococcum ssp. monococcum. Plant J 2017. [PMID: 28628250 DOI: 10.1111/tpj.13615] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/08/2023]
Abstract
Wheat grain storage proteins (GSPs) make up most of the protein content of grain and determine flour end-use value. The synthesis and accumulation of GSPs depend highly on nitrogen (N) and sulfur (S) availability and it is important to understand the underlying control mechanisms. Here we studied how the einkorn (Triticum monococcum ssp. monococcum) grain proteome responds to different amounts of N and S supply during grain development. GSP composition at grain maturity was clearly impacted by nutrition treatments, due to early changes in the rate of GSP accumulation during grain filling. Large-scale analysis of the nuclear and albumin-globulin subproteomes during this key developmental phase revealed that the abundance of 203 proteins was significantly modified by the nutrition treatments. Our results showed that the grain proteome was highly affected by perturbation in the N:S balance. S supply strongly increased the rate of accumulation of S-rich α/β-gliadin and γ-gliadin, and the abundance of several other proteins involved in glutathione metabolism. Post-anthesis N supply resulted in the activation of amino acid metabolism at the expense of carbohydrate metabolism and the activation of transport processes including nucleocytoplasmic transit. Protein accumulation networks were analyzed. Several central actors in the response were identified whose variation in abundance was related to variation in the amounts of many other proteins and are thus potentially important for GSP accumulation. This detailed analysis of grain subproteomes provides information on how wheat GSP composition can possibly be controlled in low-level fertilization condition.
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Affiliation(s)
- Titouan Bonnot
- UMR GDEC, INRA, Université Clermont Auvergne, 5 chemin de Beaulieu, Clermont-Ferrand, 63039, France
| | - Emmanuelle Bancel
- UMR GDEC, INRA, Université Clermont Auvergne, 5 chemin de Beaulieu, Clermont-Ferrand, 63039, France
| | - David Alvarez
- UMR GDEC, INRA, Université Clermont Auvergne, 5 chemin de Beaulieu, Clermont-Ferrand, 63039, France
| | - Marlène Davanture
- UMR GQE, INRA, Université Paris-Sud, CNRS, AgroParisTech, Université Paris-Saclay, Gif-sur-Yvette, 91190, France
| | - Julie Boudet
- UMR GDEC, INRA, Université Clermont Auvergne, 5 chemin de Beaulieu, Clermont-Ferrand, 63039, France
| | - Marie Pailloux
- LIMOS, CNRS, Université Blaise Pascal, Aubière, 63173, France
| | - Michel Zivy
- UMR GQE, INRA, Université Paris-Sud, CNRS, AgroParisTech, Université Paris-Saclay, Gif-sur-Yvette, 91190, France
| | - Catherine Ravel
- UMR GDEC, INRA, Université Clermont Auvergne, 5 chemin de Beaulieu, Clermont-Ferrand, 63039, France
| | - Pierre Martre
- UMR GDEC, INRA, Université Clermont Auvergne, 5 chemin de Beaulieu, Clermont-Ferrand, 63039, France
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Zhao C, Liu B, Piao S, Wang X, Lobell DB, Huang Y, Huang M, Yao Y, Bassu S, Ciais P, Durand JL, Elliott J, Ewert F, Janssens IA, Li T, Lin E, Liu Q, Martre P, Müller C, Peng S, Peñuelas J, Ruane AC, Wallach D, Wang T, Wu D, Liu Z, Zhu Y, Zhu Z, Asseng S. Temperature increase reduces global yields of major crops in four independent estimates. Proc Natl Acad Sci U S A 2017; 114:9326-9331. [PMID: 28811375 PMCID: PMC5584412 DOI: 10.1073/pnas.1701762114] [Citation(s) in RCA: 712] [Impact Index Per Article: 101.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Wheat, rice, maize, and soybean provide two-thirds of human caloric intake. Assessing the impact of global temperature increase on production of these crops is therefore critical to maintaining global food supply, but different studies have yielded different results. Here, we investigated the impacts of temperature on yields of the four crops by compiling extensive published results from four analytical methods: global grid-based and local point-based models, statistical regressions, and field-warming experiments. Results from the different methods consistently showed negative temperature impacts on crop yield at the global scale, generally underpinned by similar impacts at country and site scales. Without CO2 fertilization, effective adaptation, and genetic improvement, each degree-Celsius increase in global mean temperature would, on average, reduce global yields of wheat by 6.0%, rice by 3.2%, maize by 7.4%, and soybean by 3.1%. Results are highly heterogeneous across crops and geographical areas, with some positive impact estimates. Multimethod analyses improved the confidence in assessments of future climate impacts on global major crops and suggest crop- and region-specific adaptation strategies to ensure food security for an increasing world population.
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Affiliation(s)
- Chuang Zhao
- Sino-French Institute for Earth System Science, College of Urban and Environmental Sciences, Peking University, Beijing 100871, China
| | - Bing Liu
- National Engineering and Technology Center for Information Agriculture, Nanjing Agricultural University, Nanjing, Jiangsu 210095, China
- Key Laboratory for Crop System Analysis and Decision Making, Ministry of Agriculture, Nanjing Agricultural University, Nanjing, Jiangsu 210095
- Jiangsu Key Laboratory for Information Agriculture, Nanjing Agricultural University, Nanjing, Jiangsu 210095
- Jiangsu Collaborative Innovation Center for Modern Crop Production, Nanjing Agricultural University, Nanjing, Jiangsu 210095
- Agricultural and Biological Engineering Department, University of Florida, Gainesville, FL 32611
| | - Shilong Piao
- Sino-French Institute for Earth System Science, College of Urban and Environmental Sciences, Peking University, Beijing 100871, China;
- Key Laboratory of Alpine Ecology and Biodiversity, Institute of Tibetan Plateau Research, Chinese Academy of Sciences, Beijing 100085, China
- Center for Excellence in Tibetan Earth Science, Chinese Academy of Sciences, Beijing 100085, China
| | - Xuhui Wang
- Sino-French Institute for Earth System Science, College of Urban and Environmental Sciences, Peking University, Beijing 100871, China
| | - David B Lobell
- Department of Earth System Science Center on Food Security and the Environment, Stanford University, Stanford, CA 94305
| | - Yao Huang
- State Key Laboratory of Vegetation and Environmental Change, Institute of Botany, Chinese Academy of Sciences, Beijing 100093, China
| | - Mengtian Huang
- Sino-French Institute for Earth System Science, College of Urban and Environmental Sciences, Peking University, Beijing 100871, China
| | - Yitong Yao
- Sino-French Institute for Earth System Science, College of Urban and Environmental Sciences, Peking University, Beijing 100871, China
| | - Simona Bassu
- Desertification Research Centre, University of Sassari, 07100 Sassari, Italy
| | - Philippe Ciais
- Laboratoire des Sciences du Climat et de l'Environnement, Le Commissariat à l'Énergie Atomique et aux Énergies Alternatives, CNRS, Université de Versailles Saint-Quentin, Gif-sur-Yvette 91191, France
| | - Jean-Louis Durand
- Unité de Recherche Pluridisciplinaire Prairies et Plantes Fourragères, Institut National de la Recherche Agronomique, CS 80006, 86600 Lusignan, France
| | - Joshua Elliott
- University of Chicago Computation Institute, University of Chicago, Chicago, IL 60637
- Columbia University Center for Climate Systems Research, Columbia University, New York, NY 10025
| | - Frank Ewert
- Institute of Crop Science and Resource Conservation, University of Bonn, Bonn 53115, Germany
- Leibniz Centre for Agricultural Landscape Research, 15374 Müncheberg, Germany
| | - Ivan A Janssens
- Department of Biology, University of Antwerp, 2610 Wilrijk, Belgium
| | - Tao Li
- International Rice Research Institute, Los Baños, 4031 Laguna, Philippines
| | - Erda Lin
- Agro-Environment and Sustainable Development Institute, Chinese Academy of Agricultural Sciences, Beijing 100081, China
| | - Qiang Liu
- Sino-French Institute for Earth System Science, College of Urban and Environmental Sciences, Peking University, Beijing 100871, China
| | - Pierre Martre
- UMR Laboratoire d'Ecophysiologie des Plantes sous Stress Environementaux, Institut National de la Recherche Agronomique, Montpellier SupAgro, 34060 Montpellier, France
| | - Christoph Müller
- Climate Impacts and Vulnerabilities, Potsdam Institute for Climate Impact Research, 14473 Potsdam, Germany
| | - Shushi Peng
- Sino-French Institute for Earth System Science, College of Urban and Environmental Sciences, Peking University, Beijing 100871, China
| | - Josep Peñuelas
- Centre de Recerca Ecològica i Aplicacions Forestals, Cerdanyola del Valles, Barcelona 08193, Catalonia, Spain
- Global Ecology Unit CREAF-CSIC-UAB, Consejo Superior de Investigaciones Científicas, Bellaterra, Barcelona 08193, Catalonia, Spain
| | - Alex C Ruane
- National Aeronautics and Space Administration Goddard Institute for Space Studies, New York, NY 10025
- Columbia University Center for Climate Systems Research, Columbia University, New York, NY 10025
| | - Daniel Wallach
- UMR 1248 Agrosystèmes et Développement Territorial, Institut National de la Recherche Agronomique, 31326 Castanet-Tolosan Cedex, France
| | - Tao Wang
- Key Laboratory of Alpine Ecology and Biodiversity, Institute of Tibetan Plateau Research, Chinese Academy of Sciences, Beijing 100085, China
- Center for Excellence in Tibetan Earth Science, Chinese Academy of Sciences, Beijing 100085, China
| | - Donghai Wu
- Sino-French Institute for Earth System Science, College of Urban and Environmental Sciences, Peking University, Beijing 100871, China
| | - Zhuo Liu
- Sino-French Institute for Earth System Science, College of Urban and Environmental Sciences, Peking University, Beijing 100871, China
| | - Yan Zhu
- National Engineering and Technology Center for Information Agriculture, Nanjing Agricultural University, Nanjing, Jiangsu 210095, China
- Key Laboratory for Crop System Analysis and Decision Making, Ministry of Agriculture, Nanjing Agricultural University, Nanjing, Jiangsu 210095
- Jiangsu Key Laboratory for Information Agriculture, Nanjing Agricultural University, Nanjing, Jiangsu 210095
- Jiangsu Collaborative Innovation Center for Modern Crop Production, Nanjing Agricultural University, Nanjing, Jiangsu 210095
| | - Zaichun Zhu
- Sino-French Institute for Earth System Science, College of Urban and Environmental Sciences, Peking University, Beijing 100871, China
| | - Senthold Asseng
- Agricultural and Biological Engineering Department, University of Florida, Gainesville, FL 32611;
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Wang E, Martre P, Zhao Z, Ewert F, Maiorano A, Rötter RP, Kimball BA, Ottman MJ, Wall GW, White JW, Reynolds MP, Alderman PD, Aggarwal PK, Anothai J, Basso B, Biernath C, Cammarano D, Challinor AJ, De Sanctis G, Doltra J, Fereres E, Garcia-Vila M, Gayler S, Hoogenboom G, Hunt LA, Izaurralde RC, Jabloun M, Jones CD, Kersebaum KC, Koehler AK, Liu L, Müller C, Kumar SN, Nendel C, O'Leary G, Olesen JE, Palosuo T, Priesack E, Rezaei EE, Ripoche D, Ruane AC, Semenov MA, Shcherbak I, Stöckle C, Stratonovitch P, Streck T, Supit I, Tao F, Thorburn P, Waha K, Wallach D, Wang Z, Wolf J, Zhu Y, Asseng S. Erratum: The uncertainty of crop yield projections is reduced by improved temperature response functions. Nat Plants 2017; 3:17125. [PMID: 28770816 DOI: 10.1038/nplants.2017.125] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/07/2023]
Abstract
This corrects the article DOI: 10.1038/nplants.2017.102.
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37
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Wang E, Martre P, Zhao Z, Ewert F, Maiorano A, Rötter RP, Kimball BA, Ottman MJ, Wall GW, White JW, Reynolds MP, Alderman PD, Aggarwal PK, Anothai J, Basso B, Biernath C, Cammarano D, Challinor AJ, De Sanctis G, Doltra J, Dumont B, Fereres E, Garcia-Vila M, Gayler S, Hoogenboom G, Hunt LA, Izaurralde RC, Jabloun M, Jones CD, Kersebaum KC, Koehler AK, Liu L, Müller C, Naresh Kumar S, Nendel C, O'Leary G, Olesen JE, Palosuo T, Priesack E, Eyshi Rezaei E, Ripoche D, Ruane AC, Semenov MA, Shcherbak I, Stöckle C, Stratonovitch P, Streck T, Supit I, Tao F, Thorburn P, Waha K, Wallach D, Wang Z, Wolf J, Zhu Y, Asseng S. The uncertainty of crop yield projections is reduced by improved temperature response functions. Nat Plants 2017; 3:17102. [PMID: 28714956 DOI: 10.1038/nplants.2017.102] [Citation(s) in RCA: 52] [Impact Index Per Article: 7.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/06/2016] [Accepted: 06/05/2017] [Indexed: 05/22/2023]
Abstract
Increasing the accuracy of crop productivity estimates is a key element in planning adaptation strategies to ensure global food security under climate change. Process-based crop models are effective means to project climate impact on crop yield, but have large uncertainty in yield simulations. Here, we show that variations in the mathematical functions currently used to simulate temperature responses of physiological processes in 29 wheat models account for >50% of uncertainty in simulated grain yields for mean growing season temperatures from 14 °C to 33 °C. We derived a set of new temperature response functions that when substituted in four wheat models reduced the error in grain yield simulations across seven global sites with different temperature regimes by 19% to 50% (42% average). We anticipate the improved temperature responses to be a key step to improve modelling of crops under rising temperature and climate change, leading to higher skill of crop yield projections.
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Affiliation(s)
- Enli Wang
- CSIRO Agriculture and Food, Black Mountain, Australian Capital Territory 2601, Australia
| | - Pierre Martre
- UMR LEPSE, INRA, Montpellier SupAgro, 2 Place Viala, 34 060 Montpellier, France
| | - Zhigan Zhao
- College of Agronomy and Biotechnology, China Agricultural University, Beijing 100193, China
- CSIRO Agriculture and Food, Black Mountain, Australian Capital Territory 2601, Australia
| | - Frank Ewert
- Institute of Crop Science and Resource Conservation (INRES), University of Bonn, 53115 Bonn, Germany
- Institute of Landscape Systems Analysis, Leibniz Centre for Agricultural Landscape Research, 15374 Müncheberg, Germany
| | - Andrea Maiorano
- UMR LEPSE, INRA, Montpellier SupAgro, 2 Place Viala, 34 060 Montpellier, France
| | - Reimund P Rötter
- Department of Crop Sciences, University of Goettingen, Tropical Plant Production and Agricultural Systems Modelling (TROPAGS), 37077 Göttingen, Germany
- Centre of Biodiversity and Sustainable Land Use (CBL), University of Goettingen, Büsgenweg 1, 37077 Göttingen, Germany
| | - Bruce A Kimball
- USDA, Agricultural Research Service, U.S. Arid-Land Agricultural Research Center, Maricopa, Arizona 85138, USA
| | - Michael J Ottman
- The School of Plant Sciences, University of Arizona, Tucson, Arizona 85721, USA
| | - Gerard W Wall
- USDA, Agricultural Research Service, U.S. Arid-Land Agricultural Research Center, Maricopa, Arizona 85138, USA
| | - Jeffrey W White
- USDA, Agricultural Research Service, U.S. Arid-Land Agricultural Research Center, Maricopa, Arizona 85138, USA
| | - Matthew P Reynolds
- Global Wheat Program, International Maize and Wheat Improvement Center (CIMMYT) Apdo, 06600 Mexico, D.F, Mexico
| | - Phillip D Alderman
- Global Wheat Program, International Maize and Wheat Improvement Center (CIMMYT) Apdo, 06600 Mexico, D.F, Mexico
| | - Pramod K Aggarwal
- CGIAR Research Program on Climate Change, Agriculture and Food Security, Borlaug Institute for South Asia, International Maize and Wheat Improvement Center (CIMMYT), New Delhi 110012, India
| | - Jakarat Anothai
- AgWeatherNet Program, Washington State University, Prosser, Washington 99350-8694, USA
| | - Bruno Basso
- Department of Earth and Environmental Sciences and W.K. Kellogg Biological Station, Michigan State University East Lansing, Michigan 48823, USA
| | - Christian Biernath
- Helmholtz Zentrum München - German Research Center for Environmental Health, Institute of Biochemical Plant Pathology, Neuherberg, 85764, Germany
| | - Davide Cammarano
- Agricultural and Biological Engineering Department, University of Florida, Gainesville, Florida 32611, USA
| | - Andrew J Challinor
- Institute for Climate and Atmospheric Science, School of Earth and Environment, University of Leeds, Leeds LS29JT, UK
- CGIAR Research Program on Climate Change, Agriculture and Food Security (CCAFS), Km 17, Recta Cali-Palmira Apartado Aéreo 6713, Cali, Colombia
| | - Giacomo De Sanctis
- GMO Unit, European Food Safety Authority (EFSA), Via Carlo Magno, 1A, 43126 Parma, Italy
| | - Jordi Doltra
- Cantabrian Agricultural Research and Training Centre (CIFA), 39600 Muriedas, Spain
| | | | - Elias Fereres
- Dep. Agronomia, University of Cordoba, Apartado 3048, 14080 Cordoba, Spain
- IAS-CSIC, Cordoba 14080, Spain
| | - Margarita Garcia-Vila
- Dep. Agronomia, University of Cordoba, Apartado 3048, 14080 Cordoba, Spain
- IAS-CSIC, Cordoba 14080, Spain
| | - Sebastian Gayler
- Institute of Soil Science and Land Evaluation, University of Hohenheim, 70599 Stuttgart, Germany
| | - Gerrit Hoogenboom
- AgWeatherNet Program, Washington State University, Prosser, Washington 99350-8694, USA
| | - Leslie A Hunt
- Department of Plant Agriculture, University of Guelph, Guelph, Ontario N1G 2W1, Canada
| | - Roberto C Izaurralde
- Department of Geographical Sciences, University of Maryland, College Park, Maryland 20742, USA
- Texas A&M AgriLife Research and Extension Center, Texas A&M University, Temple, Texas 76502, USA
| | - Mohamed Jabloun
- Department of Agroecology, Aarhus University, 8830 Tjele, Denmark
| | - Curtis D Jones
- Department of Geographical Sciences, University of Maryland, College Park, Maryland 20742, USA
| | - Kurt C Kersebaum
- Institute of Landscape Systems Analysis, Leibniz Centre for Agricultural Landscape Research, 15374 Müncheberg, Germany
| | - Ann-Kristin Koehler
- Institute for Climate and Atmospheric Science, School of Earth and Environment, University of Leeds, Leeds LS29JT, UK
| | - Leilei Liu
- National Engineering and Technology Center for Information Agriculture, Key Laboratory for Crop System Analysis and Decision Making, Ministry of Agriculture, Jiangsu Key Laboratory for Information Agriculture, Jiangsu Collaborative Innovation Center for Modern Crop Production, Nanjing Agricultural University, Nanjing, Jiangsu 210095, China
| | - Christoph Müller
- Potsdam Institute for Climate Impact Research, 14473 Potsdam, Germany
| | - Soora Naresh Kumar
- Centre for Environment Science and Climate Resilient Agriculture, Indian Agricultural Research Institute, IARI PUSA, New Delhi 110 012, India
| | - Claas Nendel
- Institute of Landscape Systems Analysis, Leibniz Centre for Agricultural Landscape Research, 15374 Müncheberg, Germany
| | - Garry O'Leary
- Department of Economic Development, Landscape &Water Sciences, Jobs, Transport and Resources, Horsham 3400, Australia
| | - Jørgen E Olesen
- Department of Agroecology, Aarhus University, 8830 Tjele, Denmark
| | - Taru Palosuo
- Natural Resources Institute Finland (Luke), Latokartanonkaari 9, 00790 Helsinki, Finland
| | - Eckart Priesack
- Helmholtz Zentrum München - German Research Center for Environmental Health, Institute of Biochemical Plant Pathology, Neuherberg, 85764, Germany
| | - Ehsan Eyshi Rezaei
- Institute of Crop Science and Resource Conservation (INRES), University of Bonn, 53115 Bonn, Germany
| | | | - Alex C Ruane
- NASA Goddard Institute for Space Studies, New York, New York 10025, USA
| | - Mikhail A Semenov
- Computational and Systems Biology Department, Rothamsted Research, Harpenden, Herts AL5 2JQ, UK
| | - Iurii Shcherbak
- Department of Earth and Environmental Sciences and W.K. Kellogg Biological Station, Michigan State University East Lansing, Michigan 48823, USA
| | - Claudio Stöckle
- Biological Systems Engineering, Washington State University, Pullman, Washington 99164-6120, USA
| | - Pierre Stratonovitch
- Computational and Systems Biology Department, Rothamsted Research, Harpenden, Herts AL5 2JQ, UK
| | - Thilo Streck
- Institute of Soil Science and Land Evaluation, University of Hohenheim, 70599 Stuttgart, Germany
| | - Iwan Supit
- PPS and WSG &CALM, Wageningen University, 6700AA Wageningen, The Netherlands
| | - Fulu Tao
- Natural Resources Institute Finland (Luke), Latokartanonkaari 9, 00790 Helsinki, Finland
- Institute of Geographical Sciences and Natural Resources Research, Chinese Academy of Science, Beijing 100101, China
| | - Peter Thorburn
- CSIRO Agriculture and Food, St Lucia, Queensland 4067, Australia
| | - Katharina Waha
- Potsdam Institute for Climate Impact Research, 14473 Potsdam, Germany
| | - Daniel Wallach
- INRA, UMR 1248 Agrosystèmes et développement territorial (AGIR), 31 326 Castanet-Tolosan, France
| | - Zhimin Wang
- College of Agronomy and Biotechnology, China Agricultural University, Beijing 100193, China
| | - Joost Wolf
- PPS and WSG &CALM, Wageningen University, 6700AA Wageningen, The Netherlands
| | - Yan Zhu
- National Engineering and Technology Center for Information Agriculture, Key Laboratory for Crop System Analysis and Decision Making, Ministry of Agriculture, Jiangsu Key Laboratory for Information Agriculture, Jiangsu Collaborative Innovation Center for Modern Crop Production, Nanjing Agricultural University, Nanjing, Jiangsu 210095, China
| | - Senthold Asseng
- Agricultural and Biological Engineering Department, University of Florida, Gainesville, Florida 32611, USA
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Chenu K, Porter JR, Martre P, Basso B, Chapman SC, Ewert F, Bindi M, Asseng S. Contribution of Crop Models to Adaptation in Wheat. Trends Plant Sci 2017; 22:472-490. [PMID: 28389147 DOI: 10.1016/j.tplants.2017.02.003] [Citation(s) in RCA: 30] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/16/2016] [Revised: 01/10/2017] [Accepted: 02/14/2017] [Indexed: 05/21/2023]
Abstract
With world population growing quickly, agriculture needs to produce more with fewer inputs while being environmentally friendly. In a context of changing environments, crop models are useful tools to simulate crop yields. Wheat (Triticum spp.) crop models have been evolving since the 1960s to translate processes related to crop growth and development into mathematical equations. These have been used over decades for agronomic purposes, and have more recently incorporated advances in the modeling of environmental footprints, biotic constraints, trait and gene effects, climate change impact, and the upscaling of global change impacts. This review outlines the potential and limitations of modern wheat crop models in assisting agronomists, breeders, and policymakers to address the current and future challenges facing agriculture.
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Affiliation(s)
- Karine Chenu
- The University of Queensland, Queensland Alliance for Agriculture and Food Innovation (QAAFI), 203 Tor Street, Toowoomba, QLD 4350, Australia.
| | - John Roy Porter
- Department of Plant and Environmental Sciences, Faculty of Science, University of Copenhagen, 2630 Taastrup, Denmark
| | - Pierre Martre
- Unité Mixte de Recherche (UMR) Laboratoire d'Ecophysiologie des Plantes Sous Stress Environnementaux (LEPSE), Institut National de la Recherche Agronomique (INRA), Montpellier SupAgro, 34060 Montpellier, France
| | - Bruno Basso
- Department of Geological Sciences and Kellogg Biological Station, Michigan State University, East Lansing, MI 48823, USA
| | - Scott Cameron Chapman
- Commonwealth Scientific and Industrial Research Organisation (CSIRO) Agriculture and Food, Queensland Bioscience Precinct, 306 Carmody Road, St. Lucia, QLD 4067, Australia
| | - Frank Ewert
- Institute of Crop Science and Resource Conservation, Universität Bonn, 53115 Bonn, Germany
| | - Marco Bindi
- Department of Agri-food Production and Environmental Sciences, University of Florence, Piazzale delle Cascine 18, 50144 Firenze, Italy
| | - Senthold Asseng
- Agricultural and Biological Engineering Department, University of Florida, Gainesville, FL 32611, USA
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Martre P. The International Heat Stress Genotype Experiment for modeling wheat response to heat: field experiments and AgMIP-Wheat multi-model simulations. ACTA ACUST UNITED AC 2017. [DOI: 10.18174/odjar.v3i1.15766] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
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Neghliz H, Cochard H, Brunel N, Martre P. Ear Rachis Xylem Occlusion and Associated Loss in Hydraulic Conductance Coincide with the End of Grain Filling for Wheat. Front Plant Sci 2016; 7:920. [PMID: 27446150 PMCID: PMC4921477 DOI: 10.3389/fpls.2016.00920] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/30/2015] [Accepted: 06/09/2016] [Indexed: 05/19/2023]
Abstract
Seed dehydration is the normal terminal event in the development of orthodox seeds and is physiologically related to the cessation of grain dry mass accumulation and crop grain yield. For a better understanding of grain dehydration, we evaluated the hypothesis that hydraulic conductance of the ear decreases during the latter stages of development and that this decrease results from disruption or occlusion of xylem conduits. Whole ear, rachis, and stem nodes hydraulic conductance and percentage loss of xylem conductivity were measured from flowering to harvest-ripeness on bread wheat (Triticum aestivum L.) cv. Récital grown under controlled environments. Flag leaf transpiration, stomatal conductance, chlorophyll content and grain and ear water potentials were also measured during grain development. We show that grain dehydration was not related with whole plant physiology and leaf senescence, but closely correlated with the hydraulic properties of the xylem conduits irrigating the grains. Indeed, there was a substantial decrease in rachis hydraulic conductance at the onset of the grain dehydration phase. This hydraulic impairment was not caused by the presence of air embolism in xylem conduits of the stem internodes or rachis but by the occlusion of the xylem lumens by polysaccharides (pectins and callose). Our results demonstrate that xylem hydraulics plays a key role during grain maturation.
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Affiliation(s)
- Hayet Neghliz
- UMR GDEC, INRA, Blaise Pascal UniversityClermont-Ferrand, France
- Laboratoire d’Ecophysiologie Végétale, Ecole Normale SupérieureKouba, Algeria
| | | | | | - Pierre Martre
- UMR GDEC, INRA, Blaise Pascal UniversityClermont-Ferrand, France
- *Correspondence: Pierre Martre,
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Bonnot T, Bancel E, Chambon C, Boudet J, Branlard G, Martre P. Changes in the nuclear proteome of developing wheat (Triticum aestivum L.) grain. Front Plant Sci 2015; 6:905. [PMID: 26579155 PMCID: PMC4623401 DOI: 10.3389/fpls.2015.00905] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/01/2015] [Accepted: 10/10/2015] [Indexed: 05/24/2023]
Abstract
Wheat grain end-use value is determined by complex molecular interactions that occur during grain development, including those in the cell nucleus. However, our knowledge of how the nuclear proteome changes during grain development is limited. Here, we analyzed nuclear proteins of developing wheat grains collected during the cellularization, effective grain-filling, and maturation phases of development, respectively. Nuclear proteins were extracted and separated by two-dimensional gel electrophoresis. Image analysis revealed 371 and 299 reproducible spots in gels with first dimension separation along pH 4-7 and pH 6-11 isoelectric gradients, respectively. The relative abundance of 464 (67%) protein spots changed during grain development. Abundance profiles of these proteins clustered in six groups associated with the major phases and phase transitions of grain development. Using nano liquid chromatography-tandem mass spectrometry to analyse 387 variant and non-variant protein spots, 114 different proteins were identified that were classified into 16 functional classes. We noted that some proteins involved in the regulation of transcription, like HMG1/2-like protein and histone deacetylase HDAC2, were most abundant before the phase transition from cellularization to grain-filling, suggesting that major transcriptional changes occur during this key developmental phase. The maturation period was characterized by high relative abundance of proteins involved in ribosome biogenesis. Data are available via ProteomeXchange with identifier PXD002999.
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Affiliation(s)
- Titouan Bonnot
- UMR1095 Genetics, Diversity and Ecophysiology of Cereals, Institut National de la Recherche AgronomiqueClermont-Ferrand, France
- UMR1095 Genetics, Diversity and Ecophysiology of Cereals, Blaise Pascal UniversityAubière, France
| | - Emmanuelle Bancel
- UMR1095 Genetics, Diversity and Ecophysiology of Cereals, Institut National de la Recherche AgronomiqueClermont-Ferrand, France
- UMR1095 Genetics, Diversity and Ecophysiology of Cereals, Blaise Pascal UniversityAubière, France
| | - Christophe Chambon
- Metabolism Exploration Platform Proteomic Component, Institut National de la Recherche AgronomiqueSaint-Genès Champanelle, France
| | - Julie Boudet
- UMR1095 Genetics, Diversity and Ecophysiology of Cereals, Institut National de la Recherche AgronomiqueClermont-Ferrand, France
- UMR1095 Genetics, Diversity and Ecophysiology of Cereals, Blaise Pascal UniversityAubière, France
| | - Gérard Branlard
- UMR1095 Genetics, Diversity and Ecophysiology of Cereals, Institut National de la Recherche AgronomiqueClermont-Ferrand, France
- UMR1095 Genetics, Diversity and Ecophysiology of Cereals, Blaise Pascal UniversityAubière, France
| | - Pierre Martre
- UMR1095 Genetics, Diversity and Ecophysiology of Cereals, Institut National de la Recherche AgronomiqueClermont-Ferrand, France
- UMR1095 Genetics, Diversity and Ecophysiology of Cereals, Blaise Pascal UniversityAubière, France
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Affiliation(s)
- Emmanuelle Bancel
- INRA, UMR1095
Genetics, Diversity and Ecophysiology of Cereals, 5 chemin de Beaulieu, F-63 039 Clermont-Ferrand, France
- Blaise Pascal
University, UMR1095 Genetics, Diversity and Ecophysiology of Cereals, Avenue des Landais, F-63 170 Aubière, France
| | - Titouan Bonnot
- INRA, UMR1095
Genetics, Diversity and Ecophysiology of Cereals, 5 chemin de Beaulieu, F-63 039 Clermont-Ferrand, France
- Blaise Pascal
University, UMR1095 Genetics, Diversity and Ecophysiology of Cereals, Avenue des Landais, F-63 170 Aubière, France
| | - Marlène Davanture
- CNRS, PAPPSO, UMR 0320/8120 Génétique
Quantitative et Évolution - Le Moulon, F-91190 Gif-sur-Yvette, France
| | - Gérard Branlard
- INRA, UMR1095
Genetics, Diversity and Ecophysiology of Cereals, 5 chemin de Beaulieu, F-63 039 Clermont-Ferrand, France
- Blaise Pascal
University, UMR1095 Genetics, Diversity and Ecophysiology of Cereals, Avenue des Landais, F-63 170 Aubière, France
| | - Michel Zivy
- CNRS, PAPPSO, UMR 0320/8120 Génétique
Quantitative et Évolution - Le Moulon, F-91190 Gif-sur-Yvette, France
| | - Pierre Martre
- INRA, UMR1095
Genetics, Diversity and Ecophysiology of Cereals, 5 chemin de Beaulieu, F-63 039 Clermont-Ferrand, France
- Blaise Pascal
University, UMR1095 Genetics, Diversity and Ecophysiology of Cereals, Avenue des Landais, F-63 170 Aubière, France
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Dai Z, Plessis A, Vincent J, Duchateau N, Besson A, Dardevet M, Prodhomme D, Gibon Y, Hilbert G, Pailloux M, Ravel C, Martre P. Transcriptional and metabolic alternations rebalance wheat grain storage protein accumulation under variable nitrogen and sulfur supply. Plant J 2015; 83:326-43. [PMID: 25996785 DOI: 10.1111/tpj.12881] [Citation(s) in RCA: 29] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/19/2014] [Revised: 04/08/2015] [Accepted: 05/05/2015] [Indexed: 05/08/2023]
Abstract
Wheat (Triticum aestivum L.) grain storage proteins (GSPs) are major determinants of flour end-use value. Biological and molecular mechanisms underlying the developmental and nutritional determination of GSP accumulation in cereals are as yet poorly understood. Here we timed the accumulation of GSPs during wheat grain maturation relative to changes in metabolite and transcript pools in different conditions of nitrogen (N) and sulfur (S) availability. We found that the N/S supply ratio modulated the duration of accumulation of S-rich GSPs and the rate of accumulation of S-poor GSPs. These changes are likely to be the result of distinct relationships between N and S allocation, depending on the S content of the GSP. Most developmental and nutritional modifications in GSP synthesis correlated with the abundance of structural gene transcripts. Changes in the expression of transport and metabolism genes altered the concentrations of several free amino acids under variable conditions of N and S supply, and these amino acids seem to be essential in determining GSP expression. The comprehensive data set generated and analyzed here provides insights that will be useful in adapting fertilizer use to variable N and S supply, or for breeding new cultivars with balanced and robust GSP composition.
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Affiliation(s)
- Zhanwu Dai
- INRA, UMR1095 Genetics, Diversity and Ecophysiology of Cereals, 5 chemin de Beaulieu, Clermont-Ferrand, F-63 039, France
- UMR1095 Genetics, Diversity and Ecophysiology of Cereals, Blaise Pascal University, Aubière, F-63 177, France
| | - Anne Plessis
- INRA, UMR1095 Genetics, Diversity and Ecophysiology of Cereals, 5 chemin de Beaulieu, Clermont-Ferrand, F-63 039, France
- UMR1095 Genetics, Diversity and Ecophysiology of Cereals, Blaise Pascal University, Aubière, F-63 177, France
| | - Jonathan Vincent
- INRA, UMR1095 Genetics, Diversity and Ecophysiology of Cereals, 5 chemin de Beaulieu, Clermont-Ferrand, F-63 039, France
- UMR1095 Genetics, Diversity and Ecophysiology of Cereals, Blaise Pascal University, Aubière, F-63 177, France
- UMR6158 CNRS Laboratoire d'Informatique, de Modélisation et d'Optimisation des Systèmes, Blaise Pascal University, Aubière, F-63 173, France
| | - Nathalie Duchateau
- INRA, UMR1095 Genetics, Diversity and Ecophysiology of Cereals, 5 chemin de Beaulieu, Clermont-Ferrand, F-63 039, France
- UMR1095 Genetics, Diversity and Ecophysiology of Cereals, Blaise Pascal University, Aubière, F-63 177, France
| | - Alicia Besson
- INRA, UMR1095 Genetics, Diversity and Ecophysiology of Cereals, 5 chemin de Beaulieu, Clermont-Ferrand, F-63 039, France
- UMR1095 Genetics, Diversity and Ecophysiology of Cereals, Blaise Pascal University, Aubière, F-63 177, France
| | - Mireille Dardevet
- INRA, UMR1095 Genetics, Diversity and Ecophysiology of Cereals, 5 chemin de Beaulieu, Clermont-Ferrand, F-63 039, France
- UMR1095 Genetics, Diversity and Ecophysiology of Cereals, Blaise Pascal University, Aubière, F-63 177, France
| | - Duyen Prodhomme
- INRA, UMR1332 Biologie du Fruit et Pathologie, Villenave d'Ornon, F-33 882, France
| | - Yves Gibon
- INRA, UMR1332 Biologie du Fruit et Pathologie, Villenave d'Ornon, F-33 882, France
| | - Ghislaine Hilbert
- INRA, UMR1287 Ecophysiologie et Génomique Fonctionnelle de la Vigne, Institut des Sciences de la Vigne et du Vin, Villenave d'Ornon, F-33 882, France
| | - Marie Pailloux
- UMR6158 CNRS Laboratoire d'Informatique, de Modélisation et d'Optimisation des Systèmes, Blaise Pascal University, Aubière, F-63 173, France
| | - Catherine Ravel
- INRA, UMR1095 Genetics, Diversity and Ecophysiology of Cereals, 5 chemin de Beaulieu, Clermont-Ferrand, F-63 039, France
- UMR1095 Genetics, Diversity and Ecophysiology of Cereals, Blaise Pascal University, Aubière, F-63 177, France
| | - Pierre Martre
- INRA, UMR1095 Genetics, Diversity and Ecophysiology of Cereals, 5 chemin de Beaulieu, Clermont-Ferrand, F-63 039, France
- UMR1095 Genetics, Diversity and Ecophysiology of Cereals, Blaise Pascal University, Aubière, F-63 177, France
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Martre P, He J, Le Gouis J, Semenov MA. In silico system analysis of physiological traits determining grain yield and protein concentration for wheat as influenced by climate and crop management. J Exp Bot 2015; 66:3581-98. [PMID: 25810069 PMCID: PMC4463803 DOI: 10.1093/jxb/erv049] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/18/2023]
Abstract
Genetic improvement of grain yield (GY) and grain protein concentration (GPC) is impeded by large genotype×environment×management interactions and by compensatory effects between traits. Here global uncertainty and sensitivity analyses of the process-based wheat model SiriusQuality2 were conducted with the aim of identifying candidate traits to increase GY and GPC. Three contrasted European sites were selected and simulations were performed using long-term weather data and two nitrogen (N) treatments in order to quantify the effect of parameter uncertainty on GY and GPC under variable environments. The overall influence of all 75 plant parameters of SiriusQuality2 was first analysed using the Morris method. Forty-one influential parameters were identified and their individual (first-order) and total effects on the model outputs were investigated using the extended Fourier amplitude sensitivity test. The overall effect of the parameters was dominated by their interactions with other parameters. Under high N supply, a few influential parameters with respect to GY were identified (e.g. radiation use efficiency, potential duration of grain filling, and phyllochron). However, under low N, >10 parameters showed similar effects on GY and GPC. All parameters had opposite effects on GY and GPC, but leaf and stem N storage capacity appeared as good candidate traits to change the intercept of the negative relationship between GY and GPC. This study provides a system analysis of traits determining GY and GPC under variable environments and delivers valuable information to prioritize model development and experimental work.
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Affiliation(s)
- Pierre Martre
- INRA, UMR1095 Genetic, Diversity and Ecophysiology of Cereals, 5 chemin de Beaulieu, Clermont-Ferrand F-63100, France Blaise Pascal University, UMR1095 Genetic, Diversity and Ecophysiology of Cereals, Aubière F-63177, France
| | - Jianqiang He
- INRA, UMR1095 Genetic, Diversity and Ecophysiology of Cereals, 5 chemin de Beaulieu, Clermont-Ferrand F-63100, France Blaise Pascal University, UMR1095 Genetic, Diversity and Ecophysiology of Cereals, Aubière F-63177, France
| | - Jacques Le Gouis
- INRA, UMR1095 Genetic, Diversity and Ecophysiology of Cereals, 5 chemin de Beaulieu, Clermont-Ferrand F-63100, France Blaise Pascal University, UMR1095 Genetic, Diversity and Ecophysiology of Cereals, Aubière F-63177, France
| | - Mikhail A Semenov
- Department of Computational and Systems Biology, Rothamsted Research, Harpenden, Herts AL5 2JQ, UK
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Asseng S, Ewert F, Martre P, Rötter RP, Lobell DB, Cammarano D, Kimball BA, Ottman MJ, Wall GW, White JW, Reynolds MP, Alderman PD, Prasad PVV, Aggarwal PK, Anothai J, Basso B, Biernath C, Challinor AJ, De Sanctis G, Doltra J, Fereres E, Garcia-Vila M, Gayler S, Hoogenboom G, Hunt LA, Izaurralde RC, Jabloun M, Jones CD, Kersebaum KC, Koehler AK, Müller C, Naresh Kumar S, Nendel C, O’Leary G, Olesen JE, Palosuo T, Priesack E, Eyshi Rezaei E, Ruane AC, Semenov MA, Shcherbak I, Stöckle C, Stratonovitch P, Streck T, Supit I, Tao F, Thorburn PJ, Waha K, Wang E, Wallach D, Wolf J, Zhao Z, Zhu Y. Rising temperatures reduce global wheat production. Nature Clim Change 2015; 5:143-147. [PMID: 0 DOI: 10.1038/nclimate2470] [Citation(s) in RCA: 528] [Impact Index Per Article: 58.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/04/2014] [Accepted: 11/18/2014] [Indexed: 05/26/2023]
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Martre P, Wallach D, Asseng S, Ewert F, Jones JW, Rötter RP, Boote KJ, Ruane AC, Thorburn PJ, Cammarano D, Hatfield JL, Rosenzweig C, Aggarwal PK, Angulo C, Basso B, Bertuzzi P, Biernath C, Brisson N, Challinor AJ, Doltra J, Gayler S, Goldberg R, Grant RF, Heng L, Hooker J, Hunt LA, Ingwersen J, Izaurralde RC, Kersebaum KC, Müller C, Kumar SN, Nendel C, O'leary G, Olesen JE, Osborne TM, Palosuo T, Priesack E, Ripoche D, Semenov MA, Shcherbak I, Steduto P, Stöckle CO, Stratonovitch P, Streck T, Supit I, Tao F, Travasso M, Waha K, White JW, Wolf J. Multimodel ensembles of wheat growth: many models are better than one. Glob Chang Biol 2015; 21:911-25. [PMID: 25330243 DOI: 10.1111/gcb.12768] [Citation(s) in RCA: 50] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/28/2014] [Revised: 08/07/2014] [Accepted: 09/25/2014] [Indexed: 05/18/2023]
Abstract
Crop models of crop growth are increasingly used to quantify the impact of global changes due to climate or crop management. Therefore, accuracy of simulation results is a major concern. Studies with ensembles of crop models can give valuable information about model accuracy and uncertainty, but such studies are difficult to organize and have only recently begun. We report on the largest ensemble study to date, of 27 wheat models tested in four contrasting locations for their accuracy in simulating multiple crop growth and yield variables. The relative error averaged over models was 24-38% for the different end-of-season variables including grain yield (GY) and grain protein concentration (GPC). There was little relation between error of a model for GY or GPC and error for in-season variables. Thus, most models did not arrive at accurate simulations of GY and GPC by accurately simulating preceding growth dynamics. Ensemble simulations, taking either the mean (e-mean) or median (e-median) of simulated values, gave better estimates than any individual model when all variables were considered. Compared to individual models, e-median ranked first in simulating measured GY and third in GPC. The error of e-mean and e-median declined with an increasing number of ensemble members, with little decrease beyond 10 models. We conclude that multimodel ensembles can be used to create new estimators with improved accuracy and consistency in simulating growth dynamics. We argue that these results are applicable to other crop species, and hypothesize that they apply more generally to ecological system models.
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Affiliation(s)
- Pierre Martre
- INRA, UMR1095 Genetics, Diversity and Ecophysiology of Cereals (GDEC), 5 chemin de Beaulieu, F-63 100, Clermont-Ferrand, France; Blaise Pascal University, UMR1095 GDEC, F-63 170, Aubière, France
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Gaju O, Allard V, Martre P, Le Gouis J, Moreau D, Bogard M, Hubbart S, Foulkes MJ. Nitrogen partitioning and remobilization in relation to leaf senescence, grain yield and grain nitrogen concentration in wheat cultivars. Field Crops Research 2014. [PMID: 0 DOI: 10.1016/j.fcr.2013.09.003] [Citation(s) in RCA: 84] [Impact Index Per Article: 8.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/03/2023]
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Ravel C, Fiquet S, Boudet J, Dardevet M, Vincent J, Merlino M, Michard R, Martre P. Conserved cis-regulatory modules in promoters of genes encoding wheat high-molecular-weight glutenin subunits. Front Plant Sci 2014; 5:621. [PMID: 25429295 PMCID: PMC4228979 DOI: 10.3389/fpls.2014.00621] [Citation(s) in RCA: 36] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/22/2014] [Accepted: 10/21/2014] [Indexed: 05/19/2023]
Abstract
The concentration and composition of the gliadin and glutenin seed storage proteins (SSPs) in wheat flour are the most important determinants of its end-use value. In cereals, the synthesis of SSPs is predominantly regulated at the transcriptional level by a complex network involving at least five cis-elements in gene promoters. The high-molecular-weight glutenin subunits (HMW-GS) are encoded by two tightly linked genes located on the long arms of group 1 chromosomes. Here, we sequenced and annotated the HMW-GS gene promoters of 22 electrophoretic wheat alleles to identify putative cis-regulatory motifs. We focused on 24 motifs known to be involved in SSP gene regulation. Most of them were identified in at least one HMW-GS gene promoter sequence. A common regulatory framework was observed in all the HMW-GS gene promoters, as they shared conserved cis-regulatory modules (CCRMs) including all the five motifs known to regulate the transcription of SSP genes. This common regulatory framework comprises a composite box made of the GATA motifs and GCN4-like Motifs (GLMs) and was shown to be functional as the GLMs are able to bind a bZIP transcriptional factor SPA (Storage Protein Activator). In addition to this regulatory framework, each HMW-GS gene promoter had additional motifs organized differently. The promoters of most highly expressed x-type HMW-GS genes contain an additional box predicted to bind R2R3-MYB transcriptional factors. However, the differences in annotation between promoter alleles could not be related to their level of expression. In summary, we identified a common modular organization of HMW-GS gene promoters but the lack of correlation between the cis-motifs of each HMW-GS gene promoter and their level of expression suggests that other cis-elements or other mechanisms regulate HMW-GS gene expression.
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Affiliation(s)
- Catherine Ravel
- Institut National de la Recherche Agronomique, UMR1095, Genetics, Diversity and Ecophysiology of CerealsClermont-Ferrand, France
- UMR1095, Genetics, Diversity and Ecophysiology of Cereals, Department of Biology, Blaise Pascal UniversityAubière, France
- *Correspondence: Catherine Ravel, Institut National de la Recherche Agronomique, UMR1095, Genetics, Diversity and Ecophysiology of Cereals, 5 chemin de Beaulieu, F-63 100 Clermont-Ferrand, France e-mail:
| | - Samuel Fiquet
- Institut National de la Recherche Agronomique, UMR1095, Genetics, Diversity and Ecophysiology of CerealsClermont-Ferrand, France
- UMR1095, Genetics, Diversity and Ecophysiology of Cereals, Department of Biology, Blaise Pascal UniversityAubière, France
| | - Julie Boudet
- Institut National de la Recherche Agronomique, UMR1095, Genetics, Diversity and Ecophysiology of CerealsClermont-Ferrand, France
- UMR1095, Genetics, Diversity and Ecophysiology of Cereals, Department of Biology, Blaise Pascal UniversityAubière, France
| | - Mireille Dardevet
- Institut National de la Recherche Agronomique, UMR1095, Genetics, Diversity and Ecophysiology of CerealsClermont-Ferrand, France
- UMR1095, Genetics, Diversity and Ecophysiology of Cereals, Department of Biology, Blaise Pascal UniversityAubière, France
| | - Jonathan Vincent
- Institut National de la Recherche Agronomique, UMR1095, Genetics, Diversity and Ecophysiology of CerealsClermont-Ferrand, France
- UMR1095, Genetics, Diversity and Ecophysiology of Cereals, Department of Biology, Blaise Pascal UniversityAubière, France
| | - Marielle Merlino
- Institut National de la Recherche Agronomique, UMR1095, Genetics, Diversity and Ecophysiology of CerealsClermont-Ferrand, France
- UMR1095, Genetics, Diversity and Ecophysiology of Cereals, Department of Biology, Blaise Pascal UniversityAubière, France
| | - Robin Michard
- Institut National de la Recherche Agronomique, UMR1095, Genetics, Diversity and Ecophysiology of CerealsClermont-Ferrand, France
- UMR1095, Genetics, Diversity and Ecophysiology of Cereals, Department of Biology, Blaise Pascal UniversityAubière, France
| | - Pierre Martre
- Institut National de la Recherche Agronomique, UMR1095, Genetics, Diversity and Ecophysiology of CerealsClermont-Ferrand, France
- UMR1095, Genetics, Diversity and Ecophysiology of Cereals, Department of Biology, Blaise Pascal UniversityAubière, France
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Asseng S, Ewert F, Rosenzweig C, Jones JW, Hatfield JL, Ruane AC, Boote KJ, Thorburn PJ, Rötter RP, Cammarano D, Brisson N, Basso B, Martre P, Aggarwal PK, Angulo C, Bertuzzi P, Biernath C, Challinor AJ, Doltra J, Gayler S, Goldberg R, Grant R, Heng L, Hooker J, Hunt LA, Ingwersen J, Izaurralde RC, Kersebaum KC, Müller C, Naresh Kumar S, Nendel C, O’Leary G, Olesen JE, Osborne TM, Palosuo T, Priesack E, Ripoche D, Semenov MA, Shcherbak I, Steduto P, Stöckle C, Stratonovitch P, Streck T, Supit I, Tao F, Travasso M, Waha K, Wallach D, White JW, Williams JR, Wolf J. Uncertainty in simulating wheat yields under climate change. Nature Clim Change 2013. [PMID: 0 DOI: 10.1038/nclimate1916] [Citation(s) in RCA: 267] [Impact Index Per Article: 24.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/08/2023]
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Plessis A, Ravel C, Bordes J, Balfourier F, Martre P. Association study of wheat grain protein composition reveals that gliadin and glutenin composition are trans-regulated by different chromosome regions. J Exp Bot 2013; 64:3627-44. [PMID: 23881399 PMCID: PMC3745720 DOI: 10.1093/jxb/ert188] [Citation(s) in RCA: 60] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/20/2023]
Abstract
Wheat grain storage protein (GSP) content and composition are the main determinants of the end-use value of bread wheat (Triticum aestivum L.) grain. The accumulation of glutenins and gliadins, the two main classes of GSP in wheat, is believed to be mainly controlled at the transcriptional level through a network of transcription factors. This regulation network could lead to stable cross-environment allometric scaling relationships between the quantity of GSP classes/subunits and the total quantity of nitrogen per grain. This work conducted a genetic mapping study of GSP content and composition and allometric scaling parameters of grain N allocation using a bread wheat worldwide core collection grown in three environments. The core collection was genotyped with 873 markers for genome-wide association and 167 single nucleotide polymorphism markers in 51 candidate genes for candidate association. The candidate genes included 35 transcription factors (TFs) expressed in grain. This work identified 74 loci associated with 38 variables, of which 19 were candidate genes or were tightly linked with candidate genes. Besides structural GSP genes, several loci putatively trans-regulating GSP accumulation were identified. Seven candidate TFs, including four wheat orthologues of barley TFs that control hordein gene expression, were associated or in strong linkage disequilibrium with markers associated with the composition or quantity of glutenin or gliadin, or allometric grain N allocation parameters, confirming the importance of the transcriptional control of GSP accumulation. Genome-wide association results suggest that the genes regulating glutenin and gliadin compositions are mostly distinct from each other and operate differently.
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Affiliation(s)
- Anne Plessis
- INRA, UMR1095, Genetics, Diversity and Ecophysiology of Cereals, 5 Chemin de Beaulieu, F-63100 Clermont-Ferrand, France
- Blaise Pascal University, UMR1095, Genetics, Diversity and Ecophysiology of Cereals, F-63170 Aubière, France
- * These authors contributed equally to this manuscript
| | - Catherine Ravel
- INRA, UMR1095, Genetics, Diversity and Ecophysiology of Cereals, 5 Chemin de Beaulieu, F-63100 Clermont-Ferrand, France
- Blaise Pascal University, UMR1095, Genetics, Diversity and Ecophysiology of Cereals, F-63170 Aubière, France
- * These authors contributed equally to this manuscript
| | - Jacques Bordes
- INRA, UMR1095, Genetics, Diversity and Ecophysiology of Cereals, 5 Chemin de Beaulieu, F-63100 Clermont-Ferrand, France
- Blaise Pascal University, UMR1095, Genetics, Diversity and Ecophysiology of Cereals, F-63170 Aubière, France
| | - François Balfourier
- INRA, UMR1095, Genetics, Diversity and Ecophysiology of Cereals, 5 Chemin de Beaulieu, F-63100 Clermont-Ferrand, France
- Blaise Pascal University, UMR1095, Genetics, Diversity and Ecophysiology of Cereals, F-63170 Aubière, France
| | - Pierre Martre
- INRA, UMR1095, Genetics, Diversity and Ecophysiology of Cereals, 5 Chemin de Beaulieu, F-63100 Clermont-Ferrand, France
- Blaise Pascal University, UMR1095, Genetics, Diversity and Ecophysiology of Cereals, F-63170 Aubière, France
- To whom correspondence should be addressed. E-mail:
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