Identifying traits for genotypic adaptation using crop models.

Genotypic adaptation involves the incorporation of novel traits in crop varieties so as to enhance food productivity and stability and is expected to be one of the most important adaptation strategies to future climate change. Simulation modelling can provide the basis for evaluating the biophysical potential of crop traits for genotypic adaptation. This review focuses on the use of models for assessing the potential benefits of genotypic adaptation as a response strategy to projected climate change impacts. Some key crop responses to the environment, as well as the role of models and model ensembles for assessing impacts and adaptation, are first reviewed. Next, the review describes crop-climate models can help focus the development of future-adapted crop germplasm in breeding programmes. While recently published modelling studies have demonstrated the potential of genotypic adaptation strategies and ideotype design, it is argued that, for model-based studies of genotypic adaptation to be used in crop breeding, it is critical that modelled traits are better grounded in genetic and physiological knowledge. To this aim, two main goals need to be pursued in future studies: (i) a better understanding of plant processes that limit productivity under future climate change; and (ii) a coupling between genetic and crop growth models-perhaps at the expense of the number of traits analysed. Importantly, the latter may imply additional complexity (and likely uncertainty) in crop modelling studies. Hence, appropriately constraining processes and parameters in models and a shift from simply quantifying uncertainty to actually quantifying robustness towards modelling choices are two key aspects that need to be included into future crop model-based analyses of genotypic adaptation.

[1]  C. Tebaldi,et al.  Prioritizing Climate Change Adaptation Needs for Food Security in 2030 , 2008, Science.

[2]  R. Sylvester-Bradley,et al.  Ideotype design for lodging-resistant wheat , 2007, Euphytica.

[3]  J. Porter,et al.  Ozone effects on wheat in relation to CO2: modelling short‐term and long‐term responses of leaf photosynthesis and leaf duration , 2000 .

[4]  S. Long,et al.  FACE-ing the facts: inconsistencies and interdependence among field, chamber and modeling studies of elevated [CO2] impacts on crop yield and food supply. , 2008, The New phytologist.

[5]  Ralph Johnson,et al.  design patterns elements of reusable object oriented software , 2019 .

[6]  David B. Lobell,et al.  Climate change adaptation in crop production: Beware of illusions , 2014 .

[7]  A. Challinor,et al.  Adaptation of crops to climate change through genotypic responses to mean and extreme temperatures , 2007 .

[8]  F.W.T. Penning de Vries,et al.  Concepts for a new plant type for direct seeded flooded tropical rice. , 1991 .

[9]  I. R. Cowan,et al.  Stomatal conductance correlates with photosynthetic capacity , 1979, Nature.

[10]  Keith Beven,et al.  A manifesto for the equifinality thesis , 2006 .

[11]  R. Naylor,et al.  Historical Warnings of Future Food Insecurity with Unprecedented Seasonal Heat , 2009, Science.

[12]  Andrew J. Challinor,et al.  Increased crop failure due to climate change: assessing adaptation options using models and socio-economic data for wheat in China , 2010 .

[13]  A. Leakey Rising atmospheric carbon dioxide concentration and the future of C4 crops for food and fuel , 2009, Proceedings of the Royal Society B: Biological Sciences.

[14]  K. Boote,et al.  Quantifying potential benefits of drought and heat tolerance in rainy season sorghum for adapting to climate change , 2014 .

[15]  Chris Murphy,et al.  APSIM - Evolution towards a new generation of agricultural systems simulation , 2014, Environ. Model. Softw..

[16]  Chris Huntingford,et al.  Aspects of climate change prediction relevant to crop productivity , 2005, Philosophical Transactions of the Royal Society B: Biological Sciences.

[17]  J. Porter,et al.  Crop responses to climatic variation , 2005, Philosophical Transactions of the Royal Society B: Biological Sciences.

[18]  G. Edwards,et al.  Influences of leaf temperature on photosynthetic carbon metabolism in wheat. , 1987, Plant physiology.

[19]  M. Semenov,et al.  Adapting wheat in Europe for climate change , 2014, Journal of cereal science.

[20]  Brian Killough,et al.  Climate Change Impact Uncertainties for Maize in Panama: Farm Information, Climate Projections, and Yield Sensitivities , 2013 .

[21]  John M. Antle,et al.  A method for evaluating climate change adaptation strategies for small-scale farmers using survey, experimental and modeled data , 2012 .

[22]  J. I. Ortiz-Monasterio,et al.  Climate change: Can wheat beat the heat? , 2008 .

[23]  D. Lobell,et al.  A meta-analysis of crop yield under climate change and adaptation , 2014 .

[24]  R. Villegas,et al.  Genotypic adaptation of Indian groundnut cultivation to climate change:an ensemble approach , 2014 .

[25]  D. Deryng,et al.  Simulating the effects of climate and agricultural management practices on global crop yield , 2011 .

[26]  A. Rogers,et al.  Elevated CO2 effects on plant carbon, nitrogen, and water relations: six important lessons from FACE. , 2009, Journal of experimental botany.

[27]  Michael E. Salvucci,et al.  Sensitivity of Photosynthesis in a C4 Plant, Maize, to Heat Stress , 2002, Plant Physiology.

[28]  Mainassara Zaman-Allah,et al.  Crop science experiments designed to inform crop modeling , 2013 .

[29]  James W. Jones,et al.  Integrated description of agricultural field experiments and production: The ICASA Version 2.0 data standards , 2013 .

[30]  Lance R. Gibson,et al.  Yield Components of Wheat Grown under High Temperature Stress during Reproductive Growth , 1999 .

[31]  Kai Sonder,et al.  Adapting maize production to climate change in sub-Saharan Africa , 2013, Food Security.

[32]  F. Tao,et al.  Climate change, wheat productivity and water use in the North China Plain: A new super-ensemble-based probabilistic projection , 2013 .

[33]  Ed Hawkins,et al.  Addressing uncertainty in adaptation planning for agriculture , 2013, Proceedings of the National Academy of Sciences.

[34]  F. Tardieu,et al.  Temperature responses of developmental processes have not been affected by breeding in different ecological areas for 17 crop species. , 2012, The New phytologist.

[35]  Gurdev S. Khush,et al.  Progress in ideotype breeding to increase rice yield potential , 2008 .

[36]  R. Visser,et al.  The twenty-first century, the century of plant breeding , 2012, Euphytica.

[37]  A. Fredeen,et al.  Effects of phosphorus nutrition on photosynthesis in Glycine max (L.) Merr. , 1990, Planta.

[38]  G. Hammer,et al.  Simulating the Yield Impacts of Organ-Level Quantitative Trait Loci Associated With Drought Response in Maize: A “Gene-to-Phenotype” Modeling Approach , 2009, Genetics.

[39]  Leonard A. Smith,et al.  Uncertainty in predictions of the climate response to rising levels of greenhouse gases , 2005, Nature.

[40]  Martin J. Kropff,et al.  Crop modeling, QTL mapping, and their complementary role in plant breeding , 2003 .

[41]  G. Khush Green revolution: the way forward , 2001, Nature Reviews Genetics.

[42]  Jeffrey W. White,et al.  Methodologies for simulating impacts of climate change on crop production , 2011 .

[43]  D. Holzworth,et al.  Re-inventing model-based decision support with Australian dryland farmers. 4. Yield Prophet® helps farmers monitor and manage crops in a variable climate. , 2009 .

[44]  M. El-Sharkawy How can calibrated research-based models be improved for use as a tool in identifying genes controlling crop tolerance to environmental stresses in the era of genomics—from an experimentalist's perspective , 2005, Photosynthetica.

[45]  Toshichika Iizumi,et al.  Dependency of parameter values of a crop model on the spatial scale of simulation , 2014 .

[46]  C. G. McLaren,et al.  Chapter 4 Informatics in Agricultural Research for Development , 2009 .

[47]  Goldenfeld,et al.  Simple lessons from complexity , 1999, Science.

[48]  James W. Jones,et al.  Uncertainty in Simulating Wheat Yields Under Climate Change , 2013 .

[49]  Gerrit Hoogenboom,et al.  Determination and evaluation of genetic coefficients of peanut lines for breeding applications , 2004 .

[50]  James W. Jones,et al.  Evaluation of Genetic Traits for Improving Productivity and Adaptation of Groundnut to Climate Change in India , 2012 .

[51]  Andrew J. Challinor,et al.  Methods and resources for climate impacts research achieving synergy , 2009 .

[52]  L. H. Allen,et al.  Elevated Temperature and CO2 Impacts on Pollination, Reproductive Growth, and Yield of Several Globally Important Crops , 2005 .

[53]  T. Sinclair,et al.  Crop Modeling: From Infancy to Maturity , 1996 .

[54]  D. Lobell,et al.  The critical role of extreme heat for maize production in the United States , 2013 .

[55]  P. Nobel,et al.  Nutrient Influences on Leaf Photosynthesis: EFFECTS OF NITROGEN, PHOSPHORUS, AND POTASSIUM FOR GOSSYPIUM HIRSUTUM L. , 1980, Plant physiology.

[56]  Xiaoming Wang,et al.  Chapter 7 , 2003, School Health Policy & Practice.

[57]  A. Challinor,et al.  Assessing relevant climate data for agricultural applications , 2012 .

[58]  A. Challinor,et al.  Design and optimisation of a large-area process-based model for annual crops , 2004 .

[59]  S. Asseng,et al.  The impact of temperature variability on wheat yields , 2011 .

[60]  Takeshi Nagai,et al.  Differences Between Rice and Wheat in Temperature Responses of Photosynthesis and Plant Growth , 2009, Plant & cell physiology.

[61]  W. Wilhelm,et al.  Putting genes into genetic coefficients , 2004 .

[62]  R. Leegood,et al.  Effects of temperature on the regulation of photosynthetic carbon assimilation in leaves of maize and barley , 1990, Planta.

[63]  G. Fischer,et al.  Crop response to elevated CO2 and world food supply A comment on: Food for Thought... by Long et al., Science 312: 1918-1921, 2006 , 2007 .

[64]  L. Ziska,et al.  The growth response of C4 plants to rising atmospheric CO2 partial pressure: a reassessment , 2000 .

[65]  James W. Jones,et al.  The Agricultural Model Intercomparison and Improvement Project (AgMIP): Protocols and Pilot Studies , 2013 .

[66]  Philippe Tixier,et al.  Ad hoc modeling in agronomy: What have we learned in the last 15 years? , 2012 .

[67]  B. Badu‐Apraku,et al.  Comparative Performance of Early‐maturing Maize Cultivars Developed in Three Eras under Drought Stress and Well‐watered Environments in West Africa , 2013 .

[68]  D. Lobell,et al.  An assessment of wheat yield sensitivity and breeding gains in hot environments , 2013, Proceedings of the Royal Society B: Biological Sciences.

[69]  J. Topping,et al.  Mitochondrial gene expression during wheat leaf development , 1990, Planta.

[70]  J. Zhuang,et al.  Super Hybrid Rice Breeding in China: Achievements and Prospects , 2007 .

[71]  M. A. El-Sharkawy,et al.  Global warming: causes and impacts on agroecosystems productivity and food security with emphasis on cassava comparative advantage in the tropics/subtropics , 2014, Photosynthetica.

[72]  Mark E. Cooper,et al.  Gene-to-phenotype models and complex trait genetics , 2005 .

[73]  James W. Jones,et al.  A Gene‐Based Model to Simulate Soybean Development and Yield Responses to Environment , 2006 .

[74]  P. Keeling,et al.  Heat Stress during Grain Filling in Maize: Effects on Kernel Growth and Metabolism , 1999 .

[75]  Takeshi Horie,et al.  Leaf Nitrogen, Photosynthesis, and Crop Radiation Use Efficiency: A Review , 1989 .

[76]  K. Cassman,et al.  Rice yields decline with higher night temperature from global warming. , 2004, Proceedings of the National Academy of Sciences of the United States of America.

[77]  Kenneth L. McNally,et al.  Developmental Dynamics and Early Growth Vigour in Rice. I. Relationship Between Development Rate (1/Phyllochron) and Growth , 2012 .

[78]  K. Boote,et al.  Potential benefits of drought and heat tolerance in groundnut for adaptation to climate change in India and West Africa , 2014, Mitigation and Adaptation Strategies for Global Change.

[79]  G. Khush Breaking the yield frontier of rice , 1995 .

[80]  C. Donald The breeding of crop ideotypes , 1968, Euphytica.

[81]  D. T. Canvin,et al.  Effects of Temperature on Photosynthesis and CO(2) Evolution in Light and Darkness by Green Leaves. , 1969, Plant physiology.

[82]  P. Nobel,et al.  Nutrient influences on leaf photosynthesis , 1980 .

[83]  A. O'Hagan,et al.  Bayesian calibration of computer models , 2001 .

[84]  S. Long,et al.  Food for Thought: Lower-Than-Expected Crop Yield Stimulation with Rising CO2 Concentrations , 2006, Science.

[85]  R. Knutti,et al.  Robustness and uncertainties in the new CMIP5 climate model projections , 2013 .

[86]  D. Luquet,et al.  Developmental Dynamics and Early Growth Vigour in Rice 2. Modelling Genetic Diversity Using Ecomeristem , 2012 .

[87]  M. Rivington,et al.  Report on the Meta-­Analysis of Crop Modelling for Climate Change and Food Security Survey , 2010 .

[88]  Reimund P. Rötter,et al.  Adverse weather conditions for European wheat production will become more frequent with climate change , 2014 .

[89]  A. Keys,et al.  Effects of Temperature on Photosynthesis by Maize and Wheat , 1977 .

[90]  Andrew J. Challinor,et al.  Ensemble yield simulations: crop and climate uncertainties, sensitivity to temperature and genotypic adaptation to climate change , 2009 .

[91]  James W. Jones,et al.  How do various maize crop models vary in their responses to climate change factors? , 2014, Global change biology.

[92]  Xinyou Yin,et al.  Role of crop physiology in predicting gene-to-phenotype relationships. , 2004, Trends in plant science.

[93]  G. Edwards,et al.  Photosynthetic Capacity and Nitrogen Use Efficiency of Maize, Wheat, and Rice: A Comparison Between C3 and C4 Photosynthesis , 1981 .

[94]  T. Iizumi,et al.  Parameter estimation and uncertainty analysis of a large-scale crop model for paddy rice: Application of a Bayesian approach , 2009 .

[95]  Reimund P. Rötter,et al.  Characteristic ‘fingerprints’ of crop model responses to weather input data at different spatial resolutions , 2013 .

[96]  P. Pinheiro,et al.  Results of 25 Years of Upland Rice Breeding in Brazil , 2011 .

[97]  Mikhail A. Semenov,et al.  Designing high-yielding wheat ideotypes for a changing climate , 2013 .