Estimation of parameters of a biochemically based model of photosynthesis using a genetic algorithm.

Photosynthesis response to carbon dioxide concentration can provide data on a number of important parameters related to leaf physiology. The genetic algorithm (GA), which is a robust stochastic evolutionary computational algorithm inspired by both natural selection and natural genetics, is proposed to simultaneously estimate the parameters [including maximum carboxylation rate allowed by ribulose 1.5-bisphosphate carboxylase/oxygenase (Rubisco) carboxylation rate (V(cmax)), potential light-saturated electron transport rate (J(max)), triose-phosphate utilization (TPU), leaf dark respiration in the light (R(d)) and mesophyll conductance (g(m))] of the photosynthesis models presented by Farquhar, von Caemmerer and Berry, and Ethier and Livingston. The results show that by properly constraining the parameter bounds the GA-based estimate methods can effectively and efficiently obtain globally (or, at least near globally) optimal solutions, which are as good as or better than those obtained by non-linear curve fitting methods used in previous studies. More complicated problems such as taking the g(m) variation response to CO(2) into account can be easily formulated and solved by using GA. The influence of the crossover probability (P(c)), mutation probability (P(m)), population size and generation on the performance of GA was also investigated.

[1]  F. Magnani,et al.  Stomatal, mesophyll conductance and biochemical limitations to photosynthesis as affected by drought and leaf ontogeny in ash and oak trees , 2005 .

[2]  Soo-Hyung Kim,et al.  A coupled model of photosynthesis, stomatal conductance and transpiration for a rose leaf (Rosa hybrida L.). , 2003, Annals of botany.

[3]  F. Loreto,et al.  The use of low [CO2] to estimate diffusional and non‐diffusional limitations of photosynthetic capacity of salt‐stressed olive saplings , 2003 .

[4]  T. Sharkey,et al.  Carbon isotope discrimination measured concurrently with gas exchange to investigate CO2 diffusion in leaves of higher plants , 1986 .

[5]  K. Hikosaka,et al.  Seasonal change in the balance between capacities of RuBP carboxylation and RuBP regeneration affects CO2 response of photosynthesis in Polygonum cuspidatum. , 2005, Journal of experimental botany.

[6]  Dennis D. Baldocchi,et al.  Leaf age affects the seasonal pattern of photosynthetic capacity and net ecosystem exchange of carbon in a deciduous forest , 2001 .

[7]  J. Berry,et al.  A biochemical model of photosynthetic CO2 assimilation in leaves of C3 species , 1980, Planta.

[8]  H. Sinoquet,et al.  Effects of crown development on leaf irradiance, leaf morphology and photosynthetic capacity in a peach tree. , 2002, Tree physiology.

[9]  Norman H. Barth,et al.  Oceanographic Experiment Design II: Genetic Algorithms , 1992 .

[10]  James F. Reynolds,et al.  Modelling photosynthesis of cotton grown in elevated CO2 , 1992 .

[11]  S. Long,et al.  Quantum yields for uptake of carbon dioxide in C3 vascular plants of contrasting habitats and taxonomic groupings , 1993, Planta.

[12]  Jens Kattge,et al.  Temperature acclimation in a biochemical model of photosynthesis: a reanalysis of data from 36 species. , 2007, Plant, cell & environment.

[13]  Yoshiko Kosugi,et al.  Parameterization of the CO2 and H2O gas exchange of several temperate deciduous broad‐leaved trees at the leaf scale considering seasonal changes , 2003 .

[14]  D. Manter,et al.  A/C(i) curve analysis across a range of woody plant species: influence of regression analysis parameters and mesophyll conductance. , 2004, Journal of experimental botany.

[15]  G. Farquhar,et al.  Some relationships between the biochemistry of photosynthesis and the gas exchange of leaves , 1981, Planta.

[16]  S. V. Caemmerer,et al.  Biochemical models of leaf photosynthesis. , 2000 .

[17]  Susanne von Caemmerer,et al.  Temperature Response of Mesophyll Conductance. Implications for the Determination of Rubisco Enzyme Kinetics and for Limitations to Photosynthesis in Vivo , 2002, Plant Physiology.

[18]  Carl J. Bernacchi,et al.  Improved temperature response functions for models of Rubisco‐limited photosynthesis , 2001 .

[19]  J. Eheart,et al.  Using Genetic Algorithms to Solve a Multiobjective Groundwater Monitoring Problem , 1995 .

[20]  Nigel J. Livingston,et al.  On the need to incorporate sensitivity to CO2 transfer conductance into the Farquhar–von Caemmerer–Berry leaf photosynthesis model , 2004 .

[21]  P. Montpied,et al.  Temperature response of photosynthesis of silver fir (Abies alba Mill.) seedlings , 2002 .

[22]  Ryozo Ooka,et al.  Optimal design method for building energy systems using genetic algorithms , 2009 .

[23]  Denis Loustau,et al.  Temperature response of parameters of a biochemically based model of photosynthesis. II. A review of experimental data , 2002 .

[24]  John H. Holland,et al.  Adaptation in Natural and Artificial Systems: An Introductory Analysis with Applications to Biology, Control, and Artificial Intelligence , 1992 .

[25]  Seon Ki Park,et al.  Parameter estimation using the genetic algorithm and its impact on quantitative precipitation forecast , 2006 .

[26]  Xinyou Yin,et al.  Extension of a biochemical model for the generalized stoichiometry of electron transport limited C3 photosynthesis , 2004 .

[27]  Ray Leuning,et al.  Temperature dependence of two parameters in a photosynthesis model , 2002 .

[28]  J. H. M. Thornley,et al.  Temperature and CO2Responses of Leaf and Canopy Photosynthesis: a Clarification using the Non-rectangular Hyperbola Model of Photosynthesis , 1998 .

[29]  M. Flowers,et al.  Optimizing the statistical estimation of the parameters of the Farquhar-von Caemmerer-Berry model of photosynthesis. , 2007, The New phytologist.

[30]  Goldberg,et al.  Genetic algorithms , 1993, Robust Control Systems with Genetic Algorithms.

[31]  I. Terashima,et al.  Effects of HgCl(2) on CO(2) dependence of leaf photosynthesis: evidence indicating involvement of aquaporins in CO(2) diffusion across the plasma membrane. , 2002, Plant & cell physiology.

[32]  R. Leuning,et al.  A two-leaf model for canopy conductance, photosynthesis and partitioning of available energy I:: Model description and comparison with a multi-layered model , 1998 .

[33]  Carl J. Bernacchi,et al.  In vivo temperature response functions of parameters required to model RuBP-limited photosynthesis , 2003 .

[34]  Parametric inversion of viscoelastic media from VSP data using a genetic algorithm , 2007 .

[35]  D. Pury,et al.  Simple scaling of photosynthesis from leaves to canopies without the errors of big‐leaf models , 1997 .

[36]  T. Sharkey,et al.  Fitting photosynthetic carbon dioxide response curves for C(3) leaves. , 2007, Plant, cell & environment.

[37]  J. Flexas,et al.  Rapid variations of mesophyll conductance in response to changes in CO2 concentration around leaves. , 2007, Plant, cell & environment.

[38]  Zewei Miao,et al.  Comparison of the A-Cc curve fitting methods in determining maximum ribulose 1.5-bisphosphate carboxylase/oxygenase carboxylation rate, potential light saturated electron transport rate and leaf dark respiration. , 2009, Plant, cell & environment.

[39]  T. Black,et al.  Low stomatal and internal conductance to CO2 versus Rubisco deactivation as determinants of the photosynthetic decline of ageing evergreen leaves. , 2006, Plant, cell & environment.

[40]  S. Kellomäki,et al.  Acclimation of photosynthetic parameters in Scots pine after three years exposure to elevated temperature and CO2 , 1996 .

[41]  D. Whitehead,et al.  The response of photosynthetic model parameters to temperature and nitrogen concentration in Pinus radiata D. Don , 1997 .

[42]  D. M. Gates,et al.  Interactive effects of light, leaf temperature, CO2 and O2 on photosynthesis in soybean , 1985, Planta.

[43]  X. Le Roux,et al.  Temperature response of leaf photosynthetic capacity in seedlings from seven temperate tree species. , 2001, Tree physiology.

[44]  Stan D. Wullschleger,et al.  Biochemical Limitations to Carbon Assimilation in C3 Plants—A Retrospective Analysis of the A/Ci Curves from 109 Species , 1993 .

[45]  Graham D. Farquhar,et al.  Temperature dependence of whole-leaf photosynthesis in Eucalyptus pauciflora Sieb , 1984 .