A functional-structural model of rice linking quantitative genetic information with morphological development and physiological processes.
OBJECTIVE
Although quantitative trait loci (QTL) analysis of yield-related traits for rice has developed rapidly, crop models using genotype information have been proposed only relatively recently. As a first step towards a generic genotype-phenotype model, we present here a three-dimensional functional-structural plant model (FSPM) of rice, in which some model parameters are controlled by functions describing the effect of main-effect and epistatic QTLs.


METHODS
The model simulates the growth and development of rice based on selected ecophysiological processes, such as photosynthesis (source process) and organ formation, growth and extension (sink processes). It was devised using GroIMP, an interactive modelling platform based on the Relational Growth Grammar formalism (RGG). RGG rules describe the course of organ initiation and extension resulting in final morphology. The link between the phenotype (as represented by the simulated rice plant) and the QTL genotype was implemented via a data interface between the rice FSPM and the QTLNetwork software, which computes predictions of QTLs from map data and measured trait data.


RESULTS
Using plant height and grain yield, it is shown how QTL information for a given trait can be used in an FSPM, computing and visualizing the phenotypes of different lines of a mapping population. Furthermore, we demonstrate how modification of a particular trait feeds back on the entire plant phenotype via the physiological processes considered.


CONCLUSIONS
We linked a rice FSPM to a quantitative genetic model, thereby employing QTL information to refine model parameters and visualizing the dynamics of development of the entire phenotype as a result of ecophysiological processes, including the trait(s) for which genetic information is available. Possibilities for further extension of the model, for example for the purposes of ideotype breeding, are discussed.
Institute of Bioinformatics, Zhejiang University, Hangzhou, PR China.
Lifeng
L
Xu
Michael
M
Henke
Jun
J
Zhu
Winfried
W
Kurth
Gerhard
G
Buck-Sorlin
D000465:Algorithms; D002138:Calibration; D002681:China; D003198:Computer Simulation; D018556:Crops, Agricultural / Q000033:anatomy & histology / Q000235:genetics / Q000254:growth & development / Q000502:physiology*; D004777:Environment; D004843:Epistasis, Genetic; D017343:Genes, Plant; D056726:Genetic Association Studies; D008954:Models, Biological; D012275:Oryza / Q000033:anatomy & histology / Q000235:genetics / Q000254:growth & development / Q000502:physiology*; D010788:Photosynthesis; D018515:Plant Leaves / Q000033:anatomy & histology / Q000235:genetics / Q000254:growth & development; D018547:Plant Stems / Q000033:anatomy & histology / Q000235:genetics / Q000254:growth & development; D040641:Quantitative Trait Loci; D013472:Sunlight
Ann Bot. 2003 Feb;91(3):361-71
12547689
Funct Plant Biol. 2008 Dec;35(10):900-910
32688841
Nat Rev Genet. 2001 Oct;2(10):815-22
11584298
Genetics. 1998 Nov;150(3):1257-65
9799277
Heredity (Edinb). 2008 Nov;101(5):396-404
18716608
EMBO Rep. 2002 Sep;3(9):846-51
12223466
Heredity (Edinb). 1999 Apr;82 Pt 4:415-21
10383660
J Exp Bot. 2010 May;61(8):2185-202
20400531
Ann Bot. 2008 May;101(8):1185-94
17921525
Trends Plant Sci. 2006 Dec;11(12):587-93
17092764
Ann Bot. 2006 Apr;97(4):549-57
16399793
Ann Bot. 2008 May;101(8):1243-54
17766844
Yi Chuan Xue Bao. 2001;28(2):135-43
11233257
New Phytol. 2005 Jun;166(3):859-67
15869647
Ann Bot. 2008 May;101(8):1053-63
18387970
Planta. 2004 Jan;218(3):388-95
14534788
Bioinformatics. 2007 Jun 15;23(12):1527-36
17459962
Funct Plant Biol. 2008 Dec;35(10):781-796
32688832
Funct Plant Biol. 2008 Dec;35(10):739-750
32688828
New Phytol. 2005 Jun;166(3):801-12
15869643
Bioinformatics. 2008 Mar 1;24(5):721-3
18202029
Ann Bot. 2005 Jun;95(7):1131-43
15820987
J Exp Bot. 2010 May;61(8):2101-15
19995824
New Phytol. 2008;179(3):629-642
18373652
Funct Plant Biol. 2008 Oct;35(8):689-704
32688823
Trends Plant Sci. 2003 Jan;8(1):9-14
12523994
Ann Bot. 2008 May;101(8):1109-23
17766311