Modelling gene networks controlling transition to flowering in Arabidopsis

Flowering is a critical stage in plant development that initiates grain production and is vulnerable to stress. The genes controlling flowering time in the model plant Arabidopsis thaliana are reviewed. Previously, interactions between these genes were described by qualitative network diagrams. We present a generalized mathematical formalism that relates environmentally dependent transcription, RNA processing, translation, and protein-protein interaction rates to resultant phenotypes. We have developed models (reported elsewhere) based on this concept that simulate flowering times for novel A. thaliana genotype-environment combinations and critical short day lengths (CSDL) in rice (Oryza sativa ssp. japonica cv. Nipponbare). Here we show how CSDL phenotypes emerge from gene expression dynamics. Functionally different but homologous photoperiod measurement genes in rice and A. thaliana nevertheless yield similar results. Other technologies for interrelating genotypes, phenotypes, and the environment are crop simulation models and the theory of quantitative genetics (QG). Some potential synergies between genetic networking (GN) and these older approaches are discussed. Twelve contrasts are drawn between QG and GN revealing that both have equal contributions to make to an ideal theory. Such a theory is initiated by discussing epistasis, dominance, and additivity (all QG basics) in GN terms. Three or less genes can account for the first two but additivity is a complex property dependent on the structure and function of entire subnets. Finally, the utility of simple models is evidenced by 80 years of quantitative genetics and mathematical ecology.