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In silico plant modelling is the use of dynamic crop simulation models to evaluate hypothetical plant traits (phenology, processes and plant architecture) that will enhance crop growth and yield for a defined target environment and crop management (weather, soils, limited resource). To be useful for genetic improvement, crop models must realistically simulate the principles of crop physiology responses to the environment and the principles by which genetic variation affects the dynamic crop carbon, water and nutrient processes. Ideally, crop models should have sufficient physiological detail of processes to incorporate the genetic effects on these processes to allow for robust simulations of response outcomes in different environments. Yield, biomass, harvest index, flowering date and maturity are emergent outcomes of many interacting genes and processes rather than being primary traits directly driven by singular genetics. Examples will be given for several grain legumes, using the CSM-CROPGRO model, to illustrate emergent outcomes simulated as a result of single and multiple combinations of genotype-specific parameters and to illustrate genotype by environment interactions that may occur in different target environments. Specific genetically influenced traits can result in G × E interactions on crop growth and yield outcomes as affected by available water, CO2 concentration, temperature, and other factors. An emergent outcome from a given genetic trait may increase yield in one environment but have little or negative effect in another environment. Much work is needed to link genetic effects to the physiological processes for in silico modelling applications, especially for plant breeding under future climate change.

The common bean is a tropical facultative short-day legume that is now grown in tropical and temperate zones. This observation underscores how domestication and modern breeding can change the adaptive phenology of a species. A key adaptive trait is the optimal timing of the transition from the vegetative to the reproductive stage. This trait is responsive to genetically controlled signal transduction pathways and local climatic cues. A comprehensive characterization of this trait can be started by assessing the quantitative contribution of the genetic and environmental factors, and their interactions. This study aimed to locate significant QTL (G) and environmental (E) factors controlling time-to-flower in the common bean, and to identify and measure G × E interactions. Phenotypic data were collected from a biparental [Andean × Mesoamerican] recombinant inbred population (F11:14, 188 genotypes) grown at five environmentally distinct sites. QTL analysis using a dense linkage map revealed 12 QTL, five of which showed significant interactions with the environment. Dissection of G × E interactions using a linear mixed-effect model revealed that temperature, solar radiation, and photoperiod play major roles in controlling common bean flowering time directly, and indirectly by modifying the effect of certain QTL. The model predicts flowering time across five sites with an adjusted r-square of 0.89 and root-mean square error of 2.52 d. The model provides the means to disentangle the environmental dependencies of complex traits, and presents an opportunity to identify in silico QTL allele combinations that could yield desired phenotypes under different climatic conditions.

The symbiotic relationship between the soybean plant and rhizobium results in fixation of atmospheric nitrogen (N(2)) in the root nodules, with the result that nitrogenous fertilization of the soybean is unnecessary. The effectiveness of nodule formation and N(2) fixation with rhizobial strains is under genetic control with two general categories identified: (1) promiscuous, which produces functional nodules with cowpea-type rhizobial strains; and (2) nonpromiscuous, which forms no or nonfunctional nodules with these strains. The segregation pattern of this promiscuity trait was studied using nodule dry weight (NDW) and leaf color score (LCS) as indicators of N(2) fixation effectiveness. Individual plants in each of six populations [P(1) = nonpromiscuous, P(2) = promiscuous, F(1) = P(1) x P(2) (and the reciprocal cross), BC(1)(P(1)) = F(1) (female) x P(1), BC(1)(P(2)) = F(1) (female) x P(2), F(2)] were scored for these characters after inoculation with a rhizobial strain that would distinguish between both types. For NDW, nonpromiscuity was found to be partially dominant (h/d = 0.37), controlled by four loci. For LCS, nonpromiscuity was shown to be almost completely dominant (h/d = 0.74), controlled by two loci. LCS was a more meaningful estimate of N(2) fixation because it represented the total effectiveness of nodulation to provide nitrogen for the plant.

The continuing increase in atmospheric carbon dioxide concentration ([CO 2 ]) and projections of possible future increases in global air temperatures have stimulated interest in the effects of these climate variables on agriculturally important food crops. This study was conducted to determine the effects of [CO 2 ] and temperature on rice (Oryza sativa L., cv. IR-30)

The atmospheric carbon dioxide (C02) concentration has been rising and is predicted to reach double the present concentration sometime during the next century. The objective of this investigation was to determine the long-term effects of different C02 concentrations on carbohydrate status and partitioning in rice (Oryza sativa L. cv. IR-30). Rice plants were grown season-long in outdoor, naturally sunlit, environmentally controlled growth chambers with C02 concentrations of 160, 250, 330, 500, 660, and 900 /?mol C02 mor1 air. In leaf blades, the priority between the partitioning of carbon into storage carbohydrates or into export changed with developmental stage and C02 concentration. During vegetative growth, leaf sucrose and starch concentrations increased with increasing C02 concentration but tended to level off above 500 /?mol mol-1 C02. Similarly, photosynthesis also increased with C02 concentrations up to 500 /?mol mol-1 and then reached a plateau at higher concentrations. The ratio of starch to sucrose concentration was positively correlated with the C02 concentration. At maturity, increasing C02 concentration resulted in an increase in total non-structural carbohydrate (TNC) concentration in leaf blades, leaf sheaths and culms. Carbohydrates that were stored in vegetative plant parts before heading made a smaller contribution to grain dry weight at C02 concentrations below 330 /xmol mol-1 than for treatments at concentrations above ambient. Increasing C02 concentration had no effect on the carbohydrate concentration in the grain at maturity.

The changes in the internal water relations of soybean (Glycine max L. Merr.) leaves during vegetative and reproductive growth were studied by following the changes in the pressure-volume curves of soybean leaves. The results demonstrate that soybean leaves undergo a change in their osmotic properties which coincides with the onset of active reproductive growth and is not induced by water stress. The observed osmotic changes resulted in an increase in the leaf relative water content at any given bulk leaf water potential. The volume of leaf water loss needed to reduce turgor potential to zero did not change following this change in osmotic properties. The degree of turgor maintenance after the change in osmotic properties depended on the ability to maintain adequate leaf relative water content. The observed changes in bulk osmotic potential of the soybean leaves would contribute to increased leaf-soil water potential gradients and therefore to improved ability to