Rewiring Network Plasticity to Improve Crops

Plant systems show dynamic responses, such as changes in architecture and physiology, to adjust their growth in changing environments. The reconfiguration of network modules underlies these responses. There is multi-scale regulation acting on these networks that can be measured as changes in mRNA synthesis, stability, and decay; and in protein translation, activity, affinity, and decay, among others. The regulatory linkages across biological scales can be constitutive, tunable, or switchable under changing environments. The ultimate goal of breeding efforts is to create novel ideotypes with desired traits, which maintain high yield despite challenging environments. Gain of beneficial or adaptive phenotypic traits in commercial crops is often due to ideal coupling/ uncoupling of the network modules with tunable linkages from parental lines. Regulatory genomic variation of influential nodes in network modules perturbs network properties, such as hubs, topology, and clustering, and serves as a source of variation for novel traits. These critical variants that perturb network modules to create novel phenotypes can be discovered using natural diversity in wild relatives of cultivated crops, thereby aiding breeding programs for target discovery. Predictive modeling and quantitatively characterized synthetic modules provide detailed understanding on predictable and heritable behavior of complex regulatory and signaling networks, but implementation of these models in crop plants lags behind. Future efforts to incorporate multi-scale layers of information to predict systems level behavior of crop plant networks and their dynamics in changing environments are an exciting area.