On the face of the rapid advances in genome editing technology and greatly expanded knowledge on plant genome and genes, there is a strong demand to develop an effective tool to guide designing crops for higher yields. Here we developed a highly mechanistic model of Whole plAnt Carbon Nitrogen Interaction (WACNI), which predicts crop yield based on major metabolic and biophysical processes in source, sink and transport tissues. WACNI accurately predicted the yield responses of so far reported source, sink and transport related genetic manipulations on rice grain yields. Systematic sensitivity analysis with WACNI was used to classify the source, sink and transport related molecular processes into four categories, i.e. universal yield enhancers, universal yield inhibitors, conditional yield enhancers and weak yield regulators. Simulations using WACNI further show that even without a major change in leaf photosynthetic properties, 54.6% to 73% grain yield increase can be potentially achieved by optimizing these molecular processes during the rice grain filling period while simply combining all the 'superior' molecular modules together cannot achieve the optimal yield level. A common macroscopic feature in all these designed high-yield lines is that they all show 'a sustained and steady growth of grain sink', which might be used as a generic selection criteria in high-yield rice breeding. Overall, WACNI can serve as a tool to facilitate plant source sink interaction research and guide future crops breeding by design.

Systematic Optimization of Whole Plant Carbon Nitrogen Interaction (WACNI) to Support Crop Design for Greater Yield