Abstract:Sustained and stable productions of main agricultural products such as rice, wheat, and fish are essential to guarantee food security in China, which depends on innovations in breeding theories and technologies. Using genetic resources of rice as well as wheat and fish, and a combination of omics, systems biology, and synthetic biology, a strategic program named the Molecular Module-based Designer Breeding Systems was initiated in 2013 and aimed to (1) dissect molecular modules controlling complex traits including yield, stress tolerance, quality, and nutrient efficiency; (2) reveal the molecular mechanisms of complex trait formation at genome-scale, and the coupling mechanisms of diverse molecular modules, (3) develop the techniques for an optimized genome-wide multi-module assembly and an effective designer breeding scheme. Moreover, this project also aimied to establish a systematic solution for designing and breeding elite varieties. This program includes four projects: (1) mining and functional analysis of molecular modules controlling complex traits; (2) analysis of module systems and their coupling effects; (3) molecular design and breeding of elite varieties;and (4) construction of breeding bases and pipelines for designer breeding. Within the first five years of the program, it aims to obtain 16-20 molecular modules and 12-15 module systems applicable in designer breeding, 1-2 computational models used for evaluating the coupling effect of diverse modules, achieve an optimal coupling assembly of yield, quality, tolerance, and nutrient efficiency, and breed 10-15 designer varieties. So far, this program has dissected 20 modules from rice including 5 for high yield, 2 for resistance to rice blast and banded sclerotial blight, 3 for tolerance to cold, and 2 for nitrogen utilization efficiency. It has revealed several module systems controlling oil biosynthesis in soybean, and bred 14 designer rice varieties for field tests or regional trials. In addition, promising progresses have been achieved in establishing breeding bases and pipelines. The program is expected to make substantial contributions to upgrading both crop and animal breeding technologies.