作物产量品质相关性状大多为复杂性状，受多基因互作网络与环境的协同调控，其遗传规律剖析与分子设计是作物遗传育种研究的热点，也面临巨大挑战。目前，基于高密度SNP的关联分析已成为复杂性状遗传剖析的重要方法，但已有方法以SNP为检测单位，分析功效低，无法有效剖析全基因组多位点间及其与环境间互作，鉴别的显著位点也不一定是可供选择的功能基因。课题将发展整合基因组结构与注释、性状表型、转录组、代谢或蛋白质组等多组学信息的系统数量遗传学方法，以基因为检测单位，全基因组有效鉴别和分析多效性和非多效性功能基因，估算上位性及基因与环境互作的各项效应分量；发展单性状/多性状基因型设计方法，研制配套分析软件。用超级稻永久F2群体为材料，验证和完善分析方法和软件，提出目标性状改良的功能基因组配方案，推动超级稻育种。课题研究成果对作物复杂性状的遗传结构剖析与分子设计具有重要科学意义和实践应用价值。

Most crop yield and quality related traits are complex traits, controlled cooperatively by gene interaction network and environment. Genetic dissection and molecular design of complex traits is a research hot and challenge in crop genetics and improvement. Currently, association mapping based on saturated SNP of genome has been an important method to dissect genetic mechanism of complex traits; however, current methods based on testing of individual SNP exhibit very lower power and couldn’t effectively analyze interaction between SNPs and their interaction effect with environment, and the distinguished loci may not be the functional genes which could be selected in breeding. This research will develop system quantitative genetics method based on integrated analysis of genetic data on genome sequence, gene annotation, trait phenotype, transcriptome, metablism or proteomics, for effectively identifying and analyzing pleiotropy and non-pleiotropy functional genes which genetic effects are tested as basic unit, estimating epistatic effects and gene-environment interaction effects; while, genotype design method will be developed for improvement of single or multiple traits. Accordingly, software will be developed. An experiment of a super-rice permanent F2 population will be conducted for testing of the method and the software; while, genotype design of functional genes will be proposed for improving targeted traits and promoting super-rice breeding. The expected results of this research are very valuable for dissection of genetic architecture and molecular design of crop complex traits in science and breeding.