大豆是重要的食品、油脂和饲料作物，富含油脂和蛋白质。近年来，基因组测序和重测序工作的开展，对于在分子水平上改良大豆品质，并对认识其生物学机制，特别是拓宽遗传基础提供了新的契机。然而，大豆自身复杂的基因组特征，尤其是现有的软件和方法不能支持对这一复杂基因组的解构，使得对其结构和多倍化发生规模的深层次研究较为困难。该申请项目旨在建立新的解析复杂基因组的方法和软件，构建大豆作物基因组的生物信息研究平台，并用以解析大豆基因组的结构，重建多倍化过程，比较分析大豆重复基因间基因置换的发生模式和造成的结果；同时基于系统发育和进化理论的分析，探索与大豆固氮、油合成等多个重要农艺性状相关基因、基因家族和调控路径功能的进化规律。项目研究成果将有效支撑大豆相关领域的研究工作，对于认识大豆基因组从全局尺度到单基因的进化具有极为重要的理论和现实意义，同时提供其他生物基因组分析的方法和工具。

Soybean is an important food, grease and a forage plant due to its being a rich source of oil and protein. So far, the development of genome sequencing and re-sequencing has provided a new opportunity for improvement of soybean quality in molecular level and the recognition of its biological mechanism. However, the complex features of soybean genome due to recursive occurrence of polyploidizations, which is a great challenge to present bioinformatics tools, hinder efforts to understand its evolutionary history and functional innovation. Here, we proposed a valuable project aiming at creating new methods and softwares of deconvolute of the complex genome, and constructing bioinformatics platform to perform insightful soybean genomics research, reconstructing the process of polyploidizations, and generating homologous gene datasets for soybean and other legume crops, and making an integrative research into duplicated gene evolution and conversion. Meanwhile, based on phylogeny and evolutionary theoretical analysis, we will explore genes and gene families that relate to important agronomic traits, such as soybean nitrogen fixation, oil synthesis, and disease resistance, and explore into potential evolutionary rules regulating gene expression, translation, and evolution. Results from this project will effectively support efforts performed in soybean research community, and will have profound theoretical and practical significance, from whole-genome scale to single-gene evolution, which may potentially contribute to soybean improvement through molecular breeding, at least partially by offering a comparative genomics and bioinformatics platform to understand soybean genetics and biology.