以水稻为模式揭示杂种优势的功能基因组基础

Utilization of heterosis has greatly contributed to the elevated crop productivity worldwide for decades. However, the biological mechanism of heterosis has remained a mystery for over a century despite intensive research globally. Our group has been working on heterosis of rice in the last twenty years with the ultimate goal to achieve comprehensive elucidation of the biological underpinning of hybrid vigor. Using an elite hybrid Shanyou 63 as a model, we conceived a design to construct an experimental population referred to as immortalized F2 (IMF2) which is particularly suitable for genetic analysis of heterosis. We developed a method for constructing an ultrahigh density genetic map of the IMF2 population employing the new sequencing technology, based on which we finely dissected the genetic composition of heterosis of yield traits, and quantified the relative contributions of the various genetic components to heterosis of the hybrid. In this proposal, we put forward six new hypotheses speculating the biological mechanisms of heterosis, and designed corresponding experiments to test each of them using Shanyou 63 as a model. The overall strategy is to combine genomic techniques with genetic analyses to build a framework for functional genomic understanding of heterosis. To do so, we will assay various genomic attributes of the hybrid against the parents, including genome sequences, dynamic expression profiles, the epigenome, proteome etc, and associate differences observed between the hybrid and parents to the genetic maps of trait heterosis. We anticipate that the proposed study will significantly advance our understanding of the biological mechanisms of heterosis, and illustrate approaches for future undertaking. It is also expected that the outcome of the project will provide useful information for formulating new strategy in heterosis breeding.

杂种优势的利用为提高作物产量作出了巨大贡献，但杂种优势的生物学机理也是困扰生物学界的世纪难题。本课题组研究杂种优势已二十多年。我们以优良杂交稻汕优63为模式，提出了新的实验设计，构建了适于杂种优势遗传分析的“永久F2”群体，用新测序技术，制作了超高密度遗传连锁图，在全基因组水平上解析汕优63杂种优势的遗传基础，确定了杂种优势相关遗传组分的基因组位置及其对杂种优势的贡献率。本申请就杂种优势的生物学基础提出了6个新的假说，设计了相应实验逐个检验。基本途径是将基因组技术与遗传分析相结合，从基因组序列、基因表达动态、表观基因组、蛋白组等多层面比较分析杂种和亲本的差异，通过分离群体和超高密度遗传连锁图，建立这些功能基因组水平差异与农艺性状杂种优势遗传组分的联系，阐述杂种优势的功能基因组基础。课题将为杂种优势的研究探讨途径，可望在基因组水平上部分阐明杂种优势的生物学机制，为作物杂种优势利用开拓思路。

杂种优势的利用为提高作物产量作出了巨大贡献，但杂种优势的生物学机理一直是困扰生物学界的世纪难题。课题以优良杂交稻汕优63为模式，构建了适于杂种优势遗传分析的“永久F2”群体，就杂种优势的生物学基础提出了6个新的假说，将基因组技术与遗传分析相结合，从基因组序列、基因表达动态、表观基因组、蛋白组等多层面比较分析杂种和亲本的差异，通过分离群体和超高密度遗传连锁图，建立这些功能基因组水平差异与农艺性状杂种优势遗传组分的联系，阐述杂种优势的功能基因组基础。.通过课题的实施，取得了如下成果：（1）与美国亚利桑那大学合作获得了汕优63亲本珍汕97和明恢63的高精度参考基因组，为进一步在分子水平阐明杂种优势的生物学机理，提高杂种优势利用水平奠定了坚实基础。（2）开展水稻苗期杂种优势的遗传基础研究，发现苗期性状加性×加性互作类型最多，单位点超显性和两位点的显性×显性互作都存在负向作用位点。单位点超显性效应以及两位点的显性×显性互作效应的综合作用能够解释F1苗期性状的表现。（3）鉴定了杂种等位基因特异表达的基因，根据等位基因特异表达的模式对杂种优势的遗传基础提出了新的解释，并为深入研究杂种优势的遗传和分子机理提供了基因信息。（4）开发了通过基因组信息预测杂种产量性状的6种预测方法，基于转录组和代谢组数据进行杂交水稻产量的预测。（5）对“永久F2”群体的剑叶平展期材料中的mRNA和sRNA进行了测序，对sQTL表达丰度的遗传调控进行分析。利用eQTL构建基因共表达网络来辅助分析复杂的基因调控网络。基于获得的“永久F2”群体的基因型数据，利用基因组最佳线性无偏预测技术预测杂种表型的最优模型。（6）开展汕优63及其亲本的蛋白质组学比较分析，获得转录组和蛋白组数据，分析工作正在进行中。课题研究为杂种优势的研究探讨途径，在基因组水平上部分阐明杂种优势的生物学机制，为作物杂种优势利用开拓思路。