小麦D基因组在驯化过程中的演变规律及多基因作用机制研究

Common wheat (bread wheat) is one of the most important staple foods of mankind. The adding of the D genome to the hexaploid wheat plays an indispensable role for its origination and the spread all over the world. It is now a consensus that the goat grass Aegilops tauschii is the D genome donor of modern bread wheat. Therefore, the D genome of wheat has a clear domestication history. Despite this, the understanding of the D genome evolution is very limited. A genome wide comprehensive analysis of the D genome in the wild and domesticated conditions is still lacking. Under the support of a cultivation grant of this key project, the applicant of this proposal has made a significant progress by sequencing 262 wheat accessions of Chinese mini-core collection which have been extensively characterized phenotypically on yield related traits. The exome capture sequencing generated a large number of common wheat D genome SNP data that can be utilized to study wheat D genome diversity as well as to compare with those from the D genome donor Ae. tauschii, such that the role of domestication on genome evolution and the polygenic interaction mechanisms for particular traits can be studied. These early work has laid a solid foundation for the proposed project. Here, we propose to perform exome capture sequencing of 200 or so Ae. tauschii accessions that are collected from around the world and have also been phenotyped for two years. The SNP dataset produced can be used to analyze the population genetics of Ae. tauschii and the association with their geographical distribution and morphological traits. Furthermore, the comparison of Ae. tauschii genome diversity, representing genome evolution patterns under natural conditions, and the wheat D genome, representing evolution patterns under domestication conditions, will reveal artificially selected loci during D genome domestication. Linkage analysis with phenotypic traits, particularly seed traits that are related to the yield, may discover genes that are interactively working during wheat domestication. Thus, this work will provide insights into important micro-evolution questions such as the mechanisms of how genomes are diverged and selected during domestication and how multiple genes are working together to shape the morphology or agricultural traits in one of the world’s most important crops.

普通小麦是人类最重要的主粮之一。D基因组供体粗山羊草在其起源过程中发挥着不可或缺的重要作用。小麦D基因组供体种来源明确，驯化历史明确。然而截至目前，人们对D基因组演变的了解非常有限，尤其未对野生和栽培条件下D基因组演化规律加以比较，发现其在人工驯化条件下的微进化规律。本项目申请人在重大研究计划前期培育项目资助下，对具有多年多点产量表型的我国普通小麦微核心种质262份材料进行了外显子捕获测序，获得了大量普通小麦D基因组SNP数据。这些重要进展为本项目的开展奠定了扎实的基础。本项目申请拟对前期有形态学鉴定的200份左右粗山羊草进行外显子捕获测序，获得野生状态下D基因组的多样性数据，开展粗山羊草群体遗传研究及其多样性演变与表型的关联分析，及与普通小麦D基因组在多样性选择位点与农艺性状如籽粒性状等的关联性，揭示D基因组如何在基因组水平上通过基因突变与多基因交互作用影响其表型的机制等重要微进化问题。

D基因组供体粗山羊草在其起源过程中发挥着不可或缺的重要作用。然而截至目前，人们对D基因组演变的了解非常有限。本项目对具有多年多点产量表型的我国普通小麦微核心种质262份材料进行了外显子捕获测序，获得了约90万个SNPs。利用这些标记结合11个性状在8个环境下的表型数据，共获得了4031个与这些性状显著关联的SNPs，涉及约3939个基因。这些关联到的位点中，位于A和B亚基因组上的数目，远远多于位于D亚基因组上的数目。但是GO富集分析发现，关联到粒宽的位点只有D基因组附近的基因被富集为光合功能相关，暗示了D基因组基因在小麦粒宽发育调控中的重要作用；另一方面，小麦异源六倍体及其亲本籽粒发育早期的转录组分析则发现，籽粒发育早期D基因组的表达模式保守性显著低于A和B基因组。Triplet基因共表达网络分析则发现新合成六倍体中，D基因组在籽粒宽度发育调控中的可能作用。合成小麦加入D基因组以后，D基因组基因表达受抑制的比例最小。近代驯化则使合成小麦中triplet的表达关系发生巨大变化，其中D基因组抑制比例增加。完成了对223份节节麦自然群体35个性状的表型评价、方差分析、遗传力分析、相关性分析以及主成分分析。同时还完成了150份世界来源的节节麦材料的10x重测序，利用所获得的SNP，初步分析了不同来源的D基因组的进化关系，研究了D基因组的微进化特点。