稗草多倍化过程中适应性进化的基因组机制研究

Barnyardgrass (Echinochloa spp.) is regarded as the most problematic paddy weeds. Among the Echinochloa genus, E. crus-galli has become much more prevalent than its progenitor tetraploid species E. oryzicola, which is supported by our preliminary effective population size (Ne) analysis for these two species. Also, it has been proposed by previous researchers that polyploidization could be one of the main driving forces for the evolution of weeds. In this project, we plan to take Echinochloa genus as model to investigate the genomic mechanisms and consequences for weeds after polyploidization. Up to now, we have published the genome of the hexaploid weed E. crus-galli. In this project, we will compare the genome of E. crus-galli with the genomes of its progenitors (tetraploid and diploid species). In addition, population genomic analyses will be performed based on resequencing data of E. crus-galli and E. oryzicola populations. We hope to find clues to the genomic changes after polyploidization, explore the differences betwen the natural selective signatures of the two Echinochloa populations, and understand the evolutionary formation of two secondary metabolic gene clusters (DIMBOA and Momilactone) responsible for better adaptation of E. crus-galli. This project could not only help broaden our understanding of adaptive evolution, genomic consequences of polyploidization, but provide implications for paddy weed management and crop breeding.

稗属杂草为我国稻田杂草之首，其中六倍体稗草（Echinochloa crus-galli）及其祖先四倍体稗（E. oryzicola）为全世界稻田危害最严重的杂草。申请人前期对我国稻田六倍体、四倍体稗草群体分布调查、有效群体大小变化等初步研究，发现六倍体稗草为稻田优势种。申请人作为主要完成人于2017年已发表六倍体稗草基因组。本项目拟将六倍体稗草基因组与其祖先四倍体和二倍体稗草基因组进行全基因组水平比较基因组分析，并通过六倍体与四倍体稗草群体的基因组重测序展开群体基因组学研究，揭示多倍化过程中基因组的动态变化，挖掘六倍体稗草群体相对于四倍体稗草和环境适应相关的基因组选择差异，明确前期鉴定的六倍体稗草基因组中次生代谢化感物质（丁布和稻壳素）合成基因簇的进化起源及形成方式。本项目有助于从基因组水平上拓宽对杂草多倍化适应性进化的理解，也同时可为作物育种及杂草防控提供理论指导。

多倍化被认为是植物进化的重要动力之一。对农业杂草基因组多倍化的研究有助于深层次了解杂草环境适应性和入侵性的基因组机制。本项目完成了稗属中2、4、6三种不同倍性稗草的基因组组装和注释。开发了辅助多倍体组装的DipHiC方法，成功将多倍体稗草基因组的亚基因组进行准确区分并进行染色体挂载。利用比较基因组学方法，解析了稗属杂草在多倍化过程中基因家族的变化模式，以及亚基因组选择和表达偏好的特征。研究揭示了稗草在适应性进化中可能通过减少多倍化过程中形成的冗余抗性基因的消耗，获得更广泛环境的生存适合度的适应性机制。基于对不同倍性稗草的群体基因组分析，鉴定了高、低纬度地区稗草在花期、氧胁迫、氮素利用等功能通路上存在显著分化的基因。整合项目产生的基因组组装、转录组、群体变异等信息，构建了稗草基因组数据库。该研究内容对了解多倍体稗属植物系统发生及其环境适应基因组演化机制具有重要意义。相关研究结果发表在Molecular Plant、Nature Communications等期刊上发表标注论文3篇，完成了目标任务。