目的 本文对神农香菊（Chrysanthemum indicum var. aromaticum）自然居群的遗传多样性、遗传结构及特征代谢产物开展研究，并以此为依据筛选核心种质，为神农香菊的资源保护和应用提供理论依据。方法 利用21对分别来源于基因组和转录组数据的简单重复序列引物（SSR）对我国神农架林区的151份神农香菊样本、41份疑似野菊样本和武汉市洪山区11份野菊对照样本进行居群遗传多样性和遗传结构分析。基于遗传信息，采用高效液相色谱技术（HPLC）对不同遗传分组的代表性纯合样本开展9种代谢物的差异分析，利用最小距离逐步取样策略（LDSS）筛选神农香菊的核心种质。结果 21对引物在所有研究样本中共扩增出202个等位基因，每个位点平均等位基因数为9.619个。神农架5个居群的平均有效基因数（N_e）为2.518，香农多样性指数（I）为1.004，多态性信息含量（PIC）为0.526，杂合度（H）为0.246。居群间具有较低的遗传分化（F_st<0.12）和较高的基因流水平（N_m>1）。遗传结构分析显示，神农架的所有样品可分为三个遗传组。异绿原酸C、蒙花苷、木犀草苷等物质在三个组的样本间有明显的含量差异。基于遗传信息，最终筛选出了来自神农架3个地方居群的45份核心种质。结论 本研究展示了神农香菊自然居群整体存在的中高水平的遗传多样性，同时神农香菊样本与邻（混）生的疑似野菊样本具有清晰的形态差异，但两者间可能存在基因流或遗传混杂。这些信息为研究神农香菊的起源进化和对其资源的开发应用提供了理论和数据支撑。

Objective To conduct the evaluation of genetic diversity, genetic structure and characteristic metabolites of Chrysanthemum indicum var. aromaticum, and to screen core germplasm, and provide a theoretical basis for the resource conservation and application of this rare plant.Methods Twenty-one pairs of simple repetitive sequence primers (SSR) derived from both genome and transcriptome data were used to investigate the population genetic diversity and structure of 151 samples of C. indicum var. aromaticum, 41 samples of suspected C. indicum collected from Shennongjia and and 11 reference C. indicum samples from Hongshan district, Wuhan. Based on genetic information, high performance liquid chromatography (HPLC) was used to analyze the differences of metabolites in samples of different genetic groups and the minimum distance stepwise sampling strategy (LDSS) was used to screen core collections of C. indicum var. aromaticum.Results 21 pairs of SSR primers detected a total of 202 alleles in all the samples analysed, and the average number of alleles was 9.619; the average effective gene number (N_e) of the five populations was 2.518; the Shannon' s information index (I) was 1.004; the polymorphic information content (PIC) was 0.526; and the heterozygosity (H) was 0.246. The five populations derived from Shennongjia had lower genetic differentiation (F_ST <0.12) and higher inter-population gene flow (N_m>1). Genetic structure analysis showed that the samples from Shennongjia were divided into three genetic groups. There were significant differences in the contents of Isochlorogenic acid C, Linarin, Galuteolin among the three groups. Based on genetic information, 45 core collections from three Shennongjia populations were finally screened out.Conclusion This study showed that the natural populations of C. indicum var. aromaticum has a middle-to-high level of genetic diversity. At the same time, the C. indicum var. aromaticum samples has a clear morphological difference with the neighboring (mixed) suspected C. indicum samples, but there may be gene flow between them. Our results provided theoretical and data support for studying the origin and evolution of C. indicum var. aromaticum and for conservation and application of this rare medicinal plants.

国家自然科学基金委员会面上项目（31900267）：不同生境条件下神农香菊萜类挥发性物质不稳定产生的分子机制研究，负责人：张景景；湖北省自然科学基金委员会重点类项目（2019CFA097）：药用野菊的基因组遗传评价与优异种质筛选，负责人：刘义飞；补充立项部门湖北省中央引导地方科技发展专项（2019ZYYD063）：中药组学研究与资源评价创新平台，负责人：刘义飞。