Department of Entomology and Plant Pathology, The University of Tennessee, Knoxville, TN, USA.
Guizhou Key Laboratory of Agro-Bioengineering, Guizhou University, Huaxi, Guiyang, P. R. China.
Sci Rep. 2019 Feb 13;9(1):1915. doi: 10.1038/s41598-019-38532-8.
Taraxacum kok-saghyz (TKS) carries great potential as alternative natural rubber source. To better inform future breeding efforts with TKS and gain a deeper understanding of its genetic diversity, we utilized de novo sequencing to generate novel genomic simple sequence repeats markers (gSSRs). We utilized 25 gSSRs on a collection of genomic DNA (gDNA) samples from germplasm bank, and two gDNA samples from historical herbarium specimens. PCR coupled with capillary electrophoresis and an array of population genetics tools were employed to analyze the dataset of our study as well as a dataset of the recently published genic SSRs (eSSRs) generated on the same germplasm. Our results using both gSSRs and eSSRs revealed that TKS has low- to- moderate genetic diversity with most of it partitioned to the individuals and individuals within populations, whereas the species lacked population structure. Nineteen of the 25 gSSR markers cross-amplified to other Taraxacum spp. collected from Southeastern United States and identified as T. officinale by ITS sequencing. We used a subset of 14 gSSRs to estimate the genetic diversity of the T. officinale gDNA collection. In contrast to the obligatory outcrossing TKS, T. officinale presented evidence for population structure and clonal reproduction, which agreed with the species biology. We mapped the molecular markers sequences from this study and several others to the well-annotated sunflower genome. Our gSSRs present a functional tool for the biodiversity analyses in Taraxacum, but also in the related genera, as well as in the closely related tribes of the Asteraceae.
蒲公英（Taraxacum kok-saghyz）具有作为替代天然橡胶来源的巨大潜力。为了更好地指导未来对蒲公英的选育工作，深入了解其遗传多样性，我们利用从头测序技术生成了新的基因组简单序列重复标记（gSSR）。我们利用 25 个 gSSR 对来自种质库的基因组 DNA（gDNA）样本集合和两个来自历史植物标本馆的 gDNA 样本进行了分析。PCR 与毛细管电泳相结合，以及一系列群体遗传学工具，用于分析我们研究的数据组以及最近发表的同一种质基因简单重复序列（eSSR）生成的数据组。我们使用 gSSR 和 eSSR 的结果表明，蒲公英的遗传多样性较低-中等，大部分遗传多样性分布在个体和种群内的个体之间，而该物种缺乏种群结构。25 个 gSSR 标记中的 19 个与从美国东南部收集的其他蒲公英物种（Taraxacum spp.）发生交叉扩增，通过 ITS 测序鉴定为蒲公英（T. officinale）。我们使用了 14 个 gSSR 的子集来估计蒲公英 gDNA 集合的遗传多样性。与必需异交的蒲公英（TKS）相反，蒲公英（T. officinale）表现出种群结构和克隆繁殖的证据，这与该物种的生物学一致。我们将来自本研究和其他研究的分子标记序列映射到注释良好的向日葵基因组上。我们的 gSSR 不仅为蒲公英属的生物多样性分析提供了一种功能工具，也为相关属以及菊科密切相关的族提供了一种功能工具。
