To study the genetic structure of clonal plant populations, genotyping and genet detection using genetic markers are necessary to assign ramets to corresponding genets. Assignment is difficult as it involves setting a robust threshold of genetic distance for genet distinction as neighbouring genets in a plant population are often genetically related. Here, we used restriction site-associated DNA sequencing (RAD-seq) for a rhizomatous clonal herb, Cardamine leucantha [Brassicaceae] to accurately determine genet structure in a natural population. We determined a draft genome sequence of this species for the first time, which resulted in 66 617 scaffolds with N50 = 6086 bp and an estimated genome size of approximately 253 Mbp. Using genetic distances based on the RAD-seq analysis, we successfully distinguished ramets that belonged to distinct genets even from a half-sib family. We applied these methods to 372 samples of C. leucantha collected at 1-m interval grids within a 20 × 20 m plot in a natural population in Hokkaido, Japan. From these samples, we identified 61 genets with high inequality in terms of genet size and patchy distribution. Spatial autocorrelation analyses indicated significant aggregation within 7 and 4 m at ramet and genet levels, respectively. An analysis of parallel DNA microsatellite loci (simple sequence repeats) suggested that RAD-seq can provide data that allows robust genet assignment. It remains unclear whether the large genets identified here became dominant stochastically or deterministically. Precise identification of genets will assist further study and characterization of dominant genets.

中文翻译：

---

使用RAD-seq在森林地上的无性系Cardamine leucantha中进行基因分配和种群结构分析。

为了研究克隆植物种群的遗传结构，必须使用基因标记进行基因分型和基因检测，才能将分株分配给相应的基因。分配是困难的，因为它涉及为遗传区分设定可靠的遗传距离阈值，因为植物种群中的邻近遗传通常是遗传相关的。在这里，我们使用了根茎无性系草本植物Cardamine leucantha [Brassicaceae]的限制性位点相关DNA测序（RAD-seq）来准确确定自然种群中的基因结构。我们首次确定了该物种的基因组草图序列，从而产生了66 617个N50 = 6086 bp的支架，估计的基因组大小约为253 Mbp。使用基于RAD-seq分析的遗传距离，我们成功地区分了属于同一个家族的分株，甚至来自同父异母的家族。我们将这些方法应用于日本北海道自然种群中20×20 m地块内以1-m间隔网格收集的372个隐色梭菌样本中。从这些样本中，我们确定了61个在种系大小和斑块分布方面高度不平等的种系。空间自相关分析表明，在分株和种系水平分别在7和4 m内有明显的聚集。对平行DNA微卫星基因座（简单序列重复）的分析表明，RAD-seq可提供允许进行可靠基因分配的数据。尚不清楚此处确定的大型种系是随机的还是确定性的。准确鉴定种系将有助于进一步研究和鉴定优势种系。