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Title: Genet assignment and population structure analysis in a clonal forest-floor herb, Cardamine leucantha, using RAD-seq
Authors: Tsujimoto, Michiaki
Araki, Kiwako S
Honjo, Mie N
Yasugi, Masaki
Nagano, Atsushi J
Akama, Satoru
Hatakeyama, Masaomi
Shimizu-Inatsugi, Rie
Sese, Jun
Shimizu, Kentaro K
Kudoh, Hiroshi
Author's alias: 辻本, 典顯
荒木, 希和子
本庄, 三恵
八杉, 公基
永野, 惇
赤間, 悟
畠山, 剛臣
清水(稲継), 理恵
瀬々, 潤
清水, 健太郎
工藤, 洋
Keywords: Cardamine leucantha
clonal plants
forest-floor herbaceous plants
genet assignment
population structure
stoloniferous rhizome
Issue Date: Feb-2020
Publisher: Oxford University Press (OUP)
Journal title: AoB PLANTS
Volume: 12
Issue: 1
Thesis number: plz080
Abstract: 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.
Rights: © The Author(s) 2019. Published by Oxford University Press on behalf of the Annals of Botany Company. This is an Open Access article distributed under the terms of the Creative Commons Attribution License (, which permits unrestricted reuse, distribution, and reproduction in any medium, provided the original work is properly cited.
DOI(Published Version): 10.1093/aobpla/plz080
PubMed ID: 32002176
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