Genet assignment and population structure analysis in a clonal forest-floor herb, Cardamine leucantha, using RAD-seq

Author:

Tsujimoto Michiaki1,Araki Kiwako S12,Honjo Mie N1,Yasugi Masaki13,Nagano Atsushi J14,Akama Satoru5,Hatakeyama Masaomi67,Shimizu-Inatsugi Rie6,Sese Jun58,Shimizu Kentaro K69,Kudoh Hiroshi1

Affiliation:

1. Center for Ecological Research, Kyoto University, Hirano Otsu, Japan

2. Faculty of Life Sciences, Ritsumeikan University, Nojihigashi, Kusatsu, Japan

3. Faculty of Engineering, Utsunomiya University, Yoto, Utsunomiya, Japan

4. Faculty of Agriculture, Ryukoku University, Yokatani, Seta Ohe-cho, Otsu, Japan

5. National Institute of Advanced Industrial Science and Technology (AIST), Aomi, Koto-ku, Tokyo, Japan

6. Department of Evolutionary Biology and Environmental Studies, University of Zurich, Winterthurerstrasse, Zurich, Switzerland

7. Functional Genomics Center Zurich, Winterthurerstrasse, Zurich, Switzerland

8. Humanome Lab., Inc. 2-4-10-2F, Tsukiji, Chuo-ku, Tokyo, Japan

9. Kihara Institute for Biological Research, Yokohama City University, Maioka, Totsuka-ku, Yokohama, Japan

Abstract

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.

Funder

JSPS Grant-in-Aid for Scientific Research

JST CREST

Japan Science and Technology Agency

Swiss National Science Foundation and JST CREST

Core Research for Evolutional Science and Technology

Japan Society for the Promotion of Science

Publisher

Oxford University Press (OUP)

Subject

Plant Science

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