Population genetic structure of Miscanthus sacchariflorus

  • Lindsay V. Clark (Creator)
  • Xiaoli Jin (Creator)
  • Karen K. Petersen (Creator)
  • Kossonou Guillaume Anzoua (Creator)
  • Larisa Bagmet (Creator)
  • Pavel Chebukin (Creator)
  • Martin Deuter (Creator)
  • Elena Dzyubenko (Creator)
  • Nikolay Dzyubenko (Creator)
  • Kweon Heo (Creator)
  • Douglas A. Johnson (Creator)
  • Uffe Jørgensen (Creator)
  • Jens Bonderup Kjeldsen (Creator)
  • Hironori Nagano (Creator)
  • Junhua Peng (Creator)
  • Andrey Sabitov (Creator)
  • Toshihiko Yamada (Creator)
  • Ji Hye Yoo (Creator)
  • Chang Yeon Yu (Creator)
  • Stephen P Long (Creator)
  • Erik J Sacks (Creator)

Dataset

Description

This repository contains datasets and R scripts that were used in a study of the population structure of Miscanthus sacchariflorus in its native range across East Asia. Notably, genotypes of 764 individuals at 34,605 SNPs, called from reduced-representation DNA sequencing using a non-reference bioinformatics pipeline, are provided. Two similar SNP datasets, used for identifying clonal duplicates and for determining the ancestry of ornamental and hybrid Miscanthus plants identified in previous studies respectively, are also provided. There is also a spreadsheet listing the provenance and ploidy of all individuals along with their plastid (chloroplast) haplotypes. Software output for Structure, Treemix, and DIYABC is also included. See README.txt for more information about individual files. Results of this study are described in a manuscript in revision in Annals of Botany by the same authors, "Population structure of Miscanthus sacchariflorus reveals two major polyploidization events, tetraploid-mediated unidirectional introgression from diploid Miscanthus sinensis, and diversity centered around the Yellow Sea."
Date made availableJun 18 2018
PublisherUniversity of Illinois at Urbana-Champaign

Keywords

  • Miscanthus
  • restriction site-associated DNA sequencing (RAD-seq)
  • single nucleotide polymorphism (SNP)
  • population genetics
  • Miscanthus xgiganteus
  • Miscanthus sacchariflorus
  • R scripts
  • germplasm
  • plastid haplotype

Cite this

Clark, L. V. (Creator), Jin, X. (Creator), Petersen, K. K. (Creator), Anzoua, K. G. (Creator), Bagmet, L. (Creator), Chebukin, P. (Creator), Deuter, M. (Creator), Dzyubenko, E. (Creator), Dzyubenko, N. (Creator), Heo, K. (Creator), Johnson, D. A. (Creator), Jørgensen, U. (Creator), Kjeldsen, J. B. (Creator), Nagano, H. (Creator), Peng, J. (Creator), Sabitov, A. (Creator), Yamada, T. (Creator), Yoo, J. H. (Creator), Yu, C. Y. (Creator), Long, S. P. (Creator), Sacks, E. J. (Creator) (Jun 18 2018). Population genetic structure of Miscanthus sacchariflorus . University of Illinois at Urbana-Champaign. 10.13012/B2IDB-0170190_V3