University of Illinois Urbana-Champaign

Data from: Genetic structure of Miscanthus sinensis and Miscanthus sacchariflorus in Japan indicates a gradient of bidirectional but asymmetric introgression

Clark, Lindsay V.; Stewart, J. Ryan; Nishiwaki, Aya; Toma, Yo; Kjeldsen, Jens Bonderup; Jorgensen, Uffe; Zhao, Hua; Peng, Junhua; Yoo, Ji Hye; Heo, Kweon; Yu, Chang Yeon; Yamada, Toshihiko; Sacks, Erik J.

Content Files
131112infoForRadseq.csv
140317DapcK8assign.csv
140318chloroplast_analysis.R
140318chloroplast_data_LatLong.txt
140318chloroplast_data.txt
140324infoForRadseq_MsiOnly.csv
140324monmonierPrep.R
140417MsiTable.txt
140501MsaMxgTable.txt
140707downsample_exportStruct.R
140708DapcLatLong.csv
140710Statistics.R
140808spca_contd_Msi.R
141104simulate.R
141104structureresults.txt
141107filter_snp_pca.R
141116_barplots_cpstats-4.R
HapMap.fas.txt
HapMap.hmc.txt
HapMap.hmp.txt
IndividualsData.txt
IndividualsTable140410.txt
IndividualsTable140411.txt
MsiMsaDiagnosticMarkers.txt
README.txt
table1.txt

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https://hdl.handle.net/2142/73212

Description

Title
Data from: Genetic structure of Miscanthus sinensis and Miscanthus sacchariflorus in Japan indicates a gradient of bidirectional but asymmetric introgression
Author(s)
  • Clark, Lindsay V.
  • Stewart, J. Ryan
  • Nishiwaki, Aya
  • Toma, Yo
  • Kjeldsen, Jens Bonderup
  • Jorgensen, Uffe
  • Zhao, Hua
  • Peng, Junhua
  • Yoo, Ji Hye
  • Heo, Kweon
  • Yu, Chang Yeon
  • Yamada, Toshihiko
  • Sacks, Erik J.
Issue Date
2015-01-24
Keyword(s)
  • biomass crop
  • cross-ploidy introgression
  • hybridization
  • polyploidy
  • population genetics
  • RAD-seq
  • Poaceae
Date of Ingest
2015-02-12T20:03:24Z
Geographic Coverage
Japan
Abstract
Unilateral introgression from diploids to tetraploids has been hypothesized to be an important evolutionary mechanism in plants. However, few examples have been definitively identified, perhaps because data of sufficient depth and breadth were difficult to obtain prior to the advent of affordable high-density genotyping. Throughout Japan, tetraploid Miscanthus sacchariflorus and diploid M. sinensis are common, and occasionally hybridize. In this study, we characterized 667 M. sinensis and 78 M. sacchariflorus genotypes from Japan using 20,704 SNPs and ten plastid microsatellites. Similarity of SNP genotypes between diploid and tetraploid M. sacchariflorus indicated that the tetraploids originated via autopolyploidy. Structure analysis indicated a gradient of introgression from diploid M. sinensis into tetraploid M. sacchariflorus throughout Japan; most tetraploids had some M. sinensis DNA. Among phenotypically M. sacchariflorus tetraploids, M. sinensis ancestry averaged 7% and ranged from 1-39%, with introgression greatest in southern Japan. Unexpectedly, rare (~1%) diploid M. sinensis individuals from northern Japan were found with 6-27% M. sacchariflorus ancestry. Population structure of M. sinensis in Japan included three groups, and was driven primarily by distance, and secondarily by geographic barriers such as mountains and straits. Miscanthus speciation is a complex and dynamic process. In contrast to limited introgression between diploid M. sacchariflorus and M. sinensis in northern China, selection for adaptation to a moderate maritime climate likely favored cross-ploidy introgressants in southern Japan. Our results will help guide the selection of Miscanthus accessions for the breeding of biomass cultivars.
Publisher
Oxford University Press
Has Part
https://doi.org/10.1093/jxb/eru511
Type of Resource
  • text
  • dataset / spreadsheet
Genre of Resource
Data
Language
eng
Handle URL
http://hdl.handle.net/2142/73212
Sponsor(s)/Grant Number(s)
  • Energy Biosciences Institute
  • Office of Science - Biological and Environmental Research, U.S. Department of Energy [Project ID 0017582]
Copyright and License Information
All files are released under a Creative Commons Attribution-ShareAlike 4.0 International License (CC BY-SA 4.0; http://creativecommons.org/licenses/by-sa/4.0/).

Owning Collections

Miscanthus genetics PRIMARY