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text/plainREADME.txt (7kB)
Description of files included in this item.Text file

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text/plaintable1.txt (1kB)
Corrected Table 1 from main manuscript.Text file

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text/plainIndividualsData.txt (241kB)
Geographic data and genetic results for individual plants.Text file

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text/plainMsiMsaDiagnosticMarkers.txt (46kB)
DNA sequences of tag pairs diagnostic of M. sinensis vs. M. sacchariflorus.Text file

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text/plainHapMap.hmp.txt (69MB)
SNP genotypes.Text file

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text/plainHapMap.hmc.txt (153MB)
Read counts for SNP genotypes.Text file

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text/plainHapMap.fas.txt (4MB)
DNA sequences of RAD tags.Text file

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text/plain140707downsample_exportStruct.R (32kB)
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text/csv131112infoForRadseq.csv (38kB)
Table to match individual names with accession names.CSV file

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text/csv140708DapcLatLong.csv (50kB)
Genetic groupings, latitude and longitude of individuals.CSV file

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text/plain140710Statistics.R (11kB)
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text/csv140317DapcK8assign.csv (65kB)
Assignments of individuals to genetic groups.CSV file

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text/plain140318chloroplast_analysis.R (11kB)
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text/plain140318chloroplast_data.txt (39kB)
Plastid microsatellite genotypes.Text file

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text/plain140318chloroplast_data_LatLong.txt (57kB)
Plastid microsatellite genotypes, latitude and longitude.Text file

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text/plain141116_barplots_cpstats-4.R (21kB)
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text/plainIndividualsTable140410.txt (278kB)
Data for individual plants.Text file

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text/plainIndividualsTable140411.txt (281kB)
Data for individual plants.Text file

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text/plain140501MsaMxgTable.txt (7kB)
Flow cytometry results for M. sacchariflorus and M. xgiganteus.Text file

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text/plain140417MsiTable.txt (2kB)
Flow cytometry results for M. sinensis.Text file

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text/plain140324monmonierPrep.R (3kB)
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text/csv140324infoForRadseq_MsiOnly.csv (35kB)
Table to match individual names with accession names for M. sinensis.CSV file

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text/plain140808spca_contd_Msi.R (9kB)
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text/plain141104simulate.R (25kB)
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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; Jörgensen, Uffe; Zhao, Hua; Peng, Junhua; Yoo, Ji Hye; Heo, Kweon; Yu, Chang Yeon; Yamada, Toshihiko; Sacks, Erik J.
Subject(s):biomass crop
cross-ploidy introgression
hybridization
polyploidy
population genetics
RAD-seq
Poaceae
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.
Issue Date:2015-01-24
Publisher:Oxford University Press
Citation Info:Clark LV, Stewart JR, Nishiwaki A, Toma Y, Kjeldsen JB, Jørgensen U, Zhao H, Peng J, Yoo JH, Heo K, Yu CY, Yamada T, and Sacks EJ (2015) "Genetic structure of Miscanthus sinensis and Miscanthus sacchariflorus in Japan indicates a gradient of bidirectional but asymmetric introgression." Journal of Experimental Botany. DOI: 10.1093/jxb/eru511
Genre:Data
Type:Text
Dataset / Spreadsheet
Language:English
URI:http://hdl.handle.net/2142/73212
DOI:10.1093/jxb/eru511
Sponsor:Energy Biosciences Institute
Office of Science - Biological and Environmental Research, U.S. Department of Energy [Project ID 0017582]
Rights 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/).
Date Available in IDEALS:2015-02-12


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