Switchgrass (Panicum virgatum L.) Genotypes Differ between Coastal Sites and Inland Road Corridors in the Northeastern US
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{"title"=>"Switchgrass (Panicum virgatum L.) genotypes differ between coastal sites and inland road corridors in the Northeastern US", "type"=>"journal", "authors"=>[{"first_name"=>"Geoffrey", "last_name"=>"Ecker", "scopus_author_id"=>"53163614000"}, {"first_name"=>"Juan", "last_name"=>"Zalapa", "scopus_author_id"=>"14619931500"}, {"first_name"=>"Carol", "last_name"=>"Auer", "scopus_author_id"=>"7004590160"}], "year"=>2015, "source"=>"PLoS ONE", "identifiers"=>{"pui"=>"605481019", "isbn"=>"1932-6203", "issn"=>"19326203", "doi"=>"10.1371/journal.pone.0130414", "sgr"=>"84938710059", "scopus"=>"2-s2.0-84938710059", "pmid"=>"26125564"}, "id"=>"ceeccefa-ba30-3771-a70a-fcf784098b73", "abstract"=>"Switchgrass (Panicum virgatum L.) is a North American grass that exhibits vast genetic diversity across its geographic range. In the Northeastern US, local switchgrass populations were restricted to a narrow coastal zone before European settlement, but current populations inhabit inland road verges raising questions about their origin and genetics. These questions are important because switchgrass lines with novel traits are being cultivated as a biofuel feedstock, and gene flow could impact the genetic integrity and distribution of local populations. This study was designed to determine if: 1) switchgrass plants collected in the Long Island Sound Coastal Lowland coastal Level IV ecoregion represented local populations, and 2) switchgrass plants collected from road verges in the adjacent inland regions were most closely related to local coastal populations or switchgrass from other geographic regions. The study used 18microsatellitemarkers to infer the genetic relationships between 122 collected switchgrass plants and a reference dataset consisting of 28 cultivars representing ecotypes, ploidy levels, and lineages from North America. Results showed that 84% of 88 plants collected in the coastal plants were most closely aligned with the Lowland tetraploid genetic pool. Among this group, 61 coastal plants were similar to, but distinct from, all Lowland tetraploid cultivars in the reference dataset leading to the designation of a genetic sub-population called the Southern New England Lowland Tetraploids. In contrast, 67% of 34 plants collected in road verges in the inland ecoregions were most similar to two Upland octoploid cultivars; only 24% of roadside plants were Lowland tetraploid. These results suggest that cryptic, non-local genotypes exist in road verges and that gene flow from biofuels plantations could contribute to further changes in switchgrass population genetics in the Northeast.", "link"=>"http://www.mendeley.com/research/switchgrass-panicum-virgatum-l-genotypes-differ-between-coastal-sites-inland-road-corridors-northeas", "reader_count"=>11, "reader_count_by_academic_status"=>{"Researcher"=>4, "Student > Doctoral Student"=>1, "Student > Ph. D. Student"=>4, "Student > Bachelor"=>1, "Professor"=>1}, "reader_count_by_user_role"=>{"Researcher"=>4, "Student > Doctoral Student"=>1, "Student > Ph. D. Student"=>4, "Student > Bachelor"=>1, "Professor"=>1}, "reader_count_by_subject_area"=>{"Biochemistry, Genetics and Molecular Biology"=>1, "Agricultural and Biological Sciences"=>9, "Computer Science"=>1}, "reader_count_by_subdiscipline"=>{"Agricultural and Biological Sciences"=>{"Agricultural and Biological Sciences"=>9}, "Computer Science"=>{"Computer Science"=>1}, "Biochemistry, Genetics and Molecular Biology"=>{"Biochemistry, Genetics and Molecular Biology"=>1}}, "reader_count_by_country"=>{"United States"=>2}, "group_count"=>0}

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Figshare

  • {"files"=>["https://ndownloader.figshare.com/files/2156949"], "description"=>"<p>Switchgrass collection sites (open circles). Black lines represent borders of Connecticut and Rhode Island and six roads identified as Routes 63, 8, 9, 95, 84,and 2. Grey lines represent the borders of Level IV sub-ecoregions. The shaded area represents Level IV sub-ecoregion 59g Long Island Sound Coastal Lowland.</p>", "links"=>[], "tags"=>["Inland Road Corridors", "Gene flow", "Level IV ecoregion", "Upland octoploid cultivars", "Lowland tetraploid cultivars", "road verges", "Long Island Sound Coastal Lowland", "North American grass", "18 microsatellite markers", "Lowland tetraploid", "reference dataset", "Southern New England Lowland Tetraploids", "switchgrass population genetics"], "article_id"=>1469360, "categories"=>["Uncategorised"], "users"=>["Geoffrey Ecker", "Juan Zalapa", "Carol Auer"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0130414.g001", "stats"=>{"downloads"=>0, "page_views"=>7, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Map_of_the_study_site_/1469360", "title"=>"Map of the study site.", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2015-06-30 03:45:13"}
  • {"files"=>["https://ndownloader.figshare.com/files/2156950"], "description"=>"<p>Individuals are shown as a vertical line representing the membership fractions for each of the K populations and sorted according to q-value (K = 9). Switchgrass lineages abbreviated as shown in [<a href=\"http://www.plosone.org/article/info:doi/10.1371/journal.pone.0130414#pone.0130414.ref042\" target=\"_blank\">42</a>]. Other abbreviation: Southern New England Lowland Tetraploid, SNELT; UID, Unidentified. Genotype groups with an asterisk (*) include one or more individuals collected from the LISCL coastal ecoregion or inland road verges.</p>", "links"=>[], "tags"=>["Inland Road Corridors", "Gene flow", "Level IV ecoregion", "Upland octoploid cultivars", "Lowland tetraploid cultivars", "road verges", "Long Island Sound Coastal Lowland", "North American grass", "18 microsatellite markers", "Lowland tetraploid", "reference dataset", "Southern New England Lowland Tetraploids", "switchgrass population genetics"], "article_id"=>1469361, "categories"=>["Uncategorised"], "users"=>["Geoffrey Ecker", "Juan Zalapa", "Carol Auer"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0130414.g002", "stats"=>{"downloads"=>0, "page_views"=>6, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_STRUCTURE_analysis_of_SSR_markers_from_all_switchgrass_cultivars_and_collected_plants_n_365_/1469361", "title"=>"STRUCTURE analysis of SSR markers from all switchgrass cultivars and collected plants (n = 365).", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2015-06-30 03:45:13"}
  • {"files"=>["https://ndownloader.figshare.com/files/2156951"], "description"=>"<p>The circle indicates the clustering of collected LISCL plants with three L4x cultivars (‘Miami’, ‘Wabasso’, ‘Stuart’) representing the Florida Clade. Colors indicate: ‘Kanlow’ (red+), ‘Alamo’ (purple♦), ‘SG5’ (black-), ‘Timber’ (olive green■), Florida Clade cultivars (blue×), and coastal samples (light green●).</p>", "links"=>[], "tags"=>["Inland Road Corridors", "Gene flow", "Level IV ecoregion", "Upland octoploid cultivars", "Lowland tetraploid cultivars", "road verges", "Long Island Sound Coastal Lowland", "North American grass", "18 microsatellite markers", "Lowland tetraploid", "reference dataset", "Southern New England Lowland Tetraploids", "switchgrass population genetics"], "article_id"=>1469362, "categories"=>["Uncategorised"], "users"=>["Geoffrey Ecker", "Juan Zalapa", "Carol Auer"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0130414.g003", "stats"=>{"downloads"=>2, "page_views"=>19, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Principle_Coordinate_Analysis_PCA_of_SSR_markers_from_L4x_cultivars_and_plants_collected_in_the_LISCL_coastal_ecoregion_n_124_/1469362", "title"=>"Principle Coordinate Analysis (PCA) of SSR markers from L4x cultivars and plants collected in the LISCL coastal ecoregion (n = 124).", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2015-06-30 03:45:13"}
  • {"files"=>["https://ndownloader.figshare.com/files/2156952"], "description"=>"<p>Individuals are shown as a vertical line representing the membership fractions for each of the K populations and sorted according to q-value (K = 6).</p>", "links"=>[], "tags"=>["Inland Road Corridors", "Gene flow", "Level IV ecoregion", "Upland octoploid cultivars", "Lowland tetraploid cultivars", "road verges", "Long Island Sound Coastal Lowland", "North American grass", "18 microsatellite markers", "Lowland tetraploid", "reference dataset", "Southern New England Lowland Tetraploids", "switchgrass population genetics"], "article_id"=>1469363, "categories"=>["Uncategorised"], "users"=>["Geoffrey Ecker", "Juan Zalapa", "Carol Auer"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0130414.g004", "stats"=>{"downloads"=>0, "page_views"=>7, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_STRUCTURE_analysis_of_SSR_markers_from_L4x_LISCL_plants_n_46_and_seven_L4x_cultivars_/1469363", "title"=>"STRUCTURE analysis of SSR markers from L4x LISCL plants (n = 46) and seven L4x cultivars.", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2015-06-30 03:45:13"}
  • {"files"=>["https://ndownloader.figshare.com/files/2156953"], "description"=>"<p>Circles indicate inland road plants clustering with either U8x or L4x but not U4x cultivars. Colors indicate: U4X cultivars (Red■), U8X cultivars (PurpleX), L4X cultivars (Green●), plants from inland road verges (Black♦).</p>", "links"=>[], "tags"=>["Inland Road Corridors", "Gene flow", "Level IV ecoregion", "Upland octoploid cultivars", "Lowland tetraploid cultivars", "road verges", "Long Island Sound Coastal Lowland", "North American grass", "18 microsatellite markers", "Lowland tetraploid", "reference dataset", "Southern New England Lowland Tetraploids", "switchgrass population genetics"], "article_id"=>1469364, "categories"=>["Uncategorised"], "users"=>["Geoffrey Ecker", "Juan Zalapa", "Carol Auer"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0130414.g005", "stats"=>{"downloads"=>2, "page_views"=>21, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Principle_Coordinate_Analysis_PCA_of_SSR_markers_from_switchgrass_collected_from_inland_road_verges_and_18_U4x_U8x_and_L4x_switchgrass_cultivars_n_265_/1469364", "title"=>"Principle Coordinate Analysis (PCA) of SSR markers from switchgrass collected from inland road verges and 18 U4x, U8x, and L4x switchgrass cultivars (n = 265).", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2015-06-30 03:45:13"}
  • {"files"=>["https://ndownloader.figshare.com/files/2156954"], "description"=>"<p>The circle indicates the grouping of road verge samples with cultivars ‘Cave-in-Rock’ and ‘Shelter’. Colors indicate: ‘Cave-in-rock’ and ‘Shelter’ (Red♦), Other U8X cultivars (Blue■), L4X cultivars (Green●), plants from inland road verges (BlackX).</p>", "links"=>[], "tags"=>["Inland Road Corridors", "Gene flow", "Level IV ecoregion", "Upland octoploid cultivars", "Lowland tetraploid cultivars", "road verges", "Long Island Sound Coastal Lowland", "North American grass", "18 microsatellite markers", "Lowland tetraploid", "reference dataset", "Southern New England Lowland Tetraploids", "switchgrass population genetics"], "article_id"=>1469365, "categories"=>["Uncategorised"], "users"=>["Geoffrey Ecker", "Juan Zalapa", "Carol Auer"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0130414.g006", "stats"=>{"downloads"=>1, "page_views"=>9, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Principle_Coordinate_Analysis_PCA_of_SSR_markers_from_switchgrass_collected_from_inland_road_verges_and_16_cultivars_representing_U8x_and_L4x_genotypes_n_231_/1469365", "title"=>"Principle Coordinate Analysis (PCA) of SSR markers from switchgrass collected from inland road verges and 16 cultivars representing U8x and L4x genotypes (n = 231).", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2015-06-30 03:45:13"}
  • {"files"=>["https://ndownloader.figshare.com/files/2156956"], "description"=>"<p>Black lines represent borders of Connecticut and Rhode Island and six roads identified as Routes 63, 8, 9, 95, 84, and 2. Grey lines represent the borders of Level IV sub-ecoregions. The shaded area represents sub-ecoregion 59g Long Island Sound Coastal Lowland (LISCL). Green dots represent plants identified as SNELT or other L4x genotypes; red dots represent plants with an U8x genotype; yellow dots represent individuals that could not be assigned to a specific group.</p>", "links"=>[], "tags"=>["Inland Road Corridors", "Gene flow", "Level IV ecoregion", "Upland octoploid cultivars", "Lowland tetraploid cultivars", "road verges", "Long Island Sound Coastal Lowland", "North American grass", "18 microsatellite markers", "Lowland tetraploid", "reference dataset", "Southern New England Lowland Tetraploids", "switchgrass population genetics"], "article_id"=>1469367, "categories"=>["Uncategorised"], "users"=>["Geoffrey Ecker", "Juan Zalapa", "Carol Auer"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0130414.g007", "stats"=>{"downloads"=>0, "page_views"=>12, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Map_of_study_site_showing_distribution_of_switchgrass_genotypes_/1469367", "title"=>"Map of study site showing distribution of switchgrass genotypes.", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2015-06-30 03:45:13"}
  • {"files"=>["https://ndownloader.figshare.com/files/2156957"], "description"=>"<p>Information about switchgrass cultivar geographic origin, ecotype, ploidy and lineage were as previously published [<a href=\"http://www.plosone.org/article/info:doi/10.1371/journal.pone.0130414#pone.0130414.ref032\" target=\"_blank\">32</a>] and as described in the Methods. Numbers in the Tissue Extracted (TE) column represent the number of plants with DNA extraction and SSR analysis. Numbers in the Reanalyzed Electropherograms (RE) column represent the number of electropherograms re-analyzed and integrated into this study. The symbol (-) means that information was not available and (*) indicates ornamental cultivars. Abbreviations for propagule sources: USDA National Genetic Resources Program (GRIN); Ernst Seeds (Ernst); Sharpe Brothers Seed Company (Sharpe); and Broken Arrow Nursery (BAN).</p><p>Switchgrass accessions in the reference dataset.</p>", "links"=>[], "tags"=>["Inland Road Corridors", "Gene flow", "Level IV ecoregion", "Upland octoploid cultivars", "Lowland tetraploid cultivars", "road verges", "Long Island Sound Coastal Lowland", "North American grass", "18 microsatellite markers", "Lowland tetraploid", "reference dataset", "Southern New England Lowland Tetraploids", "switchgrass population genetics"], "article_id"=>1469368, "categories"=>["Uncategorised"], "users"=>["Geoffrey Ecker", "Juan Zalapa", "Carol Auer"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0130414.t001", "stats"=>{"downloads"=>2, "page_views"=>12, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Switchgrass_accessions_in_the_reference_dataset_/1469368", "title"=>"Switchgrass accessions in the reference dataset.", "pos_in_sequence"=>0, "defined_type"=>3, "published_date"=>"2015-06-30 03:45:13"}
  • {"files"=>["https://ndownloader.figshare.com/files/2156958"], "description"=>"<p>Performance of 18 SSR markers in switchgrass DNA from U4x, U8x and L4x cultivars and collected plants (coastal ecoregion and inland ecoregion).</p><p>Performance of 18 SSR markers in switchgrass.</p>", "links"=>[], "tags"=>["Inland Road Corridors", "Gene flow", "Level IV ecoregion", "Upland octoploid cultivars", "Lowland tetraploid cultivars", "road verges", "Long Island Sound Coastal Lowland", "North American grass", "18 microsatellite markers", "Lowland tetraploid", "reference dataset", "Southern New England Lowland Tetraploids", "switchgrass population genetics"], "article_id"=>1469369, "categories"=>["Uncategorised"], "users"=>["Geoffrey Ecker", "Juan Zalapa", "Carol Auer"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0130414.t002", "stats"=>{"downloads"=>13, "page_views"=>13, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Performance_of_18_SSR_markers_in_switchgrass_/1469369", "title"=>"Performance of 18 SSR markers in switchgrass.", "pos_in_sequence"=>0, "defined_type"=>3, "published_date"=>"2015-06-30 03:45:13"}
  • {"files"=>["https://ndownloader.figshare.com/files/2156959"], "description"=>"<p>Analysis of molecular variance (AMOVA): 1) within and among plants collected in the coastal or inland ecoregion, and 2) within and among all cultivars in the reference dataset.</p><p>Analysis of molecular variance.</p>", "links"=>[], "tags"=>["Inland Road Corridors", "Gene flow", "Level IV ecoregion", "Upland octoploid cultivars", "Lowland tetraploid cultivars", "road verges", "Long Island Sound Coastal Lowland", "North American grass", "18 microsatellite markers", "Lowland tetraploid", "reference dataset", "Southern New England Lowland Tetraploids", "switchgrass population genetics"], "article_id"=>1469370, "categories"=>["Uncategorised"], "users"=>["Geoffrey Ecker", "Juan Zalapa", "Carol Auer"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0130414.t003", "stats"=>{"downloads"=>1, "page_views"=>8, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Analysis_of_molecular_variance_/1469370", "title"=>"Analysis of molecular variance.", "pos_in_sequence"=>0, "defined_type"=>3, "published_date"=>"2015-06-30 03:45:13"}
  • {"files"=>["https://ndownloader.figshare.com/files/2156960"], "description"=>"<p>Percentage of switchgrass plants collected in the Long Island Sound Coastal Lowland region or the inland region road verges identified as L4X or U8X based on STRUCTURE analysis (<a href=\"http://www.plosone.org/article/info:doi/10.1371/journal.pone.0130414#pone.0130414.g002\" target=\"_blank\">Fig 2</a>). Individuals without a clear genetic assignment were put in the Unidentified group.</p><p>Percentage of switchgrass ecotypes in coastal or inland regions.</p>", "links"=>[], "tags"=>["Inland Road Corridors", "Gene flow", "Level IV ecoregion", "Upland octoploid cultivars", "Lowland tetraploid cultivars", "road verges", "Long Island Sound Coastal Lowland", "North American grass", "18 microsatellite markers", "Lowland tetraploid", "reference dataset", "Southern New England Lowland Tetraploids", "switchgrass population genetics"], "article_id"=>1469371, "categories"=>["Uncategorised"], "users"=>["Geoffrey Ecker", "Juan Zalapa", "Carol Auer"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0130414.t004", "stats"=>{"downloads"=>3, "page_views"=>13, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Percentage_of_switchgrass_ecotypes_in_coastal_or_inland_regions_/1469371", "title"=>"Percentage of switchgrass ecotypes in coastal or inland regions.", "pos_in_sequence"=>0, "defined_type"=>3, "published_date"=>"2015-06-30 03:45:13"}

PMC Usage Stats | Further Information

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Relative Metric

{"start_date"=>"2015-01-01T00:00:00Z", "end_date"=>"2015-12-31T00:00:00Z", "subject_areas"=>[]}
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