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Using Genotyping by Sequencing to Map Two Novel Anthracnose Resistance Loci in Sorghum bicolor

Terry J. Felderhoff, View ORCID ProfileLauren M. McIntyre, Ana Saballos and View ORCID ProfileWilfred Vermerris
G3: Genes, Genomes, Genetics July 1, 2016 vol. 6 no. 7 1935-1946; https://doi.org/10.1534/g3.116.030510
Terry J. Felderhoff
UF Genetics Institute, University of Florida, Gainesville, Florida 32611Department of Microbiology and Cell Science—IFAS, University of Florida, Gainesville, Florida 32611
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Lauren M. McIntyre
UF Genetics Institute, University of Florida, Gainesville, Florida 32611Genetics and Genomics Graduate Program, University of Florida, Gainesville, Florida 32611
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  • ORCID record for Lauren M. McIntyre
Ana Saballos
UF Genetics Institute, University of Florida, Gainesville, Florida 32611
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Wilfred Vermerris
UF Genetics Institute, University of Florida, Gainesville, Florida 32611Department of Molecular Genetics and Microbiology, University of Florida, Gainesville, Florida 32611
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  • ORCID record for Wilfred Vermerris
  • For correspondence: wev@ufl.edu
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Data supplements

  • Supplemental Material for Felderhoff et al., 2016

    Files in this Data Supplement:

    • Figure S5 - Association analysis overlaying different transformations used for association analysis. (.pdf, 243 KB)
    • File S9 - Legends for supplemental material. (.pdf, 486 KB)
    • Table S1 - Disease scores for the different lines in the original five-point scale. (.csv, 23 KB)
    • Table S2 - Phenotypic scores for the different transformations and locations. (.csv, 4 KB)
    • Table S3 - SNP markers associated with anthracnose resistance based on a -log10(p-value) above the FDR significance threshold. (.csv, 14 KB)
    • Table S4 - Comparison of the effect on the loci due to the different phenotypic scales and approaches for labeling the heterozygous markers. (.csv, 17 KB)
    • Table S5 - Allele-specific PCR to identify 'Bk7'-derived alleles on chromosome 9 in four anthracnose-resistant cultivars. (.csv, 1 KB)
    • Table S6 - Complete distribution of phenotypes based on the parental origin of the marker alleles. (.csv, 1 KB)
    • Table S7 - Proteins and gene ontology groups identified from the sorghum transcripts within the loci of interest. (.csv, 168 KB)
    • Table S8 - Curated reference R-genes aligned to the identified anthracnose resistance loci. (.csv, 5 KB)
    • Table S9 - Reference R-genes with similarity to the sorghum reference genome identified via BLAST. (.csv, 928 B)
    • Figure S1 - Visual representation of the development of the mapping population. (.tif, 541 KB)
    • Figure S2 - Flowchart for the steps used in the filtering of GBS markers. (.tif, 56 KB)
    • Figure S3 - Histograms displaying the distribution of plant height across the population in the three environments. (.tif, 52 KB)
    • Figure S4 - Comparison between the marker order on chromosome 7 generated by JoinMap and the marker order based on the reference genome. (.tif, 51 KB)
    • Figure S6 - Two-tailed Fisher's exact test for association analysis. (.tif, 176 KB)
    • File S1 - SAS code for the 2013 GBS marker filtering steps and Fisher exact test. (.txt, 139 KB)
    • File S2 - Final GBS markers from 2013 after all filtering steps are applied. (.csv, 1 MB)
    • File S3 - Final GBS markers from 2015 after all filtering steps are applied. (.csv, 570 KB)
    • File S4 - The -log10(p-value) of the Fisher's exact test for every marker, location in 2013, phenotypic scale, and heterozygous call. (.csv, 2 MB)
    • File S5 - The -log10(p-value) of the Fisher's exact test for every marker, phenotypic scale, and classification of heterozygous markers for the Live Oak 2015 location. (.csv, 493 KB)
    • File S6 - Original GBS data from 2013 in hapmat format. (.txt, 40 MB)
    • File S7 - Original GBS data from 2015 in hapmat format. (.txt, 23 MB)
    • File S8 - List of markers with identical GBS genotypic data. (.txt, 23 KB)
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PUBLICATION INFORMATION

Volume 6 Issue 7, July 2016

G3: Genes|Genomes|Genetics: 6 (7)

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Using Genotyping by Sequencing to Map Two Novel Anthracnose Resistance Loci in Sorghum bicolor

Terry J. Felderhoff, View ORCID ProfileLauren M. McIntyre, Ana Saballos and View ORCID ProfileWilfred Vermerris
G3: Genes, Genomes, Genetics July 1, 2016 vol. 6 no. 7 1935-1946; https://doi.org/10.1534/g3.116.030510
Terry J. Felderhoff
UF Genetics Institute, University of Florida, Gainesville, Florida 32611Department of Microbiology and Cell Science—IFAS, University of Florida, Gainesville, Florida 32611
  • Find this author on Google Scholar
  • Find this author on PubMed
  • Search for this author on this site
Lauren M. McIntyre
UF Genetics Institute, University of Florida, Gainesville, Florida 32611Genetics and Genomics Graduate Program, University of Florida, Gainesville, Florida 32611
  • Find this author on Google Scholar
  • Find this author on PubMed
  • Search for this author on this site
  • ORCID record for Lauren M. McIntyre
Ana Saballos
UF Genetics Institute, University of Florida, Gainesville, Florida 32611
  • Find this author on Google Scholar
  • Find this author on PubMed
  • Search for this author on this site
Wilfred Vermerris
UF Genetics Institute, University of Florida, Gainesville, Florida 32611Department of Molecular Genetics and Microbiology, University of Florida, Gainesville, Florida 32611
  • Find this author on Google Scholar
  • Find this author on PubMed
  • Search for this author on this site
  • ORCID record for Wilfred Vermerris
  • For correspondence: wev@ufl.edu
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Citation

Using Genotyping by Sequencing to Map Two Novel Anthracnose Resistance Loci in Sorghum bicolor

Terry J. Felderhoff, View ORCID ProfileLauren M. McIntyre, Ana Saballos and View ORCID ProfileWilfred Vermerris
G3: Genes, Genomes, Genetics July 1, 2016 vol. 6 no. 7 1935-1946; https://doi.org/10.1534/g3.116.030510
Terry J. Felderhoff
UF Genetics Institute, University of Florida, Gainesville, Florida 32611Department of Microbiology and Cell Science—IFAS, University of Florida, Gainesville, Florida 32611
  • Find this author on Google Scholar
  • Find this author on PubMed
  • Search for this author on this site
Lauren M. McIntyre
UF Genetics Institute, University of Florida, Gainesville, Florida 32611Genetics and Genomics Graduate Program, University of Florida, Gainesville, Florida 32611
  • Find this author on Google Scholar
  • Find this author on PubMed
  • Search for this author on this site
  • ORCID record for Lauren M. McIntyre
Ana Saballos
UF Genetics Institute, University of Florida, Gainesville, Florida 32611
  • Find this author on Google Scholar
  • Find this author on PubMed
  • Search for this author on this site
Wilfred Vermerris
UF Genetics Institute, University of Florida, Gainesville, Florida 32611Department of Molecular Genetics and Microbiology, University of Florida, Gainesville, Florida 32611
  • Find this author on Google Scholar
  • Find this author on PubMed
  • Search for this author on this site
  • ORCID record for Wilfred Vermerris
  • For correspondence: wev@ufl.edu

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