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Parsimony tree of 15 996 soybean accessions with high confidence data at all single nucleotide polymorphisms (SNPs) in the S2 linkage disequilibrium block surrounding Rhg1 . The four terminal branches containing all <t>germplasm</t> accessions described elsewhere in the manuscript are labelled, together with the number of accessions carrying the same combination of SNPs.
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1) Product Images from "Evolution and selection of Rhg1, a copy-number variant nematode-resistance locus"

Article Title: Evolution and selection of Rhg1, a copy-number variant nematode-resistance locus

Journal: Molecular Ecology

doi: 10.1111/mec.13138

Parsimony tree of 15 996 soybean accessions with high confidence data at all single nucleotide polymorphisms (SNPs) in the S2 linkage disequilibrium block surrounding Rhg1 . The four terminal branches containing all germplasm accessions described elsewhere in the manuscript are labelled, together with the number of accessions carrying the same combination of SNPs.
Figure Legend Snippet: Parsimony tree of 15 996 soybean accessions with high confidence data at all single nucleotide polymorphisms (SNPs) in the S2 linkage disequilibrium block surrounding Rhg1 . The four terminal branches containing all germplasm accessions described elsewhere in the manuscript are labelled, together with the number of accessions carrying the same combination of SNPs.

Techniques Used: Blocking Assay

Signatures of selection at the Rhg1 locus. (a) Nucleotide diversity (π and θ), Tajima's D and linkage disequilibrium were measured in the 1.5-Mbp region across the locus in 19 548 accessions (18 383 Glycine max 1165 Glycine soja ). The mean and 75th and 95th percentiles of whole-genome Tajima's D are marked by horizontal lines in corresponding graphs. (b) F ST was calculated for lines with experimentally determined copy number (46 single copy vs. 48 multiple copy). Direction of telomere = ‘tel’. The mean and 95th percentile of whole-genome F ST are marked by horizontal lines. Red marks indicates statistical significance. (c) F ST between geographic subpopulations. One hundred and thirty-five single nucleotide polymorphisms were used to compare: Top graph, between 3311 germplasm accessions from Korea and 3855 from China; centre, between 3311 from Korea and 2466 from Japan; bottom, between 3855 from China and 2466 from Japan. The mean and 95th percentile values of whole-genome F ST are marked by a horizontal line in the corresponding graphs.
Figure Legend Snippet: Signatures of selection at the Rhg1 locus. (a) Nucleotide diversity (π and θ), Tajima's D and linkage disequilibrium were measured in the 1.5-Mbp region across the locus in 19 548 accessions (18 383 Glycine max 1165 Glycine soja ). The mean and 75th and 95th percentiles of whole-genome Tajima's D are marked by horizontal lines in corresponding graphs. (b) F ST was calculated for lines with experimentally determined copy number (46 single copy vs. 48 multiple copy). Direction of telomere = ‘tel’. The mean and 95th percentile of whole-genome F ST are marked by horizontal lines. Red marks indicates statistical significance. (c) F ST between geographic subpopulations. One hundred and thirty-five single nucleotide polymorphisms were used to compare: Top graph, between 3311 germplasm accessions from Korea and 3855 from China; centre, between 3311 from Korea and 2466 from Japan; bottom, between 3855 from China and 2466 from Japan. The mean and 95th percentile values of whole-genome F ST are marked by a horizontal line in the corresponding graphs.

Techniques Used: Selection

Diversity, linkage disequilibrium (LD) and sequence analysis of the region surrounding the Rhg1 locus. (a) Nucleotide diversity within 38 protein-coding genes surrounding Rhg1 in eighteen germplasm accessions (with 1–10 copies at Rhg1 ) is displayed in the uppermost graph. Those accessions with three copies (centre graph) and nine and ten copies (bottom graph) were also analysed separately. The average nucleotide diversity (π; 0.00053) of all coding regions in Glycine max is marked by a horizontal line. (b) LD plot using the r 2 metric for the 400-kb region surrounding the Rhg1 locus. The same 18 accessions were used. Regions S1, S2 and S3 represent three linkage blocks used in further analysis. tel: telomere. (c) Phylogenetic trees derived from parsimony analysis of the three LD blocks. The tree for the region of linkage block S2 that contains Rhg1 is consistent with the analysis of the repeat sequence (Fig. 2 ). The copy number of each accession is in parentheses. The consensus trees were created after collapsing branches with bootstrap values
Figure Legend Snippet: Diversity, linkage disequilibrium (LD) and sequence analysis of the region surrounding the Rhg1 locus. (a) Nucleotide diversity within 38 protein-coding genes surrounding Rhg1 in eighteen germplasm accessions (with 1–10 copies at Rhg1 ) is displayed in the uppermost graph. Those accessions with three copies (centre graph) and nine and ten copies (bottom graph) were also analysed separately. The average nucleotide diversity (π; 0.00053) of all coding regions in Glycine max is marked by a horizontal line. (b) LD plot using the r 2 metric for the 400-kb region surrounding the Rhg1 locus. The same 18 accessions were used. Regions S1, S2 and S3 represent three linkage blocks used in further analysis. tel: telomere. (c) Phylogenetic trees derived from parsimony analysis of the three LD blocks. The tree for the region of linkage block S2 that contains Rhg1 is consistent with the analysis of the repeat sequence (Fig. 2 ). The copy number of each accession is in parentheses. The consensus trees were created after collapsing branches with bootstrap values

Techniques Used: Sequencing, Derivative Assay, Blocking Assay

2) Product Images from "Evolution and selection of Rhg1, a copy-number variant nematode-resistance locus"

Article Title: Evolution and selection of Rhg1, a copy-number variant nematode-resistance locus

Journal: Molecular Ecology

doi: 10.1111/mec.13138

Parsimony tree of 15 996 soybean accessions with high confidence data at all single nucleotide polymorphisms (SNPs) in the S2 linkage disequilibrium block surrounding Rhg1 . The four terminal branches containing all germplasm accessions described elsewhere in the manuscript are labelled, together with the number of accessions carrying the same combination of SNPs.
Figure Legend Snippet: Parsimony tree of 15 996 soybean accessions with high confidence data at all single nucleotide polymorphisms (SNPs) in the S2 linkage disequilibrium block surrounding Rhg1 . The four terminal branches containing all germplasm accessions described elsewhere in the manuscript are labelled, together with the number of accessions carrying the same combination of SNPs.

Techniques Used: Blocking Assay

Signatures of selection at the Rhg1 locus. (a) Nucleotide diversity (π and θ), Tajima's D and linkage disequilibrium were measured in the 1.5-Mbp region across the locus in 19 548 accessions (18 383 Glycine max 1165 Glycine soja ). The mean and 75th and 95th percentiles of whole-genome Tajima's D are marked by horizontal lines in corresponding graphs. (b) F ST was calculated for lines with experimentally determined copy number (46 single copy vs. 48 multiple copy). Direction of telomere = ‘tel’. The mean and 95th percentile of whole-genome F ST are marked by horizontal lines. Red marks indicates statistical significance. (c) F ST between geographic subpopulations. One hundred and thirty-five single nucleotide polymorphisms were used to compare: Top graph, between 3311 germplasm accessions from Korea and 3855 from China; centre, between 3311 from Korea and 2466 from Japan; bottom, between 3855 from China and 2466 from Japan. The mean and 95th percentile values of whole-genome F ST are marked by a horizontal line in the corresponding graphs.
Figure Legend Snippet: Signatures of selection at the Rhg1 locus. (a) Nucleotide diversity (π and θ), Tajima's D and linkage disequilibrium were measured in the 1.5-Mbp region across the locus in 19 548 accessions (18 383 Glycine max 1165 Glycine soja ). The mean and 75th and 95th percentiles of whole-genome Tajima's D are marked by horizontal lines in corresponding graphs. (b) F ST was calculated for lines with experimentally determined copy number (46 single copy vs. 48 multiple copy). Direction of telomere = ‘tel’. The mean and 95th percentile of whole-genome F ST are marked by horizontal lines. Red marks indicates statistical significance. (c) F ST between geographic subpopulations. One hundred and thirty-five single nucleotide polymorphisms were used to compare: Top graph, between 3311 germplasm accessions from Korea and 3855 from China; centre, between 3311 from Korea and 2466 from Japan; bottom, between 3855 from China and 2466 from Japan. The mean and 95th percentile values of whole-genome F ST are marked by a horizontal line in the corresponding graphs.

Techniques Used: Selection

Diversity, linkage disequilibrium (LD) and sequence analysis of the region surrounding the Rhg1 locus. (a) Nucleotide diversity within 38 protein-coding genes surrounding Rhg1 in eighteen germplasm accessions (with 1–10 copies at Rhg1 ) is displayed in the uppermost graph. Those accessions with three copies (centre graph) and nine and ten copies (bottom graph) were also analysed separately. The average nucleotide diversity (π; 0.00053) of all coding regions in Glycine max is marked by a horizontal line. (b) LD plot using the r 2 metric for the 400-kb region surrounding the Rhg1 locus. The same 18 accessions were used. Regions S1, S2 and S3 represent three linkage blocks used in further analysis. tel: telomere. (c) Phylogenetic trees derived from parsimony analysis of the three LD blocks. The tree for the region of linkage block S2 that contains Rhg1 is consistent with the analysis of the repeat sequence (Fig. 2 ). The copy number of each accession is in parentheses. The consensus trees were created after collapsing branches with bootstrap values
Figure Legend Snippet: Diversity, linkage disequilibrium (LD) and sequence analysis of the region surrounding the Rhg1 locus. (a) Nucleotide diversity within 38 protein-coding genes surrounding Rhg1 in eighteen germplasm accessions (with 1–10 copies at Rhg1 ) is displayed in the uppermost graph. Those accessions with three copies (centre graph) and nine and ten copies (bottom graph) were also analysed separately. The average nucleotide diversity (π; 0.00053) of all coding regions in Glycine max is marked by a horizontal line. (b) LD plot using the r 2 metric for the 400-kb region surrounding the Rhg1 locus. The same 18 accessions were used. Regions S1, S2 and S3 represent three linkage blocks used in further analysis. tel: telomere. (c) Phylogenetic trees derived from parsimony analysis of the three LD blocks. The tree for the region of linkage block S2 that contains Rhg1 is consistent with the analysis of the repeat sequence (Fig. 2 ). The copy number of each accession is in parentheses. The consensus trees were created after collapsing branches with bootstrap values

Techniques Used: Sequencing, Derivative Assay, Blocking Assay

3) Product Images from "Evolution and selection of Rhg1, a copy-number variant nematode-resistance locus"

Article Title: Evolution and selection of Rhg1, a copy-number variant nematode-resistance locus

Journal: Molecular Ecology

doi: 10.1111/mec.13138

Parsimony tree of 15 996 soybean accessions with high confidence data at all single nucleotide polymorphisms (SNPs) in the S2 linkage disequilibrium block surrounding Rhg1 . The four terminal branches containing all germplasm accessions described elsewhere in the manuscript are labelled, together with the number of accessions carrying the same combination of SNPs.
Figure Legend Snippet: Parsimony tree of 15 996 soybean accessions with high confidence data at all single nucleotide polymorphisms (SNPs) in the S2 linkage disequilibrium block surrounding Rhg1 . The four terminal branches containing all germplasm accessions described elsewhere in the manuscript are labelled, together with the number of accessions carrying the same combination of SNPs.

Techniques Used: Blocking Assay

Signatures of selection at the Rhg1 locus. (a) Nucleotide diversity (π and θ), Tajima's D and linkage disequilibrium were measured in the 1.5-Mbp region across the locus in 19 548 accessions (18 383 Glycine max 1165 Glycine soja ). The mean and 75th and 95th percentiles of whole-genome Tajima's D are marked by horizontal lines in corresponding graphs. (b) F ST was calculated for lines with experimentally determined copy number (46 single copy vs. 48 multiple copy). Direction of telomere = ‘tel’. The mean and 95th percentile of whole-genome F ST are marked by horizontal lines. Red marks indicates statistical significance. (c) F ST between geographic subpopulations. One hundred and thirty-five single nucleotide polymorphisms were used to compare: Top graph, between 3311 germplasm accessions from Korea and 3855 from China; centre, between 3311 from Korea and 2466 from Japan; bottom, between 3855 from China and 2466 from Japan. The mean and 95th percentile values of whole-genome F ST are marked by a horizontal line in the corresponding graphs.
Figure Legend Snippet: Signatures of selection at the Rhg1 locus. (a) Nucleotide diversity (π and θ), Tajima's D and linkage disequilibrium were measured in the 1.5-Mbp region across the locus in 19 548 accessions (18 383 Glycine max 1165 Glycine soja ). The mean and 75th and 95th percentiles of whole-genome Tajima's D are marked by horizontal lines in corresponding graphs. (b) F ST was calculated for lines with experimentally determined copy number (46 single copy vs. 48 multiple copy). Direction of telomere = ‘tel’. The mean and 95th percentile of whole-genome F ST are marked by horizontal lines. Red marks indicates statistical significance. (c) F ST between geographic subpopulations. One hundred and thirty-five single nucleotide polymorphisms were used to compare: Top graph, between 3311 germplasm accessions from Korea and 3855 from China; centre, between 3311 from Korea and 2466 from Japan; bottom, between 3855 from China and 2466 from Japan. The mean and 95th percentile values of whole-genome F ST are marked by a horizontal line in the corresponding graphs.

Techniques Used: Selection

Diversity, linkage disequilibrium (LD) and sequence analysis of the region surrounding the Rhg1 locus. (a) Nucleotide diversity within 38 protein-coding genes surrounding Rhg1 in eighteen germplasm accessions (with 1–10 copies at Rhg1 ) is displayed in the uppermost graph. Those accessions with three copies (centre graph) and nine and ten copies (bottom graph) were also analysed separately. The average nucleotide diversity (π; 0.00053) of all coding regions in Glycine max is marked by a horizontal line. (b) LD plot using the r 2 metric for the 400-kb region surrounding the Rhg1 locus. The same 18 accessions were used. Regions S1, S2 and S3 represent three linkage blocks used in further analysis. tel: telomere. (c) Phylogenetic trees derived from parsimony analysis of the three LD blocks. The tree for the region of linkage block S2 that contains Rhg1 is consistent with the analysis of the repeat sequence (Fig. 2 ). The copy number of each accession is in parentheses. The consensus trees were created after collapsing branches with bootstrap values
Figure Legend Snippet: Diversity, linkage disequilibrium (LD) and sequence analysis of the region surrounding the Rhg1 locus. (a) Nucleotide diversity within 38 protein-coding genes surrounding Rhg1 in eighteen germplasm accessions (with 1–10 copies at Rhg1 ) is displayed in the uppermost graph. Those accessions with three copies (centre graph) and nine and ten copies (bottom graph) were also analysed separately. The average nucleotide diversity (π; 0.00053) of all coding regions in Glycine max is marked by a horizontal line. (b) LD plot using the r 2 metric for the 400-kb region surrounding the Rhg1 locus. The same 18 accessions were used. Regions S1, S2 and S3 represent three linkage blocks used in further analysis. tel: telomere. (c) Phylogenetic trees derived from parsimony analysis of the three LD blocks. The tree for the region of linkage block S2 that contains Rhg1 is consistent with the analysis of the repeat sequence (Fig. 2 ). The copy number of each accession is in parentheses. The consensus trees were created after collapsing branches with bootstrap values

Techniques Used: Sequencing, Derivative Assay, Blocking Assay

4) Product Images from "Evolution and selection of Rhg1, a copy-number variant nematode-resistance locus"

Article Title: Evolution and selection of Rhg1, a copy-number variant nematode-resistance locus

Journal: Molecular Ecology

doi: 10.1111/mec.13138

Parsimony tree of 15 996 soybean accessions with high confidence data at all single nucleotide polymorphisms (SNPs) in the S2 linkage disequilibrium block surrounding Rhg1 . The four terminal branches containing all germplasm accessions described elsewhere in the manuscript are labelled, together with the number of accessions carrying the same combination of SNPs.
Figure Legend Snippet: Parsimony tree of 15 996 soybean accessions with high confidence data at all single nucleotide polymorphisms (SNPs) in the S2 linkage disequilibrium block surrounding Rhg1 . The four terminal branches containing all germplasm accessions described elsewhere in the manuscript are labelled, together with the number of accessions carrying the same combination of SNPs.

Techniques Used: Blocking Assay

Signatures of selection at the Rhg1 locus. (a) Nucleotide diversity (π and θ), Tajima's D and linkage disequilibrium were measured in the 1.5-Mbp region across the locus in 19 548 accessions (18 383 Glycine max 1165 Glycine soja ). The mean and 75th and 95th percentiles of whole-genome Tajima's D are marked by horizontal lines in corresponding graphs. (b) F ST was calculated for lines with experimentally determined copy number (46 single copy vs. 48 multiple copy). Direction of telomere = ‘tel’. The mean and 95th percentile of whole-genome F ST are marked by horizontal lines. Red marks indicates statistical significance. (c) F ST between geographic subpopulations. One hundred and thirty-five single nucleotide polymorphisms were used to compare: Top graph, between 3311 germplasm accessions from Korea and 3855 from China; centre, between 3311 from Korea and 2466 from Japan; bottom, between 3855 from China and 2466 from Japan. The mean and 95th percentile values of whole-genome F ST are marked by a horizontal line in the corresponding graphs.
Figure Legend Snippet: Signatures of selection at the Rhg1 locus. (a) Nucleotide diversity (π and θ), Tajima's D and linkage disequilibrium were measured in the 1.5-Mbp region across the locus in 19 548 accessions (18 383 Glycine max 1165 Glycine soja ). The mean and 75th and 95th percentiles of whole-genome Tajima's D are marked by horizontal lines in corresponding graphs. (b) F ST was calculated for lines with experimentally determined copy number (46 single copy vs. 48 multiple copy). Direction of telomere = ‘tel’. The mean and 95th percentile of whole-genome F ST are marked by horizontal lines. Red marks indicates statistical significance. (c) F ST between geographic subpopulations. One hundred and thirty-five single nucleotide polymorphisms were used to compare: Top graph, between 3311 germplasm accessions from Korea and 3855 from China; centre, between 3311 from Korea and 2466 from Japan; bottom, between 3855 from China and 2466 from Japan. The mean and 95th percentile values of whole-genome F ST are marked by a horizontal line in the corresponding graphs.

Techniques Used: Selection

Diversity, linkage disequilibrium (LD) and sequence analysis of the region surrounding the Rhg1 locus. (a) Nucleotide diversity within 38 protein-coding genes surrounding Rhg1 in eighteen germplasm accessions (with 1–10 copies at Rhg1 ) is displayed in the uppermost graph. Those accessions with three copies (centre graph) and nine and ten copies (bottom graph) were also analysed separately. The average nucleotide diversity (π; 0.00053) of all coding regions in Glycine max is marked by a horizontal line. (b) LD plot using the r 2 metric for the 400-kb region surrounding the Rhg1 locus. The same 18 accessions were used. Regions S1, S2 and S3 represent three linkage blocks used in further analysis. tel: telomere. (c) Phylogenetic trees derived from parsimony analysis of the three LD blocks. The tree for the region of linkage block S2 that contains Rhg1 is consistent with the analysis of the repeat sequence (Fig. 2 ). The copy number of each accession is in parentheses. The consensus trees were created after collapsing branches with bootstrap values
Figure Legend Snippet: Diversity, linkage disequilibrium (LD) and sequence analysis of the region surrounding the Rhg1 locus. (a) Nucleotide diversity within 38 protein-coding genes surrounding Rhg1 in eighteen germplasm accessions (with 1–10 copies at Rhg1 ) is displayed in the uppermost graph. Those accessions with three copies (centre graph) and nine and ten copies (bottom graph) were also analysed separately. The average nucleotide diversity (π; 0.00053) of all coding regions in Glycine max is marked by a horizontal line. (b) LD plot using the r 2 metric for the 400-kb region surrounding the Rhg1 locus. The same 18 accessions were used. Regions S1, S2 and S3 represent three linkage blocks used in further analysis. tel: telomere. (c) Phylogenetic trees derived from parsimony analysis of the three LD blocks. The tree for the region of linkage block S2 that contains Rhg1 is consistent with the analysis of the repeat sequence (Fig. 2 ). The copy number of each accession is in parentheses. The consensus trees were created after collapsing branches with bootstrap values

Techniques Used: Sequencing, Derivative Assay, Blocking Assay

5) Product Images from "Evolution and selection of Rhg1, a copy-number variant nematode-resistance locus"

Article Title: Evolution and selection of Rhg1, a copy-number variant nematode-resistance locus

Journal: Molecular Ecology

doi: 10.1111/mec.13138

Parsimony tree of 15 996 soybean accessions with high confidence data at all single nucleotide polymorphisms (SNPs) in the S2 linkage disequilibrium block surrounding Rhg1 . The four terminal branches containing all germplasm accessions described elsewhere in the manuscript are labelled, together with the number of accessions carrying the same combination of SNPs.
Figure Legend Snippet: Parsimony tree of 15 996 soybean accessions with high confidence data at all single nucleotide polymorphisms (SNPs) in the S2 linkage disequilibrium block surrounding Rhg1 . The four terminal branches containing all germplasm accessions described elsewhere in the manuscript are labelled, together with the number of accessions carrying the same combination of SNPs.

Techniques Used: Blocking Assay

Signatures of selection at the Rhg1 locus. (a) Nucleotide diversity (π and θ), Tajima's D and linkage disequilibrium were measured in the 1.5-Mbp region across the locus in 19 548 accessions (18 383 Glycine max 1165 Glycine soja ). The mean and 75th and 95th percentiles of whole-genome Tajima's D are marked by horizontal lines in corresponding graphs. (b) F ST was calculated for lines with experimentally determined copy number (46 single copy vs. 48 multiple copy). Direction of telomere = ‘tel’. The mean and 95th percentile of whole-genome F ST are marked by horizontal lines. Red marks indicates statistical significance. (c) F ST between geographic subpopulations. One hundred and thirty-five single nucleotide polymorphisms were used to compare: Top graph, between 3311 germplasm accessions from Korea and 3855 from China; centre, between 3311 from Korea and 2466 from Japan; bottom, between 3855 from China and 2466 from Japan. The mean and 95th percentile values of whole-genome F ST are marked by a horizontal line in the corresponding graphs.
Figure Legend Snippet: Signatures of selection at the Rhg1 locus. (a) Nucleotide diversity (π and θ), Tajima's D and linkage disequilibrium were measured in the 1.5-Mbp region across the locus in 19 548 accessions (18 383 Glycine max 1165 Glycine soja ). The mean and 75th and 95th percentiles of whole-genome Tajima's D are marked by horizontal lines in corresponding graphs. (b) F ST was calculated for lines with experimentally determined copy number (46 single copy vs. 48 multiple copy). Direction of telomere = ‘tel’. The mean and 95th percentile of whole-genome F ST are marked by horizontal lines. Red marks indicates statistical significance. (c) F ST between geographic subpopulations. One hundred and thirty-five single nucleotide polymorphisms were used to compare: Top graph, between 3311 germplasm accessions from Korea and 3855 from China; centre, between 3311 from Korea and 2466 from Japan; bottom, between 3855 from China and 2466 from Japan. The mean and 95th percentile values of whole-genome F ST are marked by a horizontal line in the corresponding graphs.

Techniques Used: Selection

Diversity, linkage disequilibrium (LD) and sequence analysis of the region surrounding the Rhg1 locus. (a) Nucleotide diversity within 38 protein-coding genes surrounding Rhg1 in eighteen germplasm accessions (with 1–10 copies at Rhg1 ) is displayed in the uppermost graph. Those accessions with three copies (centre graph) and nine and ten copies (bottom graph) were also analysed separately. The average nucleotide diversity (π; 0.00053) of all coding regions in Glycine max is marked by a horizontal line. (b) LD plot using the r 2 metric for the 400-kb region surrounding the Rhg1 locus. The same 18 accessions were used. Regions S1, S2 and S3 represent three linkage blocks used in further analysis. tel: telomere. (c) Phylogenetic trees derived from parsimony analysis of the three LD blocks. The tree for the region of linkage block S2 that contains Rhg1 is consistent with the analysis of the repeat sequence (Fig. 2 ). The copy number of each accession is in parentheses. The consensus trees were created after collapsing branches with bootstrap values
Figure Legend Snippet: Diversity, linkage disequilibrium (LD) and sequence analysis of the region surrounding the Rhg1 locus. (a) Nucleotide diversity within 38 protein-coding genes surrounding Rhg1 in eighteen germplasm accessions (with 1–10 copies at Rhg1 ) is displayed in the uppermost graph. Those accessions with three copies (centre graph) and nine and ten copies (bottom graph) were also analysed separately. The average nucleotide diversity (π; 0.00053) of all coding regions in Glycine max is marked by a horizontal line. (b) LD plot using the r 2 metric for the 400-kb region surrounding the Rhg1 locus. The same 18 accessions were used. Regions S1, S2 and S3 represent three linkage blocks used in further analysis. tel: telomere. (c) Phylogenetic trees derived from parsimony analysis of the three LD blocks. The tree for the region of linkage block S2 that contains Rhg1 is consistent with the analysis of the repeat sequence (Fig. 2 ). The copy number of each accession is in parentheses. The consensus trees were created after collapsing branches with bootstrap values

Techniques Used: Sequencing, Derivative Assay, Blocking Assay

6) Product Images from "Evolution and selection of Rhg1, a copy-number variant nematode-resistance locus"

Article Title: Evolution and selection of Rhg1, a copy-number variant nematode-resistance locus

Journal: Molecular Ecology

doi: 10.1111/mec.13138

Parsimony tree of 15 996 soybean accessions with high confidence data at all single nucleotide polymorphisms (SNPs) in the S2 linkage disequilibrium block surrounding Rhg1 . The four terminal branches containing all germplasm accessions described elsewhere in the manuscript are labelled, together with the number of accessions carrying the same combination of SNPs.
Figure Legend Snippet: Parsimony tree of 15 996 soybean accessions with high confidence data at all single nucleotide polymorphisms (SNPs) in the S2 linkage disequilibrium block surrounding Rhg1 . The four terminal branches containing all germplasm accessions described elsewhere in the manuscript are labelled, together with the number of accessions carrying the same combination of SNPs.

Techniques Used: Blocking Assay

Signatures of selection at the Rhg1 locus. (a) Nucleotide diversity (π and θ), Tajima's D and linkage disequilibrium were measured in the 1.5-Mbp region across the locus in 19 548 accessions (18 383 Glycine max 1165 Glycine soja ). The mean and 75th and 95th percentiles of whole-genome Tajima's D are marked by horizontal lines in corresponding graphs. (b) F ST was calculated for lines with experimentally determined copy number (46 single copy vs. 48 multiple copy). Direction of telomere = ‘tel’. The mean and 95th percentile of whole-genome F ST are marked by horizontal lines. Red marks indicates statistical significance. (c) F ST between geographic subpopulations. One hundred and thirty-five single nucleotide polymorphisms were used to compare: Top graph, between 3311 germplasm accessions from Korea and 3855 from China; centre, between 3311 from Korea and 2466 from Japan; bottom, between 3855 from China and 2466 from Japan. The mean and 95th percentile values of whole-genome F ST are marked by a horizontal line in the corresponding graphs.
Figure Legend Snippet: Signatures of selection at the Rhg1 locus. (a) Nucleotide diversity (π and θ), Tajima's D and linkage disequilibrium were measured in the 1.5-Mbp region across the locus in 19 548 accessions (18 383 Glycine max 1165 Glycine soja ). The mean and 75th and 95th percentiles of whole-genome Tajima's D are marked by horizontal lines in corresponding graphs. (b) F ST was calculated for lines with experimentally determined copy number (46 single copy vs. 48 multiple copy). Direction of telomere = ‘tel’. The mean and 95th percentile of whole-genome F ST are marked by horizontal lines. Red marks indicates statistical significance. (c) F ST between geographic subpopulations. One hundred and thirty-five single nucleotide polymorphisms were used to compare: Top graph, between 3311 germplasm accessions from Korea and 3855 from China; centre, between 3311 from Korea and 2466 from Japan; bottom, between 3855 from China and 2466 from Japan. The mean and 95th percentile values of whole-genome F ST are marked by a horizontal line in the corresponding graphs.

Techniques Used: Selection

Diversity, linkage disequilibrium (LD) and sequence analysis of the region surrounding the Rhg1 locus. (a) Nucleotide diversity within 38 protein-coding genes surrounding Rhg1 in eighteen germplasm accessions (with 1–10 copies at Rhg1 ) is displayed in the uppermost graph. Those accessions with three copies (centre graph) and nine and ten copies (bottom graph) were also analysed separately. The average nucleotide diversity (π; 0.00053) of all coding regions in Glycine max is marked by a horizontal line. (b) LD plot using the r 2 metric for the 400-kb region surrounding the Rhg1 locus. The same 18 accessions were used. Regions S1, S2 and S3 represent three linkage blocks used in further analysis. tel: telomere. (c) Phylogenetic trees derived from parsimony analysis of the three LD blocks. The tree for the region of linkage block S2 that contains Rhg1 is consistent with the analysis of the repeat sequence (Fig. 2 ). The copy number of each accession is in parentheses. The consensus trees were created after collapsing branches with bootstrap values
Figure Legend Snippet: Diversity, linkage disequilibrium (LD) and sequence analysis of the region surrounding the Rhg1 locus. (a) Nucleotide diversity within 38 protein-coding genes surrounding Rhg1 in eighteen germplasm accessions (with 1–10 copies at Rhg1 ) is displayed in the uppermost graph. Those accessions with three copies (centre graph) and nine and ten copies (bottom graph) were also analysed separately. The average nucleotide diversity (π; 0.00053) of all coding regions in Glycine max is marked by a horizontal line. (b) LD plot using the r 2 metric for the 400-kb region surrounding the Rhg1 locus. The same 18 accessions were used. Regions S1, S2 and S3 represent three linkage blocks used in further analysis. tel: telomere. (c) Phylogenetic trees derived from parsimony analysis of the three LD blocks. The tree for the region of linkage block S2 that contains Rhg1 is consistent with the analysis of the repeat sequence (Fig. 2 ). The copy number of each accession is in parentheses. The consensus trees were created after collapsing branches with bootstrap values

Techniques Used: Sequencing, Derivative Assay, Blocking Assay

7) Product Images from "Evolution and selection of Rhg1, a copy-number variant nematode-resistance locus"

Article Title: Evolution and selection of Rhg1, a copy-number variant nematode-resistance locus

Journal: Molecular Ecology

doi: 10.1111/mec.13138

Parsimony tree of 15 996 soybean accessions with high confidence data at all single nucleotide polymorphisms (SNPs) in the S2 linkage disequilibrium block surrounding Rhg1 . The four terminal branches containing all germplasm accessions described elsewhere in the manuscript are labelled, together with the number of accessions carrying the same combination of SNPs.
Figure Legend Snippet: Parsimony tree of 15 996 soybean accessions with high confidence data at all single nucleotide polymorphisms (SNPs) in the S2 linkage disequilibrium block surrounding Rhg1 . The four terminal branches containing all germplasm accessions described elsewhere in the manuscript are labelled, together with the number of accessions carrying the same combination of SNPs.

Techniques Used: Blocking Assay

Signatures of selection at the Rhg1 locus. (a) Nucleotide diversity (π and θ), Tajima's D and linkage disequilibrium were measured in the 1.5-Mbp region across the locus in 19 548 accessions (18 383 Glycine max 1165 Glycine soja ). The mean and 75th and 95th percentiles of whole-genome Tajima's D are marked by horizontal lines in corresponding graphs. (b) F ST was calculated for lines with experimentally determined copy number (46 single copy vs. 48 multiple copy). Direction of telomere = ‘tel’. The mean and 95th percentile of whole-genome F ST are marked by horizontal lines. Red marks indicates statistical significance. (c) F ST between geographic subpopulations. One hundred and thirty-five single nucleotide polymorphisms were used to compare: Top graph, between 3311 germplasm accessions from Korea and 3855 from China; centre, between 3311 from Korea and 2466 from Japan; bottom, between 3855 from China and 2466 from Japan. The mean and 95th percentile values of whole-genome F ST are marked by a horizontal line in the corresponding graphs.
Figure Legend Snippet: Signatures of selection at the Rhg1 locus. (a) Nucleotide diversity (π and θ), Tajima's D and linkage disequilibrium were measured in the 1.5-Mbp region across the locus in 19 548 accessions (18 383 Glycine max 1165 Glycine soja ). The mean and 75th and 95th percentiles of whole-genome Tajima's D are marked by horizontal lines in corresponding graphs. (b) F ST was calculated for lines with experimentally determined copy number (46 single copy vs. 48 multiple copy). Direction of telomere = ‘tel’. The mean and 95th percentile of whole-genome F ST are marked by horizontal lines. Red marks indicates statistical significance. (c) F ST between geographic subpopulations. One hundred and thirty-five single nucleotide polymorphisms were used to compare: Top graph, between 3311 germplasm accessions from Korea and 3855 from China; centre, between 3311 from Korea and 2466 from Japan; bottom, between 3855 from China and 2466 from Japan. The mean and 95th percentile values of whole-genome F ST are marked by a horizontal line in the corresponding graphs.

Techniques Used: Selection

Diversity, linkage disequilibrium (LD) and sequence analysis of the region surrounding the Rhg1 locus. (a) Nucleotide diversity within 38 protein-coding genes surrounding Rhg1 in eighteen germplasm accessions (with 1–10 copies at Rhg1 ) is displayed in the uppermost graph. Those accessions with three copies (centre graph) and nine and ten copies (bottom graph) were also analysed separately. The average nucleotide diversity (π; 0.00053) of all coding regions in Glycine max is marked by a horizontal line. (b) LD plot using the r 2 metric for the 400-kb region surrounding the Rhg1 locus. The same 18 accessions were used. Regions S1, S2 and S3 represent three linkage blocks used in further analysis. tel: telomere. (c) Phylogenetic trees derived from parsimony analysis of the three LD blocks. The tree for the region of linkage block S2 that contains Rhg1 is consistent with the analysis of the repeat sequence (Fig. 2 ). The copy number of each accession is in parentheses. The consensus trees were created after collapsing branches with bootstrap values
Figure Legend Snippet: Diversity, linkage disequilibrium (LD) and sequence analysis of the region surrounding the Rhg1 locus. (a) Nucleotide diversity within 38 protein-coding genes surrounding Rhg1 in eighteen germplasm accessions (with 1–10 copies at Rhg1 ) is displayed in the uppermost graph. Those accessions with three copies (centre graph) and nine and ten copies (bottom graph) were also analysed separately. The average nucleotide diversity (π; 0.00053) of all coding regions in Glycine max is marked by a horizontal line. (b) LD plot using the r 2 metric for the 400-kb region surrounding the Rhg1 locus. The same 18 accessions were used. Regions S1, S2 and S3 represent three linkage blocks used in further analysis. tel: telomere. (c) Phylogenetic trees derived from parsimony analysis of the three LD blocks. The tree for the region of linkage block S2 that contains Rhg1 is consistent with the analysis of the repeat sequence (Fig. 2 ). The copy number of each accession is in parentheses. The consensus trees were created after collapsing branches with bootstrap values

Techniques Used: Sequencing, Derivative Assay, Blocking Assay

8) Product Images from "Evolution and selection of Rhg1, a copy-number variant nematode-resistance locus"

Article Title: Evolution and selection of Rhg1, a copy-number variant nematode-resistance locus

Journal: Molecular Ecology

doi: 10.1111/mec.13138

Parsimony tree of 15 996 soybean accessions with high confidence data at all single nucleotide polymorphisms (SNPs) in the S2 linkage disequilibrium block surrounding Rhg1 . The four terminal branches containing all germplasm accessions described elsewhere in the manuscript are labelled, together with the number of accessions carrying the same combination of SNPs.
Figure Legend Snippet: Parsimony tree of 15 996 soybean accessions with high confidence data at all single nucleotide polymorphisms (SNPs) in the S2 linkage disequilibrium block surrounding Rhg1 . The four terminal branches containing all germplasm accessions described elsewhere in the manuscript are labelled, together with the number of accessions carrying the same combination of SNPs.

Techniques Used: Blocking Assay

Signatures of selection at the Rhg1 locus. (a) Nucleotide diversity (π and θ), Tajima's D and linkage disequilibrium were measured in the 1.5-Mbp region across the locus in 19 548 accessions (18 383 Glycine max 1165 Glycine soja ). The mean and 75th and 95th percentiles of whole-genome Tajima's D are marked by horizontal lines in corresponding graphs. (b) F ST was calculated for lines with experimentally determined copy number (46 single copy vs. 48 multiple copy). Direction of telomere = ‘tel’. The mean and 95th percentile of whole-genome F ST are marked by horizontal lines. Red marks indicates statistical significance. (c) F ST between geographic subpopulations. One hundred and thirty-five single nucleotide polymorphisms were used to compare: Top graph, between 3311 germplasm accessions from Korea and 3855 from China; centre, between 3311 from Korea and 2466 from Japan; bottom, between 3855 from China and 2466 from Japan. The mean and 95th percentile values of whole-genome F ST are marked by a horizontal line in the corresponding graphs.
Figure Legend Snippet: Signatures of selection at the Rhg1 locus. (a) Nucleotide diversity (π and θ), Tajima's D and linkage disequilibrium were measured in the 1.5-Mbp region across the locus in 19 548 accessions (18 383 Glycine max 1165 Glycine soja ). The mean and 75th and 95th percentiles of whole-genome Tajima's D are marked by horizontal lines in corresponding graphs. (b) F ST was calculated for lines with experimentally determined copy number (46 single copy vs. 48 multiple copy). Direction of telomere = ‘tel’. The mean and 95th percentile of whole-genome F ST are marked by horizontal lines. Red marks indicates statistical significance. (c) F ST between geographic subpopulations. One hundred and thirty-five single nucleotide polymorphisms were used to compare: Top graph, between 3311 germplasm accessions from Korea and 3855 from China; centre, between 3311 from Korea and 2466 from Japan; bottom, between 3855 from China and 2466 from Japan. The mean and 95th percentile values of whole-genome F ST are marked by a horizontal line in the corresponding graphs.

Techniques Used: Selection

Diversity, linkage disequilibrium (LD) and sequence analysis of the region surrounding the Rhg1 locus. (a) Nucleotide diversity within 38 protein-coding genes surrounding Rhg1 in eighteen germplasm accessions (with 1–10 copies at Rhg1 ) is displayed in the uppermost graph. Those accessions with three copies (centre graph) and nine and ten copies (bottom graph) were also analysed separately. The average nucleotide diversity (π; 0.00053) of all coding regions in Glycine max is marked by a horizontal line. (b) LD plot using the r 2 metric for the 400-kb region surrounding the Rhg1 locus. The same 18 accessions were used. Regions S1, S2 and S3 represent three linkage blocks used in further analysis. tel: telomere. (c) Phylogenetic trees derived from parsimony analysis of the three LD blocks. The tree for the region of linkage block S2 that contains Rhg1 is consistent with the analysis of the repeat sequence (Fig. 2 ). The copy number of each accession is in parentheses. The consensus trees were created after collapsing branches with bootstrap values
Figure Legend Snippet: Diversity, linkage disequilibrium (LD) and sequence analysis of the region surrounding the Rhg1 locus. (a) Nucleotide diversity within 38 protein-coding genes surrounding Rhg1 in eighteen germplasm accessions (with 1–10 copies at Rhg1 ) is displayed in the uppermost graph. Those accessions with three copies (centre graph) and nine and ten copies (bottom graph) were also analysed separately. The average nucleotide diversity (π; 0.00053) of all coding regions in Glycine max is marked by a horizontal line. (b) LD plot using the r 2 metric for the 400-kb region surrounding the Rhg1 locus. The same 18 accessions were used. Regions S1, S2 and S3 represent three linkage blocks used in further analysis. tel: telomere. (c) Phylogenetic trees derived from parsimony analysis of the three LD blocks. The tree for the region of linkage block S2 that contains Rhg1 is consistent with the analysis of the repeat sequence (Fig. 2 ). The copy number of each accession is in parentheses. The consensus trees were created after collapsing branches with bootstrap values

Techniques Used: Sequencing, Derivative Assay, Blocking Assay

9) Product Images from "Evolution and selection of Rhg1, a copy-number variant nematode-resistance locus"

Article Title: Evolution and selection of Rhg1, a copy-number variant nematode-resistance locus

Journal: Molecular Ecology

doi: 10.1111/mec.13138

Parsimony tree of 15 996 soybean accessions with high confidence data at all single nucleotide polymorphisms (SNPs) in the S2 linkage disequilibrium block surrounding Rhg1 . The four terminal branches containing all germplasm accessions described elsewhere in the manuscript are labelled, together with the number of accessions carrying the same combination of SNPs.
Figure Legend Snippet: Parsimony tree of 15 996 soybean accessions with high confidence data at all single nucleotide polymorphisms (SNPs) in the S2 linkage disequilibrium block surrounding Rhg1 . The four terminal branches containing all germplasm accessions described elsewhere in the manuscript are labelled, together with the number of accessions carrying the same combination of SNPs.

Techniques Used: Blocking Assay

Signatures of selection at the Rhg1 locus. (a) Nucleotide diversity (π and θ), Tajima's D and linkage disequilibrium were measured in the 1.5-Mbp region across the locus in 19 548 accessions (18 383 Glycine max 1165 Glycine soja ). The mean and 75th and 95th percentiles of whole-genome Tajima's D are marked by horizontal lines in corresponding graphs. (b) F ST was calculated for lines with experimentally determined copy number (46 single copy vs. 48 multiple copy). Direction of telomere = ‘tel’. The mean and 95th percentile of whole-genome F ST are marked by horizontal lines. Red marks indicates statistical significance. (c) F ST between geographic subpopulations. One hundred and thirty-five single nucleotide polymorphisms were used to compare: Top graph, between 3311 germplasm accessions from Korea and 3855 from China; centre, between 3311 from Korea and 2466 from Japan; bottom, between 3855 from China and 2466 from Japan. The mean and 95th percentile values of whole-genome F ST are marked by a horizontal line in the corresponding graphs.
Figure Legend Snippet: Signatures of selection at the Rhg1 locus. (a) Nucleotide diversity (π and θ), Tajima's D and linkage disequilibrium were measured in the 1.5-Mbp region across the locus in 19 548 accessions (18 383 Glycine max 1165 Glycine soja ). The mean and 75th and 95th percentiles of whole-genome Tajima's D are marked by horizontal lines in corresponding graphs. (b) F ST was calculated for lines with experimentally determined copy number (46 single copy vs. 48 multiple copy). Direction of telomere = ‘tel’. The mean and 95th percentile of whole-genome F ST are marked by horizontal lines. Red marks indicates statistical significance. (c) F ST between geographic subpopulations. One hundred and thirty-five single nucleotide polymorphisms were used to compare: Top graph, between 3311 germplasm accessions from Korea and 3855 from China; centre, between 3311 from Korea and 2466 from Japan; bottom, between 3855 from China and 2466 from Japan. The mean and 95th percentile values of whole-genome F ST are marked by a horizontal line in the corresponding graphs.

Techniques Used: Selection

Diversity, linkage disequilibrium (LD) and sequence analysis of the region surrounding the Rhg1 locus. (a) Nucleotide diversity within 38 protein-coding genes surrounding Rhg1 in eighteen germplasm accessions (with 1–10 copies at Rhg1 ) is displayed in the uppermost graph. Those accessions with three copies (centre graph) and nine and ten copies (bottom graph) were also analysed separately. The average nucleotide diversity (π; 0.00053) of all coding regions in Glycine max is marked by a horizontal line. (b) LD plot using the r 2 metric for the 400-kb region surrounding the Rhg1 locus. The same 18 accessions were used. Regions S1, S2 and S3 represent three linkage blocks used in further analysis. tel: telomere. (c) Phylogenetic trees derived from parsimony analysis of the three LD blocks. The tree for the region of linkage block S2 that contains Rhg1 is consistent with the analysis of the repeat sequence (Fig. 2 ). The copy number of each accession is in parentheses. The consensus trees were created after collapsing branches with bootstrap values
Figure Legend Snippet: Diversity, linkage disequilibrium (LD) and sequence analysis of the region surrounding the Rhg1 locus. (a) Nucleotide diversity within 38 protein-coding genes surrounding Rhg1 in eighteen germplasm accessions (with 1–10 copies at Rhg1 ) is displayed in the uppermost graph. Those accessions with three copies (centre graph) and nine and ten copies (bottom graph) were also analysed separately. The average nucleotide diversity (π; 0.00053) of all coding regions in Glycine max is marked by a horizontal line. (b) LD plot using the r 2 metric for the 400-kb region surrounding the Rhg1 locus. The same 18 accessions were used. Regions S1, S2 and S3 represent three linkage blocks used in further analysis. tel: telomere. (c) Phylogenetic trees derived from parsimony analysis of the three LD blocks. The tree for the region of linkage block S2 that contains Rhg1 is consistent with the analysis of the repeat sequence (Fig. 2 ). The copy number of each accession is in parentheses. The consensus trees were created after collapsing branches with bootstrap values

Techniques Used: Sequencing, Derivative Assay, Blocking Assay

10) Product Images from "Evolution and selection of Rhg1, a copy-number variant nematode-resistance locus"

Article Title: Evolution and selection of Rhg1, a copy-number variant nematode-resistance locus

Journal: Molecular Ecology

doi: 10.1111/mec.13138

Parsimony tree of 15 996 soybean accessions with high confidence data at all single nucleotide polymorphisms (SNPs) in the S2 linkage disequilibrium block surrounding Rhg1 . The four terminal branches containing all germplasm accessions described elsewhere in the manuscript are labelled, together with the number of accessions carrying the same combination of SNPs.
Figure Legend Snippet: Parsimony tree of 15 996 soybean accessions with high confidence data at all single nucleotide polymorphisms (SNPs) in the S2 linkage disequilibrium block surrounding Rhg1 . The four terminal branches containing all germplasm accessions described elsewhere in the manuscript are labelled, together with the number of accessions carrying the same combination of SNPs.

Techniques Used: Blocking Assay

Signatures of selection at the Rhg1 locus. (a) Nucleotide diversity (π and θ), Tajima's D and linkage disequilibrium were measured in the 1.5-Mbp region across the locus in 19 548 accessions (18 383 Glycine max 1165 Glycine soja ). The mean and 75th and 95th percentiles of whole-genome Tajima's D are marked by horizontal lines in corresponding graphs. (b) F ST was calculated for lines with experimentally determined copy number (46 single copy vs. 48 multiple copy). Direction of telomere = ‘tel’. The mean and 95th percentile of whole-genome F ST are marked by horizontal lines. Red marks indicates statistical significance. (c) F ST between geographic subpopulations. One hundred and thirty-five single nucleotide polymorphisms were used to compare: Top graph, between 3311 germplasm accessions from Korea and 3855 from China; centre, between 3311 from Korea and 2466 from Japan; bottom, between 3855 from China and 2466 from Japan. The mean and 95th percentile values of whole-genome F ST are marked by a horizontal line in the corresponding graphs.
Figure Legend Snippet: Signatures of selection at the Rhg1 locus. (a) Nucleotide diversity (π and θ), Tajima's D and linkage disequilibrium were measured in the 1.5-Mbp region across the locus in 19 548 accessions (18 383 Glycine max 1165 Glycine soja ). The mean and 75th and 95th percentiles of whole-genome Tajima's D are marked by horizontal lines in corresponding graphs. (b) F ST was calculated for lines with experimentally determined copy number (46 single copy vs. 48 multiple copy). Direction of telomere = ‘tel’. The mean and 95th percentile of whole-genome F ST are marked by horizontal lines. Red marks indicates statistical significance. (c) F ST between geographic subpopulations. One hundred and thirty-five single nucleotide polymorphisms were used to compare: Top graph, between 3311 germplasm accessions from Korea and 3855 from China; centre, between 3311 from Korea and 2466 from Japan; bottom, between 3855 from China and 2466 from Japan. The mean and 95th percentile values of whole-genome F ST are marked by a horizontal line in the corresponding graphs.

Techniques Used: Selection

Diversity, linkage disequilibrium (LD) and sequence analysis of the region surrounding the Rhg1 locus. (a) Nucleotide diversity within 38 protein-coding genes surrounding Rhg1 in eighteen germplasm accessions (with 1–10 copies at Rhg1 ) is displayed in the uppermost graph. Those accessions with three copies (centre graph) and nine and ten copies (bottom graph) were also analysed separately. The average nucleotide diversity (π; 0.00053) of all coding regions in Glycine max is marked by a horizontal line. (b) LD plot using the r 2 metric for the 400-kb region surrounding the Rhg1 locus. The same 18 accessions were used. Regions S1, S2 and S3 represent three linkage blocks used in further analysis. tel: telomere. (c) Phylogenetic trees derived from parsimony analysis of the three LD blocks. The tree for the region of linkage block S2 that contains Rhg1 is consistent with the analysis of the repeat sequence (Fig. 2 ). The copy number of each accession is in parentheses. The consensus trees were created after collapsing branches with bootstrap values
Figure Legend Snippet: Diversity, linkage disequilibrium (LD) and sequence analysis of the region surrounding the Rhg1 locus. (a) Nucleotide diversity within 38 protein-coding genes surrounding Rhg1 in eighteen germplasm accessions (with 1–10 copies at Rhg1 ) is displayed in the uppermost graph. Those accessions with three copies (centre graph) and nine and ten copies (bottom graph) were also analysed separately. The average nucleotide diversity (π; 0.00053) of all coding regions in Glycine max is marked by a horizontal line. (b) LD plot using the r 2 metric for the 400-kb region surrounding the Rhg1 locus. The same 18 accessions were used. Regions S1, S2 and S3 represent three linkage blocks used in further analysis. tel: telomere. (c) Phylogenetic trees derived from parsimony analysis of the three LD blocks. The tree for the region of linkage block S2 that contains Rhg1 is consistent with the analysis of the repeat sequence (Fig. 2 ). The copy number of each accession is in parentheses. The consensus trees were created after collapsing branches with bootstrap values

Techniques Used: Sequencing, Derivative Assay, Blocking Assay

11) Product Images from "Evolution and selection of Rhg1, a copy-number variant nematode-resistance locus"

Article Title: Evolution and selection of Rhg1, a copy-number variant nematode-resistance locus

Journal: Molecular Ecology

doi: 10.1111/mec.13138

Parsimony tree of 15 996 soybean accessions with high confidence data at all single nucleotide polymorphisms (SNPs) in the S2 linkage disequilibrium block surrounding Rhg1 . The four terminal branches containing all germplasm accessions described elsewhere in the manuscript are labelled, together with the number of accessions carrying the same combination of SNPs.
Figure Legend Snippet: Parsimony tree of 15 996 soybean accessions with high confidence data at all single nucleotide polymorphisms (SNPs) in the S2 linkage disequilibrium block surrounding Rhg1 . The four terminal branches containing all germplasm accessions described elsewhere in the manuscript are labelled, together with the number of accessions carrying the same combination of SNPs.

Techniques Used: Blocking Assay

Signatures of selection at the Rhg1 locus. (a) Nucleotide diversity (π and θ), Tajima's D and linkage disequilibrium were measured in the 1.5-Mbp region across the locus in 19 548 accessions (18 383 Glycine max 1165 Glycine soja ). The mean and 75th and 95th percentiles of whole-genome Tajima's D are marked by horizontal lines in corresponding graphs. (b) F ST was calculated for lines with experimentally determined copy number (46 single copy vs. 48 multiple copy). Direction of telomere = ‘tel’. The mean and 95th percentile of whole-genome F ST are marked by horizontal lines. Red marks indicates statistical significance. (c) F ST between geographic subpopulations. One hundred and thirty-five single nucleotide polymorphisms were used to compare: Top graph, between 3311 germplasm accessions from Korea and 3855 from China; centre, between 3311 from Korea and 2466 from Japan; bottom, between 3855 from China and 2466 from Japan. The mean and 95th percentile values of whole-genome F ST are marked by a horizontal line in the corresponding graphs.
Figure Legend Snippet: Signatures of selection at the Rhg1 locus. (a) Nucleotide diversity (π and θ), Tajima's D and linkage disequilibrium were measured in the 1.5-Mbp region across the locus in 19 548 accessions (18 383 Glycine max 1165 Glycine soja ). The mean and 75th and 95th percentiles of whole-genome Tajima's D are marked by horizontal lines in corresponding graphs. (b) F ST was calculated for lines with experimentally determined copy number (46 single copy vs. 48 multiple copy). Direction of telomere = ‘tel’. The mean and 95th percentile of whole-genome F ST are marked by horizontal lines. Red marks indicates statistical significance. (c) F ST between geographic subpopulations. One hundred and thirty-five single nucleotide polymorphisms were used to compare: Top graph, between 3311 germplasm accessions from Korea and 3855 from China; centre, between 3311 from Korea and 2466 from Japan; bottom, between 3855 from China and 2466 from Japan. The mean and 95th percentile values of whole-genome F ST are marked by a horizontal line in the corresponding graphs.

Techniques Used: Selection

Diversity, linkage disequilibrium (LD) and sequence analysis of the region surrounding the Rhg1 locus. (a) Nucleotide diversity within 38 protein-coding genes surrounding Rhg1 in eighteen germplasm accessions (with 1–10 copies at Rhg1 ) is displayed in the uppermost graph. Those accessions with three copies (centre graph) and nine and ten copies (bottom graph) were also analysed separately. The average nucleotide diversity (π; 0.00053) of all coding regions in Glycine max is marked by a horizontal line. (b) LD plot using the r 2 metric for the 400-kb region surrounding the Rhg1 locus. The same 18 accessions were used. Regions S1, S2 and S3 represent three linkage blocks used in further analysis. tel: telomere. (c) Phylogenetic trees derived from parsimony analysis of the three LD blocks. The tree for the region of linkage block S2 that contains Rhg1 is consistent with the analysis of the repeat sequence (Fig. 2 ). The copy number of each accession is in parentheses. The consensus trees were created after collapsing branches with bootstrap values
Figure Legend Snippet: Diversity, linkage disequilibrium (LD) and sequence analysis of the region surrounding the Rhg1 locus. (a) Nucleotide diversity within 38 protein-coding genes surrounding Rhg1 in eighteen germplasm accessions (with 1–10 copies at Rhg1 ) is displayed in the uppermost graph. Those accessions with three copies (centre graph) and nine and ten copies (bottom graph) were also analysed separately. The average nucleotide diversity (π; 0.00053) of all coding regions in Glycine max is marked by a horizontal line. (b) LD plot using the r 2 metric for the 400-kb region surrounding the Rhg1 locus. The same 18 accessions were used. Regions S1, S2 and S3 represent three linkage blocks used in further analysis. tel: telomere. (c) Phylogenetic trees derived from parsimony analysis of the three LD blocks. The tree for the region of linkage block S2 that contains Rhg1 is consistent with the analysis of the repeat sequence (Fig. 2 ). The copy number of each accession is in parentheses. The consensus trees were created after collapsing branches with bootstrap values

Techniques Used: Sequencing, Derivative Assay, Blocking Assay

12) Product Images from "Evolution and selection of Rhg1, a copy-number variant nematode-resistance locus"

Article Title: Evolution and selection of Rhg1, a copy-number variant nematode-resistance locus

Journal: Molecular Ecology

doi: 10.1111/mec.13138

Parsimony tree of 15 996 soybean accessions with high confidence data at all single nucleotide polymorphisms (SNPs) in the S2 linkage disequilibrium block surrounding Rhg1 . The four terminal branches containing all germplasm accessions described elsewhere in the manuscript are labelled, together with the number of accessions carrying the same combination of SNPs.
Figure Legend Snippet: Parsimony tree of 15 996 soybean accessions with high confidence data at all single nucleotide polymorphisms (SNPs) in the S2 linkage disequilibrium block surrounding Rhg1 . The four terminal branches containing all germplasm accessions described elsewhere in the manuscript are labelled, together with the number of accessions carrying the same combination of SNPs.

Techniques Used: Blocking Assay

Signatures of selection at the Rhg1 locus. (a) Nucleotide diversity (π and θ), Tajima's D and linkage disequilibrium were measured in the 1.5-Mbp region across the locus in 19 548 accessions (18 383 Glycine max 1165 Glycine soja ). The mean and 75th and 95th percentiles of whole-genome Tajima's D are marked by horizontal lines in corresponding graphs. (b) F ST was calculated for lines with experimentally determined copy number (46 single copy vs. 48 multiple copy). Direction of telomere = ‘tel’. The mean and 95th percentile of whole-genome F ST are marked by horizontal lines. Red marks indicates statistical significance. (c) F ST between geographic subpopulations. One hundred and thirty-five single nucleotide polymorphisms were used to compare: Top graph, between 3311 germplasm accessions from Korea and 3855 from China; centre, between 3311 from Korea and 2466 from Japan; bottom, between 3855 from China and 2466 from Japan. The mean and 95th percentile values of whole-genome F ST are marked by a horizontal line in the corresponding graphs.
Figure Legend Snippet: Signatures of selection at the Rhg1 locus. (a) Nucleotide diversity (π and θ), Tajima's D and linkage disequilibrium were measured in the 1.5-Mbp region across the locus in 19 548 accessions (18 383 Glycine max 1165 Glycine soja ). The mean and 75th and 95th percentiles of whole-genome Tajima's D are marked by horizontal lines in corresponding graphs. (b) F ST was calculated for lines with experimentally determined copy number (46 single copy vs. 48 multiple copy). Direction of telomere = ‘tel’. The mean and 95th percentile of whole-genome F ST are marked by horizontal lines. Red marks indicates statistical significance. (c) F ST between geographic subpopulations. One hundred and thirty-five single nucleotide polymorphisms were used to compare: Top graph, between 3311 germplasm accessions from Korea and 3855 from China; centre, between 3311 from Korea and 2466 from Japan; bottom, between 3855 from China and 2466 from Japan. The mean and 95th percentile values of whole-genome F ST are marked by a horizontal line in the corresponding graphs.

Techniques Used: Selection

Diversity, linkage disequilibrium (LD) and sequence analysis of the region surrounding the Rhg1 locus. (a) Nucleotide diversity within 38 protein-coding genes surrounding Rhg1 in eighteen germplasm accessions (with 1–10 copies at Rhg1 ) is displayed in the uppermost graph. Those accessions with three copies (centre graph) and nine and ten copies (bottom graph) were also analysed separately. The average nucleotide diversity (π; 0.00053) of all coding regions in Glycine max is marked by a horizontal line. (b) LD plot using the r 2 metric for the 400-kb region surrounding the Rhg1 locus. The same 18 accessions were used. Regions S1, S2 and S3 represent three linkage blocks used in further analysis. tel: telomere. (c) Phylogenetic trees derived from parsimony analysis of the three LD blocks. The tree for the region of linkage block S2 that contains Rhg1 is consistent with the analysis of the repeat sequence (Fig. 2 ). The copy number of each accession is in parentheses. The consensus trees were created after collapsing branches with bootstrap values
Figure Legend Snippet: Diversity, linkage disequilibrium (LD) and sequence analysis of the region surrounding the Rhg1 locus. (a) Nucleotide diversity within 38 protein-coding genes surrounding Rhg1 in eighteen germplasm accessions (with 1–10 copies at Rhg1 ) is displayed in the uppermost graph. Those accessions with three copies (centre graph) and nine and ten copies (bottom graph) were also analysed separately. The average nucleotide diversity (π; 0.00053) of all coding regions in Glycine max is marked by a horizontal line. (b) LD plot using the r 2 metric for the 400-kb region surrounding the Rhg1 locus. The same 18 accessions were used. Regions S1, S2 and S3 represent three linkage blocks used in further analysis. tel: telomere. (c) Phylogenetic trees derived from parsimony analysis of the three LD blocks. The tree for the region of linkage block S2 that contains Rhg1 is consistent with the analysis of the repeat sequence (Fig. 2 ). The copy number of each accession is in parentheses. The consensus trees were created after collapsing branches with bootstrap values

Techniques Used: Sequencing, Derivative Assay, Blocking Assay

Related Articles

Sequencing:

Article Title: Evolution and selection of Rhg1, a copy-number variant nematode-resistance locus
Article Snippet: .. Table S3 A total of 15 996 soybean germplasm accessions clustered by maximum parsimony phylogenetic analysis of the sequence region near the Rhg1 allele, indicating germplasm accessions predicted to carry Rhg1 . ..

Article Title: Evolution and selection of Rhg1, a copy-number variant nematode-resistance locus
Article Snippet: .. Repeat composition of different Rhg1 alleles By combining data on the frequency of sequence variants in different germplasm accessions with different repeat composition ( b, Supporting information) and using Sanger sequencing ( c, Supporting information) to confirm the presence of SNP variants, the composition of repeat subtypes within each Rhg1 allele was estimated (Fig. c). ..

Article Title: Evolution and selection of Rhg1, a copy-number variant nematode-resistance locus
Article Snippet: .. A total of ten SNPs, nine located in sequence region S2 in Fig. and one within the Rhg1 repeat unit, formed 89 distinct combinations among 15 996 germplasm accessions (all accessions with high confidence data for all ten SNPs; Fig. ; , Supporting information). ..

other:

Article Title: Evolution and selection of Rhg1, a copy-number variant nematode-resistance locus
Article Snippet: Clustering of germplasm accessions from the much larger Infinium data set was performed using parsimonator version 1.0.2 ( https://github.com/stamatak/Parsimonator-1.0.2 ).

Article Title: Evolution and selection of Rhg1, a copy-number variant nematode-resistance locus
Article Snippet: Of these, a set of 19 548 germplasm accessions with high-quality, mono-allelic SNP analysis results was used as the main data set (hereafter, Infinium data).

Article Title: Evolution and selection of Rhg1, a copy-number variant nematode-resistance locus
Article Snippet: The germplasm accessions in the WGS data are as follows: three single-copy germplasm accessions (Williams 82, PI 427136, & PI 518751), one 2 copy (PI 438489 B), three 3 copy (PI 467327, Peking, & PI 89772), one 4 copy (PI 89008), three 6 copy (PI 87631-1, PI 461509, & PI 467332), two 7 copy (PI 92720 & Cloud), one 9 copy (PI 88788) and four 10 copy (PI 209332, LD10-30036, LD09-15087a, & LD00-3309).

Article Title: Evolution and selection of Rhg1, a copy-number variant nematode-resistance locus
Article Snippet: Relationship between CNV and SCN resistance reactions We selected nine germplasm accessions with validated CNVs at the Rhg1 locus where complete data for resistance to diverse SCN types are available ( , Supporting information).

Selection:

Article Title: Evolution and selection of Rhg1, a copy-number variant nematode-resistance locus
Article Snippet: .. Wild soybean G. soja , also showed a very similar selection signature to the whole population of germplasm accessions (bottom graph in Fig. a). ..

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    Parsimony tree of 15 996 soybean accessions with high confidence data at all single nucleotide polymorphisms (SNPs) in the S2 linkage disequilibrium block surrounding Rhg1 . The four terminal branches containing all <t>germplasm</t> accessions described elsewhere in the manuscript are labelled, together with the number of accessions carrying the same combination of SNPs.
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    Parsimony tree of 15 996 soybean accessions with high confidence data at all single nucleotide polymorphisms (SNPs) in the S2 linkage disequilibrium block surrounding Rhg1 . The four terminal branches containing all germplasm accessions described elsewhere in the manuscript are labelled, together with the number of accessions carrying the same combination of SNPs.

    Journal: Molecular Ecology

    Article Title: Evolution and selection of Rhg1, a copy-number variant nematode-resistance locus

    doi: 10.1111/mec.13138

    Figure Lengend Snippet: Parsimony tree of 15 996 soybean accessions with high confidence data at all single nucleotide polymorphisms (SNPs) in the S2 linkage disequilibrium block surrounding Rhg1 . The four terminal branches containing all germplasm accessions described elsewhere in the manuscript are labelled, together with the number of accessions carrying the same combination of SNPs.

    Article Snippet: Of these, a set of 19 548 germplasm accessions with high-quality, mono-allelic SNP analysis results was used as the main data set (hereafter, Infinium data).

    Techniques: Blocking Assay

    Signatures of selection at the Rhg1 locus. (a) Nucleotide diversity (π and θ), Tajima's D and linkage disequilibrium were measured in the 1.5-Mbp region across the locus in 19 548 accessions (18 383 Glycine max 1165 Glycine soja ). The mean and 75th and 95th percentiles of whole-genome Tajima's D are marked by horizontal lines in corresponding graphs. (b) F ST was calculated for lines with experimentally determined copy number (46 single copy vs. 48 multiple copy). Direction of telomere = ‘tel’. The mean and 95th percentile of whole-genome F ST are marked by horizontal lines. Red marks indicates statistical significance. (c) F ST between geographic subpopulations. One hundred and thirty-five single nucleotide polymorphisms were used to compare: Top graph, between 3311 germplasm accessions from Korea and 3855 from China; centre, between 3311 from Korea and 2466 from Japan; bottom, between 3855 from China and 2466 from Japan. The mean and 95th percentile values of whole-genome F ST are marked by a horizontal line in the corresponding graphs.

    Journal: Molecular Ecology

    Article Title: Evolution and selection of Rhg1, a copy-number variant nematode-resistance locus

    doi: 10.1111/mec.13138

    Figure Lengend Snippet: Signatures of selection at the Rhg1 locus. (a) Nucleotide diversity (π and θ), Tajima's D and linkage disequilibrium were measured in the 1.5-Mbp region across the locus in 19 548 accessions (18 383 Glycine max 1165 Glycine soja ). The mean and 75th and 95th percentiles of whole-genome Tajima's D are marked by horizontal lines in corresponding graphs. (b) F ST was calculated for lines with experimentally determined copy number (46 single copy vs. 48 multiple copy). Direction of telomere = ‘tel’. The mean and 95th percentile of whole-genome F ST are marked by horizontal lines. Red marks indicates statistical significance. (c) F ST between geographic subpopulations. One hundred and thirty-five single nucleotide polymorphisms were used to compare: Top graph, between 3311 germplasm accessions from Korea and 3855 from China; centre, between 3311 from Korea and 2466 from Japan; bottom, between 3855 from China and 2466 from Japan. The mean and 95th percentile values of whole-genome F ST are marked by a horizontal line in the corresponding graphs.

    Article Snippet: Of these, a set of 19 548 germplasm accessions with high-quality, mono-allelic SNP analysis results was used as the main data set (hereafter, Infinium data).

    Techniques: Selection

    Diversity, linkage disequilibrium (LD) and sequence analysis of the region surrounding the Rhg1 locus. (a) Nucleotide diversity within 38 protein-coding genes surrounding Rhg1 in eighteen germplasm accessions (with 1–10 copies at Rhg1 ) is displayed in the uppermost graph. Those accessions with three copies (centre graph) and nine and ten copies (bottom graph) were also analysed separately. The average nucleotide diversity (π; 0.00053) of all coding regions in Glycine max is marked by a horizontal line. (b) LD plot using the r 2 metric for the 400-kb region surrounding the Rhg1 locus. The same 18 accessions were used. Regions S1, S2 and S3 represent three linkage blocks used in further analysis. tel: telomere. (c) Phylogenetic trees derived from parsimony analysis of the three LD blocks. The tree for the region of linkage block S2 that contains Rhg1 is consistent with the analysis of the repeat sequence (Fig. 2 ). The copy number of each accession is in parentheses. The consensus trees were created after collapsing branches with bootstrap values

    Journal: Molecular Ecology

    Article Title: Evolution and selection of Rhg1, a copy-number variant nematode-resistance locus

    doi: 10.1111/mec.13138

    Figure Lengend Snippet: Diversity, linkage disequilibrium (LD) and sequence analysis of the region surrounding the Rhg1 locus. (a) Nucleotide diversity within 38 protein-coding genes surrounding Rhg1 in eighteen germplasm accessions (with 1–10 copies at Rhg1 ) is displayed in the uppermost graph. Those accessions with three copies (centre graph) and nine and ten copies (bottom graph) were also analysed separately. The average nucleotide diversity (π; 0.00053) of all coding regions in Glycine max is marked by a horizontal line. (b) LD plot using the r 2 metric for the 400-kb region surrounding the Rhg1 locus. The same 18 accessions were used. Regions S1, S2 and S3 represent three linkage blocks used in further analysis. tel: telomere. (c) Phylogenetic trees derived from parsimony analysis of the three LD blocks. The tree for the region of linkage block S2 that contains Rhg1 is consistent with the analysis of the repeat sequence (Fig. 2 ). The copy number of each accession is in parentheses. The consensus trees were created after collapsing branches with bootstrap values

    Article Snippet: Of these, a set of 19 548 germplasm accessions with high-quality, mono-allelic SNP analysis results was used as the main data set (hereafter, Infinium data).

    Techniques: Sequencing, Derivative Assay, Blocking Assay