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Figure 2. Number of SNPs detected from empirical ddRAD-Seq analysis

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Presentation on theme: "Figure 2. Number of SNPs detected from empirical ddRAD-Seq analysis"— Presentation transcript:

1 Figure 2. Number of SNPs detected from empirical ddRAD-Seq analysis
Figure 2. Number of SNPs detected from empirical ddRAD-Seq analysis. Line chart indicates numbers of SNPs between Micro-Tom and Regina with four combinations of restriction enzymes (A) and SNPs of six cultivars with respect to SL2.50 using the PstI/MspI combination (B). From: Analytical workflow of double-digest restriction site-associated DNA sequencing based on empirical and in silico optimization in tomato DNA Res. 2016;23(2): doi: /dnares/dsw004 DNA Res | © The Author Published by Oxford University Press on behalf of Kazusa DNA Research Institute.This is an Open Access article distributed under the terms of the Creative Commons Attribution License ( which permits unrestricted reuse, distribution, and reproduction in any medium, provided the original work is properly cited.

2 Figure 1. Numbers of restriction sites and restriction fragments in the tomato genome (SL2.50). Bars indicate the numbers of restriction sites (A) and 300–900 bp restriction fragments (B) predicted from the SL2.50 tomato genome sequence by in silico analysis. From: Analytical workflow of double-digest restriction site-associated DNA sequencing based on empirical and in silico optimization in tomato DNA Res. 2016;23(2): doi: /dnares/dsw004 DNA Res | © The Author Published by Oxford University Press on behalf of Kazusa DNA Research Institute.This is an Open Access article distributed under the terms of the Creative Commons Attribution License ( which permits unrestricted reuse, distribution, and reproduction in any medium, provided the original work is properly cited.

3 Figure 3. Proportions of SNPs detected from empirical ddRAD-Seq analysis. SNPs from empirical ddRAD-Seq libraries are distributed in genic and intergenic regions (A) and repeat and non-repeat sequences (B). Proportions of SNPs between Micro-Tom and Regina (MT vs REG) detected from WGS data is shown as a control. From: Analytical workflow of double-digest restriction site-associated DNA sequencing based on empirical and in silico optimization in tomato DNA Res. 2016;23(2): doi: /dnares/dsw004 DNA Res | © The Author Published by Oxford University Press on behalf of Kazusa DNA Research Institute.This is an Open Access article distributed under the terms of the Creative Commons Attribution License ( which permits unrestricted reuse, distribution, and reproduction in any medium, provided the original work is properly cited.

4 Figure 4. Genetic linkage maps of RMF2, an F<sub>2</sub> population derived from a cross between Micro-Tom and Regina. Bars on the left and right sides indicate linkage group maps based on SNP loci detected in the tomato reference genome (red lines) and a de novo assembly of ddRAD-Seq data (blue lines). Bars between the two maps indicate the physical map of the tomato genome. The density of SNPs detected using WGS data for the two cultivars is indicated by the darkness of green lines. Loci that are identical between the genetic and physical maps are connected by lines. From: Analytical workflow of double-digest restriction site-associated DNA sequencing based on empirical and in silico optimization in tomato DNA Res. 2016;23(2): doi: /dnares/dsw004 DNA Res | © The Author Published by Oxford University Press on behalf of Kazusa DNA Research Institute.This is an Open Access article distributed under the terms of the Creative Commons Attribution License ( which permits unrestricted reuse, distribution, and reproduction in any medium, provided the original work is properly cited.

5 Figure 5. The ddRAD-Seq analytical workflow based on empirical and in silico optimization.
From: Analytical workflow of double-digest restriction site-associated DNA sequencing based on empirical and in silico optimization in tomato DNA Res. 2016;23(2): doi: /dnares/dsw004 DNA Res | © The Author Published by Oxford University Press on behalf of Kazusa DNA Research Institute.This is an Open Access article distributed under the terms of the Creative Commons Attribution License ( which permits unrestricted reuse, distribution, and reproduction in any medium, provided the original work is properly cited.

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