Figure 1.
Adapter Design, PCR amplification of fragments.
1) The ligation product of a genomic DNA fragment (black) containing a PstI restriction site and a MspI restriction site. The forward adapter (blue) binds to a PstI generated overhang. The 4–9 bp barcode for this adapter is in bold with “X”. The MspI generated overhang corresponds to the reverse Y-adapter (green). The unpaired tail of the Y-adapter is underlined. 2) During the first round of PCR only the forward primer (red) can anneal. PCR synthesis of the complementary strand proceeds to the end of the fragment synthesizing the compliment of the Y-adapter tail. 3) During the second round of PCR the reverse primer (orange) can anneal to the newly synthesized compliment of the Y-adapter tail. This PCR reaction then proceeds to fill in the compliment of the forward adapter/primer on the other end of the same fragment.
Figure 2.
Distribution of GBS SNP markers in the Oregon Wolfe Barley (OWB) bin map.
Histogram showing the number of markers from the set of GBS SNPs mapping to each bin in the OWB bin map. The number of SNPs mapping to a single bin is shown by the height of the blue bars. Additional markers that could not be placed in a single bin are show in grey. If a marker mapped to more than one bin (due to missing data), that marker was attributed to its middle bin. Bins that did not have definitive placement of any GBS SNP marker are noted with a red triangle below the plot.
Figure 3.
Histogram of number of markers in the three wheat genomes for DArT and GBS SNP genetic maps.
A) The number of markers assigned to each genome from the DArT genetic map [25] and B) the number of markers in each genome from the de novo genetic map constructed using GBS SNP markers and the AntMap Algorithm. C) The total number of SNPs assigned to each genome using the bin mapping approach in SynOpDH (note different units on vertical axis).
Figure 4.
Marker number per chromosome correlates with physical chromosome size.
The size of each hexaploid wheat chromosome [28] was compared with the number of genotyping-by-sequencing SNP markers on that respective chromosome. Using AntMap the de novo constructed map has 1,485 GBS SNP markers while the full set of mapped GBS markers is 19,720. The correlation coefficient between the marker number and the chromosome size is shown in the upper left of each graph. The legend shows the color-coding for chromosomes from each genome.
Figure 5.
Example of placement of GBS SNP markers into genetic bins of the double haploid mapping populations.
A) A GBS SNP without missing data will be precisely placed when all bin genotypes are known (Bin 4). B) When the bin genotypes are “unresolved” (i.e. there is no informative marker in that genetic bin, then a GBS SNP without missing data can again be placed into a single recombination bin in a two step process (Bin 3). C) In the case of missing data in the GBS SNP a range of possible bins (Bin 3–4) were assigned to that GBS SNP.