The data displayed in this applet is derived from next generation sequencing of 120 soybean lines. Seventy-nine new lines were sequenced as part of this project and represent plant introductions and milestone cultivars. The remaining sequences represent the 41 parents used for developing the soybean NAM population. NAM parent sequences were provided by Dr. Perry Cregan (USDA-ARS) and the Soybean NAM project. For the new sequences generated by this project, twenty seeds from each line were acquired from the USDA Soybean Germplasm Collection. Seeds were planted in the USDA greenhouse at Iowa State University. Once plants reached the trifoliolate stage, leaves from up to 10 plants were pooled and genomic DNA was extracted. DNA was sent to Hudson Alpha Institute for Biotechnology for next-generation sequencing. In addition, replicated field trials were conducted on a subset of lines (30 of the 79 lines, plus ancestral varieties that were not sequenced) to measure protein, oil, yield, and other characteristics under standard growth conditions, to dissociate the effect of on-farm improvements from genetic gain ,.
MarkDuplicatesfunctions in picard tools.
IndelRealignerfunction in GATK . The
ReduceReadsfunction was used to compress the alignment files by removing non-informative and redundant reads (default parameters except for downsample_coverage=1).
HaplotypeCallerfunction in GATK (version 2.7-2-g6bda569).
SNPS displayed in this applet are reliable SNPs from 120 lines. 86944 unique SNPs were identified for further analysis.
The lines included in this analysis are:
Need to delineate "reliable" criterion.
Kinship matrices were generated with TASSEL  using a subset of the SNP data, where one random SNP was taken from every 10,000 base interval in the genome or the next closest SNP (Supplementary Script 1).
These matrices were then clustered using Ward's method, using the distance (2- similarity). Clusters were used to lay out the rows and columns of the heatmap.
The clusters were then formatted for plotting and plotted using ggplot2.
Need more detail here from Andrew. Also, need QTL results?
Using the combined, phased and imputed VCF file generated as a result of the SNP sampling, the following steps are performed.
Plots in this applet were generated using ggplot2 , and are rendered interactively using Shiny .
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