Whole genome resequencing is being carried out on ~400 sorghum accessions to understand the landscape of genetic variation in the selected germplasm and enable high-resolution mapping of bioenergy traits with genome wide association studies (GWAS). Additionally, ~200 sorghum recombinant inbred lines (RILs) will be characterized with ~400,000 genetic markers using genotyping-by-sequencing (Morris et al., 2013) for trait dissection in the RIL population and testcross hybrids of the RIL population.
Shotgun sequencing (127-bp paired-end) was done using an Illumina X10 instrument at the HudsonAlpha Institute for Biotechnology.
Variant calling was done using a computational pipeline at the Danforth Center.
768 RIL samples were sequenced using a GBS approach.
These data are available in the CyVerse Data Commons
CoGe has integrated the tools that make up the Danforth Center’s variant calling pipeline into their easy point and click GUI, allowing users to reproduce a majority of the TERRA SNP analysis. Below, we detail how to run sequence data through CoGe’s system.