> For the complete documentation index, see [llms.txt](https://docs.terraref.org/llms.txt). Markdown versions of documentation pages are available by appending `.md` to page URLs; this page is available as [Markdown](https://docs.terraref.org/experimental-design/experimental-design-genomics.md).

# Genomics

[Whole genome resequencing](/experimental-design/experimental-design-genomics.md) was 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) were characterized with \~400,000 genetic markers using genotyping-by-sequencing ([Morris et al., 2013](http://www.g3journal.org/content/early/2013/09/13/g3.113.008417)) for trait dissection in the RIL population and testcross hybrids of the RIL population.

## Whole-genome resequencing

**Experimental Design:**

* 384 BAP samples were sequenced to an average depth of \~25x.
  * [List of BAP accessions in BETYdb](https://terraref.org/bety/api/v1/cultivars?ecotype=BAP)
* 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](/protocols/genomic-data.md) at the Danforth Center. 
* Data were aligned against the BTx623 reference genotype
  * NCBI <https://www.ncbi.nlm.nih.gov/assembly/GCF_000003195.3/>
  * Phytozome <https://phytozome.jgi.doe.gov/pz/portal.html#!info?alias=Org_Sbicolor>

## Genotyping-by-sequencing

**Experimental Design:**

* [768 RIL samples](https://terraref.org/bety/api/v1/cultivars?ecotype=RIL) were sequenced using a GBS approach.

## See Also

* [Genomics Protocols](/user-manual/data-products/genomics-data.md)
* [Genomics Data Availability](/user-manual/data-products/genomics-data.md)

###