> 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.md).

# Experimental Design

## Overview

### Phenotyping

The TERRA-REF project is collecting phenotype data from 852 sorghum genotypes grown in three locations:

* [Maricopa Agricultural Center (MAC), Maricopa, Arizona](/experimental-design/experimental-design-mac.md)
* Kansas State University (KSU), Ashland, KS
* [Donald Danforth Plant Science Center, Missouri](/experimental-design/experimental-design-danforth.md)

| Data source                                                            | MAC | KSU | Danforth |
| ---------------------------------------------------------------------- | --- | --- | -------- |
| Scanalyzer Field System                                                | X   |     |          |
| [Scanalyzer 3D System](/protocols/controlled-environment-protocols.md) |     |     | X        |
| [Phenotractor](/protocols/phenotractor-protocols.md)                   | X   | X   |          |
| [UAV (drone)](/protocols/uav-protocols.md)                             | X   | X   |          |
| [Manual field data](/protocols/manual-field-data-protocols.md)         | X   | X   |          |

### Genotyping

[Whole genome resequencing](https://app.gitbook.com/s/-L9HQFTifPjun_Gj6_At-887967055/experimental-design/experimental-design-genomics/) is being carried out on \~[400 sorghum accessions](https://app.gitbook.com/s/-L9HQFTifPjun_Gj6_At-887967055/experimental-design/experimental-design-genomics/sorghum-lines-genomics-year-1.md) 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](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.