# Scientific Objectives and Experimental Design ### Phenotyping The TERRA-REF project is phenotyping the same genotypes of sorghum at multiple locations * Automated Lemnatec Scanalyzer Field System at [Maricopa Agricultural Center ](/revisions/scientific-objectives-and-experimental-design/experimental-design/experimental-design-mac.md)(MAC) * [PhenoTractors ](/revisions/scientific-objectives-and-experimental-design/protocols/phenotractor-protocols.md)on parallel plots at [MAC ](/revisions/scientific-objectives-and-experimental-design/experimental-design/experimental-design-mac.md)and Kansas State University (KSU) * [UAV ](/revisions/scientific-objectives-and-experimental-design/protocols/uav-protocols.md)platform on parallel plots at KSU * [Controlled-environment phenotyping systems](/revisions/scientific-objectives-and-experimental-design/protocols/controlled-environment-protocols.md) at the [Danforth Center](/revisions/scientific-objectives-and-experimental-design/experimental-design/experimental-design-danforth.md) * [Manually collected field data](/revisions/scientific-objectives-and-experimental-design/protocols/manual-field-data-protocols.md) at all locations ### Genotyping [Whole genome resequencing](/revisions/scientific-objectives-and-experimental-design/experimental-design/experimental-design-genomics.md) is being carried out on \~[400 sorghum accessions](/revisions/scientific-objectives-and-experimental-design/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. ## Maricopa Agricultural Center (MAC), Arizona Three hundred thirty one [lines were planted in 2016](https://docs.google.com/spreadsheets/d/1Nfabx_n1rNlO6NW3olD8MAibJ3KHnOMmMwOYYw4wwGc/pubhtml?gid=239932660\&single=true\&widget=true\&headers=false). Plantings occurred both under and west of the gantry system. * [Experiments planned for 2016](https://docs.google.com/spreadsheets/d/1Nfabx_n1rNlO6NW3olD8MAibJ3KHnOMmMwOYYw4wwGc/pubhtml?gid=890543376\&single=true\&widget=true\&headers=false) * Field layouts [under the gantry](https://docs.google.com/spreadsheets/d/1Nfabx_n1rNlO6NW3olD8MAibJ3KHnOMmMwOYYw4wwGc/pubhtml?gid=1231399646\&single=true\&widget=true\&headers=false) and [west of the gantry](https://docs.google.com/spreadsheets/d/1Nfabx_n1rNlO6NW3olD8MAibJ3KHnOMmMwOYYw4wwGc/pubhtml?gid=728631369\&single=true\&widget=true\&headers=false) in 2016. ### Automated Field Scanner System The [Lemnatec Scanalyzer Field Scanner System](http://www.lemnatec.com/products/hardware-solutions/scanalyzer-field/) is the largest field crop analytics robot in the world. This high-throughput phenotyping field-scanning robot has a 30-ton steel gantry that autonomously moves along two 200-meter steel rails while continuously imaging the crops growing below it with a diverse array of [cameras and sensors](http://terraref.org/articles/lemnatec-scanalyzer-field-sensors/). Twelve sensors are attached to the system. Detailed information for each sensor including name, variable measured, and field of view are [available here](https://docs.google.com/spreadsheets/d/1Nfabx_n1rNlO6NW3olD8MAibJ3KHnOMmMwOYYw4wwGc/pubhtml?gid=1886254108\&single=true\&widget=true\&headers=false). The planned sensor missions and their objectives for 2016 are [available here](https://docs.google.com/spreadsheets/d/1Nfabx_n1rNlO6NW3olD8MAibJ3KHnOMmMwOYYw4wwGc/pubhtml?gid=2092320800\&single=true\&widget=true\&headers=false). ### Phenotractor The PhenoTractor at MAC is fitted with a sensor frame that supports a real time kinematic (RTK) satellite navigation antenna, a sonar transducer, an infrared temperature (IRT) scanner, and [three GreenSeeker crop sensing systems](https://www.gitbook.com/book/terraref/terraref-documentation/edit). ### UAV Coming 2017 ### Manually collected field data In progress ## Automated controlled-environment phenotyping, Missouri The Scanalyzer 3D platform at the [Bellwether Foundation Phenotyping Facility at the Donald Danforth Plant Science Center ](https://www.danforthcenter.org/scientists-research/core-technologies/phenotyping)consists of multiple digital imaging chambers connected to the Conviron growth house by a conveyor belt system, resulting in a continuous imaging loop. Plants are imaged from the top and/or multiple sides, followed by digital construction of images for analysis. * RGB imaging allows visualization and quantification of plant color and structural morphology, such as leaf area, stem diameter and plant height. * NIR imaging enables visualization of water distribution in plants in the near infrared spectrum of 900–1700 nm. * Fluorescent imaging uses red light excitation to visualize chlorophyll fluorescence between 680 – 900 nm. The system is equipped with a dark adaptation tunnel preceding the fluorescent imaging chamber, allowing the analysis of photosystem II efficiency. The LemnaTec software suite is used to program and control the Scanalyzer platform, analyze the digital images and mine resulting data. Data and images are saved and stored on a secure server for further review or reanalysis. ## Kansas State University * **PhenoTractor** - Coming 2017 * **UAV** - Coming 2017 * **Manually collected field data** - Coming 2017 ## HudsonAlpha - Genomics * Coming 2017 --- # Agent Instructions: Querying This Documentation If you need additional information that is not directly available in this page, you can query the documentation dynamically by asking a question. Perform an HTTP GET request on the current page URL with the `ask` query parameter: ``` GET https://docs.terraref.org/revisions/scientific-objectives-and-experimental-design.md?ask= ``` The question should be specific, self-contained, and written in natural language. The response will contain a direct answer to the question and relevant excerpts and sources from the documentation. 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