TERRA-REF Documentation
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Primary version
  • Introduction
  • Scientific Objectives
  • Experimental Design
    • The Maricopa Agricultural Center (MAC)
    • Controlled Environment Phenotyping
    • Genomics
  • Data
    • How to Access Data
    • Data Products
      • Environmental conditions
      • Phenotype Data
      • Genomics data
      • Fluorescence intensity imaging
      • Geospatial information
      • Hyperspectral imaging data
      • Infrared heat imaging data
      • Meteorological data
      • Point Cloud Data
      • Controlled Environment phenotype data
    • Data Use Policy
    • Manuscripts and Authorship Guidelines
  • Protocols
    • Field Scanner
    • Sensor Calibration
    • Hyperspectral Data
    • Controlled Environment Protocols
    • Manual Field Data Protocols
    • Phenotractor Protocols
    • UAV Protocols
    • Genomic Protocols
  • Technical Documentation
    • Software
    • Data Standards
      • Existing Data Standards
      • Agronomic and Phenotype Data Standards
      • Genomic Data Standards
      • Sensor Data Standards
      • Data Standards Committee
    • Data Product Levels
    • Directory Structure
    • Data Transfer
    • Data Processing Pipeline
    • Time Series Data in Geostreams
    • Data Backup
    • Systems Configuration
  • Code of Conduct
  • Appendix
    • Glossary
    • Accessing BETYdb with GIS Software
  • References
  • Archived Documentation
    • Developer Manual
      • Submitting data to Clowder
      • Submitting data to BETYdb
      • Submitting Data to CoGe
      • Developing Clowder Extractors
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  • Whole-genome resequencing
  • Genotyping-by-sequencing
  • See Also
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  1. Experimental Design

Genomics

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Last updated 5 years ago

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 () 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.

  • 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 at the Danforth Center.

  • Data were aligned against the BTx623 reference genotype

    • NCBI

    • Phytozome

Genotyping-by-sequencing

Experimental Design:

  • were sequenced using a GBS approach.

See Also

Whole genome resequencing
Morris et al., 2013
List of BAP accessions in BETYdb
computational pipeline
https://www.ncbi.nlm.nih.gov/assembly/GCF_000003195.3/
https://phytozome.jgi.doe.gov/pz/portal.html#!info?alias=Org_Sbicolor
768 RIL samples
Genomics Protocols
Genomics Data Availability