Guided Phenotype Upload Workflow



  1. Intro
  2. Breeding Program
  3. Locations
  4. Accessions
  5. Trials
  6. Observations
  7. Finish
  1. Introduction

    This workflow will guide your through the basic steps required for adding one or more phenotyping / field trials to the database:



    Download Templates  


  2. Breeding Program(s)

    Trials are associated with a single Breeding Program. Before a Trial can be added, the Breeding Program must already exist in the database.

    Check the table below to see if your Breeding Program has already been created.



    Breeding Programs:

    NameDescription
    AAFCAgriculture and Agri-Food Canada
    Ackermann GmbHInstitution: Ackermann GmbH. Collaborator: Claus Einfeldt.
    AgriPro SyngentaInstitution: Syngenta.
    Busch Agricultural Resources IncPlant breeder Institution: Busch Agricultural Resources Inc..
    CapCoremapping program
    CIMMYTInstitution: CIMMYT.
    Cornell UniversityPlant breeder Institution: Cornell University. Collaborator: Mark Sorrells.
    Crop Development CentreInstitution: University of Saskatchewan. Collaborator: Aaron Beattie.
    ICARDAInstitution: ICARDA.
    James HuttonInstitution: James Hutton Institute. Collaborator: Joanne Russell.
    Kansas State / USDA Genotyping LabInstitution: Kansas State University. Collaborator: Jesse Poland.
    KWS SaatInstitution: KWS Saat SE.
    Leibniz Institute of Plant Genetics and Crop Plant ResearchInstitution: Leibniz Institute of Plant Genetics and Crop Plant Research. Collaborator: Martin Mascher.
    Limagrain Cereal SeedsInstitution: Limagrain Cereal Seeds.
    Montana State Drought TrialsDrought and Irrigation Trials Institution: Montana State University. Collaborator: Tom Blake.
    Montana State UniversityPlant breeder Institution: Montana State University. Collaborator: Tom Blake.
    Morex-Barkemapping program
    NABSENThe North American Barley Scab Evaluation Nursery
    NDSU Plant PathologyPathologist Institution: North Dakota State University. Collaborator: Stephen Neate.
    NDSU Plant ScienceMalting Quality Institution: North Dakota State University. Collaborator: Paul Schwarz.
    N.I.Vavilov Research Institute of Plant IndustryInstitution: N.I.Vavilov Research Institute of Plant Industry.
    North Dakota State (NDSU 2-Row)Plant breeder Institution: North Dakota State University. Collaborator: Richard Horsley.
    North Dakota State (NDSU 6-Row)Plant breeder Institution: North Dakota State University. Collaborator: Richard Horsley.
    NSGC BarleyGermplasm Collection Institution: National Small Grains Collection - Barley. Collaborator: Harold Bockelman.
    Oregon State UniversityPlant breeder Institution: Oregon State University. Collaborator: Patrick Hayes.
    Oregon Wolfe Barleymapping program
    Research Institute for BioresourcesInstitution: Okayama Univeristy. Collaborator: Kaz Sato.
    Secobra RecherchesInstitution: Secobra Recherches.
    Spanish National Research Council (CSIC)Institution: Spanish National Research Council (CSIC). Collaborator: Luis Cistue, Ignacio Romagosa.
    Steptoe-Morexmapping program
    UC Davis PathologyPathologist Institution: University of California. Collaborator: Lee Jackson.
    UC Riverside Close LabGenotype Institution: University of California, Riverside. Collaborator: Tim Close.
    UMN PathologyPathologist Institution: University of Minnesota. Collaborator: Brian Steffenson.
    University of CaliforniaInstitution: University of California.
    University of Minnesota AgronomyPlant breeder Institution: University of Minnesota. Collaborator: Kevin Smith.
    University of Minnesota GenomicsInstitution: University of Minnesota.
    University of Minnesota PathologyPlant Pathology Institution: University of Minnesota. Collaborator: Eva Henningsen.
    University of NebraskaInstitution: University of Nebraska.
    University of Wisconsin MadisonInstitution: University of Wisconsin. Collaborator: Lucia Gutierrez.
    UnknownTo accommodate germplasm of unknown origin Institution: Unknown.
    USDA AberdeenPlant breeder Institution: USDA/ARS-Aberdeen, ID. Collaborator: Jianli Chen.
    USDA-ARS Aberdeen IDElite 2 rows Institution: USDA/ARS-Aberdeen, ID. Collaborator: Gongshe Hu.
    USDA-ARS Fargo NDGenotyper Institution: USDA-Agricultural Research. Collaborator: Shiaoman Chao.
    USDA-ARS Madison WIResearch Chemist Institution: USDA-ARS. Collaborator: Mitch Wise.
    USDA-ARS Raleigh NCInstitution: Eastern Regional Small Grains Genotyping Lab. Collaborator: Gina Brown-Guedira.
    Utah StatePlant breeder Institution: Utah State University. Collaborator: David Hole.
    Virginia TechPlant breeder Institution: Virginia Tech. Collaborator: Carl Griffey.
    Virginia Tech PathologyPathologist Institution: Virginia Tech. Collaborator: Carl Griffey.
    Virginia Tech Winter HardinessWinter hardiness Traits Institution: Virginia Tech. Collaborator: Carl Griffey.
    Washington State UniversityPlant breeder Institution: Washington State University. Collaborator: Steve Ullrich.
    Western Regional Barley NurseryUSDA WRBN
    WSU Food QualityFood Quality Institution: Washington State University. Collaborator: Byung-Kee Baik.


    If your Breeding Program exists:

    Continue to the next step


    If your Breeding Program does not exist:

    1. Go to the Manage > Breeding Programs page
    2. Click the Add New Program button at the bottom of the page to add your Breeding Program to the database


    Detailed Instructions  


  3. Locations

    Each Trial needs to be associated with a single Location and the Location needs to exist in the database before adding a Trial. Most of our trials are associated with a location of the closest town to the field site. However, more specific locations can be used (such as a separate location for each field).

    Check the table below to see if the Location(s) of your Trial(s) have already been created.



    Locations:

    NameAbbreviationCountryTrials
    AberdeenABRDUnited Kingdom0 trials
    Aberdeen, IDABEIDUnited States of America37 trials
    Alburgh, VTALBVTUnited States of America9 trials
    Alma, WIALMWIUnited States of America8 trials
    Arlington, WIARLWIUnited States of America4 trials
    Athens, GAATHGAUnited States of America1 trials
    Aurora, NYAURNYUnited States of America1 trials
    Aurora, ORAURORUnited States0 trials
    Beiseker, ABBEIALCanada2 trials
    Blacksburg, VABLAVAUnited States of America30 trials
    Bottineau, NDBOTNDUnited States of America3 trials
    Bozeman, MTBOZMTUnited States of America29 trials
    Brandon, MBBRAMBCanada20 trials
    Carpio, NDCARNDUnited States of America1 trials
    Carrington, NDCARRIUnited States of America14 trials
    Cartwright, NDCARTWUnited States of America1 trials
    Casselton, NDCASNDUnited States of America26 trials
    Center, COCENCOUnited States of America1 trials
    Charlottetown, PECHAPECanada2 trials
    Chatham, MICHAMIUnited States of America2 trials
    Clarksville, MDCLAMDUnited States of America4 trials
    Cochabamba, BoliviaCOCBOBolivia6 trials
    Conrad, MTCONMTUnited States of America2 trials
    Corvallis, ORCORORUnited States of America41 trials
    Crookston, MNCROMNUnited States of America104 trials
    Custar, OHCUSOHUnited States of America2 trials
    Davis, CADAVCAUnited States of America9 trials
    Debre Zeit, EthiopiaDEBETEthiopia2 trials
    Edmonton, ABEDMALCanada1 trials
    El Batan, Texcoco, MexicoELBATUnited States of America2 trials
    Elora, ONELOONCanada2 trials
    Fairfield, MTFAIMTUnited States of America14 trials
    Fargo, NDFARNDUnited States of America95 trials
    Farmington, NMFARNMUnited States of America3 trials
    Fayetteville, ARFAYARUnited States of America3 trials
    Fenn, IDFENIDUnited States1 trials
    Fergus Falls, MNFERMNUnited States of America1 trials
    Filer, IDFILIDUnited States of America8 trials
    Fort Collins, COFORCOUnited States of America18 trials
    Freeville, NYFRENYUnited States3 trials
    Genesee, IDGENIDUnited States of America6 trials
    Genesee, WAGENWAUnited States of America3 trials
    Georgetown, DEGEODEUnited States of America3 trials
    Glen Mills, PAGLEPAUnited States of America1 trials
    Glendive, MTGLEMTUnited States of America3 trials
    Grand Rhonde Valley, ORGRAORUnited States of America1 trials
    Greytown, South AfricaGRESOSouth Africa6 trials
    Hallock, MNHALMNUnited States of America1 trials
    Hangzhou, ChinaHANCHChina1 trials
    Hickory Corners, MIHICMIUnited States of America4 trials
    Huntley, MTHUNMTUnited States of America10 trials
    Idaho Falls, IDIDAIDUnited States of America16 trials
    Ithaca, NEITHNEUnited States of America0 trials
    Ithaca, NYITHNYUnited States8 trials
    Ithaca, NY - BluegrassITHNY-BLGUnited States0 trials
    Ithaca, NY - CaldwellITHNY-CALUnited States4 trials
    Ithaca, NY - HelferITHNY-HELUnited States3 trials
    Ithaca, NY - KetolaITHNY-KETUnited States4 trials
    Ithaca, NY - TailbyITHNY-TAIUnited States0 trials
    Kawkawlin, MIKAWMIUnited States of America2 trials
    Kimball, MNKIMMNUnited States of America1 trials
    Lacombe, ABLACALCanada1 trials
    Lamberton, MNLAMMNUnited States of America1 trials
    Landisville, PALANPAUnited States of America2 trials
    Langdon, NDLANNDUnited States of America62 trials
    Laurel Springs, NCLAUNCUnited States of America6 trials
    Lincoln, NELINNEUnited States of America1 trials
    Logan County, KYLOGKYUnited States of America1 trials
    Logan, UTLOGUTUnited States of America14 trials
    Madison, WIMADWIUnited States of America17 trials
    Maricopa, AZMARAZUnited States of America1 trials
    Martonvasar, HungaryMARHUHungary1 trials
    McGregor, TXMCGTXUnited States of America1 trials
    McVille, NDMCVNDUnited States of America21 trials
    Mead, NEMEANEUnited States of America7 trials
    Memphis, TNMEMTNUnited States of America1 trials
    Mills River, NCMILNCUnited States of America4 trials
    Minot, NDMINNDUnited States of America21 trials
    Morris, MNMORMNUnited States of America21 trials
    Mount Sterling, UTMOUUTUnited States of America2 trials
    Mt. Holly, VAMT.VAUnited States of America3 trials
    Nanjing, ChinaNANCHChina2 trials
    Njoro, KenyaNJOKEKenya5 trials
    Oklee, MNOKLMNUnited States of America1 trials
    Olds, ABOLDALCanada7 trials
    OregonOREGONCanada1 trials
    Orton, ONORTONCanada1 trials
    Osnabrock, NDOSNNDUnited States of America48 trials
    Pendleton, ORPENORUnited States of America6 trials
    Plains, GAPLAGAUnited States of America4 trials
    Powell, WYPOWWYUnited States of America1 trials
    Princeville, QCPRIQCUnited States of America2 trials
    Prosper, NDPRONDUnited States of America4 trials
    Pullman, WAPULWAUnited States of America33 trials
    Queenstown, MDQUEMDUnited States of America2 trials
    Raleigh, NCRALNCUnited States of America8 trials
    Ray, NDRAYNDUnited States of America24 trials
    Rexburg, IDREXIDUnited States of America3 trials
    River Falls, WIRIVWIUnited States of America5 trials
    Rock Springs, PAROCPAUnited States of America1 trials
    Rosalia, WAROSWAUnited States of America1 trials
    Roseau, MNROSMNUnited States of America3 trials
    Rupert, IDRUPIDUnited States of America2 trials
    Saint Paul, MNSAIMNUnited States174 trials
    Saskatoon, SKSASSKCanada1 trials
    Schochoh, KYSCHKYUnited States of America2 trials
    Sidney, MTSIDMTUnited States of America15 trials
    Soda Springs, IDSODIDUnited States1 trials
    South Deerfield, MASOUMAUnited States of America6 trials
    Stephen, MNSTEMNUnited States of America3 trials
    Sturgeon Bay, WISTUWIUnited States of America2 trials
    Tetonia, IDTETIDUnited States2 trials
    Tioga (Nesson Valley), NDTIONDUnited States of America4 trials
    Toluca, MexicoTOLMEMexico4 trials
    Twin Falls, IDTWIIDUnited States of America3 trials
    Velva, NDVELNDUnited States of America3 trials
    Versailles, KYVERKYUnited States of America2 trials
    VirginiaVIRGINIAUnited States of America1 trials
    Warsaw, VAWARVAUnited States of America22 trials
    West Lafayette, INWESINUnited States of America3 trials
    Williston, NDWILNDUnited States of America12 trials
    Wooster, OHWOOOHUnited States of America6 trials
    Wye, MDWYEMDUnited States of America1 trials


    If your Location(s) exist:

    Continue to the next step


    If your Location(s) do not exist:

    1. Go to the Manage > Locations page
    2. Click the [Upload New Locations] link in the top right corner of the page to upload a Locations Excel Template


    Detailed Instructions  


  4. Accessions

    The contents of each plot must be associated with a single Accession (germplasm line). The Accession must exist in the database before a Trial can be created. Also, you must refer to the exact spelling and letter-case of the Accession's name (or synonym) in the database when creating the Trial.

    We try very hard to avoid creating duplicate entries of an Accession based on variations in the spelling and/or characters used in the Accession name. Therefore, we highly recommend using the BrAPI Germplasm Search Tool to search for existing Accession entries in the database and any that match possible variations in spelling and/or punctuation.



    Search for existing Accession entries:



    If all of your Accessions already exist:

    Continue to the next step


    Add any new Accessions to the database:

    1. Go to the Manage > Accessions page
    2. Click the [Add Accessions or Upload Accession Info] link in the top right corner of the page
    3. Select the Uploading a File tab to upload an Accessions Excel template


    Detailed Instructions  


  5. Trials

    A Trial (a single location & year environment) must exist in the database before Trait Observations can be added. When a Trial is created, the folllowing information is added to the database:

    • Trial Metadata, such as:
      • the Breeding Program that performed the Trial
      • the Location
      • the Design Type
      • the Planting/Harvest Date(s)
    • Plot Metadata, such as:
      • the Accession grown in the Plot
      • Plot number
      • Block number
      • Rep number
      • Whether or not the Plot is used as a control
      • Row/Column position of the Plot within the field


    Upload a Multi-Trial Upload Template:

    1. Go to the Manage > Field Trials page
    2. Click the Upload Existing Trial(s) button in the top right corner of the page
    3. On Step 2, select the Multiple Trial Designs tab
    4. Upload a Multi-Trial Excel Template


    Detailed Instructions  


  6. Trait Observations

    Once the Trial(s) have been added to the database, Trait Observations can be added to the Plots within the Trial(s).

    To add Trait Observations, you will need:

    • The Plot Name (used when creating the Trial)
    • The Trait Name of each observation (from the Search > Traits page)
    • The Trait ID of each observation (from the Search > Traits page)

    It is important to note the units/scale used by the trait in the database. If your observations were recorded using a different scale, you will need to convert them to the scale used by the database first.

    File Format:

    • The first column has the header observationunit_name and contains the Plot Name (or Subplot Name or Plant Name, but it is almost always going to be the Plot Name)
    • Add an additional column for each trait being stored. The column header follows the format {Trait Name}|{Trait ID} and contains the trait values for each Plot. Unobserved plots should be left blank.


    Upload a Trait Observations Template:

    1. Go to the Manage > Phenotyping Results page
    2. Click the [Upload Spreadsheet] link in the top right corner of the page
    3. Change the Spreadsheet Format format to Simple
    4. Upload a Trait Observations Excel Template


    Detailed Instructions  


  7. Finish

    At this point your Trial(s) and Phenotyping Data have been stored in the database!


    The final step is to organize similar Trials together into Folders, which are used to group Trials into Experiments:

    1. Go to the Manage > Field Trials page
    2. Click the Refresh button above the Trial tree to load the new Trials
    3. Click the Create new folder button to create a new folder within a Breeding Program
    4. Click the Move trial(s) to folder to add one or more Trial(s) to a folder
    5. Click the Refresh button again to display the changes


Complete!
Complete!