Guided Phenotype Upload Workflow
- Intro
- Breeding Program
- Locations
- Accessions
- Trials
- Observations
- Finish
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Introduction
This workflow will guide your through the basic steps required for adding one or more phenotyping / field trials to the database:
- Ensuring the Breeding Program(s) exist
- Adding new Locations where the trials were performed
- Adding new or updated Accessions (germplasm lines)
- Creating Trials and their plot layouts
- Adding Phenotype Observations to the plots
Download Templates
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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:
Name Description Agricultural Biotechnology Research Institute, Faisalabad Shahid Nazir Agriculture and Agri-Food Canada Ron Knox Agriculture and Agri-Food Canada Alberta Dean Spaner Agriculture and Agri-Food Canada Manitoba Stephen Fox Agriculture and Agri-Food Canada Saskatchewan Ron Depauw AgriPro-Syngenta Allele Based Breeding Cooperative ABB trials performed by various Universities Applied Wheat Pathology FHB Resistance Trials Cereal Research Institute Non-Profit Ltd. Akos Mesterhazy CIMMYT Hans Braun Clemson Colorado State University Esten Mason Cornell University Mark Sorrells Designing Future Wheat Cristobal Uauy Dow AgroSciences Clay Sneller Durum Genome Sequencing Consortium International Durum Wheat Genome Sequencing Consortium EVIGEZ Czech Republic Five State Cooperative Cooperative trials of elite SRWW lines Genesis Seeds Clay Sneller Gortzen Gulf Atlantic Wheat Nursery Cooperative Cooperative trials of elite SRWW lines Hard Winter Wheat Fusarium Head Blight Nursery Cooperative Cooperative nursery of HWW FHB trials Kansas State University Eduard Akhunov Kansas State University - Hays Eduard Akhunov KWS Cereals Clay Sneller Limagrain Cereal Seed LMG Limagrain Cereal Seed Louisiana State University Michigan State University Montana State University Luther Talbert National Agricultural Research Development Institute Marianna Ittu National SGC National Small Grains Collection National Small Grains Collection Harold Bockelman National Small Grains Collection - Barley Harold Bockelman Nebraska USDA North Carolina State University North Dakota State University Ohio State University Oklahoma State University Brett Carver Oregon State University Pioneer PSB Collection Purdue University Regional Scab Nursery Cooperative Cooperative nursery of scab trials Septoria Nursery Cooperative Cooperative nursery of septoria trials Soft Red Winter Wheat Nursery Cooperative Cooperative nursery of SRWW trials Soft White Winter Wheat Nursery Cooperative South Dakota State University- Spring Wheat Karl Glover South Dakota State University- Winter Wheat Sunish Sehgal Sunbeam Extract Clay Sneller TAMU Texas A&M University, Jackie Rudd TCAP Cooperative Cooperative trials for TCAP Trio Hybrids UC Davis Jorge Dubcovsky UniSouth Genetics University of Arkansas University of Florida University of Georgia University of Guelph Clay Sneller University of Idaho Jianli Chen University of Illinois University of Kentucky University of Maryland University of Minnesota Jim Anderson University of Missouri University of Nebraska Steve Baenziger University of Tennessee University of Wisconsin Lucia Gutierrez Unknown USDA-ARS National USDA-ARS North Dakota NDG, Shiaoman Chao, Illumina genotyping lab Utah State University Margaret Krause Virginia Tech Nicholas Santantonio Washington State University Michael Pumphrey WestBred Dale Clark Winter Wheat Scab Nursery Cooperative Cooperative trials from uniform scab nurseries
If your Breeding Program exists:
Continue to the next step
If your Breeding Program does not exist:
- Go to the Manage > Breeding Programs page
- Click the Add New Program button at the bottom of the page to add your Breeding Program to the database
Detailed Instructions
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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:
Name Abbreviation Country Trials Aberdeen, ID ABEID United States of America 39 trials Aberdeen, SD ABESD United States 1 trials Addieville, IL AddieIL Unite States of America 1 trials Agar, SD AGASD United States 1 trials Akron, CO AKRCO United States of America 18 trials Alliance, NE ALLNE United States of America 30 trials Altus, OK ALTOK United States of America 8 trials Ames, IA AMEIA United States of America 10 trials Archer, WY ARCWY United States of America 17 trials Ardmore, OK ARDOK United States of America 1 trials Arlington, WI ARLWI United States of America 1 trials Aurora, SD AURSD United States of America 2 trials Baton Rouge, LA BATLA United States of America 6 trials Bay, AR BAYAR United States of America 9 trials Becker, MN BECMN United States 1 trials Belle Mina, AL BELAL United States of America 4 trials Belleville, IL BELIL United States of America 22 trials Bellfield, ND BELND United States of America 2 trials Beresford, SD BERSD United States of America 5 trials Billings, MT BILMT United States of America 1 trials Bison, SD BISSD United States of America 8 trials Blacksburg, VA BLAVA United States of America 50 trials Blackville, SC BLASC United States of America 1 trials Bluffton, IN BLUIN United States of America 1 trials Bozeman, MT BOZMT United States of America 44 trials Britton, SD BRISD United States of America 1 trials Brookings, SD BROSD United States of America 73 trials Brookston, IN BROIN United States of America 14 trials Brownstown, IL BROIL United States of America 37 trials Burlington, CO BURCO United States of America 15 trials Bushland, TX BUSTX United States of America 17 trials Bushland, TX - Dryland BUSTX-DRY United States of America 0 trials Bushland, TX - Irrigated BUSTX-IRR United States 15 trials Calhoun, KY CALKY United States of America 1 trials Carmi, IL CARIL United States 6 trials Carrington, ND CARND United States of America 16 trials Casselton, ND CASND United States of America 10 trials Castle Co, DE CASDE United States of America 1 trials Castroville, TX CASTX United States of America 2 trials Centralia, IL CENIL United States of America 2 trials Champaign, IL CHAIL United States of America 22 trials Charleston, MO CHAMO United States of America 1 trials Chillicothe, TX CHITX United States of America 13 trials Claire City, SD CLASD United States 1 trials Clarkston, MI CLAMI United States of America 1 trials Clarksville, MD CLAMD United States of America 6 trials Clay Center, NE CLANE United States of America 21 trials Cleveland, MS CLEMS United States of America 8 trials Clinton, MI CLIMI United States of America 1 trials Clovis, NM CLONM United States of America 20 trials Colby, KS COLKS United States of America 16 trials Columbia, MO COLMO United States of America 94 trials Crawfordsville, IA CRAIA United States of America 10 trials Crawfordsville, IN CRAIN United States of America 1 trials Crookston, MN CROMN United States of America 25 trials Crowley, LA CROLA United States of America 1 trials Custar, OH CUSOH United States 24 trials Dailey, CO DAILEY United States of America 0 trials Dakota Lakes, SD DAKSD United States of America 30 trials Danforth, IL DANIL United States 2 trials Danforth,IL DAN.IL United States of America 0 trials Davis, CA DAVCA United States of America 30 trials DeKalb, IL DEKIL United States of America 19 trials Debre-Zeit, Ethiopia DEBET Ethiopia 1 trials Dickinson, ND DICND United States of America 13 trials Dixon Springs, IL DIXIL United States of America 16 trials Draper, SD DRASD United States 1 trials Dundee, MI DUNMI United States of America 1 trials East Lansing, MI EASMI United States of America 59 trials El Centro, CA EL CA United States of America 4 trials Elkville, IL ELKIL United States of America 3 trials Enid, OK ENIOK United States of America 1 trials Etter, TX ETTTX United States of America 0 trials Evansville, IN EVAIN United States of America 6 trials Example, NY - DMM EXANY-DMM United States of America 1 trials Example, NY - JL7 EXANY-JL7 United States of America 1 trials Example, NY - KR-USDA-ARS EXANY-KR-USDA-ARS United States of America 1 trials Example, NY - LBM EXANY-LBM United States of America 1 trials Example, NY - LT21992K EXANY-LT21992K United States of America 1 trials Example, NY - MIK EXANY-MIK United States of America 1 trials Example, NY - MW EXANY-MW United States of America 1 trials Example, NY - PJK EXANY-PJK United States of America 1 trials Example, NY - TPM EXANY-TPM United States of America 1 trials FARGO, ND NCSLFAR United States 2 trials Faith, SD FAISD United States of America 3 trials Fargo, ND FARND United States of America 1 trials Farmington, NM FARNM United States of America 16 trials Fayetteville, AR FAYAR United States of America 12 trials Flora, IL FLOIL United States of America 1 trials Florence, SC FLOSC United States of America 3 trials Forman, ND FORND United States of America 7 trials Fort Cobb, OK FOROK United States of America 8 trials Fort Collins, CO FORCO United States of America 20 trials Fremont, OH FREOH United States 11 trials Ft. Branch, IN FT.IN United States of America 4 trials Fundulea, Romania FUNRO Romania 13 trials Garden City, KS GARKS United States of America 12 trials Geddes, SD GEDSD United States of America 3 trials Glenlea, MB, Canada GLEMB Canada 4 trials Goodland, KS GOOKS United States of America 5 trials Goodwell, OK GOOOK United States of America 17 trials Granite, OK GRAOK United States of America 2 trials Grant, NE GRANE United States of America 3 trials Greeley, CO GRECO United States of America 2 trials Greensburg, IN GREIN United States of America 2 trials Griffin, GA GRIGA United States of America 15 trials Groton, SD GROSD United States of America 2 trials Halcomb, KY HALKY United States 46 trials Hamel, IL HMLIL United States of America 2 trials Hampshire, IL HAMIL United States of America 2 trials Havre, MT HAVMT United States of America 1 trials Hayes, SD HAYSD United States of America 9 trials Hays, KS HAYKS United States of America 21 trials Henderson, KY HENKY United States of America 2 trials Hettinger, ND HETND United States of America 23 trials Highland, IL HIGIL United States 9 trials Highmore, SD HIGSD United States of America 5 trials Hildreth, NE HILNE United States of America 1 trials Hillman, MI HILMI United States of America 2 trials Hopkinsville, KY HOPKY United States of America 2 trials Horse Heaven, WA HORWA United States of America 1 trials Hugoton, KS HUGKS United States of America 2 trials Huntley, MT HUNMT United States of America 9 trials Huron County, MI HURMI United States 8 trials Hutchinson, KS HUTKS United States of America 12 trials Independence, KS INDKS United States of America 2 trials Ingham, MI INGMI United States of America 3 trials Irvington, IL IRVIL United States of America 2 trials Isabella County, MI ISAMI United States 2 trials Ithaca, NE ITHNE United States of America 8 trials Ithaca, NY ITHNY United States of America 27 trials Ithaca, NY - Caldwell ITHNY-CAL United States of America 13 trials Ithaca, NY - Helfer ITHNY-HEL United States 17 trials Ithaca, NY - Ketola ITHNY-KET United States 17 trials Ithaca, NY - McGowan ITHNY-MCG United States 7 trials Ithaca, NY - Snyder ITHNY-SNY United States 11 trials Julesburg, CO JULCO United States of America 16 trials Kalispell, MT KALMT United States of America 3 trials Kennebec, SD KENSD United States of America 8 trials Kibler, AR KIBAR United States of America 4 trials Kimball, MN KIMMN United States of America 4 trials Kinston, NC KINNC United States of America 34 trials Kinston, NC - Caswell KINNC-CAS United States of America 1 trials Knoxville, TN KNOTN United States of America 4 trials Lafayette, IN LAFIN United States of America 50 trials Lahoma, OK LAHOK United States of America 17 trials Lake Wheeler, NC LAKNC United States of America 2 trials Lamberton, MN LAMMN United States of America 9 trials Langdon, ND LANND United States of America 20 trials Laporte, MI LAPMI United States of America 1 trials Larned, KS LARKS United States of America 1 trials Laurel Springs, NC LAUNC United States of America 4 trials Le Center, MN LE MN United States of America 8 trials Lenawee County, MI LENMI United States 2 trials Lethbridge, AB LETAB Canada 12 trials Lexington, KY LEXKY United States of America 74 trials Lexington, NC LEXNC United States of America 0 trials Lima, OH LIMOH United States of America 1 trials Lincoln, NE LINNE United States of America 49 trials Lind, WA LINWA United States of America 8 trials Lisbon, ND LISND United States of America 5 trials Logan Co, KY LOGKY United States of America 19 trials Madison,WI MADWI United States 4 trials Mandan, ND MANND United States of America 7 trials Manhattan, KS MANKS United States of America 42 trials Maricopa, AZ MARAZ United States of America 10 trials Martin, SD MARSD United States of America 11 trials Mason, MI MASMI United States 34 trials McCook, NE MCCNE United States of America 2 trials McGregor, TX MCGTX United States of America 3 trials McLaughlin, SD MCLSD United States of America 2 trials Mead, NE MEANE United States of America 23 trials Merrill, MI MERMI United States of America 2 trials Mexico City Mexico 0 trials Mexico, MO MEXMO United States of America 2 trials Middletown, DE MIDDE United States of America 1 trials Minot, ND MINND United States of America 16 trials Moccasin, MT MOCMT United States of America 17 trials Monroe County, MI MONMI United States 5 trials Montcalm County, MI MNTMI United States 2 trials Morden, MB, Canada MORMB Canada 2 trials Morris, MN MORMN United States of America 2 trials Mount Holly, VA MOHVA United States 4 trials Mt Vernon, SD MT SD United States of America 1 trials Mt. Vernon, WA MT.WA United States of America 39 trials Mulkeytown, IL MULIL United States of America 1 trials NWBranch, OH NWBOH United States of America 22 trials Nairn, ON NAION Canada 3 trials Napoleon, OH NAPOH United States of America 9 trials Neoga, IL NEOIL United States of America 8 trials New Haven, IN NEWIN United States of America 1 trials Newport, AR NEWAR United States of America 7 trials Newton, MS NEWMS United States of America 4 trials Njoro, Kenya NJOKE Kenya 1 trials North Platte, NE NORNE United States of America 35 trials Norwich, UK NUK 0 trials Oconto, WI OCOWI United States of America 6 trials Oelrichs, SD OELSD United States of America 4 trials Onida, SD ONISD United States of America 8 trials Othello, WA OTHWA United States 2 trials Ottawa, ON OTTON Canada 1 trials Owensville, IN OWEIN United States of America 2 trials Palmer, KS PALKS United States of America 5 trials Pendleton, OR PENOR United States of America 7 trials Perry, IL PERIL United States of America 22 trials Pierre, SD PIESD United States of America 8 trials Pine Bluffs, WY PINWY United States of America 1 trials Plains, GA PLAGA United States of America 16 trials Plankinton, SD PLASD United States of America 2 trials Platte, SD PLTSD United States of America 7 trials Plymouth, NC PLYNC United States of America 4 trials Pole Barn 0 trials Pole Barn 0 trials Pole Barn 0 trials Pomeroy, WA POMWA United States of America 2 trials Portageville, MO PORMO United States of America 13 trials Princeton, IN PRIIN United States of America 1 trials Princeton, KY PRNKY United States of America 46 trials Princetown, KY PRIKY United States 0 trials Prosper, ND PROND United States of America 24 trials Prosper, TX PROTX United States of America 13 trials Pullman, WA PULWA United States of America 44 trials Queenstown, MD QUEMD United States of America 4 trials Quincy, FL QUIFL United States of America 10 trials Raleigh, NC RALNC United States of America 1 trials Raleigh, NC - Midpines RALNC-MID United States of America 1 trials Ridgetown, ON RIDON United States of America 22 trials Rodney, ON RODON United States of America 1 trials Roseau, MN ROSMN United States of America 7 trials Rosemount, MN ROSEMN 17 trials Saginaw Valley Research and Extension Center, MI SVREC United States 21 trials Salina, KS SALKS United States of America 15 trials Salisbury, MD SALMD United States of America 13 trials Salisbury, NC SALNC United States of America 4 trials Sample, NY - DMM SAMNY-DMM United States of America 1 trials Sample, NY - JL7 SAMNY-JL7 United States of America 1 trials Sample, NY - KR-USDA-ARS SAMNY-KR-USDA-ARS United States of America 1 trials Sample, NY - LBM SAMNY-LBM United States of America 1 trials Sample, NY - LT21992K SAMNY-LT21992K United States of America 1 trials Sample, NY - MIK SAMNY-MIK United States of America 1 trials Sample, NY - MW SAMNY-MW United States of America 1 trials Sample, NY - PJK SAMNY-PJK United States of America 1 trials Sample, NY - TPM SAMNY-TPM United States of America 1 trials Sanilac County, MI SANMI United States 9 trials Saskatoon, SK, Canada SASSK Canada 1 trials Schochoh, KY SCHKY United States of America 7 trials Selby, SD SELSD United States 15 trials Sheridan Lake, CO SHER United States of America 0 trials Sidney, MT SIDMT United States of America 1 trials Sidney, NE SIDNE United States of America 34 trials South Charleston, OH SCHOH United States of America 1 trials South Shore, SD SOUSD United States 7 trials St Peter, IL StpIL Unite States of America 1 trials St. Jacob, IL STJIL United States 8 trials St. Paul, MN ST.MN United States of America 39 trials Stillwater, OK STIOK United States of America 17 trials Storage A 0 trials Sturgis, SD STUSD United States of America 12 trials Stuttgart, AR STUAR United States of America 8 trials Sussex Co, DE SUSDE United States of America 2 trials Szeged, Hungary SZEHU Hungary 4 trials Test Location TL United States 0 trials Tiffin, OH TIFOH United States 2 trials Tipton, IN TIPIN United States of America 4 trials Tipton, OK TIPOK United States of America 2 trials Tripp County, SD TRISD United States of America 4 trials Trumansburg, NY TRUNY United States of America 0 trials Trumansburg, NY - Field A TRUNY-A United States of America 1 trials Urbana, IL URBIL United States 129 trials VCBranch, OH VCBOH United States 24 trials Vincennes, IN VININ United States 5 trials Vivian, SD VIVSD United States of America 2 trials Volga, SD VOLSD United States 1 trials Wabash, IN WABIN United States of America 3 trials Wall, SD WALSD United States of America 14 trials Walla Walla, WA WALWA United States of America 4 trials Walsh, CO WALCO United States of America 10 trials Warsaw, VA WARVA United States of America 22 trials Waseca, MN WASMN United States of America 9 trials Watertown, SD WATSD United States of America 2 trials West Lafayette, IN WESIN United States of America 110 trials Wichita, KS WICKS United States of America 21 trials Williston, ND WILND United States of America 29 trials Windfall, IN WININ United States of America 1 trials Winfield, KS WINKS United States of America 17 trials Winner intensive, SD WINSD United States of America 2 trials Winner, SD WIISD United States of America 46 trials Winnsboro, LA WINLA United States of America 15 trials Wishek, ND WISND United States of America 5 trials Woodford Co, KY WOOKY United States 50 trials Woodford, KY WODKY United States of America 14 trials Wooster, OH WOOOH United States of America 150 trials Yaqui Valley, Sonora, Mexico YAQSO Mexico 4 trials
If your Location(s) exist:
Continue to the next step
If your Location(s) do not exist:
- Go to the Manage > Locations page
- Click the [Upload New Locations] link in the top right corner of the page to upload a Locations Excel Template
Detailed Instructions
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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:
- Search for exact matches of individual entries using the Search > Accessions and Plots page
- Search for exact matches of multiple entries using the Search > Bulk Search page
- Search for multiple entries (and variations in spelling and/or punctuation) using the BrAPI Germplasm Search Tool
If all of your Accessions already exist:
Continue to the next step
Add any new Accessions to the database:
- Go to the Manage > Accessions page
- Click the [Add Accessions or Upload Accession Info] link in the top right corner of the page
- Select the Uploading a File tab to upload an Accessions Excel template
Detailed Instructions
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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:
- Go to the Manage > Field Trials page
- Click the Upload Existing Trial(s) button in the top right corner of the page
- On Step 2, select the Multiple Trial Designs tab
- Upload a Multi-Trial Excel Template
Detailed Instructions
- Trial Metadata, such as:
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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:
- Go to the Manage > Phenotyping Results page
- Click the [Upload Spreadsheet] link in the top right corner of the page
- Change the Spreadsheet Format format to Simple
- Upload a Trait Observations Excel Template
Detailed Instructions
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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:
- Go to the Manage > Field Trials page
- Click the Refresh button above the Trial tree to load the new Trials
- Click the Create new folder button to create a new folder within a Breeding Program
- Click the Move trial(s) to folder to add one or more Trial(s) to a folder
- Click the Refresh button again to display the changes