Germplasm Search

1. Perform germplasm search using wildcard (e.g., CROP%).

2. Filter the results to find germplasm from a specific germplasm state, year, and/or program.

3. Select 10 germplasm and save them in a germplasm list.

4. You can use additional search parameters in the input list and add a condition.

5. Check your new list in the List Manager tool.

6. Share the list with Trainer (read/write rights)

Inventory Search

1. Search for seeds using the Search Parameter. Choose the field type from “Season”, “Experiment Year”, “Experiment Type”, “Occurrence”, “Facility”, and/or “Sub-facility”.

2. Manage the results by sorting items based on Entry No and Entry Code. Then, select the items and add them to the Working List.

3. Reserve seeds for an upcoming experiment by creating a package list. Give it an appropriate name.

4. Check your new package in the List Manager tool.

5. Share the list with Trainer (read/write rights).

Trait Search

1. Search for specific traits associated with your crop trial objectives (e.g., Plant height, Yield, Weight, etc.)

2. Manage results by selecting the traits for use in the trial and saving the selected traits as a new list.

3. Check your new trait list in the List Manager tool.

4. d. Share the list with Trainer (read/write rights).

List Manager

Option 1

1. Merge your two lists (of the same type) and give a new name.

2. Add items to the merged list.

Option 2

1. Split the list into two.

2. Share your list with another program of the same crop and another person, giving them read/write permission.

Experiment Creation

Option 1: Create a Breeding Trial experiment.

1. In Basic Information, enter the name using: Year_[Your initials]_BT. Add stage, Year, Season, Experiment Sub-type, objective, and description.

2. In the Entry List tab, use the saved list option and choose your package list.

   1. Modify the entry type of entries 1 and 2 to be checks.\

      1. Also, modify entry 1 as a local check and entry 2 as a performance check.

3. In the Design tab, select the design to use, the number of parameters and occurrences, the number of replicates, and the number of plots per block.

   1. Toggle the define shape/dimension button to “yes”. Add field layout details and finally generate the design.

4. In the Protocols tab, set up the plot sizes and planting instructions, then save the parameters.

   1. Still in the protocols tab, use the “trait lists” and add your saved trait list.

5. In the Sites tab, add sites and add the contact person for each occurrence.

6. Review the experiment and complete creation.

7. See your experiment in the Experiment Manager tool.

Option 2: Create a Cross Parent Nursery/Generation Nursery experiment

1. In Basic Information, enter the basic information for your nursery.

2. In the Parent List tab, add parents using your saved list.

3. In the Planting Arrangement tab, use the toggle button and switch to Entry Order.

4. In the Protocols tab, add Planting, Pollination, Traits, Management, and Harvest protocols

5. In the Site tab, add the site and the contact person for your nursery experiment.

6. Review the experiment and if okay, proceed to complete creation.

7. Go to the Experiment Manager tool to see your nursery and ensure that it is planted.

8. To create crosses from the CPN experiment, go to Cross Manager tool.

Cross Manager

1. Create a new cross list.

   1. Add basic information for your cross list: the name ([your first name]_Crosslist_01), Year (current year), Season, and Site of the occurrence where you get your parents.

   2. In the Add Parents tab, click the eye icon next to your occurrence and click the download button to see a list of the germplasm attributes associated with these parents.

   3. Select all the parents and add them as female-and-male. Then click on “Manage Parents”

   4. In the Add Crosses tab, select entries 1 and 2 as female, and 3 and 4 as male. Then click Pair and then Add. Select Add More to continue adding more crosses.

   5. In the Manage Crosses tab, add your cross method to each cross, or use the Bulk Update button.

2. Review the crosses and finalize to save the cross list.

Experiment Manager

1. Map the breeding trial created earlier

   1. Check if the design layout matches the planting area and field layout. If so, click the check button and next, then expand to see your plots. If satisfied, click Confirm.

2. Once the status is “Mapped”, proceed to commit your occurrence and have it planted.

3. Click the pencil icon and create changes to the occurrence as needed.

Planting Instructions Manager

1. In the Experiment Manager tool, select the trial you created with the status Created and access the Planting Instructions Manager tool through the Access Breeding Tools.

2. In the Envelopes tab, specify the quantity of seeds per envelope (in grams) and the number of envelopes per plot.

3. Manage the entries in the Entry Management tab by checking if all entries have sufficient seeds.

4. Review the Summary and additional instructions for your occurrence and submit the packing job.

5. Once it has the status Ready for Packing, click the eye icon and update the status to Packed.

6. Check that this reflects in your occurrence in the Experiment Manager tool.

Data Collection and Quality Control (~Field book)

Option 1: Plots

1. In the Experiment Manager tool, confirm that the occurrence’s trait protocols are updated.

2. Open the Field book app in your data collection gadget (Phone, tablet).

   1. In Settings, ensure you have BrAPI enabled and configured with the correct link for the following: Base URL, OIDC Discovery URL, and OIDC Flow.

   2. In Fields, go to BrAPI Field Import and click Load Fields. Use your EBS login credentials to log in to the site.

   3. Once done, click Load Fields, select your occurrence, preview, and load it to be ready for data collection. Ensure that your occurrence is selected under the fields.

3. Check the traits to ensure they are the ones set for data collection.

4. Proceed to collect data. After a successful data collection, go to “Export” and under BrAPI Export, click Export to sync the collected data back to the occurrence in EBS.

5. In the Data Collection tool, the status of the data collected from the Field Book will be Uploaded.

6. Click the QC button on the left to conduct a quality check on the uploaded data.

7. Review the data. Once satisfied, proceed to the Complete Transaction tab and click Complete to commit the data.

8. Check that the status of the occurrence is now Trait Data Collected in the Experiment Manager tool.

Option 2: Crosses

1. In the Cross Manager tool, select the cross list, then go to trait data collection.

2. Once in the “Traits” tab, search for Harvest Date and Harvest Method, then add. Select the traits and download the CSV file “With trait abbreviations”.

3. Update the data in the csv file and upload it back to the Data Collection tool.

4. Review the data. Once satisfied, proceed to the Complete Transaction tab and click Complete to commit the data.

5. Check that the status of the occurrence is now Trait Data Collected in the Experiment Manager tool.

Harvest Manager

Option 1: Plots

1. In the Experiment Manager tool, select a Breeding Trial occurrence, click the “Access Breeding Tools” button to select “Harvest Manager”, then “Harvest plots”.

2. In the Harvest Data tab, update the harvest date and harvest method.

3. Go to the Creation tab and first commit the harvest data. Once it is “For Creation”, click “Create” and see the plots ready for harvest. Then, “Proceed” to create new packages, seeds, germplasm, and related records.

4. Once notified that the harvest is complete, go to the Management tab to check your germplasm, seed, and package information.

5. Use the “Save to list” button to save the new list in a seed list, package, or germplasm list.

Option 2:Crosses

1. In the Experiment Manager tool, select an Intentional Crossing Nursery occurrence, click the “Access Breeding Tools” button to select “Harvest Manager”, then “Harvest crosses”.

2. In the Harvest Data tab, use the “Bulk update” button to add the harvest method and harvest date to the crosses. Click on next.

3. First commit the harvest, then create new germplasm and/or inventory items.

4. Once notified that the harvest is complete, go to the Management tab to check your germplasm, seed, and package information.

5. Use the “Save to list” button to save the new list in a seed list, package, or germplasm list.

Phenotypic Data Manager

1. In the Experiment Manager tool, select a Breeding Trial occurrence, click the “Access Breeding Tools” button to select “Phenotypic Data Manager”.

2. Perform quality check for your occurrence(s), to ensure for Missing, Questionable, Bad, and Good data. Then, mark the traits as Quality Checked.

3. View the Summary Statistics of your occurrence.

4. View the visualizations (Boxplots, Scatterplots, Histograms, and Heatmaps) of your occurrence.

Analysis Request Manager

Option 1: Single-Occurrence Analysis (SOA)

1. Submit a request for analysis of your single-occurrence data.

2. Track the progress of your analysis request and review the final output.

3. Download the analysis results and integrate them into the breeding decision-making.

4. Repeat the processes 1-3 for the other occurrences in that experiment if you need to create a Multi-occurrence analysis (MOA).

Option 2: Multi-Occurrence Analysis

1. Select two or more occurrences (those listed have undergone single-occurrence analyses) that have one or more similar traits.

2. Submit the request for analysis of your multi-occurrence data.

3. Track the progress of your analysis request.

4. Review the final output and the downloaded analysis results.

Shipment tool

a. Create a shipment request (Open Service Manager > Shipment tool).

b. Click New shipment. (Enter title, purpose, sender program/site, expected ship date)

c. Add recipient details (program, site, contact, address).

d. Select items/package from inventory or lists

e. Complete required compliance fields (permits, MTAs, phytosanitary, BIOSAFETY as applicable).

f. Submit shipment (add approvers and notes).