Trials
Field trials are a central concept in Breedbase, and provide a structure for linking phenotypic observations to the experimental layout to the germplasm information. A field layout represents the germplasm tested in the experiment under a specific experimental design. Usually, the field layout is created, based on a given randomization method that is deemed appropriate, using the field creation and randomization methods in Breedbase, and then the trial is planted according to the design obtained.
There are two ways for adding a field layout into Breedbase. The first is by using an interactive interface on Breedbase for designing a new field layout, while the second is by uploading an Excel spreadsheet of the field layout. The first method ensures a path of least resistance for the researcher by performing the design calculation and randomization on Breedbase.
To begin designing a new field trial in Breedbase, a breeding program, location, unique trial name, trial type, year, description, and design type must be specified; optionally, the plot width, plot length, and field size can be specified. The trial type is simply a tag for the kind of trial being performed and must be selected from the following terms: phenotyping trial, seedling nursery, clonal evaluation, advanced yield trial, preliminary yield trial, uniform yield trial, variety release trial, regional trial, seed multiplication, screenhouse, or crossing block trial.
The design type specifies the calculation and randomization to be performed on the distribution of germplasm in the field experiment and must be one of the following: completely randomized, complete block, alpha lattice, lattice, augmented, modified augmented design, nursery/greenhouse, split plot, partially replicated, or Westcott design. Next, design type parameters must be provided depending on the design type specified.
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For the completely randomized design, only a list of germplasm and the number of replicates is required.
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For the complete block design, only a list of germplasm and the number of blocks is required.
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The alpha lattice design requires a list of germplasm, the number of replicates, and the block size, while the lattice design requires only a list of germplasm and the number of replicates.
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The modified augmented design requires a list of germplasm, a second list of germplasm to use as checks, and the maximum block size.
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The nursery/greenhouse design is not plot replicated or randomized and only requires a list of germplasm and input for the number of plants for each germplasm.
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The split plot design requires a list of germplasm, the number of blocks, the number of plants per split-plot factor, and names for all the split-plot factors being tested; the split-plot design is unique in that it will create plots, sub-plots, and plant entries in a nested design and will assign the given split-plot factors as field management factors to the generated sub-plots and plant entries. More on field management factors is found in the section below.
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The partially replicated design requires a list of unreplicated germplasm, a list of replicated germplasm, the number of rows and columns in the design, a replicate number, a block sequence, and a sub-block sequence.
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The Westcott design requires a list of germplasm, two germplasm names to use as checks, the number columns, and the number of columns between the two checks.
After providing the design parameters, Breedbase will calculate the design using R libraries, including ‘agricolae’. A Perl library called R::YapRI (https://metacpan.org/pod/R::YapRI) is used to interface with R, providing in-memory translation of data objects between Perl and R. The calculated layout is then interactively drawn on Breedbase and the researcher can review the layout before saving it into the database; it is possible to redo randomizations in this step. During this review process, though uptional, it is possible to add field management factors to the field trial; more on field management factors is in the following section. The review process will also warn whether the designed layout is larger than the specified field size if the plot length, plot width, and field size were provided.
The second method for creating field trials in Breedbase is by uploading an Excel spreadsheet. This method is useful for uploading experiments that have previously been performed and for uploading experiments for which Breedbase cannot calculate the design. Both methods produce the same result. During upload of the Excel spreadsheet it is also possible to include field management factors as additional columns in the spreadsheet. Also, during upload of the Excel spreadsheet it is possible to indicate the seedlots that were planted in specific plots; when seedlots are provided, a transaction between the seedlot and plot is created to subtract the specified number or weight of seed from the seedlot.
The end result of both methods is a field trial created in Breedbase with defined plots arranged over a number of blocks and replicates. Every plot has a plot number that is unique only to the field trial and increments linearly across all plots; the plot number can be defined in a serpentine or zig-zag fashion. Breedbase offers an interactive field layout for viewing the field trial spatially; this same interactive interface works as a heatmap to overlay phenotypic measurements for each plot in the field trial.
If it is desired to phenotype individual plants alongside individual plots, Breedbase can link plant entries to plot entries for the field trial. Plant entries can be added by either simply indicating the number of plants to create for each plot in the field trial or by uploading an Excel file. The uploaded Excel file can be of three forms. The first is a spreadsheet with a column specifying an existing plot name and a column defining the name of the new plant entry; in this way, the uploader can control the number of plants to create for each plot and their new plant name. The second way is using a spreadsheet with a column specifying an existing plot name and a column defining a plant index number; this way will create new plant entries with names that are a concatenation of the plot name and the specified index number, allowing the uploader control of how many plant entries to create per plot and the index numbers to use. The third way is using a spreadsheet where the first column specifies an existing plot name and the second column defines how many plants to create for that plot; in this case, new plant entries are created with names that are concatenations of the plot name and an index number, allowing the uploader control of how many plant entries to create for each plot.
Similarly, if it is desired to collect tissue samples from plants in the field trial, Breedbase can link tissue sample entries to plant entries for the field trial. Tissue samples can be created only after plant entries have been created. Tissue samples can be created by specifying how many tissue samples to create for each plant in the field trial. The user can then define a tissue type for each of the tissue samples they will collect, for example leaf and stem. Breedbase will then create tissue sample entries for every plant entry in the field trial; the new tissue sample names are a concatenation of the plant name, the provided tissue type, and an incrementing tissue sample index number.
By creating plot entries, and optionally plant entries and tissue sample entries, for the field trial, it is then possible to print barcodes from Breedbase and it is possible to associate phenotype values to any of these entities. An interactive barcode label design tool is available on Breedbase, allowing researchers to design reusable custom label formats on an easy drag-and-drop templating interface.
In the case where the field trial is used for crossing experiments, for example if the field trial is a crossing block, it is possible to utilize the plot names, or optionally plant names, to track parentage; this is an additional level of parentage tracking on top of tracking germplasm names, as was discussed in detail in the crossing experiments section.
A field trial is stored as an entry in the project table with entries in the projectprop table following an EAV model; entries in projectprop include the year, location, field size, plot width, plot length, design type, and trial type, with all type names coming from the ‘project_property’ controlled vocabulary. The field trial project entry is connected to the breeding program project entry via the project_relationship table using the type name ‘breeding_program_trial_relationship’ from the ‘project_relationship’ controlled vocabulary. The field trial is created with a link to nd_experiment via the nd_experiment_project linking table; the nd_experiment entry has the type name ‘field_layout’ from the ‘experiment_type’ controlled vocabulary. All plot entries are saved individually in the stock table using the type name ‘plot’ from the ‘stock_type’ controlled vocabulary; the plot entries are all linked to the same field trial nd_experiment entry via the nd_experiment_stock linking table. The plot stock entry is linked to its germplasm stock entry via the stock_relationship table using the type name ‘plot_of’ from the ‘stock_relationship’ controlled vocabulary. Each plot’s stock entry has stockprop entries in an EAV model describing the plot’s plot number, row number, column number, block number, replicate number, and whether the plot contains a check germplasm; all of these stockprop terms are from the ‘stock_property’ controlled vocabulary. Optionally, when plant entries are saved in a field trial they are saved as stock entries with the type name ‘plant’ from the ‘stock_type’ controlled vocabulary; the plant entries have a stockprop entry in an EAV model with the type name ‘plant_index_number’ from the ‘stock_property’ controlled vocabulary. The plant entries also inherit all design related stockprop values from their related plot, such as plot number and block number. The plant entries are linked to their germplasm and plot via stock_relationship entries using the type name ‘plant_of’ from the ‘stock_relationship’ controlled vocabulary. Optionally, when tissue sample entries are saved in a field trial they are saved as stock entries with the type name ‘tissue_sample’ from the ‘stock_type’ controlled vocabulary; the tissue sample stock entries are linked to a stockprop in an EAV model using the type name ‘tissue_sample_index_number’ from the ‘stock_property’ controlled vocabulary. The tissue sample entries also inherit all design related stockprop values from their related plot. Field trial tissue sample entries are linked to their related germplasm, plot, and plant entries via stock_relationship entries using the type name ‘tissue_sample_of’ from the ‘stock_relationship’ controlled vocabulary. For ease of determination, additional projectprop entries are added to the field trial indicating whether the field trial contains plant or tissue sample entries, with type names coming from the ‘project_property’ controlled vocabulary.
For performance reasons, a cached representation of the field trial is generated for every field trial layout; the cached layout is stored as a JSON encoded string in a projectprop entry using the type name ‘trial_layout_json’ from the ‘project_property’ controlled vocabulary. The cached layout is a JSON object of objects, where the top-level key is the plot number and the corresponding objects contain all design information, such as block number and replicate, as well all related plant and tissue sample information for each plot. The cached layout is regenerated when there are changes to the underlying field layout and is used throughout Breedbase, such as when drawing the field map and printing barcode labels.
