Module 8: Design, Implement, and Import Data from Single ...
Module 8: Design, Implement, and Import Data from Single Site Trial (SST) using Trial ManagerLearning ObjectivesGain understanding of how to design field trials using the appropriate experimental design to avoid undesirable variation, accommodate appropriate testing without replication to ensure good data are collected for making the right decisions. To reinforce how to export data collection sheets, make filed maps, collect and import data into the BMS databaseModule MapIntroductionStart New TrialSettings ConfigurationAdd Germplasm ListAdd Treatment FactorsAdd EnvironmentSelect ExperimentalAdd Trial MeasurementsExport Trial Field BookDesign and Manage TrialTrial SettingsGermplasmTreatment FactorsEnvironmentExperimental DesignMeasurementsExport Trial BookImport Trial DataIntroductionThe primary goal of any plant breeding program is for the plant breeder to successfully identify and select superior genotypes from among and within the highly variable genetic material available in order to develop material better in performance than the currently available competition for the trait of interest (which can be yield, resistance/tolerance to biotic/abiotic stress, or quality, etc.). Because of the broad array of variation in entries, it is inevitable that some entries will produce insufficient planting material for replicated testing. Hence it is a critical requirement that the plant breeder develops/uses trial/selection designs that can handle both unreplicated and replicated material. Having identified populations from F2 nurseries, further advancement of families/lines depends on conducting field trials to collect yield and other agronomic trait data to assist in decision making. In this module, you will use the Trial Manager (a tool for designing field trials which uses standardized crop ontology terms to describe treatments, factors, and trait measurements) to:Design and manage a yield trial planted at multiple sites (locations) using one of the supported experimental designs, for example, randomized complete block design (RCBD) with two or more replicates, row-column (RC),etc. Export data collection sheetsAdd data to data collection sheetsImport data collected back to the database The steps that follow describe how to design a field trial to evaluate a 32 entries germplasm for 7 phenotypic traits replicated 3 times at 4 locations. The experimental design is a resolvable incomplete block design, specifically an alpha lattice design. The module also covers the export of data collection sheets and import of phenotypic data back to the BMS database.Starting a New Trial You will access Trial Manager to, configure settings, add germplasm list, add treatment factors, add environments, select experimental design, add measurements to be taken, export trial field book, and import trial data,Settings ConfigurationClick ‘Manage Trials’ under Breeding Activities at the left (Fig. 1)Click the blue ‘Start a New Trial’ button to the right (Fig. 1)Figure 1Complete the ‘Basic Details section with required fields: trial name and description, and accept the default settings (Fig. 1)Check the box by ‘Use a previously created trial as template’ at lower leftClick blue ‘Save’ at top left to save regularly (recommended) at any point in trial design process Click the blue ‘Choose’ button (Fig. 1) to open ‘Trials window (Fig. 2) Expand the Public Trials folder (Program Trials in version 4.0) (Fig. 2)Next expand the ‘Templates’ sub-folder, highlight ‘Basic Trial template’ and Click ‘Select’ (Fig. 2)Figure 2Click ‘Select (Fig. 2) to populate the trial with customizable trial design displaying by default, information on the Settings tab (Fig. 3)Select the desired information from the dropdown menu options available for each field - Study_Status, and PI_Name (Fig. 3)Figure 3Adding Germplasm ListClick the Germplasm tab (Fig. 4)Click ‘Browse’ under Trial List to open the program list window (Fig. 4)Click ‘Trial Germplasm List’ and click ‘Select’ (Fig. 5) to populate the germplasm list that will be included in the trial for review (Fig. 6) Figure 4Figure 5Figure 6Adding Treatment FactorsIf trial will not have treatment factors, then leave blank. Click the ‘Treatment Factors’ tab and specify name, description and levels (Fig. 7)Figure 7Adding Environments (Figure 8)Click ‘Environments’ tab. This trial will be planted at three sites (locations)Enter 3 for number of environments and click ‘OK’ to add boxes for three environmentsClick the dropdown menu and add the appropriate three location cooperators names and saveFigure 8Selecting Experimental Design (Fig. 9)Click on the ‘Experimental Design’ tabChoose Randomized Complete Block Design, for this example, from dropdown menuEnter 3 for number of replicationsClick on ‘Generate Design’ button at lower left for populating the ‘Measurement’ tabFigure 9Adding Measurements (Fig. 10)Click on the ‘Measurements’ tab, review the list to make sure that traits of interest are included, e.g. weight of 100 seeds (g) and 50% maturity (days) (SDWT100 and MAT50). Review the list of traits preselected in the template, e.g SDWT100 and MAT50 Click the ‘Add’ button and include additional traitsClick ‘Save’ button to save the empty trial design Figure 10At this point the trial is ready for field mapping, label printing, and file export for data collection.Exporting Trial Field Book (Fig. 11)Click ‘Manage Trials’ under ‘Breeding Activities’Click ‘Browse’ hyperlink to open Trials windowExpand Program Trials folderSelect your trial name, Multi-Site (3) Trial for this exampleFigure 11Click the orange ‘Open’ button (Fig. 11) to open the Manage Trials window (Fig. 12)Click the ‘Actions’ button and select ‘Export Trial Book’ from the menu displayed (Fig. 12) to export a field data collection file (Fig. 13) Figure 12Click the orange ‘Export’ button to export files corresponding to all three locations to a specified location on your PC and open them (Fig. 14)Figure 13Figure 14Design & Manage Field TrialNow you will design the?field trial mentioned earlier to?evaluate 32 germplasm?entries for 7?phenotypic traits?replicated 3 times at?4 locations, using a?resolvable incomplete block design, specifically an alpha lattice design.?You will then export data collection sheets, add phenotypic data and other notes or comments, and then import the data back to the BMS database.Trial SettingsClick ‘Manage Trials’ hyperlink’ and click ‘Start a New Trial’ button (Fig. 15)Figure 15Click the ‘Add’ button at lower middle to establish basic trial details - Name the trial as it applies to your program, e.g. ‘CIMMYT 2012 Trial’ and give a meaningful description to the trial, e.g. ‘‘2012’. Leave the default settings for the other optional details (Fig. 15) Click the blue ‘Save’ button at any point in trial design and management process (Fig. 15)Select new folder to create new list (Fig. 16) (double check this)Figure 16Add a management detail to the trial setting (Fig. 17)Figure 17GermplasmClick ‘Import’ hyperlink at lower left of window to bring in a formatted?trial germplasm?list (.xls) (Fig. 18)?Figure 18Click ‘Browse’ hyperlink (Fig. 18) to the list, e.g. 'CIMMYT Trial Germplasm'iii. Click ‘Next’ to import?(Fig. 19)?Figure 19iv. Specify germplasm details (Fig. 20)Breeding Method: Unknown generative methodLocation:?Unknown?Date: BlankName Type: Line Name?Figure 20Set the?pedigree options to ‘Select existing germplasm?whenever found’ and click Finish (Fig. 21)Figure 21Click the orange ‘Save’ button to save the list with the imported list details (Fig. 22)Figure 22The germplasm list can now be viewed from the trial manager (Fig. 23)Figure 23?Treatment FactorsSince the trial in this example has no treatment factors, leave ‘Treatment Factors section blank (Fig. 24), else indicate as appropriate for the design chosenFigure 24EnvironmentsSpecify four environments for the trial and click ‘OK’. Four environments will now populate the screen (Fig. 25) Click the middle ‘Add’ button to specify location name as an environment detail (Fig. 25)Figure 25Search for ‘location’ in the dropdown menu and Add LOCATION_NAME (Fig. 26)Figure 26Add the location names to each environment.? Type the location name and select the match from the dropdown menu (Fig. 27). For this exercise, location names are: Environment 1: Agua Fria, Environment 2: Sabana Del Medio, Environment 3: Jutiapa, and Environment 4: Tlaltizapan?Figure 27Experimental Design (Fig. 28)Select Incomplete Block Design from the dropdown menu.Specify 3?replicates and a block size of 4Specifically this is an alpha lattice design, where all germplasm and replicates are represented at every location in incomplete blocks. ?The advantage of the alpha lattice design over a randomized complete block is the ability to control for environmental heterogeneity within a location.?For an alpha lattice design the number of germplasm entries must be evenly divisible by the size of?the block (32?germplasm / 4 plots per block = 8?blocks per replicate)Click the ‘Generate Design’ button at lower left to?populate the measurements tab with a matrix of 384 randomized trial entries (32 germplasm x 4 locations x 3 replicates = 384 plots) and associated file data Figure 28MeasurementsClick ‘Add’ button to add phenotypic traits to measure in the trial (Fig. 29)Figure 29Search for the six traits by typing details of the individual traits in the selection bar.? For example typing the first few letters of ‘Yield’ reveals all of the yield related measurements (Fig. 30)Figure 30Add the trait, GY, grain yield to the trial.?Repeat by?adding other traits of interest (Fig. 31), e.g.,Grain Yield (GY):?Shelled grain weight per plot adjusted to 12.5% grain moisture and converted to tons per hectareGrain Moisture (MOI):?Percentage of moisture as measured at harvestPlant Height (PH):?Height between the base of a plant to the insertion of the first tassel branch of the same plant in centimeters (cm)Average?Shelling Percentage?(aSP)?Ear Height (EH):?Height between the base of a plant to the insertion of the top (uppermost) ear of the same plant in centimeters (cm)Field Weight of Grain (FW)?Anthesis?Date (AD):?Days between planting and anthesisFigure 31Notice that the 384 trial entries are now associated with empty columns of trait data (Fig. 32)??Figure 32At this point the trial design is complete. The next task is to export data collection sheets, enter data, and import data back to the database in preparation for analysis. Export Trial BookClick the blue ‘Save’ to save the trial (Fig. 33)Click the ‘Actions’ button and select ‘Export Trial Book’ from the menu to export data collection sheets (Fig. 33)Figure 33Choose Excel from the list of export formats compatible with different handheld devices (Fig. 34)Set data collection order by plot. Serpentine order options are only available after a field map has been created (Fig. 34)Click ‘Export’ and choose a location for the file (Fig. 34)?Figure 34The export file is a single?zipped, or compressed, folder containing four Excel workbooks corresponding to each location?Navigate to the compressed folder and open to view the individual files (Fig. 35)Figure 35Import Trial DataClick the ‘Actions’ button and select ‘Import Measurements’ from the menu to import field observations (Fig. 36)Figure 36Browse and select the pre-formatted Site 1 Aqua Fria location data Click the orange ‘Import’ button. You must save the trial after the import of each location or subsequent imports will overwrite previous data (Fig. 37)Repeat the import process for the other locations Agua Fria Observations (xls)Sabana Observations (xls)Jutiapa Observations (xls)Tlaltizapan Observations (xls)Figure 37Confirm that the data has been uploaded by scrolling through the trait columns in the measurements tab (Fig. 38)Figure 38Click the blue ‘Save’ button before leaving the trial manager (Fig. 39)Figure 39 ................
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