Chapter 7: Prepare a field trial and analyze results

Chapter 7: Prepare a field trial and analyze results

1


Introduction ........................................................................................................................................... 2

Preparation ............................................................................................................................................ 2

Create a germplasm list for the trial ....................................................................................................... 2

Prepare the trial fieldbook ..................................................................................................................... 6

Basic details .............................................................................................................................................. 7

Settings ..................................................................................................................................................... 8

Germplasm ............................................................................................................................................... 9

Environments ......................................................................................................................................... 11

Experimental Design ............................................................................................................................... 12

Measurements ....................................................................................................................................... 12

Save the trial ........................................................................................................................................... 13

Export a file for data collection ............................................................................................................ 14

Import data into a trial ......................................................................................................................... 17

Analyze data ........................................................................................................................................ 19

View data ............................................................................................................................................. 26


2

Introduction In this tutorial the user will use the List Manager to choose lines from a nursery harvest

list, form a list of trial entries for a replicated field trial, prepare the Fieldbook for the

trial, load some data and do a single site analysis.

Preparation This tutorial continues from Sorghum_Tutorial_006 and the database status can be

restored to the end of that tutorial by restoring the file C:\Breeding Management

System\Documents\BMS Workbench_Nursery & Trial

Managers\Tutorials\Sorghum\Sorghum_Tutorial_006-201409.sql

Create a germplasm list for the trial

Click Manage Lists under the Breeding Activities menu and Browse for the F3B List

(click once to select).


3

Close the Browse for Lists window.

Click Show List Builder on the top right of the screen.

Select the first 20 entries from F3B List and drag them across to the new list on the

right.


4

We will now add a check entry to the 20 entries in the new list by selecting a line from

the female parent list. Click Browse again in the top part of the List Manager ssscreen,

select the list 2008FEMALE.


5

Tag the first entry, TIANDOUGOU-4, and drag it to the new list.

Click Save at the bottom of the new list and fill in the header information.

First click the (add folder) icon and name the folder as Trial Lists. Click to

save the folder.


6

Enter the list name Trial 1 Entries and description Germplasm entries for Trial 1.

Click Save.

Prepare the trial fieldbook

Click Manage Trials under the Breeding Activities menu, then Start a New Trial.


7

Basic details Complete the edit boxes in the Basic Details section:

Trial name = 2011T1

Description = Phenotyping Trial 1 in 2011

Objective = Germplasm evaluation

Creation date = 2011-06-05

Check the Use previously created trial as a template checkbox. Then click Choose.

Any trial which was created with the Trial Manager application may be

used as a template, or special formats may be created with the Trial

Manager and saved specifically as templates.

Navigate to the Templates folder in the Public Trials section and highlight Basic Trial

Template. Then click Select.


8

Settings Variables for recording management details have been retrieved from the template

and displayed on the Settings tab.

Specify the PI_NAME (name of Principal Investigator) and set the date.

Leave the study status as visible to all users with access.


9

The PMKEY is designed to record a link to a project management system containing

administrative information about the project to which this trial belongs. We do not

have a project management system for the Productivity improvement in Mali program

so remove the variable by clicking on the icon to the left of the variable name. The

Settings tab now looks like this:

You could add other Trial Settings variables by clicking on the Add button but we will

accept the defaults from the template.

Germplasm Click on the Germplasm tab to specify germplasm variables and entries. A table of

variables from the template is shown. We will include all the variables in this section.


10

Click Browse below the list of variables and click to highlight the Trial 1 Entries

germplasm list. Click Select.

The list of germplasm entries is displayed below the list of variables.

This trial is a pure variety trial so we will not add any other Treatment Factors. Click on

the Environments tab to proceed.


11

Environments The list of Trial Management variables and Trial Condition variables from the template

is shown. We will use all the variables from the template and we could add more

management variables or conditions by clicking Add at the top right of the appropriate

section and choosing variables from the ontology picker.

Set the number of environments to 1 (since this is a single site trial) and click Ok.

Variable entry boxes will be displayed for all variables and each environment.

Choose the Cooperator and the Site.

Leave the Soil pH blank as we generally don’t know conditions before actually

conducting the trial. Any variables (management or conditions) may be left blank on

this screen and their values can be added later when they are known.


12

Experimental Design Click on the Experimental Design tab and select Randomized Complete Block Design,

with 3 replications. Click Generate Design.

Measurements A randomized layout will be generated for each environment and you will be

transferred to the Measurements tab. The list of traits from the template will be

displayed.


13

A preview of the randomized measurements table is shown below the list of traits

which also appear as columns in the Measurements table.

Save the trial Click Save at the top left of the Trial Manager.


14

You can save a trial at any stage of the creation process and resume later.

Since this is the first time this trial has been saved, you are asked to choose a folder.

We will create a new folder Phenotyping Trials.

When the new folder appears under Program Trials, highlight it and click Select.

Export a file for data collection

From the Actions menu, select Export Trial Book.

Select Excel as the format, Plot order as the data collection order. Select trial

environment number 1 for export. Click Export to generate the data collection file.


15

The exported file has a Description sheet where management details and environment

conditions can be recorded if they were not entered during the trial creation process.

Enter the pH of the site 7.6 in the cell under the heading VALUE on line 32.

It also contains an Observation sheet where the measurements are recorded.


16

The file C:\Breeding Management System\Examples\sorghum\Sample Files\2011T1-

Data.csv contains fictitious data for the 2011T1 trial for trait DTFL (days to flag leaf).

Open this file with Excel, and also open the file you exported in the last section

(2011T1.xls). Copy and paste the data for DTFL column from the csv file into the trial

book 2011T1.xls:

Save your changes.


17

Import data into a trial

From the Actions menu, select Import Measurements.

Browse and navigate to the trial book file (2011T1.xls). Click Open, then Import.


18

The data will be loaded from the Excel file into the Measurements tab.

Click Save at the top of the page to store the data in the database.


19

Analyze data

Click Single-Site Analysis under the Statistical Analysis menu. Browse for a dataset to

analyze.


20

Expand the Phenotyping Trials folder and the 2011T1 trial (by clicking on the ► symbol

on both occasions). Highlight the PLOTDATA dataset then click Select.

Review the lists of variables in the dataset. Select the trait DTFL for analysis. (Check

then uncheck Select all, then tick the box next to DTFL).


21

Click Next at the bottom of the screen.

Specify options for the Breeding View analysis:

The default name is acceptable.

Select SITE as the factor which defines the environment (There is only one site

so check the SELECT box for this site)


22

The design type is Randomized block design.

The REP factor is already selected.

Select DESIGNATION for the germplasm factor to be used in the analysis.

Click Run Breeding View at the bottom of the screen.


23

Maximize the Breeding View application which appears in the task tray. Right-click on

the Quality control – phenotypes box and select Run pipeline from the popup menu.

The complete analysis will run for the selected trait(s) and a report will be generated:


24

The report contains a section summarizing the results of the analysis of all traits, and

then a section with the detailed results for each trait. Near the top of the report is a

link to a file of estimates of line means (BLUPS on one sheet and BLUES on another) for

the each trait which can be opened by clicking on the link. The report, graphs and file of

BLUPS are all stored in the directory

C:\Breeding Management System\workspace\Productivity improvement in

Mali\breeding_view\output\Sotuba\

One of the tabs is Quality Assurance which shows data points detected as potential

outliers.


25

When satisfied with the analysis, click Upload to BMS on the menu bar at the top of

the Breeding View screen.


26

The means will be loaded into the database.

Close the Breeding View application.

View data

Click Browse Studies under the Information Management menu.

Search for a study to view.


27

Type in 2011 as the year of the Start Date, then click Search.

Click on the 2011T1 study. Notice that a tab for study 2011T1 has appeared in the

background. Close the Search Studies window.

Expand the Datasets section by clicking once on the header.


28

Click the PLOTDATA dataset to view measurements for study 2011T1.


29

Click the MEANS dataset to view the trait means generated by Breeding View. A large

number of summary statistics are saved on the trial environment dataset including

overall means, variances and heritability.

Chapter 7: Prepare a field trial and analyze results

Documents

Transcript of Chapter 7: Prepare a field trial and analyze results