The BMS links with a Statistical Analysis package called Breeding View. This package is propriety software developed by VSNi and is based on Genstat and uses ASREML for mixed model analysis of plant breeding trials. Breeding View is designed to perform routine analysis for plant breeding quickly. It is not as versatile as a statistical package, such as the full version of Genstat, which is required for research analysis.

Objectives

At the end of this tutorial, the user should be able to:

1. Specify single site analysis for a trial in BMS
2. Run Single site analysis with Breeding View and save the means back to BMS
3. Specify a GxE analysis for trial means for a study in BMS
4. Run the GxE analysis with Breeding View.

Install and License Breeding View

Breeding View is a stand alone program which must be downloaded to your windows 64 bit computer, and installed. Before you can use it you must supply a license key by clicking Help>Activate license:

Once the license is activated, you can use Breeding View, but it usually requires an internet connection to check the validity of the license before running. More information about installing and licensing Breeding View is in the manual.
https://bmspro.io/1937/breeding-management-system-manual-40/install-breeding-view-statistical-application

Specify single site analysis for a trial in BMS

From the STUDIES menu select Single-Site Analysis:

Browse for the study containing the data to be analyzed. We will select the trial “SimTrial” which has 16 genotypes x 3 reps at 5 sites, and the randomization for a Randomised Complete Block design has been imported for the trial.

Highlight the file and click Select.
The Study will open and display the factors it contains:

By default, all the traits are selected for Analysis – only one trait in the example. Deselect those which do not require analysis.

Any of the non-analyzed variables can be specified to be covariates in an analysis of covariance for the analysed variables. We will not specify any covariates. Click Next.

On the form to Specify Options for Breeding View Analysis, you must

1. Site/Environment: first select the variable which distinguishes between sites. You often will select the LOCATION_NAME. We will select TRIAL_INSTANCE and select all sites.
2. Design details: These fields will be filled out if you have designed the trial in the BMS. You need to specify the design type if you have imported the trial design – here Randomised Complete Block. Only the fields with “*” need filling.
3. Genotypes: Usually the best is “DESIGNATION”

Note : BV (Breeding View) icon on the desktop

Once complete, click on the bottom button “Download Input files”.  This will download a zip file with the name of the study.zip – SimTrial.zip in the example.

Notice the green and white “BV” button on the desktop toolbar at the bottom outside the BMS.

You need to extract the files from this zip file into a directory where the analysis will be performed. There are two files in the zip, one csv file which contains the data to be analysed and an xml file which contains the instructions for the analysis.

Running Breeding View for Single Site Analysis

You now leave the BMS as it is and open the Breeding View (BV) on your desktop.  In BV you go to “Open project “on the top toolbar and browse for the xml file you just created and open.

The Single Site Analysis pipeline is now populated.

Clicking on the “Quality control phenotypes” box reveals two options:

“Settings” – you can add extra statistics to be displayed in the output eg “Boxplots”

“Run selected environment pipelines” -this will begin the analysis and you will see its progress on your screen in the bottom left-hand corner.  Wait until you see “Pipeline complete”.

In the report, you will see the heritability for each site – take note of the values.

A quality Assurance report is there for each site and shows outliers.

You should check if there are reasons why these outliers are identified such as part to the bag of grain spilt or part of the plot missing. Once you have eliminated these possibilities, you can choose to make these outliers as missing.  The other reps of the entry with an outlier are tabled at the bottom to aid in your decision. You can set a plot to “missing” and rerun the pipeline.  If the heritability is improved by removing outliers, this seems good reason to leave them out.  If the heritability is worse or not improved, put the outliers back in and re-run.

In this example, the outlier in environment 3 is set to missing.  Note the other reps of this entry “12” are at the bottom.

Running it again shows an improved heritability for this site - so keep it out.

When you save the project, a directory is found in your download saying “Upload”. 

Within that directory will be at least one zip file (choose last one as there will be one there from each time you ran the pipeline.) 

Now return to the BMS where you left it.  Upload the zip file (note you don’t unzip) by browsing for it within the BMS and upload.

The Single Site Data analysis is now in the BMS and when you open the “SimTrial” study under “Manage studies”, you will see a tab “SSA Results” with summary statistics of Heritability and CV for each site/trait.  There are also the Means (BLUES) for each site/trait.

Multi-site Analysis

From the STUDIES menu on the BMS, select Multi-Site Analysis and browse to the study for which you have uploaded means and for which you wish to do a multi-site analysis. You need at least three sites for a GxE analysis and four or more is better.

As with the single site analysis you are asked to specify the variable defining sites as before and for genotypes – usually DESIGNATION. Next the form asks if your environments are already grouped in some way which would account for significant GxE interactions. Usually, we do not know about groupings at the early stage, and mostly do not have enough environments for subsets, so leave this as is.

Next is a form for the Details of the selected Dataset

This allows you to eliminate environments for which there is insufficient data or for which the heritability is too low, and similarly at the bottom you can eliminate traits. 

Click “Download Input files”.  This will download a zip file with three files, one of which is the xml file for means that will be the input to Breeding View. You will unzip this file.

As before, leave the BMS and open Breeding View on your desktop. In BV open the project by browsing for the xml means file. This will populate BV but this time with the Multi-site Analysis flow diagram.

Once you run the pipeline, there will be a directory with a date-stamp as shown.

Within this directory are files of what is generated about association of sites (eg, heat maps) and stability measures. There is a detailed explanation about the report in the manual at: v21 Genotype by Environment Analyses

The most important of these files encompasses this correlation of sites and the stability of lines.  They are

• GxE_Means and
• GGE biplot mega environs

The GxE means table looks like this.

It needs simplification and rearranging to group sites according to the GGE biplot mega environs.

The GGE Biplot cluster showed sites 1, 3 and 4 were giving similar ranking and should be considered together, and they were different to sites 2 and 5. 

Thus, presenting the data according to these clusters reveals some interesting conclusions. So, the GxE table above then is arranged as:

So, putting sites 1,3 and 4 together reveals patterns that may be overlooked otherwise eg Meghan1 is very high yield in cluster one only, Bert1 has good yield but is very variable and Meghan5 Check is only adapted to site 5.