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Users guide for Multi Environment Trial analysis with CloneSelector

Genotype by environment interaction, GxE, is one of the challenges in plant breeding and other experiments with plants. Testing across multiple environments is therefore a standard procedure in plant breeding as well as other experiments. The outcome of these experiments is data sets from multiple environments, and these need to be analyzed using statistical methods that allows the scientist to draw conclusions for example related to stability of a genotype across target environments or in relation to the genotypic performance with less interference of GxE. These different types of analysis have in CloneSelector been automated as MET analysis or Multi environment trial analysis.

It should be noted that the MET analysis generates many analytical outputs; however, the researcher must select the analytical outputs that are relevant to the particular trial or experiment, and ensure all assumptions are fulfilled. The MET analysis will for example produce different ANOVA tables, but you must choose the one that have the right combination of fixed and random effects. The MET analysis also produces for example plots of the data or residuals, and other types of analytical tools to assess if the assumptions for a particular analysis are fulfilled. CloneSelector aims to automate the task of carrying out the statistical analysis of a multi-environment trial, however, the researcher must interpret the outputs and ensure they are valid in relation to the particular experiment.

Before you can do the MET analysis you must have a series of experiments in CloneSelector where you have tested at least 3 clones in the same three 3 environments. Some of the tests can also be done for only 2 clones in 2 environments, but most of the analysis requires at least 3 clones that have been tested in at least 3 environments, if you have more clones and more environments that obviously also work. If your data is not in CloneSelector you may still be able to use the MET analysis, but it will require a bit of manual copy/paste – and we cannot guarantee that you will not have problems when trying to analyze non-CloneSelector data.