GGE analyses for multi-environment studies

Published at May 31, 2023 · 12 min read

In a recent post we have seen that we can use Principal Component Analyses (PCA) to elucidate the â€˜genotype by environmentâ€™ relationship (see this post). Whenever the starting point for PCA is the doubly-centered (centered by rows and columns) matrix of yields across environments, we talk about AMMI analysis, which is often used to get insight into the stability of genotype yields across environments.

By changing the starting matrix, we can obtain a different perspective and put focus on the definition of macroenvironments and on the selection of winning genotypes. In particular, if the two-way matrix of yields across environments is only column-centered before PCA, we talk about GGE analysis (Yan et al., 2000). In spite of some academic debate (see Gauch, 2006, Yan et al., 2007, Gauch et al., 2008), AMMI and GGE analyses are both useful and can be used as two complementary tools for the analysis of multi-environment genotype data.

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