Two-mode clustering of genotype by trait and genotype by environment data

Abstract

In this paper, we demonstrate the use of two-mode clustering for genotype by trait and genotype by environment data. In contrast to two separate (one mode) clusterings on genotypes or traits/environments, two-mode clustering simultaneously produces homogeneous groups of genotypes and traits/environments. For two-mode clustering, we first scan all two-mode cluster solutions with all possible numbers of clusters using k-means. After deciding on the final numbers of clusters, we continue with a two-mode clustering algorithm based on a genetic algorithm. This ensures optimal solutions even for large data sets. We discuss the application of two-mode clustering to multiple trait data stemming from genomic research on tomatoes as well as an application to multi-environment data on barley. © 2010 The Author(s).