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

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.

Authors: 
J.A. Hageman, M. Malosetti, F.A. van Eeuwijk
Authors from the NMC: 
DOI: 
10.1007/s10681-010-0236-6
Pages: 
2012; 183 (3): 349-359
Published in: 
Euphytica
Date of publication: 
February, 2012
Status of the publication: 
Published/accepted