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

Hageman, J A and Malosetti, M and van Eeuwijk, F A (2010) Two-mode clustering of genotype by trait and genotype by environment data. Euphytica, 183 (3). pp. 349-359.

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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.

Item Type: Article
Additional Information: This project was (co)financed by the Centre for BioSystems Genomics (CBSG) which is part of the Netherlands Genomics Initiative/Netherlands Organisation for Scientific Research.
Uncontrolled Keywords: Two-mode clustering, Biclustering, Genotype by trait interaction, Genotype by environment interaction, Metabolomics, Tomato, Barley, Two-mode k-means,Genetic algorithm
Author Affiliation: Biometris-Applied Statistics, P.O. Box 100, 6700 AC Wageningen, The Netherlands
Subjects: Crop Improvement
Divisions: Other Crops
Depositing User: Mr Siva Shankar
Date Deposited: 27 Mar 2012 05:30
Last Modified: 27 Mar 2012 05:37
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