Staff Publications

Staff Publications

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    'Staff publications' is the digital repository of Wageningen University & Research

    'Staff publications' contains references to publications authored by Wageningen University staff from 1976 onward.

    Publications authored by the staff of the Research Institutes are available from 1995 onwards.

    Full text documents are added when available. The database is updated daily and currently holds about 240,000 items, of which 72,000 in open access.

    We have a manual that explains all the features 

Record number 406592
Title Determination of genetic structure of germplasm collections: are traditional hierarchical clustering methods appropriate for molecular marker data?
Author(s) Odong, T.L.; Heerwaarden, J. van; Jansen, J.; Hintum, T.J.L. van; Eeuwijk, F.A. van
Source Theoretical and Applied Genetics 123 (2011)2. - ISSN 0040-5752 - p. 195 - 205.
DOI http://dx.doi.org/10.1007/s00122-011-1576-x
Department(s) Biometris (WU MAT)
Biometris (PPO/PRI)
Centre for Genetic Resources, The Netherlands
PE&RC
Publication type Refereed Article in a scientific journal
Publication year 2011
Keyword(s) multilocus genotype data - genome-wide association - forming core subsets - population-structure - data set - linkage disequilibrium - f-statistics - number - inference - diversity
Abstract Despite the availability of newer approaches, traditional hierarchical clustering remains very popular in genetic diversity studies in plants. However, little is known about its suitability for molecular marker data. We studied the performance of traditional hierarchical clustering techniques using real and simulated molecular marker data. Our study also compared the performance of traditional hierarchical clustering with model-based clustering (STRUCTURE). We showed that the cophenetic correlation coefficient is directly related to subgroup differentiation and can thus be used as an indicator of the presence of genetically distinct subgroups in germplasm collections. Whereas UPGMA performed well in preserving distances between accessions, Ward excelled in recovering groups. Our results also showed a close similarity between clusters obtained by Ward and by STRUCTURE. Traditional cluster analysis can provide an easy and effective way of determining structure in germplasm collections using molecular marker data, and, the output can be used for sampling core collections or for association studies.
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