NDLI: Determination of genetic structure of germplasm collections: are traditional hierarchical clustering methods appropriate for molecular marker data?

Content Provider	Springer Nature Link
Author	Odong, T. L. Heerwaarden, J. Jansen, J. Hintum, T. J. L. Eeuwijk, F. A.
Copyright Year	2011
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.
Starting Page	195
Ending Page	205
Page Count	11
File Format	PDF
ISSN	00405752
Journal	Theoretical and Applied Genetics
Volume Number	123
Issue Number	2
e-ISSN	14322242
Language	English
Publisher	Springer-Verlag
Publisher Date	2011-04-07
Publisher Place	Berlin/Heidelberg
Access Restriction	One Nation One Subscription (ONOS)
Subject Keyword	Biotechnology Biochemistry Plant Biochemistry Plant Genetics & Genomics Plant Breeding/Biotechnology Agriculture
Content Type	Text
Resource Type	Article
Subject	Genetics Medicine Biotechnology Agronomy and Crop Science

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