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

We studied the performance of traditional hierarchical clustering techniques using molecular marker data. In this study, 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 model-based cluster method (STRUCTURE). Traditional cluster analysis can provide an easy and effective way of determining structure in germplasm collections using molecular marker data.
Nous avons étudié la performance des techniques traditionnelles de classification hiérarchique en utilisant des données de marqueurs moléculaires. Dans cette étude, nous avons montré que le coefficient de corrélation cophénétique est directement lié à la différenciation des sous-groupes et peut donc être utilisé comme un indicateur de la présence de sous-groupes génétiquement distincts dans les collections du matériel génétique. Tandis qu’UPGMA a donné de bons résultats dans la préservation de distances entre les accessions, Ward a excellé dans la récupération des groupes. Nos résultats ont également montré une similitude étroite entre les groupes obtenue par Ward et par la méthode de groupe basée sur un modèle (STRUCTURE). L’analyse traditionnelle de groupes peut constituer un moyen facile et efficace de détermination de la structure dans les collections du matériel génétique à partir des données de marqueurs moléculaires.
Are traditional hierarchical clustering methods appropriate for genetic marker data?
Date of publication: 
Region Focus: 
East Africa
RUFORUM Conferences and Workshops
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Open Access
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Printed resource

About the RUFORUM 2010 Biennal Conference
"The 2010 RUFORUM Biennial Conference was the second in the series. The main objective of the Biennial conferences is to provide a platform for agricultural research for development stakeholders in Africa and beyond to actively exchange findings and experiences, while at the same time learning lessons towards improving performance of the agricultural sector and ultimately people’s livelihoods. The biennial conference is RUFORUM’s most comprehensive meeting for the diversity of stakeholders in agriculture. It is especially dedicated to graduate students and their supervisors, grantees in RUFORUM member universities and alumni. It is a platform for peer review, quality control, mentorship, networking and shared learning. This record contains an extended abstract accepted under the theme of Plant Breeding"