Hotel Estoril Eden, Monte Estoril,
5-8 October 2005



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nvestigating Linkage Disequilibrium in Collections of Plant Cultivars and Accessions

Maria Joćo Paulo and Fred van Eeuwijk
Max Plack Institute for Plant Breeding Research, Cologne, Germany
Lab. of Plant Breeding, Wageningen University, Wageningen, The Netherlands

In recent years plant geneticists have started to genotype historical collections of plant cultivars and accessions for which they possessed already phenotypic information Subsequently, diversity analyses and linkage disequilibrium analyses are performed on the genotypic and phenotypic data. These analyses raise a number of problems like;

How to detect and quantify population substructure?
How to detect and quantify linkage disequilibrium between markers?
How to detect association between markers and traits?
How to account for multiple testing in linkage disequilibrium and association analyses?

How to account for population substructure in marker - trait association analyses?  

In the presentation we will look at the analysis of a data set and discuss problems and solutions related to the above questions.