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An entropy-based measure of founder informativeness

Published online by Cambridge University Press:  14 April 2005

M. HUMBERTO REYES-VALDÉS  and
CLAIRE G. WILLIAMS
M. HUMBERTO REYES-VALDÉS
Affiliation:
Departamento de Fitomejoramiento, Universidad Autónoma Agraria Antonio Narro, Buenavista, Saltillo, Coah., Mexico, C.P. 25315
CLAIRE G. WILLIAMS
Affiliation:
Nicholas School of the Environment and Earth Sciences, Duke University, Durham NC 27708, USA
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Abstract

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Optimizing quantitative trait locus (QTL) mapping experiments requires a generalized measure of marker informativeness because variable information is obtained from different marker systems, marker distribution and pedigree types. Such a measure can be derived from the concept of Shannon entropy, a central concept in information theory. Here we introduce entropy-based founder informativeness(EFI), a new measure of information content generalized across pedigrees, maps, marker systems and mating configurations. We derived equations for inbred- and outbred-derived mapping populations. Mathematical properties of EFI include enhanced sensitivity to mapping population type and extension to any number of founders. To illustrate the use of EFI, we compared experimental designs for QTL mapping for three examples: (i) different marker systems for an F2 pedigree, (ii) different marker densities and sampling sizes for a BC1 pedigree and (iii) a comparison of haplotypic versus zygotic analyses of an outbred pedigree. As an a priori generalized measure of information content, EFI does not require phenotypic data for optimizing experimental designs for QTL mapping.

Type
Research Article
Information
Genetics Research , Volume 85 , Issue 1 , February 2005 , pp. 81 - 88
Copyright
© 2005 Cambridge University Press