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A strategy for QTL detection in half-sib populations

Published online by Cambridge University Press:  02 September 2010

D. J. de Koning ,
P. M. Visscher ,
S. A. Knott  and
C. S. Haley
D. J. de Koning
Affiliation:
Roslin Institute (Edinburgh), Roslin, Midlothian EH25 9PS Wageningen Agricultural University, Department of Animal Breeding, PO Box 338, 6700 AH Wageningen, The Netherlands
P. M. Visscher
Affiliation:
Institute of Ecology and Resource Management, University of Edinburgh, West Mains Road, Edinburgh EH9 3JG
S. A. Knott
Affiliation:
Institute of Cell, Animal and Population Biology, University of Edinburgh, West Mains Road, Edinburgh EH9 3JT
C. S. Haley
Affiliation:
Roslin Institute (Edinburgh), Roslin, Midlothian EH25 9PS
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Abstract

A statistical analysis strategy for the detection of quantitative trait loci (QTLs) in half-sib populations is outlined. The initial exploratory analysis is a multiple regression of the trait score on a subset of markers to allow a rapid identification of possible chromosomal regions of interest. This is followed by multiple marker interval mapping with regression methods within and across families fitting one or two QTLs. Empirical thresholds are determined by experiment-wise permutation tests for different significance levels and empirical confidence intervals for the QTLs' positions are obtained by bootstrapping methods. For traits with evidence for a significant single-QTL effect, an approximate maximum likelihood analysis is performed to obtain estimates of QTL effect and the probability of the QTL genotype for each parent of a group of half-sibs. The strategy is demonstrated in an analysis of previously published data on chromosome 6 and five production traits from a granddaughter design in dairy cattle. The results confirm and extend evidence for QTLs affecting protein percentage. Informativeness of markers limited the possibility of mapping more than one QTL on the same linkage group.

Keywords

dairy cattlegene mappingmilk proteinquantitative trait loci
Type
Research Article
Information
Animal Science , Volume 67 , Issue 2 , October 1998 , pp. 257 - 268
Copyright
Copyright © British Society of Animal Science 1998

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