Free Access
Genet. Sel. Evol.
Volume 39, Number 6, November-December 2007
Page(s) 685 - 709
Published online 06 December 2007
Genet. Sel. Evol. 39 (2007) 685-709
DOI: 10.1051/gse:2007026

Interval mapping of quantitative trait loci with selective DNA pooling data

Jing Wanga, b, Kenneth J. Koehlerb and Jack C.M. Dekkersa

a  Department of Animal Science and Center for Integrated Animal Genomics, Iowa State University, Ames, Iowa 50011, USA
b  Department of Statistics, Iowa State University, Ames, Iowa 50011, USA

(Received 10 October 2006; accepted 21 May 2007; published online 6 December 2007)

Abstract - Selective DNA pooling is an efficient method to identify chromosomal regions that harbor quantitative trait loci (QTL) by comparing marker allele frequencies in pooled DNA from phenotypically extreme individuals. Currently used single marker analysis methods can detect linkage of markers to a QTL but do not provide separate estimates of QTL position and effect, nor do they utilize the joint information from multiple markers. In this study, two interval mapping methods for analysis of selective DNA pooling data were developed and evaluated. One was based on least squares regression (LS-pool) and the other on approximate maximum likelihood (ML-pool). Both methods simultaneously utilize information from multiple markers and multiple families and can be applied to different family structures (half-sib, F2 cross and backcross). The results from these two interval mapping methods were compared with results from single marker analysis by simulation. The results indicate that both LS-pool and ML-pool provided greater power to detect the QTL than single marker analysis. They also provide separate estimates of QTL location and effect. With large family sizes, both LS-pool and ML-pool provided similar power and estimates of QTL location and effect as selective genotyping. With small family sizes, however, the LS-pool method resulted in severely biased estimates of QTL location for distal QTL but this bias was reduced with the ML-pool.

Key words: selective DNA pooling / interval mapping / QTL

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© INRA, EDP Sciences 2007