Genet. Sel. Evol. 39 (2007) 267-283
DOI: 10.1051/gse:2007003

Empirical evaluation of selective DNA pooling to map QTL in dairy cattle using a half-sib design by comparison to individual genotyping and interval mapping

Maxy Mariasegaram^{a, b}, Nicholas Andrew Robinson^b and Michael Edward Goddard<sup>b, c

a</sup>  CSIRO Livestock Industries, Queensland Biosciences Precinct, 306 Carmody Road, St Lucia QLD 4067, Australia
^b  Animal Genetics and Genomics Platform, Department of Primary Industries, Victoria 3049, Australia
^c  Institute of Land and Food Resources, University of Melbourne, Victoria 3010, Australia

(Received 2 March 2006; accepted 17 November 2006 ; published online 14 April 2007)

Abstract - This study represents the first attempt at an empirical evaluation of the DNA pooling methodology by comparing it to individual genotyping and interval mapping to detect QTL in a dairy half-sib design. The findings indicated that the use of peak heights from the pool electropherograms without correction for stutter (shadow) product and preferential amplification performed as well as corrected estimates of frequencies. However, errors were found to decrease the power of the experiment at every stage of the pooling and analysis. The main sources of errors include technical errors from DNA quantification, pool construction, inconsistent differential amplification, and from the prevalence of sire alleles in the dams. Additionally, interval mapping using individual genotyping gains information from phenotypic differences between individuals in the same pool and from neighbouring markers, which is lost in a DNA pooling design. These errors cause some differences between the markers detected as significant by pooling and those found significant by interval mapping based on individual selective genotyping. Therefore, it is recommended that pooled genotyping only be used as part of an initial screen with significant results to be confirmed by individual genotyping. Strategies for improving the efficiency of the DNA pooling design are also presented.

Key words: selective DNA pooling / dairy half-sib design / genome scan / individual selective genotyping

Correspondence and reprints: maxy.mariasegaram@csiro.au

© INRA, EDP Sciences 2007