Open Access

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 Mariasegaram1, 2Email author,
  • Nicholas Andrew Robinson2 and
  • Michael Edward Goddard2, 3
Genetics Selection Evolution200739:267

https://doi.org/10.1186/1297-9686-39-3-267

Received: 2 March 2006

Accepted: 17 November 2006

Published: 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.

Keywords

selective DNA poolingdairy half-sib designgenome scanindividual selective genotyping

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Authors’ Affiliations

(1)
CSIRO Livestock Industries, Queensland Biosciences Precinct
(2)
Department of Primary Industries, Animal Genetics and Genomics Platform
(3)
Institute of Land and Food Resources, University of Melbourne

Copyright

© INRA, EDP Sciences 2007

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