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

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.selective DNA pooling / dairy half-sib design / genome scan / individual selective genotyping

Detection of QTL for growth rate in the blacklip abalone (Haliotis rubra Leach) using selective DNA pooling

“…1998). Although using raw heights without such corrections could conceivably result in a loss in accuracy, the assumption that PCR amplification of pools from the same parents, under identical conditions, produces similar stutter and differential amplification patterns were found to be valid, as also observed by Mariasegaram et al. (2007).…”

“…A variant of this problem has been noted before when selective DNA pooling has been applied to half‐sib mapping populations in livestock, where the contribution of sire‐type alleles by the dams can cause significant bias to the pooled allele ratios (Cobanoglu et al. 2005; Mariasegaram et al. 2007), in some cases causing false positive results.…”

“…the larger‐sized allele in base pairs, or H L ) to obtain H S / H L . A linear model was used to analyse the ratio of allele heights in each of the two DNA pools (Mariasegaram et al. 2007) and a single F ‐test was used to accept or reject the null hypothesis that there were no overall differences in the parental allele ratio between the high and low pools for any of the markers analysed.…”

“…2002). In addition, methods to simplify analysis of allele ratio differences using pooled DNA have been successfully employed (Mariasegaram et al. 2007); however, to date these have not been evaluated in pooling designs using large full‐sib families that are typical in aquaculture species.…”

A Whole Genome Scanning for QTL Affecting Leg Weakness and Its Related Traits in a White Duroc × Erhualian Resource Population

“…The natural populations from farms can be applied in QTL mapping in these species with less statistical power. The half-sib design and the grand-daughter design are two mainly methods used in QTL mapping of dairy cattle (Heyen et al, 1999;Bennewitz et al, 2003;Mariasegaram et al, 2007).…”