Format

Send to

Choose Destination
See comment in PubMed Commons below
Genetics. 2009 Feb;181(2):755-65. doi: 10.1534/genetics.108.099218. Epub 2008 Dec 15.

Association mapping in outbred populations: power and efficiency when genotyping parents and phenotyping progeny.

Author information

1
Queensland Statistical Genetics, Queensland Institute of Medical Research, Brisbane, QLD 4029, Australia. s.chenoweth@uq.edu.au

Abstract

We develop expressions for the power to detect associations between parental genotypes and offspring phenotypes for quantitative traits. Three different "indirect" experimental designs are considered: full-sib, half-sib, and full-sib-half-sib families. We compare the power of these designs to detect genotype-phenotype associations relative to the common, "direct," approach of genotyping and phenotyping the same individuals. When heritability is low, the indirect designs can outperform the direct method. However, the extra power comes at a cost due to an increased phenotyping effort. By developing expressions for optimal experimental designs given the cost of phenotyping relative to genotyping, we show how the extra costs associated with phenotyping a large number of individuals will influence experimental design decisions. Our results suggest that indirect association studies can be a powerful means of detecting allelic associations in outbred populations of species for which genotyping and phenotyping the same individuals is impractical and for life history and behavioral traits that are heavily influenced by environmental variance and therefore best measured on groups of individuals. Indirect association studies are likely to be favored only on purely economical grounds, however, when phenotyping is substantially less expensive than genotyping. A web-based application implementing our expressions has been developed to aid in the design of indirect association studies.

PMID:
19087954
PMCID:
PMC2644963
DOI:
10.1534/genetics.108.099218
[Indexed for MEDLINE]
Free PMC Article
PubMed Commons home

PubMed Commons

0 comments
How to join PubMed Commons

    Supplemental Content

    Full text links

    Icon for HighWire Icon for PubMed Central
    Loading ...
    Support Center