Yi. Ronin et al., Selective genotyping to detect quantitative trait loci affecting multiple traits: interval mapping analysis, THEOR A GEN, 97(7), 1998, pp. 1169-1178
Segregating quantitative trait loci can be detected via linkage to genetic
markers. By selectively genotyping individuals with extreme phenotypes for
the quantitative trait, the power per individual genotyped is increased at
the expense of the power per individual phenotyped, but linear-model estima
tes of the quantitative-locus effect will be biased. The properties of sing
le- and multiple-trait maximum-likelihood estimates of quantitative-loci pa
rameters derived from selectively genotyped samples were investigated using
Monte-Carlo simulations of backcross populations. All individuals with tra
it records were included in the analyses. All quantitative-locus parameters
and the residual correlation were unbiasedly estimated by multiple-trait m
aximum-likelihood methodology. With single-trait maximum-likelihood, unbias
ed estimates for quantitative-locus effect and location, and the residual v
ariance, were obtained for the trait under selection, but biased estimates
were derived for a correlated trait that was analyzed separately. When an e
ffect of the QTL was simulated only on the trait under selection, a "ghost"
effect was also found for the correlated trait. Furthermore, if an effect
was simulated only for the correlated trait, then the statistical power was
less than that obtained with a random sample of equal size. With multiple-
trait analyses, the power of quantitative-trait locus detection was always
greater with selective genotyping.