Bias correction for estimated QTL effects using the penalized maximum likelihood method.

Abstract:

:A penalized maximum likelihood method has been proposed as an important approach to the detection of epistatic quantitative trait loci (QTL). However, this approach is not optimal in two special situations: (1) closely linked QTL with effects in opposite directions and (2) small-effect QTL, because the method produces downwardly biased estimates of QTL effects. The present study aims to correct the bias by using correction coefficients and shifting from the use of a uniform prior on the variance parameter of a QTL effect to that of a scaled inverse chi-square prior. The results of Monte Carlo simulation experiments show that the improved method increases the power from 25 to 88% in the detection of two closely linked QTL of equal size in opposite directions and from 60 to 80% in the identification of QTL with small effects (0.5% of the total phenotypic variance). We used the improved method to detect QTL responsible for the barley kernel weight trait using 145 doubled haploid lines developed in the North American Barley Genome Mapping Project. Application of the proposed method to other shrinkage estimation of QTL effects is discussed.

journal_name

Heredity (Edinb)

journal_title

Heredity

authors

Zhang J,Yue C,Zhang YM

doi

10.1038/hdy.2011.86

subject

Has Abstract

pub_date

2012-04-01 00:00:00

pages

396-402

issue

4

eissn

0018-067X

issn

1365-2540

pii

hdy201186

journal_volume

108

pub_type

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