Non-iterative variance component estimation in QTL analysis

• In variance component quantitative trait loci (QTL) analysis, a mixed model is used to detect the most likely chromosome position of a QTL. The putative QTL is included as a random effect and a method is needed to estimate the QTL variance. The standard estimation method used is an iterative method based on the restricted maximum likelihood (REML). In this paper, we present a novel non-iterative variance component estimation method. This method is based on Henderson's method 3, but relaxes the condition of unbiasedness. Two similar estimators were compared, which were developed from two different partitions of the sum of squares in Henderson's method 3. The approach was compared with REML on data from a European wild boar x domestic pig intercross. A meat quality trait was studied on chromosome 6 where a functional gene was known to be located. Both partitions resulted in estimated QTL variances close to the REML estimates. From the non-iterative estimates, we could also compute good approximations of the likelihood ratio curve on the studied chromosome.

Subject headings

NATURVETENSKAP  -- Biologi (hsv//swe)

NATURAL SCIENCES  -- Biological Sciences (hsv//eng)

LANTBRUKSVETENSKAPER  -- Veterinärmedicin (hsv//swe)

AGRICULTURAL SCIENCES  -- Veterinary Science (hsv//eng)

LANTBRUKSVETENSKAPER  -- Husdjursvetenskap (hsv//swe)

AGRICULTURAL SCIENCES  -- Animal and Dairy Sience (hsv//eng)

NATURVETENSKAP  -- Matematik -- Sannolikhetsteori och statistik (hsv//swe)

NATURAL SCIENCES  -- Mathematics -- Probability Theory and Statistics (hsv//eng)

Keyword

Henderson's method 3

minimized mean square error

quantitative trait loci analysis

restricted maximum likelihood

variance components

Biology

Biologi

Complex Systems – Microdata Analysis

Publication and Content Type

ref (subject category)

art (subject category)