Genome-wide linkage scan on estimated breeding values for a quantitative trait

BACKGROUND: A genome-wide linkage scan was performed on Replicate 1 of the simulated data for fasting triglyceride levels. The aim of this study was to implement mixed-model methodology to estimate breeding values for each individual for this trait and to assess the merit of these breeding values in linkage analysis. These breeding values utilize all the pedigree information, and the genetic and phenotypic correlations with other measured traits across the two cohorts. A genome-wide linkage scan was run on both the new breeding value traits and the original traits. RESULTS: Using breeding values, a maximum LOD of 7.78 was found on chromosome 5 at a position very close to a gene underlying the triglyceride levels. This effect was not detected using the original trait. CONCLUSION: The results imply that estimating breeding values may be a suitable method of deriving traits for use in genome-wide scans.