Visually-aided interpretation of results from a genome scan

Abstract

The availability of extensively phenotyped and deeply pedigreed animal datasets, together withcheap genotyping of genome-wide markers, leads to viable high-density genome scans. Thedesign of such a program can be critical. Steps should be taken to reduce bias fromconfounding polygenic effects, while generating high phenotypic variation amongst theanimals genotyped. Data analysis is a challenging area, with the need for balance between thespeed required to get timely results across the genome and the complexity required to exploitlinkage disequilibrium and haplotypes. With thousands of markers genotyped acrosspopulations and traits, the volume of results can become unwieldy. This is especially truewhere marker interactions or QTL epistasis are fitted. This paper reports on a tool used to helpinterpret such results.