Effects of the number of markers per haplotype and clustering of haplotypes on the accuracy of QTL mapping and prediction of genomic breeding values

Mario Pl Calus,Theo He Meuwissen,Egbert F Knol,Jack J Windig,Addie Lj Vereijken,Chris Schrooten,Roel F Veerkamp

doi:10.1186/1297-9686-41-11

Abstract

The aim of this paper was to compare the effect of haplotype definition on the precision of QTL-mapping and on the accuracy of predicted genomic breeding values. In a multiple QTL model using identity-by-descent (IBD) probabilities between haplotypes, various haplotype definitions were tested i.e. including 2, 6, 12 or 20 marker alleles and clustering base haplotypes related with an IBD probability of > 0.55, 0.75 or 0.95. Simulated data contained 1100 animals with known genotypes and phenotypes and 1000 animals with known genotypes and unknown phenotypes. Genomes comprising 3 Morgan were simulated and contained 74 polymorphic QTL and 383 polymorphic SNP markers with an average r2 value of 0.14 between adjacent markers. The total number of haplotypes decreased up to 50% when the window size was increased from two to 20 markers and decreased by at least 50% when haplotypes related with an IBD probability of > 0.55 instead of > 0.95 were clustered. An intermediate window size led to more precise QTL mapping. Window size and clustering had a limited effect on the accuracy of predicted total breeding values, ranging from 0.79 to 0.81. Our conclusion is that different optimal window sizes should be used in QTL-mapping versus genome-wide breeding value prediction.

Highlights

The use of genome-wide dense marker maps in animal breeding is becoming more common for both genomewide breeding value prediction and QTL detection
Increasing window sizes and lowering limitIBD for clustering haplotypes decreased the number of base and non-base haplotypes
Haplotype clustering and window size The aim of this paper was to investigate the effect of the number of surrounding marker alleles included in base haplotypes and the effect of clustering of base haplotypes based on IBD probabilities, on the accu

Summary

Introduction

The use of genome-wide dense marker maps in animal breeding is becoming more common for both genomewide breeding value prediction and QTL detection. In genome-wide breeding value prediction, the simplest model assumes that each allele of a marker locus has an effect on the trait of interest, i.e. that a simple regression on single or multiple SNP markers can be used as predictive model for the breeding value. Haplotypes can be constructed using marker alleles of two or more loci on the same chromosome. In this type of analysis, haplotypes are associated to the phenotypic values, and the summation of all haplotype effects gives the genomic breeding value of an animal.

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