Whole-genome evaluation of complex traits using SNP, haplotype, or QTL information
Whole-genome technologies provide rich data for dissection of complex traits. While gene discovery is still largely limited, the data at hand can be successfully used for evaluation of genetic merit. The aim of this work was to demonstrate the value of different sources of information (pedigrees, Single Nucleotide Polymorphisms – SNP, haplotypes, or Quantitative Trait Loci – QTL) for genetic evaluation of non-phenotyped individuals in a typical animal breeding scenario via simulation. In the first step a coalescent simulation was used to create a base population with structured chromosomes that were in the second step dropped and recombined through the pedigree of 10 generations with 50 sires per generation, 10 dams per sire, and 2 offspring per dam. Phenotypic values were simulated with different genetic architectures (QTL effects were sampled from Gaussian or gamma distribution and minor allele frequency less than 0.3) and heritability of 0.25. Genotypic data was available for all individuals from generation 4 onwards, while phenotypic data was available for individuals in generations 4 and 5. Genetic evaluation was based on linear mixed models with relationship matrix between individuals. This matrix was built using pedigree, SNP, haplotype, or QTL data. Haplotypes of different length were considered (from 5 to all the way up to 2000 SNP) with an option to account for similarities between haplotypes while building relationship matrices. The accuracy of different methods was assessed by correlation between true and evaluated additive genetic values for individuals in generations 6, 8 and 10. Average accuracy over ten replications for Gaussian trait over generations was between 0.45 to 0.10 for pedigree data, 0.50 to 0.35 for SNP and haplotype data and 0.6 to 0.4 for QTL data. In the case of long haplotypes accuracies dropped considerably, but accounting for similarities between haplotypes prevented this drop. In the case of gamma trait accuracies were slightly higher in generation 6 and dropped faster in the later generations in the case of pedigree, SNP, and haplotype data due to recombinations. On the other hand accuracies were substantially higher with QTL data and quite stable over generations (from 0.75 to 0.65) though still far from perfect (even though QTL genotypes are known), due to estimation errors. Results demonstrate the value and limitations of genotypic information for the evaluation of additive genetic merit in animal populations.