Abstract
BackgroundThe potential of combining multiple populations in genomic prediction is depending on the consistency of linkage disequilibrium (LD) between SNPs and QTL across populations. We investigated consistency of multi-locus LD across populations using selection index theory and investigated the relationship between consistency of multi-locus LD and accuracy of genomic prediction across different simulated scenarios. In the selection index, QTL genotypes were considered as breeding goal traits and SNP genotypes as index traits, based on LD among SNPs and between SNPs and QTL. The consistency of multi-locus LD across populations was computed as the accuracy of predicting QTL genotypes in selection candidates using a selection index derived in the reference population. Different scenarios of within and across population genomic prediction were evaluated, using all SNPs or only the four neighboring SNPs of a simulated QTL. Phenotypes were simulated using different numbers of QTL underlying the trait. The relationship between the calculated consistency of multi-locus LD and accuracy of genomic prediction using a GBLUP type of model was investigated.ResultsThe accuracy of predicting QTL genotypes, i.e. the measure describing consistency of multi-locus LD, was much lower for across population scenarios compared to within population scenarios, and was lower when QTL had a low MAF compared to QTL randomly selected from the SNPs. Consistency of multi-locus LD was highly correlated with the realized accuracy of genomic prediction across different scenarios and the correlation was higher when QTL were weighted according to their effects in the selection index instead of weighting QTL equally. By only considering neighboring SNPs of QTL, accuracy of predicting QTL genotypes within population decreased, but it substantially increased the accuracy across populations.ConclusionsConsistency of multi-locus LD across populations is a characteristic of the properties of the QTL in the investigated populations and can provide more insight in underlying reasons for a low empirical accuracy of across population genomic prediction. By focusing in genomic prediction models only on neighboring SNPs of QTL, multi-locus LD is more consistent across populations since only short-range LD is considered, and accuracy of predicting QTL genotypes of individuals from another population is increased.Electronic supplementary materialThe online version of this article (doi:10.1186/s12863-015-0252-6) contains supplementary material, which is available to authorized users.
Highlights
The potential of combining multiple populations in genomic prediction is depending on the consistency of linkage disequilibrium (LD) between single nucleotide polymorphism (SNP) and quantitative trait loci (QTL) across populations
When focusing in genomic prediction models only on the SNPs closely located to a QTL, the accuracy of predicting the QTL genotypes of individuals from another population increased, indicating that consistency of LD across populations is higher at shorter distances on the genome
The results do show that the accuracy of across and multi population genomic prediction could potentially be increased by focusing only on the neighboring SNPs of a QTL, for which the consistency of LD is higher across populations
Summary
The potential of combining multiple populations in genomic prediction is depending on the consistency of linkage disequilibrium (LD) between SNPs and QTL across populations. We investigated consistency of multi-locus LD across populations using selection index theory and investigated the relationship between consistency of multi-locus LD and accuracy of genomic prediction across different simulated scenarios. Marker information is used to predict breeding values for selection candidates based on estimated marker effects in a reference population consisting of individuals with phenotypes and marker genotypes. The accuracy of predicting genomic breeding values depends on the size of the reference population, the heritability of the trait, and on the level of family relationships between the reference population and selection candidates, e.g. The consistency of linkage phase across populations is found to be reasonable high at short distances on the genome [9, 12, 15], and depending on the degree of relatedness between the populations; the higher the relatedness between the populations, the higher the consistency of LD [12]
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