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Haplotype-assisted genomic evaluations in Nordic Red dairy cattle
In admixed populations originating from different base breeds, such as Nordic Red dairy cattle, haplotypes of chromosomal segments instead of single SNP are expected to improve prediction accuracy in genomic evaluations, because linkage disequilibrium with QTL is likely to be more consistent for haplotypes than for SNP. The suggested evaluation approach consists of (i) pre-selecting a limited number of chromosomal segments based on a genome-wide QTL-scan with BayesB, (ii) estimating relative variances of haplotype markers with BayesA, and (iii) obtaining solutions for haplotype effects from mixed model equations including pedigree-based animal effects. For three production traits (milk, protein, fat) and fertility, the highest validation test reliabilities R2 were 0.48, 0.41, 0.42 and 0.33, respectively. For milk, protein and fertility, we observed an improvement over G-BLUP of 3, 1 and 3 %-units, respectively, whereas for fat, a decline of 1 %-unit.
Keywords:
Nordic Red dairy cattle
genomic evaluation
haplotype
