Genome-wide association mapping for dominance effects in female fertility using real and simulated data from Danish Holstein cattle

Exploring dominance variance and loci contributing to dominance variation is important to understand the genetic architecture behind quantitative traits. The objectives of this study were i) to estimate dominance variances, ii) to detect quantitative trait loci (QTL) with dominant effects, and iii) to evaluate the power and the precision of identifying loci with dominance effect through post-hoc simulations, with applications for female fertility in Danish Holstein cattle. The female fertility records analyzed were number of inseminations (NINS), days from calving to first insemination (ICF), and days from the first to last insemination (IFL), covering both abilities to recycle and to get pregnant in the female reproductive cycle. There were 3,040 heifers and 4,483 cows with both female fertility records and Illumina BovineSNP50 BeadChip genotypes (35,391 single nucleotide polymorphisms (SNP) after quality control). Genomic best linear unbiased prediction (BLUP) models were used to estimate additive and dominance genetic variances. Linear mixed models were used for association analyses. A post-hoc simulation study was performed using genotyped heifers’ data. In heifers, estimates of dominance genetic variances for female fertility traits were larger than additive genetic variances, but had large standard errors. The variance components for fertility traits in cows could not be estimated due to non-convergence of the statistical model. In total, five QTL located on chromosomes 9, 11 (2 QTL), 19, and 28 were identified and all of them showed both additive and dominance genetic effects. Among them, the SNP rs29018921 on chromosome 9 is close to a previously identified QTL in Nordic Holstein for interval between first and last insemination. This SNP is located in the 3’ untranslated region of gene peptidylprolyl isomerase like 4 (PPIL4), which was shown to be associated with milk production traits in US Holstein cattle but not known for fertility-related functions. Simulations indicated that the current sample size had limited power to detect QTL with dominance effects for female fertility probably due to low QTL variance. More females need to be genotyped to achieve reliable mapping of QTL with dominance effects for female fertility.