Mapping of Female Fertility Traits in Nordic Red Dairy Cattle Using 50K and High Density Genotypes

Fertility disorders are causing economic losses to dairy farms due to replacement costs, veterinary costs and longer intervals between calving and next pregnancy.  Detected LD markers could be placed on genotyping chips in order to be typed in the cow population. We have performed genome-wide association analysis in a sample of 4115 admixed Nordic red dairy cattle AI bulls with Illumina 50K genotypes. In addition HD genotypes were available for 706 bulls and these were used to impute the rest of the data to HD using Beagle software.  The mapping was carried out using single marker association with a mixed model  where the admixture was accounted for by a group effect from the output of the STRUCTURE software.  All except the sex chromosome were analyzed using the 50K data.  Areas with significant or close to significant associations were re-analyzed using HD data. Significant associations were detected on BTA 1, 6, 12, 17, and 18 using 50K data. In addition areas close to significant were found on BTA 2, 8, and 9. Out of these associations the areas on BTA6, 9, and 12 showed stronger associations with new SNPs on the HD chip. The QTL on BTA12 has earlier been shown to be a deletion affecting embryo mortality.