Breeding and Genetics: Dairy Cattle Breeding II– Applied molecular biology and genomics

The objective of the present study was to assess the effects of genomic inbreeding on production, reproduction, and udder health in Holstein dairy cows. First and second lactation data were collected from 1,061 Holstein dairy cows, which were born between 2006 and 2008, from 5 commercial herds across the United States. All cows were genotyped for 54,609 single nucleotide polymorphism (SNP) markers. SNPs were edited based on call rate and allele frequency. The remaining SNPs were separated into SNPs that were or were not in Hardy-Weinberg (HW) equilibrium. The SNPs that were not in HW equilibrium were assumed to be under selection and were removed from the analysis of genomic inbreeding. Homozygosity of the remaining 43,398 SNPs that were in HW equilibrium was calculated and utilized as the measure of genomic inbreeding in this study. Average homozygosity was 66.7 ± 1.6%, with a minimum and maximum of 60.4 and 75.3% respectively, and cows with a greater percentage homozygous loci were assumed to be more highly inbred. Total lactation milk, fat, and protein yield decreased by 15.8, 1.4, and 0.6 kg, respectively, per 1% increase in homozygosity. Furthermore, days open increased by an average of 1.96 d per 1% increase in homozygosity, but somatic cell score did not change with an increase in homozygosity. The results presented herein suggest a possible relationship between increasing homozygosity and decreasing lactation performance and reproductive ability.