Impact of increased heterozygosity on Nordic Total Merit traits in dairy cattle:Potential for mating strategy optimization

Mating decisions in dairy cattle are traditionally based on pedigree information. However, genomic information offers the potential to minimize inbreeding and increase heterozygosity in mating decisions by providing more precise estimates of the expected heterozygosity (eHe) and realized heterozygosity (rHe) compared to pedigree information. The underlying hypothesis is that increased heterozygosity in dairy cattle heifers results in a larger dominance effect and reduced inbreeding depression in purebred cattle. The aim of this study was to estimate the size of eHe and rHe using information from SNP markers. We assessed the effect of increased heterozygosity on milk, fat, and protein yields; overall conformation score for body, legs, and udder; milkability, and functional traits included in Nordic Total Merit Index in Holstein (HOL), Red Dairy Cattle (RDC), and Jersey (JER) cows. We calculated eHe SNP by SNP for all pairs of genotyped parents, and genome-wide eHe was determined as the mean heterozygosity across all SNPs. Pedigree inbreeding was also computed by tracing the pedigree back for 5 generations. Data from 5,423 HOL, 2,245 RDC, and 5,975 JER genotyped cows born in 2015, 2016, and 2017 were analyzed. The parents of all these cows were genotyped. Mean eHe and rHe levels were both 0.328 for HOL, 0.336 for RDC and 0.308 for JER, with SD between 0.007 and 0.008 for eHe and between 0.009 and 0.012 for rHe. Results indicated a significant effect of eHe, rHe, and pedigree inbreeding on milk, fat, and protein yields across all breeds. For HOL, a 1 percentage-point increase in eHe corresponded to an increase in 305-d yield of 125 kg of milk, 2.74 kg of fat, and 3.52 kg of protein. For RDC, the corresponding increases were 100 kg of milk, 2.96 kg of fat, and 2.88 kg of protein. For JER the effects were 53 kg of milk, 3.63 kg of fat and 2.35 kg of protein per heterozygosity percentage point. While effects of eHe were observed on conformation and functional traits, these effects were only significant for a subset of ...