Comparison of homozygosity in SNP and ROH sites in Holstein dairy cows with high and low production levels.

Increased homozygosity resulted from mating of relatives is considered as one of the challenges faced in dairy farming industry which has attracted the attentions. This research has been conducted to measure homozygosity based on SNP and ROH in high- and low-producing Holstein cows. In current research, both random regression and pedigree index approaches were used to obtain candidate animals for genotyping process. The samples were obtained from 150 Holstein dairy cows (75 by high- and 75 by low-EBV for milk production). We proposed a suitable method, by integrating breeding value estimation calculated by random regression and pedigree index, to select the candidate animals for genotyping. The results showed that putting too much emphasis on production traits in high-producing dairy cows had negative impact on the traits associated with fertility (DPR = -0.55) and productive life (PL = 0.1). The calculated homozygosity based on ROH showed different amount of variation in different chromosomes in the cows with high and low production which may be related to uneven distribution of genes influencing production traits in different chromosomes.