Impact of Genome-Wide and Regional Inbreeding on Semen Production Traits in Beef and Dairy Bulls

To evaluate inbreeding depression, which is a reduction in the phenotypic mean of a population due to mating between close relatives, for semen production traits in cattle, it is necessary to understand inbreeding depression both regionally and across the genome. This study aimed to investigate genome-wide and regional inbreeding depression in semen production traits in Japanese Black bulls (JB) and Holstein bulls (HOL). The present study used 615 JB and 873 HOL with a 50K single-nucleotide polymorphism (SNP) BeadChip and five semen production traits. First, we estimated the regression coefficients of the semen production traits on pedigree-based and genomic inbreeding coefficients. Our results indicated significant negative effects of inbreeding on four semen production traits in JB, whereas only one trait was significantly affected in HOL. Second, we performed genome-wide association studies to identify run of homozygosity (ROH) regions that had an unfavorable effect on the traits. Our results showed no significant SNPs in JB; however, SNPs on chromosomes 7 and 17 were significantly associated with sperm quality in HOL. This study revealed that semen production traits are influenced by genome-wide and regional inbreeding depression in JB and HOL, although the effects vary depending on the target population.