Inbreeding depression has become an urgent issue in cosmopolitan breeds where the massive genetic progress achieved in the latest generations is counterbalanced by a dramatic loss of genetic diversity causing increased health issues. Thus, the aim of this study was to estimate inbreeding depression on productive traits in Holstein dairy cattle. More precisely, we aimed to i) determine the level of inbreeding in 27,735 Italian Holstein dairy cows using pedigree and genotype data, ii) quantify the effect of inbreeding on 305-d in milk yield (MY; kg), fat yield (FY; kg), and protein yield (PY; kg) based on different statistical approaches, iii) determine if recent inbreeding has a more harmful impact than ancestral ones, and iv) quantify chromosomal homozygosity effect on productive traits. Quality control was performed on the autosomal chromosomes resulting in a final dataset of 84,443 single nucleotide polymorphisms. Four statistical models were used to evaluate the presence of inbreeding depression, which included linear regression analysis and division of FPED and FROH into percentile classes. Moreover, FROH was partitioned into i) length classes to assess the role of recent and ancestral inbreeding and ii) chromosome-specific contributions (FROH-CHR). Results evidenced that inbreeding negatively impacted the productive performance of Italian Holstein Friesian cows. However, differences between the estimated FPED and FROH coefficients resulted in different estimates of inbreeding depression. For instance, a 1% increase in FPED and FROH was associated with a decrease in MY of about 44 and 61 kg (P < 0.01). Further, when considering the extreme inbreeding percentile classes moving from the 5th lowest to the 95th highest, there was a reduction of -263 kg and -561 kg per lactation for FPED and FROH. Increased inbreeding, estimated by FPED and FROH, had also a negative effect on PY and FY, either fit as a regressor or percentile classes. When evaluating the impact of inbreeding based on runs of homozygosity (ROH) length classes, longer ROH (over 8 Mb) had a negative effect in all traits, indicating that recent inbreeding might be more harmful than the ancestral one. Finally, results within chromosome homozygosity highlighted specific chromosomes with a more deleterious effect on productive traits.
Keywords: FPED; FROH; dairy cattle; genomics; inbreeding depression; production.
Inbreeding depression is a reduction in performance or health due to the mating of closely related individuals. The overall aim of this study was to investigate the level of inbreeding in the Italian Holstein dairy cow breed and quantify its negative effect on productive performances. The level of inbreeding was estimated by pedigree (FPED) and genomic data by looking at stretches of homozygosity (FROH). Both methods revealed a reduction in milk yield, fat yield, and protein yield when inbreeding increased. Moreover, the study demonstrated that FROH was able to capture more inbreeding depression compared to FPED. In addition, the more recent inbreeding had a stronger negative impact on productive performances compared to ancestral ones. Then, since the amount of runs of homozygosity can vary across the chromosomes of an individual, the effect of each chromosomal homozygosity region on productive traits was also evaluated. The chromosome-level results might be included in breeding programs to limit the accumulation of homozygosity in particular regions that appear to have a more detrimental effect on productive traits. Overall, this study highlights the importance of avoiding inbreeding in animal breeding programs to keep productive animals in the long term.
© The Author(s) 2023. Published by Oxford University Press on behalf of the American Society of Animal Science.