Abstract
Inbreeding depression in dairy production is an extensively studied phenomenon. However, we are not aware of a single study that has estimated inbreeding depression concerning sex-chromosome. Using Bayesian inference, we analyzed inbreeding depression in milk yield (4,749 Czech Holstein cows genotyped for >40,000 SNPs with milk yield in the first lactation) in terms of the combined effect of inbreeding (per 1% increase) obtained from autosomes and sex-chromosome. We used three models, each based on different estimated inbreeding coefficients (pedigree, ROH>4Mb, or ROH>8Mb). Significant inbreeding depression estimates for autosomes were observed in all three models (medians; bFPED=-13.2 kg, bFROH>4Mb=-30.0, and bFROH>8Mb=-34.4 kg), while significant inbreeding depression was observed only for pedigree sexchromosome estimates (medians; bFPED-sex=-7.6 kg, bFROH>4Mb-sex=-0.1 kg, and bFROH>8Mb-sex=3.9 kg). Low genomic correlations between inbreeding estimated from autosomes and sex-chromosome argue for the need to estimate inbreeding depression from sex-chromosome.
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