Inbreeding depression of reproductive traits in Japanese Black cattle using genomic information

The objective of this study was to evaluate genomic inbreeding in Japanese Black cattle and its effects on reproductive traits. The study analyzed reproductive records and SNP data from Japanese Black cattle born between 2001 and 2005, resulting in 8,553 records from large farms. Genomic inbreeding was assessed using SNP data from 782 animals. Key reproductive traits analyzed included age at first calving (AFC) and calf production index (CPI). Statistical models were employed to estimate fixed effects and inbreeding depression. Findings indicated that genomic inbreeding levels were generally higher than traditional inbreeding coefficients. Significant inbreeding depression was observed in CPI but not in AFC. Specific chromosomes (12, 15, 27 for CPI and 4 for AFC) showed significant associations with inbreeding depression. Key genes related to reproduction were identified, particularly on chromosome 15. The study concludes that genomic inbreeding effectively detects inbreeding depression related to reproductive abilities in Japanese Black cattle. The results highlight the importance of genomic assessment in breeding practices to enhance reproductive performance while maintaining genetic diversity in the breed.