Genomic insights into young stock survival in Danish Jersey cattle: A breed-specific QTL on chromosome 10 and its regulatory potential.

Calf mortality during the rearing period is a major concern for dairy producers, impacting both profitability and animal welfare. A genome-wide association analysis of young stock survival (YSS) in Jersey cattle using whole-genome sequence variants identified a major QTL on chromosome 10 influencing survival at an early age. Within the QTL region, 27 variants were segregated in Jersey cattle but not in Holstein, suggesting a Jersey breed-specific locus associated with calf mortality. A strong colocalization signals were observed in lymph nodes between eQTL signals and five candidate variants. Gene-based association analysis identified several candidate genes. Comparison with Bos taurus assemblies revealed a 2 Mb gap region (BTA10:22499414-24,826,764), within which a 1 Mb segment remained unaligned to the Jersey-specific assembly, resulting in the absence of four lncRNA genes. Candidate genetic variants can be utilized in genetic selection to lower calf mortality to improve herd health in Jersey cattle.