Genomic signatures of long-term selection in the Langhill dairy herd: the power of a five-decade experiment for sustainable dairy cattle breeding

The Langhill dairy herd experiment, initiated in 1973, is one of the longest-running dairy cattle selection trials in the world, with a control line maintained under similar management conditions. Researchers compared two genetic lines, a Select line sire by top-performing bulls and a Control line sire by average-performing bulls.

The Select line exhibited expected gains in milk yield traits, while both lines showed equivalent inbreeding rates. Effective population size, determined by the inbreeding rate, was approximately 33. Linkage disequilibrium was higher in the Select line across marker distances ranging from 2 to 300 kb. The Select line also demonstrated 24.7% higher autozygosity than the Control line (0.078 versus 0.063).

This observed excess was confined to runs of homozygosity greater than 2 Mb, suggesting that the divergence occurred after the lines were split, not due to a narrower sire pool or different numbers of sires. Twenty-eight regions on thirteen chromosomes exhibited strong differentiation, with five scans converging on a four-method signal on chromosome 21 associated with the SERPINA gene cluster.

The study concludes that selection in the Langhill herd left two genomic footprints: diffuse inbreeding resulting from the narrow ancestry of the elite sire pool, and localized differentiation at specific loci. Autozygosity itself did not localize to any region.