Dairy cattle

Runs of Homozygosity, Conception Rate, and Calf Traits in Reconstituted Lost-Y Holstein Lineages

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Abstract

Y-chromosome lineages of all modern Holstein (HO) sires trace back to three bulls born in the 1960s. Using semen from the USDA National Animal Germplasm Repository mated to modern HO dams, we generated five bulls from two lost Y-chromosome lineages that had been present in the 1960s; semen from the five bulls was collected and distributed to commercial farms. This project aimed to: (1) assess sire fertility differences among Y-chromosome lineages, (2) evaluate differences in gestation length and birth weight, and (3) examine how reintroducing lost-Y lineages affected genomic inbreeding patterns. Inseminations (n=11,132) were performed on four commercial dairy farms using Holstein cows and service sires from three breed groups: modern HO (n=8,140), lost-Y (n=557), and Angus (n=2,435). Farm records provided 2,589 gestation lengths and 672 birth weights in total from the resulting outcross (75% modern HO, 25% lost-Y), modern HO, and Angus calves. Additionally, 128 lost-Y progeny and 172 modern HO herd mates were genotyped using 777K DNA markers. Data were analyzed with linear mixed models for gestation length and birth weight, or generalized linear mixed models for conception rate. Fixed effects included genetic lineage (modern HO, lost-Y, Angus), contemporary group, dam parity, insemination number (conception rate only), and calf sex (gestation length and birth weight only); random effects included dam and service sire. Estimated marginal means (EMM) were calculated for continuous traits, while logistic regression coefficients were back-transformed to probabilities for conception rate. Runs of homozygosity (ROH) were identified in PLINK (v1.9) to assess genome-wide and chromosomal homozygosity rates, and to distinguish ancient versus recent inbreeding. Significance was declared at P< 0.05 for all analyses. Conception probabilities ranged from 0.43 (Angus) to 0.53 (lost-Y) and did not differ significantly among lineages. Calves born to lost-Y sires had significantly longer gestation lengths (278.4 days) and higher birth weights (42.6 kg) than modern HO (275.7 days, 40.3 kg) or Angus (275.5 days, 40.2 kg). Outcross calves exhibited lower genome-wide homozygosity (11.87%) than modern HO (18.75%), with significantly reduced homozygosity on all autosomes except 25, 27, and 28. In particular, outcross calves showed less inbreeding from long (2.34% for ROH ≥16 Mb) and moderately long (2.69% for 8-16 Mb) ROH segments compared to modern HO (4.19% and 4.91%, respectively), indicating higher recent inbreeding in modern HO. We conclude that poor semen fertility due to variation in the Y-chromosome was an unlikely cause for the loss of these lineages from the modern HO breed. Additionally, selection for calving ease in modern HO may have concurrently reduced gestation lengths and birth weights. Germplasm repositories offer a valuable resource for reintroducing lost genetic diversity into livestock populations under intense selection.

Keywords: 2026

How to Cite:

Dechow, C., Liu, W., Kelley, H. & Blackburn, H., (2026) “Runs of Homozygosity, Conception Rate, and Calf Traits in Reconstituted Lost-Y Holstein Lineages”, World Congress on Genetics Applied to Livestock Production Digital Archive 2026(1): 2287345. doi: https://doi.org/10.31274/wcgalp.24270

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