Genetic gain & Inbreeding

Inbreeding trends from 1991 to 2025 in > 1.1 million genotyped purebred beef and dairy cattle.

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Abstract

Widespread genotyping and genomic selection have enabled more intensive selection and wider dissemination of elite sires, this raises concerns about losses in genetic diversity and increased accumulation of population-level inbreeding. The aim of this study was to quantify inbreeding trends estimated from runs of homozygosity (FROH) called from medium-density single nucleotide polymorphism (SNP) data and separately from pedigree-based estimates of inbreeding (FPED) in a large multibreed population of purebred beef and dairy cattle. In 2024, average FROH ranged from 2.65% in Limousin calves up to 7.41% in Holstein calves. In most analysed breeds, FROH levels accumulated year-on-year; with the fastest rate of accumulation observed in the Holsteins with an average annual increase of 0.14% over the previous 30 years. This corresponded to an effective population size of 66 and indicated that the Holsteins, of the analysed breeds, were the most vulnerable to further losses in genetic diversity. Across breeds, FPED consistently underestimated FROH. While the difference between FPED and FROH decreased with increasing pedigree depth, considerable between-breed variation remained even at the same degree of pedigree completeness. Notably, FPED did not converge to FROH even when 17 complete generation equivalents of ancestry records were available. Of the analysed breeds, the Holsteins had among the highest prevalence of runs of homozygosity (ROH) >10 Mb. Unlike the other breeds, the proportion of ROH >10 Mb in Holsteins had steadily declined since the early 2000's, suggesting that inbreeding had shifted from recent to more distant co-ancestry. In contrast, ROH >10 Mb increased by approximately 25% in Charolais and Limousins over the same period. The results of this study demonstrated that even though FPED became a less biased estimator of observed autozygosity as pedigree depth increased, this bias was not completely eliminated even with the deepest pedigree available. When genomic data are available the expected FROH of progeny should inform mating decisions; otherwise, all available pedigree data should be used to estimate co-ancestry to limit unintended accumulation of inbreeding and prevent further erosion of genetic diversity.

Keywords: 2026

How to Cite:

Rafter, P., Ryan, C. & Evans, R., (2026) “Inbreeding trends from 1991 to 2025 in > 1.1 million genotyped purebred beef and dairy cattle.”, World Congress on Genetics Applied to Livestock Production Digital Archive 2026(1): 2286482. doi: https://doi.org/10.31274/wcgalp.24024

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