29 Effects of Recent and Ancient Inbreeding on Growth in American Angus Cattle

Abstract

The accumulation of inbreeding can lead to an unfavorable change in the phenotypic value of individuals for traits related to fitness, also known as inbreeding depression. However, inbreeding accumulated at a more distant past (ancient inbreeding) is expected to have a smaller depressive effect than that accumulated more recently due to the loss of detrimental alleles caused by purifying selection. Therefore, the aim of this study was to quantify the inbreeding depression caused by recent and ancient inbreeding for birth weight, weaning weight, and post-weaning gain. Pedigree and genomic information were obtained from Angus Genetics, Inc. (St. Joseph, MO) for 569,364 individuals from the American Angus breed. Pedigree inbreeding and genomic inbreeding based on runs of homozygosity (ROH) were estimated using the SNP1101 software. Model-based genomic inbreeding based on the probability a marker is part of a homozygous-by-descent segment (HBD) was estimated using the RZooROH in R. The generational cutoffs for designating inbreeding as recent was that acquired 5 generations ago or sooner for pedigree, 6.25 generations ago or sooner for ROH, and 8 generations ago or sooner for HBD inbreeding. The effect of a 1% increase in inbreeding was modeled in males and females using a linear mixed model approach. Recent pedigree inbreeding was found to decrease birth weight by 0.04 and 0.03 kg, decrease weaning weight by 0.50 and 0.48 kg, and decrease post-weaning gain by 0.62 and 0.32 kg, in males and females respectively. Ancient pedigree inbreeding was generally found to have no effect on growth. For genomic inbreeding, when both recent and ancient inbreeding had a detrimental effect on growth, recent inbreeding generally had a larger effect. The results of this study demonstrate that inbreeding accumulated recently should be quantified and managed in beef cattle populations to avoid economic losses.