239 The genetic cost of inbreeding: Evaluating the impact of inbreeding on Angus traits.

Abstract Inbreeding depression, defined as the reduction in mean performance due to increased homozygosity, has been extensively studied across various livestock species. With the advent of genomic information, inbreeding estimation has evolved beyond pedigree-based calculations to incorporate more precise genomic-based metrics. This study aimed to: 1) assess six different inbreeding metrics in Brazilian Angus cattle, using both pedigree and genomic information; and 2) estimate the impact of inbreeding depression on 12 traits currently evaluated by the Brazilian Angus Association. A dataset comprising 13,777 Brazilian Angus cattle genotypes imputed to the density of 78,837 markers was made available for this study. Phenotypic data included birth weight, weaning weight gain, post-weaning weight gain, yearling conformation, hair coat scores, scrotal circumference, ribeye area, back fat thickness, rump fat thickness, intramuscular fat, and tick count. Inbreeding coefficients were calculated using pedigree-based (entire population – FPEDtotal; genotyped individuals – FPEDgen), and genomic-based (genotype additive variance - FGRM, homozygous genotypes 1 - FHOM1, homozygous genotypes 2 - FHOM2, correlation between uniting gametes - FUNI, and runs of homozygosity - ROH) methods. Inbreeding depression was estimated using single-trait linear models, regressing phenotypic traits on inbreeding coefficients. Inbreeding coefficients ranged from -0.33 to 0.71 across different metrics, with the lowest mean values observed for FPEDtotal, FPEDgen, FGRM, FHOM1, FHOM2, FUNI, and ROH < 2Mb (all = 0.01), while the highest mean value was observed for FROH (0.13 ± 0.03). Correlations among inbreeding metrics varied from weak (-0.26; between FGRM and ROH 2-4Mb) to strong (0.97; between FROH and FHOM2), with pedigree-based inbreeding showing weak correlations with genomic-based metrics overall. The estimation of inbreeding depression revealed predominantly unfavorable effects, with the most pronounced impact observed for rump fat thickness, where a 1% increase in inbreeding (F8-16Mb) led to a 1.13% phenotypic reduction. However, increased effects were noted for intramuscular fat (FHOM2) and birth weight (F2Mb), with the latter rising by up to 0.83%. Additionally, birth weight exhibited differential responses based on ROH length, with shorter ROHs (F2Mb) increasing the effect, whereas longer ROHs (F8-16Mb) decreasing the effects. These findings highlight the complexity of inbreeding depression, emphasizing the importance of considering both the length and historical depth of inbreeding when assessing its impact on economically relevant traits.