Exploring inbreeding depression in Brazilian Angus cattle population using pedigree and genomic data

Abstract

Introduction: Inbreeding depression refers to the decline in performance caused by increased levels of inbreeding, which results from mating individuals with common ancestors. This study aimed to estimate inbreeding coefficients based on both pedigree and genomic information using six different metrics and evaluate, the inbreeding depression on different traits officially evaluated by the Brazilian Angus Association.

Material and methods: A total of 13,777 genotyped animals, imputed to a density of 78,837 SNPs, and 530,327 animals in the pedigree file, extending up to 17 generations, were used in the analysis. The inbreeding metrics evaluated included: pedigree-based inbreeding (F_PED), genomic relationship matrix-based inbreeding (F_GRM), observed vs. expected homozygosity (F_HOM1), genotyped homozygosity (F_HOM2), correlation between uniting gametes (F_UNI), and runs of homozygosity (F_ROH). Traits related to growth, conformation, meat quality, reproduction, resistance to ectoparasites, and heat stress were analyzed.

Results: The results revealed a range of inbreeding coefficients, with inbreeding estimated using ROHs showing the highest values (0.13). The impact of inbreeding on various traits was predominantly negative, with significant inbreeding depression observed for traits such as hair coat. Some traits, such as intramuscular fat and birth weight, had positive associations with inbreeding, indicating a complex trait-specific relationship. Shorter ROH segments (<2 Mb) generally had smaller or beneficial effects compared to longer ROH segments (>16 Mb).

Discussion: These findings underscore the complexity of inbreeding depression and highlight the importance of considering both the extent and historical depth of inbreeding when evaluating its effects on various traits. Overall, this research provides valuable insights into the genetic basis of inbreeding depression in the Brazilian Angus population and demonstrates the usefulness of genomic data in understanding and mitigating the impacts of inbreeding in livestock populations.

Keywords: animal breeding; genetic diversity; genomic inbreeding; genomic relationship matrix; genomic selection; livestock genetics; quantitative traits.

FIGURE 1

Trend of average population inbreeding over the year for the Brazilian Angus Population and the overlap of the top 10% most inbred animals using genomic dats. (A) Trend of the average pedigree inbreeding (red line) and number of individuals in the population (blue columns). (B) Average inbreeding coefficient for the genotyped population over the years for the different metrics of inbreeding evaluated. (C) Average inbreeding coefficient for the genotyped population over the years based on the classes of runs of homozygosity (FROH). (D) Venn diagram display the overlapping of the top 10% of the most inbreed animals for which genomic metric. FPED, inbreeding coefficient based on pedigree for the genotyped animals; FGRM, inbreeding coefficient based on the genotyped additive variance; FHOM1, inbreeding coefficient based on the homozygous genotyped observed and expected; FHOM2, inbreeding coefficient based on homozygous genotyped; FUNI, inbreeding coefficient based on the correlation between uniting gametes; FROH, inbreeding coefficient based on the length of the ROH’s and the total length of the autosomal genome.

FIGURE 2

Distribution frequency (A) and correlation among the inbreeding metrics (B) evaluated for the Brazilian Angus population. FPED, inbreeding coefficient based on pedigree for the genotyped animals; FGRM, inbreeding coefficient based on the genotyped additive variance; FHOM1, inbreeding coefficient based on the homozygous genotyped observed and expected; FHOM2, inbreeding coefficient based on homozygous genotyped; FUNI, inbreeding coefficient based on the correlation between uniting gametes; FROH, inbreeding coefficient based on the length of the ROH’s and the total length of the autosomal genome.