Estimating inbreeding depression for growth and reproductive traits using pedigree and genomic methods in Argentinean Brangus cattle

Abstract

Inbreeding depression reduces the mean phenotypic value of important traits in livestock populations. The goal of this work was to estimate the level of inbreeding and inbreeding depression for growth and reproductive traits in Argentinean Brangus cattle, in order to obtain a diagnosis and monitor breed management. Data comprised 359,257 (from which 1,990 were genotyped for 40,678 single nucleotide polymorphisms [SNPs]) animals with phenotypic records for at least one of three growth traits: birth weight (BW), weaning weight (WW), and finishing weight (FW). For scrotal circumference (SC), 52,399 phenotypic records (of which 256 had genotype) were available. There were 530,938 animals in pedigree. Three methods to estimate inbreeding coefficients were used. Pedigree-based inbreeding coefficients were estimated accounting for missing parents. Inbreeding coefficients combining genotyped and nongenotyped animal information were also computed from matrix H of the single-step approach. Genomic inbreeding coefficients were estimated using homozygous segments obtained from a Hidden Markov model (HMM) approach. Inbreeding depression was estimated from the regression of the phenotype on inbreeding coefficients in a multiple-trait mixed model framework, either for the whole dataset or for the dataset of genotyped animals. All traits were unfavorably affected by inbreeding depression. A 10% increase in pedigree-based or combined inbreeding would result in a reduction of 0.34 to 0.39 kg in BW, 2.77 to 3.28 kg in WW, and 0.23 cm in SC. For FW, a 10% increase in pedigree-based, genomic, or combined inbreeding would result in a decrease of 8.05 to 11.57 kg. Genomic inbreeding based on the HMM was able to capture inbreeding depression, even in such a compressed genotyped dataset.

Keywords: Argentinean Brangus beef cattle; growth and reproductive traits; inbreeding depression; pedigree-based and genomic inbreeding coefficients.

Figure 1.

Year of birth counts on the Brangus genotyped set (n = 1,990).

Figure 2.

Year of birth counts (dashed line) and average pedigree-based inbreeding coefficient, % (black line), for animals in the national evaluation between years 1950 and 2019.

Figure 3.

Distributions of the estimated inbreeding contributions (proportion of the individual genomes) $F_{\mathrm{G}}^{(c)}$ assigned to each of the eight predefined homozygous-by-descent (HBD) classes (over the 1,990 genotyped individuals).

Figure 4.

Average estimated proportions of inbreeding contribution (a) and corresponding average cumulative inbreeding (b) of a set of eight predefined homozygous-by-descent (HBD) classes for the Brangus population.