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

Abstract

Inbreeding depression reduces 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 SNP) 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 data set or the data set 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 - 0.39 kg in BW, of 2.77 - 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 - 11.57 kg. Genomic inbreeding based on the HMM was able to capture inbreeding depression, even in such a compressed genotyped data set.

Genome‐wide scan for signatures of selection in the Brangus cattle genome

“…The concordance between our results for BTA6 and BTA14 and other works in tropical composite breeds may be a consequence of strong selection pressure in Brangus towards Angus for growth, meat quality and fertility characteristics. This selection pressure is evidenced by the positive genetic trends for growth and scrotal circumference in the Argentinean Brangus reported in the paper by Forneris et al (2021). In turn, the data available for carcass traits are still scarce to display any genetic trend.…”

Analysis of Family Structure and Paternity Test of Tan Sheep in Yanchi Area, China

“…The inbreeding coefficient is usually used to evaluate the degree of inbreeding of individuals. By comparing various methods for calculating the inbreeding coefficient, it was found that the ROH-based inbreeding coefficient was the most accurate and could best reflect the true inbreeding level of individuals [ 32 , 33 , 34 , 35 ]. The average of the samples in this study was 0.049, which showed an upward trend compared with that in 2019 [ 36 ].…”