Genetic evaluation of tropical climate-adapted sheep for carcass traits including genomic information

•Moderate genomic parameters for ultrasound-based carcass traits were obtained for hair sheep adapted to harsh environments.•Carcass traits evaluated in vivo are feasible for selection in Santa Inês sheep.•Genetic evaluation for carcass traits is favored by adding genomic information.•Single-step GBLUP outperforms BLUP based on the accuracy of genomic breeding values. Santa Inês is a locally adapted hair sheep breed that is under large expansion in Brazil and other Tropical countries. This study aimed to evaluate the effect of different relationship matrices (A or H) on the estimation of genetic parameters and accuracy of (genomic) breeding values [(G)EBVs] for carcass traits measured in vivo in Santa Inês sheep. A total of 977, 890, 894, and 882 records for loin eye area (LEA), marbling score (MLE), subcutaneous fat thickness (SFT), and leg circumference (LEC), respectively, were included in this study. There were 1637 animals in the numerator relationship matrix (A). A total of 389 animals with phenotypic information were genotyped using the OvineSNP50 BeadChip. After the genotyping quality control, 388 samples and 42,748 SNPs remained in the dataset. The (co)variance components were estimated via Bayesian inference through single- and multi-trait analyses using the animal model with either the A or H matrix. The theoretical accuracies of (G)EBVs, Pearson correlation between breeding values estimated including or not genomic information, and Spearman rank correlation were used to evaluate the feasibility of incorporating genomic information in the analyses. Heritability estimates ranged from 0.12 ± 0.06 (SFT, using the A matrix) to 0.29 ± 0.07 (LEA, using the H matrix), in the single-trait analyses, and from 0.17 ± 0.05 (SFT, using A) to 0.33 ± 0.07 (LEA, using H), in a multi-trait setting. Direct genetic additive variance and heritability estimates were higher when including genomic information. Unfavorable and high genetic correlation was observed between LEA and SFT. The estimates of theoretical accuracy of (G)EBVs were higher in all the scenarios when genomic information was incorporated in the model. Gains in accuracy ranged from 0.013 to 0.039 units when genomic information was included in the analyses. Thus, if available, genomic information should be incorporated in the estimation of genetic parameters and breeding values for carcass traits measured in vivo in Santa Inês sheep.