Genome-wide association study of the reproductive, body size, and carcass-related latent and directly measured traits in admixed beef heifers.

Latent variables derived through factor analysis reveal the underlying biological traits (UBT) in organisms. However, research on UBT development and genomic applications in beef cattle is limited. This study aimed to model previously identified economically important UBT in genome-wide association studies (GWAS) using univariate and multivariate approaches. Data on 35 traits related to the body size, reproduction, and carcass characteristics from 297 admixed beef heifers were analyzed using two models. Due to the sample-size constraints, the two models utilized were: 1) all traits included (n = 161) and 2) optimized record numbers by segregating the reproductive and body size traits (n = 297) from carcass traits (n = 161). The UBT identified from a prior study included body size (BS) and body composition (BC) in model 1 and BS, ovary size (OS), and yield grade (YG) in model 2, along with non-contributing but economically relevant traits such as body density (DENS) and intra-muscular fat (IMF). Genotypically adjusted causal networks showed that BS influenced BC (model 1) and OS (model 2). Multi-trait and structural equation modeling (SEM) GWAS approaches were used to integrate BS with BC and OS, while univariate modeling was used for unrelated UBT and direct traits, such as YG, IMF, and DENS. Across all the approaches, 1,911 SNP from nine different regions were identified and mapped to 98 features, including genes, pseudogenes, and multiple non-coding and translational RNA. Enrichment analysis highlighted extracellular matrix-receptors, HERC family genes in cellular growth, desmosomes in morphogenesis, and energy metabolism related to PIGY genes. Genes linked to muscle and carcass traits, including FAM184B, NCAPG, and LCORL, were also identified. The heritability of UBT (0.46-0.84) was higher than that of individual traits, particularly for reproductive and carcass-related traits. This study provides insights into the relationships of body and carcass-oriented traits in admixed beef heifers that are directly relevant to phenotyping and genetic evaluations being conducted in the beef industry.