A comprehensive genomic characterization of Nellore cattle

Indicine cattle (Bos taurus indicus) are found primarily in tropical and subtropical regions, with Brazil hosting one of the largest Zebu cattle populations in the world. Understanding the genetic makeup of Nellore cattle is crucial for enhancing genomic predictions, performing association studies, and maintaining genetic diversity. This study aims to characterize Brazilian Nellore cattle via genomic information. Linkage disequilibrium, effective population size (Ne), and runs of homozygosity (ROH) were used to characterize the population. The generation proxy selection method (GPSM) was used to detect alleles with changing frequencies over time. The average linkage disequilibrium across all chromosomes was 0.28, and the Ne was 225 in the most recent generation. Only one ROH island, which is related mainly to carcass quality and fertility traits, was identified in this study. In total, the GPSM method identified 77 significant SNPs and 142 quantitative trait loci (QTLs). These regions are associated with tick resistance, carcass and growth traits, maternal ability, and reproduction. The level of linkage disequilibrium estimated in the Nellore population supports the successful implementation of genomic selection in the Nellore breed. Moreover, the Ne estimated via genomic information was found to be large enough to maintain desirable levels of genetic diversity within the breed. Most ROHs identified in this study were created in more ancient generations. Moreover, significant SNPs identified via the GPSM method confirmed that genetic selection was effective in Nellore cattle, and genomic changes were observed.