Genomic Regions Associated with Heifer Pregnancy in Nellore Beef Cattle

Considering the economic importance of sexual precocity in beef cattle production system, the objective of this study was to develop strategies for improving the trait heifer pregnancy (HP) in a population of Nelore cattle (Bos primigenius indicus). The phenotype was measured in 1,337 animals, which were daughters of 78 sires, coming from three different herds in Brazil. The animals were genotyped by the GeneSeek Genomic Profiler (GGP-HDi), keeping 64,800 after quality control analyses. Genotypic information of 42 sires were also available, and non-genotyped sires with more than 5 genotyped progenies in the dataset were imputed for the same marker density of the heifers. A Genome-wide Association Study (GWAS) was used to identify potential genomic windows (1 Mb) that explained at least 1% of the total genetic variance of the trait. Haplotype blocks that span these potential QTL regions were fitted as classificatory effects in a BayesB model, aiming to estimate the effect of each allele of the heterozygous sires for these regions. The estimated effects of the two paternally-inherited haplotype alleles were then contrasted considering significance level of p <0.10. The GWAS results pointed to genomic windows on chromosomes 5, 14 and 18 that accounted for more than 1% of the total genetic variance. A total of 15 haplotype alleles performed better than its alternative copy, suggesting a favorable effect on the HP. These haplotype alleles could be selected to improve the early pregnancy rates in Nelore heifers.