Abstract
Simple SummaryIn this study, we investigated the association between single nucleotide polymorphisms (SNPs) and reproductive traits in order to identify candidate genes and biological pathways associated with these traits in Nelore beef cattle. The genome-wide association analysis revealed genomic regions that could explain part of the genetic variance of the studied traits. The results revealed genes with important functions for reproductive traits, such as fertility and precocity. Some genes were associated with more than one trait, being important for reproductive efficiency. The identification of candidate genes that were associated with the studied traits as well as genes enriched in the functional terms and pathways may be useful for exploring the genetic architecture underlying reproductive traits and may be used in Nelore breeding programs.The identification of genomic regions associated with reproductive traits as well as their biological processes allows a better understanding of the phenotypic variability of these traits. This information could be applied to animal breeding programs to accelerate genetic gain. The aim of this study was to evaluate the association between single nucleotide polymorphisms (SNP) with a scrotal circumference at 365 days of age (SC365) and at 450 days of age (SC450), gestation length (GL) as a calf trait, age at first calving (AFC), accumulated productivity (ACP), heifer early calving until 30 months (HC30), and stayability (STAY) traits, in order to identify candidate genes and biological pathways associated with reproductive traits in Nelore cattle. The data set consisted of pedigree, phenotypes, and genotypes of Nelore cattle from the “Associação Nacional de Criadores e Pesquisadores” (ANCP). The association analyses were performed using the Weighted Single-Step Genome-Wide Association method; the regions, consisting of 10 consecutive SNP, which explained more than 0.5% of additive genetic variance, were considered as a significant association. A total of 3, 6, 7, 5, 10, 25, and 12 windows were associated with SC355, SC450, GL, AFC, ACP, HC30, and STAY, respectively. The results revealed genes with important functions for reproductive traits, such as fertility and precocity. Some genes were associated with more than one trait, among them CAMK1D, TASP1, ACOXL, RAB11FIP5, and SFXN5. Moreover, the genes were enriched in functional terms, like negative regulation of fat cell differentiation, fatty acid alpha-oxidation, and sphingolipids signaling pathway. The identification of the genes associated with the traits, as well as genes enriched in the terms and pathway mentioned above, should contribute to future biological validation studies and may be used as candidate genes in Nelore breeding programs.
Highlights
Greater inclusion of animal protein in human food has increased demand for beef production
The results in the present study provide a better understanding of the genes associated with reproductive traits studied in Nelore cattle
The CAMK1D and Threonine aspartase 1 (TASP1) genes were associated with heifer early calving until 30 months (HC30) and STAY; the acyl-CoA oxidase like (ACOXL)
Summary
Greater inclusion of animal protein in human food has increased demand for beef production. Producers and researchers have been working, using the benefits of genetics, nutrition, and animal reproduction, on the search for a performance that is compatible with the growth of beef cattle production and that results in an increase in productivity [1,2]. Sexual precocity is especially important for Bos taurus indicus breeds that are commonly less precocious than Bos taurus taurus breeds [4]. Zebu breeds have adaptive advantages in tropical production in comparison with Taurine breeds [5,6]. Reproductive inefficiency results in monetary losses caused by decreased production and detained reproduction, which impacts the costs and the sustainability of cattle production systems [7]
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