Genome-wide association study provides insights into genes related with horn development in Nelore beef cattle

Nedenia Bonvino Stafuzza,Cláudio De Ulhoa Magnabosco,Fernando Baldi,Rafael Medeiros De Oliveira Silva,Danísio Prado Munari,Jason B Osterstock,Daniela A Lino Lourenco,Luiz Antônio Framartino Bezerra,Raysildo Barbosa Lôbo,Elisa Peripolli,Fernando A Di Croce

doi:10.1371/journal.pone.0202978

Abstract

The causal mutation for polledness in Nelore (Bos taurus indicus) breed seems to have appeared first in Brazil in 1957. The expression of the polled trait is known to be ruled by a few groups of alleles in taurine breeds; however, the genetic basis of this trait in indicine cattle is still unclear. The aim of this study was to identify genomic regions associated with the hornless trait in a commercial Nelore population. A total of 107,294 animals had phenotypes recorded and 2,238 were genotyped/imputed for 777k SNP. The weighted single-step approach for genome-wide association study (WssGWAS) was used to estimate the SNP effects and variances accounted for by 1 Mb sliding SNP windows. A centromeric region of chromosome 1 with 3.11 Mb size (BTA1: 878,631–3,987,104 bp) was found to be associated with hornless in the studied population. A total of 28 protein-coding genes are mapped in this region, including the taurine Polled locus and the IFNAR1, IFNAR2, IFNGR2, KRTAP11-1, MIS18A, OLIG1, OLIG2, and SOD1 genes, which expression can be related to the horn formation as described in literature. The functional enrichment analysis by DAVID tool revealed cytokine-cytokine receptor interaction, JAK-STAT signaling, natural killer cell mediated cytotoxicity, and osteoclast differentiation pathways as significant (P < 0.05). In addition, a runs of homozygosity (ROH) analysis identified a ROH island in polled animals with 2.47 Mb inside the region identified by WssGWAS. Polledness in Nelore cattle is associated with one region in the genome with 3.1 Mb size in chromosome 1. Several genes are harbored in this region, and they may act together in the determination of the polled/horned phenotype. Fine mapping the locus responsible for polled trait in Nelore breed and the identification of the molecular mechanisms regulating the horn growth deserve further investigation.

Highlights

Brazil has the world’s largest commercial beef cattle herd, which is estimated at 215.2 million head [1]
A total of three adjacent windows were found to be associated with the polled trait in Nelore beef cattle, represented by one peak on BTA1 formed by 824 SNPs (Fig 1)
Within the first window identified on BTA1 (8978,631–1,873,922 bp) that explained 47.18% of the genetic variance, a total of 15 protein-coding genes were identified, some having been associated with the polled trait in taurine breeds

Summary

Introduction

Brazil has the world’s largest commercial beef cattle herd, which is estimated at 215.2 million head [1]. The vast majority of Brazilian beef cattle production is based in extensive grazing systems in challenging environments due to tropical climate. Because of their resistance to parasites, adaptability towards the tropical climate and extensive production systems, indicine breeds are widely used in Brazilian beef cattle production systems [2]. The genetic makeup of Nelore breed in Brazil is mainly the result of less than 7,000 animals imported from India from the end of the 19th century up until 1963, when the importation of animals, embryos and semen was banned [3]. The herd multiplied quickly, mainly due to its high rates of productive and reproductive performance in tropical climates [4]

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