A genome‐wide scan for selection signatures in Nellore cattle

Abstract

Brazilian Nellore cattle (Bos indicus) have been selected for growth traits for over more than four decades. In recent years, reproductive and meat quality traits have become more important because of increasing consumption, exports and consumer demand. The identification of genome regions altered by artificial selection can potentially permit a better understanding of the biology of specific phenotypes that are useful for the development of tools designed to increase selection efficiency. Therefore, the aims of this study were to detect evidence of recent selection signatures in Nellore cattle using extended haplotype homozygosity methodology and BovineHD marker genotypes (>777,000 single nucleotide polymorphisms) as well as to identify corresponding genes underlying these signals. Thirty-one significant regions (P < 0.0001) of possible recent selection signatures were detected, and 19 of these overlapped quantitative trait loci related to reproductive traits, growth, feed efficiency, meat quality, fatty acid profiles and immunity. In addition, 545 genes were identified in regions harboring selection signatures. Within this group, 58 genes were associated with growth, muscle and adipose tissue metabolism, reproductive traits or the immune system. Using relative extended haplotype homozygosity to analyze high-density single nucleotide polymorphism marker data allowed for the identification of regions potentially under artificial selection pressure in the Nellore genome, which might be used to better understand autozygosity and the effects of selection on the Nellore genome.

Identification of genome‐wide selection signatures in the Limousin beef cattle breed

“…30 months), as well as ease of calving (according to the statements included in breeding program of Polish Association of Breeders and Producers of Beef Cattle). Until now, with application of different statistical methods, several cattle breeds have received studies aiming to identify the footprints of directional selection (Qanbari et al 2010;Fan et al 2014;Porto-Neto et al 2014;Somavilla et al 2014;Bomba et al 2015;Gurgul et al 2015). Among them are a limited number of Limousin cattle (Gibbs et al 2009;Druet et al 2013;Porto-Neto et al 2013;Ramey et al 2013;Kemper et al 2014) and a comprehensive study focused exclusively on this breed is virtually unavailable.…”

Runs of homozygosity for autozygosity estimation and genomic analysis in production animals

“…Fuller et al (2015) identified ROHs related to adaptive characteristics of commercial bee species, observing the effect of environmental temperature on honey production. In bovine, O'Brien et al (2014), Somavilla et al (2014), and Zavarez et al (2015) identified ROHs associated to the adaptive potential and reproductive and productive characteristics of zebu breeds, whereas Kim et al (2015a) identified more than 15 regions related to milk production in Jersey herds.…”

An interpretive review of selective sweep studies in Bos taurus cattle populations: identification of unique and shared selection signals across breeds

“…As an initial attempt to perform a systematic review of the available literature on cattle selection signals, this review targets the genome-wide selective sweep scans described in Bos taurus breeds of European origin and mainly focuses on the interpretation of selection sweeps associated with dairy and beef production specialization. Hence, some studies have not been considered, including studies limited to specific chromosomes (e.g., Hayes et al, 2008 ; Prasad et al, 2008 ), or studies mainly addressing Bos indicus (Somavilla et al, 2014 ), African taurine cattle breeds (Gautier et al, 2009 ) or cross-bred cattle (Flori et al, 2012 ) or studies focusing on Bos taurus-Bos indicus comparisons (Porto-Neto et al, 2013 ; Utsunomiya et al, 2013a ). Exceptions were four studies that included in their larger-scale analysis some Bos indicus and hybrid breeds (Bovine HapMap Consortium, 2009 ; Qanbari et al, 2011 ; Ramey et al, 2013 ; Porto-Neto et al, 2014 ), although we have only considered the results reported for the European Bos taurus breeds.…”