Selection signatures in three lines of Nellore cattle selected for growth traits

Author(s)

Diercles Francisco Cardoso

• Document type: Doctoral Thesis
• Press: Jaboticabal. 2016-08-31.
• Institution: Universidade Estadual Paulista (Unesp). Faculdade de Ciências Agrárias e Veterinárias. Jaboticabal
• Defense date: 2016-07-28
• Advisor: Humberto Tonhati

Abstract

Analyses of selection signatures are valuable tools to identify genomic patterns formed by the interaction between humans and domestic animals. In some situations, the within-breed stratification enables genomic comparisons between groups of the same breed in order to study genetic mechanisms underlying given phenotypes under selection. The current study aimed to analyze the genomic stratification in an experimental population of Nellore cattle that keeps three selection lines, and highlight selection signatures pertinent to the practiced directional selection. To this end, was used a sample of animals genotyped with high density SNPs panel (Illumina® BovineHD beadchip – 777K), being 674 animals from two lines kept under directional selection for higher yearling body weight and 89 animals from one line kept under stabilizing selection based on the same trait. The population structure was assessed with multidimensional analysis based on the genomic distances matrix and with Admixture analyses based on genotype matrix. Selection signatures scans were based on three complementary methods the Wright’s fixation index (FST), Cross Population Extended Haplotype Homozygosity (XP-EHH) and the integrated Haplotype score (iHS). The different approaches used in order to assess the population structure were largely consistent, revealing the population separation in three clusters equivalent to the three selection lines. The line under stabilizing selection was represented by an isolated cluster, whilst the lines under directional selection presented some overlapping level. The three applied methods of selection signatures presented no accordance regarding found selection signatures. However, each of them highlighted selection signatures co-localized with previously known QTL affecting growth traits, as such as some genes already known as having a metabolic function important to growth metabolism. (AU)

• FAPESP's process: 12/24600-4 - Identification of signature selection in three lineages of Nellore cattle selected for growth
• Grantee: Diercles Francisco Cardoso
• Support Opportunities: Scholarships in Brazil - Doctorate