Genome-wide scan reveals population stratification and footprints of recent selection in Nelore cattle

Diercles F Cardoso,Maria E Zerlotti Mercadante,Henner Simianer,Humberto Tonhati,Malena Erbe,Gregório M Ferreira De Camargo,Daiane C Becker Scalez,André V Do Nascimento,Joslaine N Do Santos Gonçalves Cyrillo,Guilherme C Venturini,Saber Qanbari,Christian Reimer,Lucia Galvão De Albuquerque,Fernando Baldi

doi:10.1186/s12711-018-0381-2

Abstract

BackgroundThis study aimed at (1) assessing the genomic stratification of experimental lines of Nelore cattle that have experienced different selection regimes for growth traits, and (2) identifying genomic regions that have undergone recent selection. We used a sample of 763 animals genotyped with the Illumina BovineHD BeadChip, among which 674 animals originated from two lines that are maintained under directional selection for increased yearling body weight and 89 animals from a control line that is maintained under stabilizing selection.ResultsMultidimensional analysis of the genomic dissimilarity matrix and admixture analysis revealed a substantial level of population stratification between the directional selection lines and the stabilizing selection control line. Two of the three tests used to detect selection signatures (FST, XP-EHH and iHS) revealed six candidate regions with indications of selection, which strongly indicates truly positive signals. The set of identified candidate genes included several genes with roles that are functionally related to growth metabolism, such as COL14A1, CPT1C, CRH, TBC1D1, and XKR4.ConclusionsThe current study identified genetic stratification that resulted from almost four decades of divergent selection in an experimental Nelore population, and highlighted autosomal genomic regions that present patterns of recent selection. Our findings provide a basis for a better understanding of the metabolic mechanism that underlies the growth traits, which are modified by selection for yearling body weight.

Highlights

This study aimed at (1) assessing the genomic stratification of experimental lines of Nelore cattle that have experienced different selection regimes for growth traits, and (2) identifying genomic regions that have undergone recent selection
The Nelore Control (NeC) line presented the largest number of monomorphic single nucleotide polymorphism (SNP) and the lowest heterozygosity (Table 2), which may be due to its smaller effective population size (Ne) relative to the population sizes of the other two lines
The first two principal coordinates obtained from multidimensional scaling (MDS) accounted for 7.88% of the total genomic variance in the subsample used in this study. PCO1 completely separates NeC from Nelore Selection (NeS) and Nelore Traditional (NeT), while P CO2 partially separates the NeS and NeT lines (Fig. 2a)

Summary

Introduction

This study aimed at (1) assessing the genomic stratification of experimental lines of Nelore cattle that have experienced different selection regimes for growth traits, and (2) identifying genomic regions that have undergone recent selection. One common strategy for investigating past selection in cattle involves the systematic comparison of the genomes of breeds that have evolved under different selection regimes, e.g., dairy versus beef breeds [4, 5] The motivation behind such comparisons is to identify strongly differentiated genomic regions between different groups of animals. Cardoso et al Genet Sel Evol (2018) 50:22 analysis of within-breed stratification may allow the identification of signatures of selection within a single breed for which genetically distinct lines have been established One example of such a study in cattle involved Holstein lines that were divergently selected for milk yield, in which the identified signatures of selection co-localized with known quantitative trait loci (QTL) that affect milk traits [6, 7]

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