Population structure of eleven Spanish ovine breeds and detection of selective sweeps with BayeScan and hapFLK

A Manunza,A Pons,V Landi,J Capote,T F Cardoso,M Amills,A Martínez,A Noce,E Ugarte,O Vidal,J V Delgado,J Jordana,S Adán,J H Calvo,J J Arranz,J Casellas,A Sànchez,L A Bermejo

doi:10.1038/srep27296

Abstract

The goals of the current work were to analyse the population structure of 11 Spanish ovine breeds and to detect genomic regions that may have been targeted by selection. A total of 141 individuals were genotyped with the Infinium 50 K Ovine SNP BeadChip (Illumina). We combined this dataset with Spanish ovine data previously reported by the International Sheep Genomics Consortium (N = 229). Multidimensional scaling and Admixture analyses revealed that Canaria de Pelo and, to a lesser extent, Roja Mallorquina, Latxa and Churra are clearly differentiated populations, while the remaining seven breeds (Ojalada, Castellana, Gallega, Xisqueta, Ripollesa, Rasa Aragonesa and Segureña) share a similar genetic background. Performance of a genome scan with BayeScan and hapFLK allowed us identifying three genomic regions that are consistently detected with both methods i.e. Oar3 (150–154 Mb), Oar6 (4–49 Mb) and Oar13 (68–74 Mb). Neighbor-joining trees based on polymorphisms mapping to these three selective sweeps did not show a clustering of breeds according to their predominant productive specialization (except the local tree based on Oar13 SNPs). Such cryptic signatures of selection have been also found in the bovine genome, posing a considerable challenge to understand the biological consequences of artificial selection.

Highlights

Since their domestication in the Fertile Crescent, sheep have been bred for producing milk, meat and wool[1]
Given the quantitative nature of production traits, it can be anticipated that most of the genetic changes introduced by artificial selection in the genomes of meat and dairy sheep are driven by polygenic adaptation i.e. shifts in the allele frequencies of hundreds or thousands of loci that have small effects on the selected trait[3]
Several genome scans aimed to identify selection signatures related with fat deposition[6], morphology and color[7], dairy production[7,8], presence of horns[2] and adaptation to climate conditions[9] have been carried out so far, leading to the identification of a diverse array of selective sweeps scattered throughout the ovine genome

Summary

Introduction

Since their domestication in the Fertile Crescent, sheep have been bred for producing milk, meat and wool[1] Artificial selection for these and other phenotypic traits probably began thousands of years ago by keeping as breeders individuals with certain external features (e.g. color, size, morphology etc) and productive abilities (rapid growth and high fertility). The speed of this process of genetic change accelerated enormously in the last decades as a consequence of the implantation of intensive breeding schemes based on artificial insemination, extensive trait and genealogical recording, and the introduction of best linear unbiased predictor approaches to estimate genetic values[2]. The aim of the current work was to analyse the population structure of eleven Spanish sheep breeds and to identify selection signatures produced by artificial selection for growth and milk traits

Objectives

Methods

Results