Application of selection mapping to identify genomic regions associated with dairy production in sheep.

Bernhard Kaltenboeck,Beatriz Gutiérrez-Gil,Ricardo Pong-Wong,Juan Jose Arranz,James Kijas,Pamela Wiener,Elsa García-Gámez

doi:10.1371/journal.pone.0094623

Abstract

In Europe, especially in Mediterranean areas, the sheep has been traditionally exploited as a dual purpose species, with income from both meat and milk. Modernization of husbandry methods and the establishment of breeding schemes focused on milk production have led to the development of “dairy breeds.” This study investigated selective sweeps specifically related to dairy production in sheep by searching for regions commonly identified in different European dairy breeds. With this aim, genotypes from 44,545 SNP markers covering the sheep autosomes were analysed in both European dairy and non-dairy sheep breeds using two approaches: (i) identification of genomic regions showing extreme genetic differentiation between each dairy breed and a closely related non-dairy breed, and (ii) identification of regions with reduced variation (heterozygosity) in the dairy breeds using two methods. Regions detected in at least two breeds (breed pairs) by the two approaches (genetic differentiation and at least one of the heterozygosity-based analyses) were labeled as core candidate convergence regions and further investigated for candidate genes. Following this approach six regions were detected. For some of them, strong candidate genes have been proposed (e.g. ABCG2, SPP1), whereas some other genes designated as candidates based on their association with sheep and cattle dairy traits (e.g. LALBA, DGAT1A) were not associated with a detectable sweep signal. Few of the identified regions were coincident with QTL previously reported in sheep, although many of them corresponded to orthologous regions in cattle where QTL for dairy traits have been identified. Due to the limited number of QTL studies reported in sheep compared with cattle, the results illustrate the potential value of selection mapping to identify genomic regions associated with dairy traits in sheep.

Highlights

Since their domestication 8 000–9 000 years ago, sheep (Ovis aries) have been used by humans for the production of wool, meat and milk
In order to search for genomic regions that have been under divergent selection in dairy and non-dairy breeds, we examined genetic differentiation across the genome for five breed pairs
We evaluated correspondence of the Convergence Candidate Regions (CCR) with QTL reported for milk production and other functional traits related to dairy production in sheep

Summary

Introduction

Since their domestication 8 000–9 000 years ago (reviewed by [1]), sheep (Ovis aries) have been used by humans for the production of wool, meat and milk. The first documented modifications to sheep by human-imposed selection had taken place by the time that illustrations and records first appeared c. Sheep were kept solely for meat, milk and skins. Archaeological evidence suggests that selection for woolly sheep may have begun around 6000 BC. Dairy sheep are mainly found in Europe, especially in Mediterranean areas, where they have been traditionally exploited as a dual purpose species, with income from both meat and milk. Most sheep milk has been produced by multipurpose local breeds with low-to-medium milk yields and raised under traditional husbandry conditions [3]. The market for sheep milk and sheep dairy products appears to be growing, even in those countries without a history of sheep dairying [4]

Methods

Results

Discussion

Conclusion