Contents lists available at ScienceDirect Livestock Science journal homepage: www.elsevier.com/locate/livsci Genome-wide search for signatures of selection in three major Brazilian locally adapted sheep breeds João José de Simoni Gouveia a,b, ⁎ , Samuel Rezende Paiva c , Concepta M. McManus d , Alexandre Rodrigues Caetano e , James W. Kijas f , Olivardo Facó g , Hymerson Costa Azevedo h , Adriana Mello de Araujo i , Carlos José Hoff de Souza j , Michel Eduardo B. Yamagishi k , Paulo Luiz Souza Carneiro l , Raimundo Nonato Braga Lôbo g , Sônia Maria Pinheiro de Oliveira m , Marcos Vinicius G.B. da Silva n a Colegiado Acadêmico de Zootecnia, Universidade Federal do Vale do São Francisco, Petrolina/PE 56300-000, Brazil b Programa de Doutorado Integrado em Zootecnia (PDIZ-UFC/UFPB/UFRPE), Universidade Federal do Ceará, Fortaleza/CE 60020-181, Brazil c Secretaria de Relações Internacionais, Embrapa Sede, Brasília/DF 70770-901, Brazil d INCT Pecuária, Faculdade de Agronomia e Medicina Veterinária, Universidade de Brasília, Brasília/DF 70910-900, Brazil e Embrapa Recursos Genéticos e Biotecnologia, Brasília/DF 70770-917, Brazil f CSIRO Animal, Food and Health Sciences, St Lucia, Brisbane, Queensland 4067, Australia g Embrapa Caprinos e Ovinos, Sobral/CE 62011-970, Brazil h Embrapa Tabuleiros Costeiros, Aracaju/SE 49025-040, Brazil i Embrapa Meio-Norte, Teresina/PI 64006-220, Brazil j Embrapa Pecuária Sul, Bagé/RS 96401-970, Brazil k Embrapa Informática Agropecuária, Campinas/SP 13083-970, Brazil l Departamento de Ciências Biológicas, Universidade Estadual do Sudoeste da Bahia, Jequié/BA 45200-000, Brazil m Departamento de Zootecnia, Universidade Federal do Ceará, Fortaleza/CE 60020-181, Brazil n Embrapa Gado de Leite, Juiz de Fora/MG 36038-330, Brazil ARTICLE INFO Keywords: Ovis aries Selective sweep Climate change Conservation animal genetic resources SNP markers ABSTRACT The study of locally adapted breeds has the potential to underpin the discovery of genes involved in economically and ecologically important traits. Brazilian locally adapted sheep breeds have distinctive characteristics that could be of value for specialized production systems. Therefore, the main objective of the present study was to identify genomic regions that may have been under selection and therefore may explain ecological and production differences observed among three important Brazilian locally adapted sheep breeds. Animals from the Brazilian Creole, Morada Nova and Santa Ines breeds were genotyped using the Illumina Ovine SNP50 BeadChip. The identification of selection signatures was based on two groups of methodologies: differentiation among populations (F ST ) and linkage disequilibrium (iHS and RsB). Taken together, these analyses allowed for the identification of 86 candidate genes. Functional analysis revealed genes related to immunity, nervous system development, reproduction and sensory perception. A number of genes are of particular interest including: RXFP2, which has recently been associated with the presence/absence and morphology of horns in sheep; the TRPM8 gene, involved in regulation of body temperature at low temperatures; DIS3L2, PLAG1 and NIPBL, associated with height variation; and finally, SPEF2 and SPAG6, important for spermatogenesis. Selective sweeps were identified using multiple methods, and in a number of cases sweep regions contained genes with a demonstrated role in phenotypic variation. The genomic distribution of the sweep regions differed between populations, suggesting that breed specific signatures were successfully identified that may reflect the consequence of local adaptation. 1. Introduction Identification of genomic regions subject to selection in livestock may assist in both understanding the processes involved in genome evolution as well as in the discovery and validation of genomic regions involved in the manifestation of traits of economic and ecological http://dx.doi.org/10.1016/j.livsci.2017.01.006 Received 3 March 2016; Received in revised form 5 January 2017; Accepted 6 January 2017 ⁎ Corresponding author at: Colegiado Acadêmico de Zootecnia, Universidade Federal do Vale do São Francisco, Petrolina/PE 56300-000, Brazil. E-mail address: joao.gouveia@univasf.edu.br (J.J. de Simoni Gouveia). Livestock Science 197 (2017) 36–45 1871-1413/ © 2017 Elsevier B.V. All rights reserved. MARK