title: Selection signatures in Canchim beef cattle.
abstract: BACKGROUND
  Recent technological advances in genomics have allowed the genotyping of cattle through single nucleotide polymorphism (SNP) panels. High-density SNP panels possess greater genome coverage and are useful for the identification of conserved regions of the genome due to selection, known as selection signatures (SS). The SS are detectable by different methods, such as the extended haplotype homozygosity (EHH); and the integrated haplotype score (iHS), which is derived from the EHH. The aim of this study was to identify SS regions in Canchim cattle (composite breed), genotyped with high-density SNP panel.
  
  
  RESULTS
  A total of 687,655 SNP markers and 396 samples remained for SS analysis after the genotype quality control. The iHS statistic for each marker was transformed into piHS for better interpretation of the results. Chromosomes BTA5 and BTA14 showed piHS > 5, with 39 and nine statistically significant SNPs (P < 0.00001), respectively. For the candidate selection regions, iHS values were computed across the genome and averaged within non-overlapping windows of 500 Kb. We have identified genes that play an important role in metabolism, melanin biosynthesis (pigmentation), and embryonic and bone development.
  
  
  CONCLUSIONS
  The observation of SS indicates that the selection processes performed in Canchim, as well as in the founder breeds (i.e. Charolais), are maintaining specific genomic regions, particularly on BTA5 and BTA14. These selection signatures regions could be associated with Canchim characterization.
authors.affiliation: Departamento de Ciências Exatas, - Univ Estadual Paulista, Faculdade de Ciências Agrárias e Veterinárias, Jaboticabal, São Paulo 14884-900 Brazil.
authors.forename: Ismael
authors.initials: I
authors.lastname: Urbinati
authors.affiliation: Departamento de Ciências Exatas, - Univ Estadual Paulista, Faculdade de Ciências Agrárias e Veterinárias, Jaboticabal, São Paulo 14884-900 Brazil.
authors.forename: Nedenia Bonvino
authors.initials: NB
authors.lastname: Stafuzza
authors.affiliation: Departamento de Tecnologia, UNESP - Univ Estadual Paulista, Faculdade de Ciências Agrárias e Veterinárias, Jaboticabal, São Paulo 14884-900 Brazil.
authors.forename: Marcos Túlio
authors.initials: MT
authors.lastname: Oliveira
authors.affiliation: Departamento de Ciências Exatas, - Univ Estadual Paulista, Faculdade de Ciências Agrárias e Veterinárias, Jaboticabal, São Paulo 14884-900 Brazil.
authors.forename: Tatiane Cristina Seleguim
authors.initials: TC
authors.lastname: Chud
authors.affiliation: Embrapa Agricultural Informatics, Campinas, São Paulo 13083-886 Brazil.
authors.forename: Roberto Hiroshi
authors.initials: RH
authors.lastname: Higa
authors.affiliation: Embrapa Southeast Livestock, São Carlos, São Paulo 13560-970 Brazil.
authors.forename: Luciana Correia de Almeida
authors.initials: LC
authors.lastname: Regitano
authors.affiliation: Embrapa Southeast Livestock, São Carlos, São Paulo 13560-970 Brazil.
authors.forename: Maurício Mello
authors.initials: MM
authors.lastname: de Alencar
authors.affiliation: Departamento de Ciências Exatas, - Univ Estadual Paulista, Faculdade de Ciências Agrárias e Veterinárias, Jaboticabal, São Paulo 14884-900 Brazil.
authors.forename: Marcos Eli
authors.initials: ME
authors.lastname: Buzanskas
authors.affiliation: Departamento de Ciências Exatas, - Univ Estadual Paulista, Faculdade de Ciências Agrárias e Veterinárias, Jaboticabal, São Paulo 14884-900 Brazil.
authors.forename: Danísio Prado
authors.initials: DP
authors.lastname: Munari
keywords: Composite breed; Extended haplotype homozygosity; Genomics; Single nucleotide polymorphism