title: Linkage disequilibrium and haplotype block structure in a composite beef cattle breed.
abstract: BACKGROUND
  The development of linkage disequilibrium (LD) maps and the characterization of haplotype block structure at the population level are useful parameters for guiding genome wide association (GWA) studies, and for understanding the nature of non-linear association between phenotypes and genes. The elucidation of haplotype block structure can reduce the information of several single nucleotide polymorphisms (SNP) into the information of a haplotype block, reducing the number of SNPs in a coherent way for consideration in GWA and genomic selection studies.
  
  
  RESULTS
  The maximum average LD, measured by r2 varied between 0.33 to 0.40 at a distance of < 2.5 kb, and the minimum average values of r2 varied between 0.05 to 0.07 at distances ranging from 400 to 500 kb, clearly showing that the average r2 reduced with the increase in SNP pair distances. The persistence of LD phase showed higher values at shorter genomic distances, decreasing with the increase in physical distance, varying from 0.96 at a distance of < 2.5 kb to 0.66 at a distance from 400 to 500 kb. A total of 78% of all SNPs were clustered into haplotype blocks, covering 1,57 Mb of the total autosomal genome size.
  
  
  CONCLUSIONS
  This study presented the first high density linkage disequilibrium map and haplotype block structure for a composite beef cattle population, and indicates that the high density SNP panel over 700 k can be used for genomic selection implementation and GWA studies for Canchim beef cattle.
authors.forename: Fabiana Barichello
authors.initials: FB
authors.lastname: Mokry
authors.forename: Marcos Eli
authors.initials: ME
authors.lastname: Buzanskas
authors.forename: Maurício
authors.initials: M
authors.lastname: de Alvarenga Mudadu
authors.forename: Daniela
authors.initials: D
authors.lastname: do Amaral Grossi
authors.forename: Roberto Hiroshi
authors.initials: RH
authors.lastname: Higa
authors.forename: Ricardo Vieira
authors.initials: RV
authors.lastname: Ventura
authors.forename: Andressa Oliveira
authors.initials: AO
authors.lastname: de Lima
authors.forename: Mehdi
authors.initials: M
authors.lastname: Sargolzaei
authors.forename: Sarah Laguna
authors.initials: SL
authors.lastname: Conceição Meirelles
authors.forename: Flávio Schramm
authors.initials: FS
authors.lastname: Schenkel
authors.forename: Marcos Vinicius Gualberto Barbosa
authors.initials: MV
authors.lastname: da Silva
authors.forename: Simone Cristina
authors.initials: SC
authors.lastname: Méo Niciura
authors.forename: Maurício Mello
authors.initials: MM
authors.lastname: de Alencar
authors.forename: Danísio
authors.initials: D
authors.lastname: Munari
authors.forename: Luciana Correia
authors.initials: LC
authors.lastname: de Almeida Regitano
mesh_terms: D000818:Animals; D001947:Breeding; D002417:Cattle / Q000235:genetics*; D002874:Chromosome Mapping / Q000662:veterinary; D006239:Haplotypes; D015810:Linkage Disequilibrium; D020641:Polymorphism, Single Nucleotide