title: Study of whole genome linkage disequilibrium in Nellore cattle.
abstract: BACKGROUND
  Knowledge of the linkage disequilibrium (LD) between markers is important to establish the number of markers necessary for association studies and genomic selection. The objective of this study was to evaluate the extent of LD in Nellore cattle using a high density SNP panel and 795 genotyped steers.
  
  
  RESULTS
  After data editing, 446,986 SNPs were used for the estimation of LD, comprising 2508.4 Mb of the genome. The mean distance between adjacent markers was 4.90 ± 2.89 kb. The minor allele frequency (MAF) was less than 0.20 in a considerable proportion of SNPs. The overall mean LD between marker pairs measured by r(2) and |D'| was 0.17 and 0.52, respectively. The LD (r(2)) decreased with increasing physical distance between markers from 0.34 (1 kb) to 0.11 (100 kb). In contrast to this clear decrease of LD measured by r(2), the changes in |D'| indicated a less pronounced decline of LD. Chromosomes BTA1, BTA27, BTA28 and BTA29 showed lower levels of LD at any distance between markers. Except for these four chromosomes, the level of LD (r(2)) was higher than 0.20 for markers separated by less than 20 kb. At distances < 3 kb, the level of LD was higher than 0.30. The LD (r(2)) between markers was higher when the MAF threshold was high (0.15), especially when the distance between markers was short.
  
  
  CONCLUSIONS
  The level of LD estimated for markers separated by less than 30 kb indicates that the High Density Bovine SNP BeadChip will likely be a suitable tool for prediction of genomic breeding values in Nellore cattle.
authors: Faculdade de Ciências Agrárias e Veterinárias, UNESP, Jaboticabal, SP, 14884-000, Brazil.
authors: Rafael
authors: R
authors: Espigolan
authors: Fernando
authors: F
authors: Baldi
authors: Arione A
authors: AA
authors: Boligon
authors: Fabio Rp
authors: FR
authors: Souza
authors: Daniel Gm
authors: DG
authors: Gordo
authors: Rafael L
authors: RL
authors: Tonussi
authors: Diércles F
authors: DF
authors: Cardoso
authors: Henrique N
authors: HN
authors: Oliveira
authors: Humberto
authors: H
authors: Tonhati
authors: Mehdi
authors: M
authors: Sargolzaei
authors: Flavio S
authors: FS
authors: Schenkel
authors: Roberto
authors: R
authors: Carvalheiro
authors: Jesus A
authors: JA
authors: Ferro
authors: Lucia G
authors: LG
authors: Albuquerque
mesh_terms: D000818:Animals; D002417:Cattle / Q000235:genetics*; D023281:Genomics; D015810:Linkage Disequilibrium / Q000235:genetics*; D020641:Polymorphism, Single Nucleotide / Q000235:genetics; D040641:Quantitative Trait Loci / Q000235:genetics
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