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Open Access Highly Accessed Research article

Study of whole genome linkage disequilibrium in Nellore cattle

Rafael Espigolan1, Fernando Baldi13, Arione A Boligon1, Fabio RP Souza1, Daniel GM Gordo1, Rafael L Tonussi1, Diércles F Cardoso1, Henrique N Oliveira125, Humberto Tonhati125, Mehdi Sargolzaei4, Flavio S Schenkel4, Roberto Carvalheiro6, Jesus A Ferro1 and Lucia G Albuquerque125*

Author Affiliations

1 Faculdade de Ciências Agrárias e Veterinárias, UNESP, Jaboticabal, SP, 14884-000, Brazil

2 Instituto Nacional de Ciência e Tecnologia - Ciência Animal (INCT- CA), Viçosa, MG, 36570 000, Brazil

3 Departamento de Nutrição e Produção Animal, Faculdade de Medicina Veterinária e Zootecnia, USP, Pirassununga, SP, Brazil

4 Centre for Genetic Improvement of Livestock, Department of Animal and Poultry Science, University of Guelph, Guelph, ON, Canada

5 CNPq Fellowship, National Council of Technological and Scientific Development, 71605-001, SHIS QI 1,Conjunto B, Brasília, DF, Brazil

6 GenSys Consultores Associados, Porto Alegre, Brazil

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BMC Genomics 2013, 14:305  doi:10.1186/1471-2164-14-305

Published: 5 May 2013

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 r2 and |D'| was 0.17 and 0.52, respectively. The LD (r2) 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 r2, 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 (r2) 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 (r2) 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.

Keywords:
Beef cattle; Genome; Linkage disequilibrium; Genome; Molecular markers