Study of whole genome linkage disequilibrium in Nellore cattle

Rafael Espigolan,Fabio Rp Souza,Lucia G Albuquerque,Rafael L Tonussi,Henrique N Oliveira,Diércles F Cardoso,Fernando Baldi,Arione A Boligon,Humberto Tonhati,Jesus A Ferro,Daniel Gm Gordo,Roberto Carvalheiro,Mehdi Sargolzaei,Flavio S Schenkel

doi:10.1186/1471-2164-14-305

Abstract

BackgroundKnowledge 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.ResultsAfter 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.ConclusionsThe 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.

Highlights

Knowledge of the linkage disequilibrium (LD) between markers is important to establish the number of markers necessary for association studies and genomic selection
The mean minor allele frequency (MAF) obtained in the present study (0.25) was slightly higher than that reported by [15] for Nellore cattle (0.19) and by the Bovine Hapmap Consortium using the Illumina Bovine SNP50K BeadChip for Nellore cattle (0.20) [16]
BTA26 presented a higher proportion of minor alleles (MAF < 0.10), whereas chromosomes BTA6, BTA8, BTA16, BTA22 and BTA23 presented a lower proportion of minor alleles (MAF < 0.10)

Summary

Introduction

Knowledge of the linkage disequilibrium (LD) between markers is important to establish the number of markers necessary for association studies and genomic selection. The first specimens of the breed arrived in Brazil at the end of the 18th century and Nellore animals rapidly became the predominant breed in the Brazilian herd [1]. There are about 200 million cattle heads in Brazil and most of them (about 80%) are Zebu animals and their crossbreds [2]. There has been an increased interest to use genetically evaluated animals in the Zebu population. Several genetic evaluation programs of Zebu breeds exist, for Nellore cattle. The main focus of these programs is growth and conformation traits, which are used as selection criteria [3]

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