Evaluation of imputation accuracy using the combination of two high-density panels in Nelore beef cattle

Priscila Arrigucci Bernardes,Guilherme Batista Do Nascimento,Luciana Correia De Almeida Regitano,Danísio Prado Munari,Cedric Gondro,Rafael Nakamura Watanabe,Luiz Lehmann Coutinho,Rodrigo Pelicioni Savegnago,Marcos Eli Buzanskas

doi:10.1038/s41598-019-54382-w

Abstract

This study compared imputation from lower-density commercial and customized panels to high-density panels and a combined panel (Illumina and Affymetrix) in Nelore beef cattle. Additionally, linkage disequilibrium and haplotype block conformation were estimated in individual high-density panels and compared with corresponding values in the combined panel after imputation. Overall, 814 animals were genotyped using BovineHD BeadChip (IllumHD), and 93 of these animals were also genotyped using the Axion Genome-Wide BOS 1 Array Plate (AffyHD). In general, customization considering linkage disequilibrium and minor allele frequency had the highest accuracies. The IllumHD panel had higher values of linkage disequilibrium for short distances between SNPs than AffyHD and the combined panel. The combined panel had an increased number of small haplotype blocks. The use of a combined panel is recommended due to its increased density and number of haplotype blocks, which in turn increase the probability of a marker being close to a quantitative trait locus of interest. Considering common SNPs between IllumHD and AffyHD for the customization of a low-density panel increases the imputation accuracy for IllumHD, AffyHD and the combined panel.

Highlights

This study compared imputation from lower-density commercial and customized panels to high-density panels and a combined panel (Illumina and Affymetrix) in Nelore beef cattle
Genomic selection is widely used in dairy cattle, but the beef industry is still trailing behind in the adoption of this technique due to the large number of breeds being used around the world and the challenge of building up a large enough reference population for each breed that will enable industry-relevant levels of accuracy for genomic breeding values[1]
The number of markers used for prediction can influence accuracy[2] since the use of a large number of markers increases the probability of finding markers in high linkage disequilibrium (LD) with the quantitative trait loci (QTL)

Summary

Introduction

This study compared imputation from lower-density commercial and customized panels to high-density panels and a combined panel (Illumina and Affymetrix) in Nelore beef cattle. There are two commercial high-density panels available for bovine species[3]: the BovineHD BeadChip (Illumina) and the Axion Genome-Wide BOS 1 Array Plate (Affymetrix). Imputation can be used to combine genotyped data from different chips[17], resulting in higher-density panels and stronger LD with QTL. This improves the identification of haplotype blocks and the accuracy of the results from methodologies that use LD - and it is a critical step for industry to homogenize heterogeneous datasets

Objectives

Methods

Results

Conclusion