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Effect of quality control, density and allele frequency of markers on the accuracy of genomic prediction for complex traits in Nellore cattle

Tiago Bresolin , Guilherme Rosa , Bruno Valente , Rafael Espigolan , Daniel Gordo , Camila Braz , Gerardo Junior , Ana Fabricia Magalhães , Diogo Garcia , Gabriela Frezarim , Guilherme Leão , Roberto Carvalheiro , Fernando Baldi , Henrique de Oliveira , L Albuquerque

Abstract

This study was designed to test the impact of quality control, density and allele frequency of SNP (single nucleotide polymorphisms) markers on the accuracy of genomic predictions, using three traits with different heritabilities and two methods of prediction in a Nellore cattle population genotyped with the Illumina Bovine HD Assay. A total of 1,756; 3,150 and 3,119 records of age at first calving (AFC); weaning weight (WW) and yearling weight (YW), respectively, were used. Three scenarios with different exclusion thresholds for minor allele frequency (MAF), deviation from Hardy-Weinberg equilibrium (HWE) and correlation between SNP pairs (r2) were constructed for all traits: 1) high rigor (S1): call rate < 0.98, MAF < 0.05, HWE with P < 10−5, and r2 > 0.999; 2) Moderate rigor (S2): call rate < 0.85 and MAF < 0.01; 3) Low rigor (S3): only non-autosomal SNPs and those mapped on the same position were excluded. Additionally, to assess the prediction accuracy from different markers density, six panels (10K, 50K, 100K, 300K, 500K and 700K) were customized using the high-density genotyping assay as reference. Finally, from the markers available in high-density genotyping assay, six groups (G) with different minor allele frequency bins were defined to estimate the accuracy of genomic prediction. The range of MAF bins was approximately equal for the traits studied: G1 (0.000-0.009), G2 (0.010-0.064), G3 (0.065-0.174), G4 (0.175-0.325), G5 (0.326-0.500) and G6 (0.000-0.500). The Genomic Best Linear Unbiased Predictor (GBLUP) and BayesCπ methods were used to estimate the SNP marker effects. Five-fold cross-validation was used to measure the accuracy of genomic prediction for all scenarios. There were no effects of genotypes quality control criteria on the accuracies of genomic predictions. For all traits, the higher density panel did not provide greater prediction accuracies than the low density one (10K panel). The groups of SNPs with low MAF (MAF ≤ 0.007 for AFC, MAF ≤ 0.009 for WW and MAF ≤ 0.008 for YW) provided lower prediction accuracies than the groups with higher allele frequencies.

AN16821  Accepted 11 September 2017

© CSIRO 2017