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

Author(s):Show less -

Bresolin, Tiago ^[1] ; Rosa, Guilherme Jordao de Magalhaes ^[2] ; Valente, Bruno Dourado ^[2] ; Espigolan, Rafael ^[1] ; Mansan Gordo, Daniel Gustavo ^[1] ; Braz, Camila Urbano ^[1] ; Fernandes Junior, Gerardo Alves ^[1] ; Braga Magalhaes, Ana Fabricia ^[1] ; Garcia, Diogo Anastacio ^[1] ; Frezarim, Gabriela Bonfa ^[1] ; Carneiro Leao, Guilherme Fonseca ^[1] ; Carvalheiro, Roberto ^{[1, 3]} ; Baldi, Fernando ^{[1, 3]} ; de Oliveira, Henrique Nunes ^{[1, 3]} ; de Albuquerque, Lucia Galvao ^{[1, 3]}

Affiliation

^[1] Univ Estadual Paulista Unesp, Fac Ciencias Agr & Vet, Dept Zootecnia, Via Acesso Prof Paulo Donato Castellane S-N, BR-14884900 Jaboticabal, SP - Brazil

^[2] Univ Wisconsin, Dept Anim Sci, 436 Anim Sci Bldg, 1675 Observ Dr, Madison, WI 53706 - USA

^[3] CNPq, Natl Counsel Technol & Sci Dev, SHIS QI 1 Conjunto B Blocos A, B, C&D, BR-71605001 Brasilia, DF - Brazil

• Document type: Journal article
• Source: ANIMAL PRODUCTION SCIENCE; v. 59, n. 1, p. 48-54, 2018.
• Web of Science Citations: 0

Abstract

This study was designed to test the impact of quality control, density and allele frequency of single nucleotide polymorphisms (SNP) 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 1756; 3150 and 3119 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 (r(2)) were constructed for all traits: (1) high rigor (S1): call rate < 0.98, MAF < 0.05, HWE with P < 10-5, and r(2) > 0.999; (2) Moderate rigor (S2): call rate < 0.85 and MAF < 0.01; (3) Low rigor (S3): only non-autosomal SNP 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 customised 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 and BayesC pi 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 SNP 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. (AU)

• FAPESP's process: 13/26264-4 - Effect of using different criteria for quality control of genotypes in studies of association and genome-wide selection
• Grantee: Tiago Bresolin
• Support Opportunities: Scholarships in Brazil - Master