Genotype imputation strategies for Portuguese Holstein cattle using different SNP panels

Alessandra Alves Silva, Fabyano Fonseca Silva, Delvan Alves Silva, Hugo Teixeira Silva, Cláudio Napolis Costa, Paulo Sávio Lopes, Renata Veroneze, Gertrude Thompson and Julio Carvalheira
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Alessandra Alves Silva: Department of Animal Science, Federal University of Viçosa, Viçosa, Brazil
Fabyano Fonseca Silva: Department of Animal Science, Federal University of Viçosa, Viçosa, Brazil
Delvan Alves Silva: Department of Animal Science, Federal University of Viçosa, Viçosa, Brazil
Hugo Teixeira Silva: Department of Animal Science, Federal University of Viçosa, Viçosa, Brazil
Cláudio Napolis Costa: Embrapa Dairy Cattle, Juiz de Fora, Brazil
Paulo Sávio Lopes: Department of Animal Science, Federal University of Viçosa, Viçosa, Brazil
Renata Veroneze: Department of Animal Science, Federal University of Viçosa, Viçosa, Brazil
Gertrude Thompson: Research Center in Biodiversity and Genetic Resources (CIBIO-InBio), University of Porto, Porto, Portugal
Julio Carvalheira: Research Center in Biodiversity and Genetic Resources (CIBIO-InBio), University of Porto, Porto, Portugal

Czech Journal of Animal Science, 2019, vol. 64, issue 9, 377-386

Abstract: Although several studies have investigated the factors affecting imputation accuracy, most of these studies involved a large number of genotyped animals. Thus, results from these studies cannot be directly applied to small populations, since the population structure affects imputation accuracy. In addition, factors affecting imputation accuracy may also be intensified in small populations. Therefore, we aimed to compare different imputation strategies for the Portuguese Holstein cattle population considering several commercially available single nucleotide polymorphism (SNP) panels in a relatively small number of genotyped animals. Data from 1359 genotyped animals were used to evaluate imputation in 7 different scenarios. In the S1 to S6 scenarios, imputations were performed from LDv1, 50Kv1, 57K, 77K, HDv3 and Ax58K panels to 50Kv2 panel. In these scenarios, the bulls in 50Kv2 were divided into reference (352) and validation (101) populations based on the year of birth. In the S7 scenario, the validation population consisted of 566 cows genotyped with the Ax58K panel with their genotypes masked to LDv1. In general, all sample imputation accuracies were high with correlations ranging from 0.94 to 0.99 and concordance rate ranging from 92.59 to 98.18%. SNP-specific accuracy was consistent with that of sample imputation. S4 (40.32% of SNPs imputed) had higher accuracy than S2 and S3, both with less than 7.59% of SNPs imputed. Most probably, this was due to the high number of imputed SNPs with minor allele frequency (MAF) < 0.05 in S2 and S3 (by 18.43% and 16.06% higher than in S4, respectively). Therefore, for these two scenarios, MAF was more relevant than the panel density. These results suggest that genotype imputation using several commercially available SNP panels is feasible for the Portuguese national genomic evaluation.

Keywords: dairy cattle; genomic evaluation; imputation accuracy (search for similar items in EconPapers)
Date: 2019
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Persistent link: https://EconPapers.repec.org/RePEc:caa:jnlcjs:v:64:y:2019:i:9:id:120-2019-cjas

DOI: 10.17221/120/2019-CJAS

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