ArticleGenetics, selection, evolution : GSE2015
Imputation of genotypes in Danish purebred and two-way crossbred pigs using low-density panels.
Article in Genetics, selection, evolution : GSE, 2015. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 8 papers, 1 of them a synthesis that pooled it.
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Who cites it
8 citing papers in PubMed, 1 synthesis or guideline pooled it.
- Large-scale association study on daily weight gain in pigs reveals overlap of genetic factors for growth in humans.BMC genomics · 2022Pooled it
- Identifying low-density, ancestry-informative SNP markers through whole genome resequencing in Indian, Chinese, and wild yak.BMC genomics · 2024Article
- Leveraging low-density crossbred genotypes to offset crossbred phenotypes and their impact on purebred predictions.Journal of animal science · 2022Article
- Impacts of additive, dominance, and inbreeding depression effects on genomic evaluation by combining two SNP chips in Canadian Yorkshire pigs bred in China.Genetics, selection, evolution : GSE · 2022Article
- Development of a low-density panel for genomic selection of pigs in Russia.Translational animal science · 2020Article
- Using a very low-density SNP panel for genomic selection in a breeding program for sheep.Genetics, selection, evolution : GSE · 2017Article
- Genomic evaluation by including dominance effects and inbreeding depression for purebred and crossbred performance with an application in pigs.Genetics, selection, evolution : GSE · 2016Article
- Increased prediction accuracy using a genomic feature model including prior information on quantitative trait locus regions in purebred Danish Duroc pigs.BMC genetics · 2016Article
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Authors and funding
5 authors.
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No grant is acknowledged in the PubMed record.
Abstract
backgroundGenotype imputation is commonly used as an initial step in genomic selection since the accuracy of genomic selection does not decline if accurately imputed genotypes are used instead of actual genotypes but for a lower cost. Performance of imputation has rarely been investigated in crossbred animals and, in particular, in pigs. The extent and pattern of linkage disequilibrium differ in crossbred versus purebred animals, which may impact the performance of imputation. In this study, first we compared different scenarios of imputation from 5 K to 8 K single nucleotide polymorphisms (SNPs) in genotyped Danish Landrace and Yorkshire and crossbred Landrace-Yorkshire datasets and, second, we compared imputation from 8 K to 60 K SNPs in genotyped purebred and simulated crossbred datasets. All imputations were done using software Beagle version 3.3.2. Then, we investigated the reasons that could explain the differences observed.
resultsGenotype imputation performs as well in crossbred animals as in purebred animals when both parental breeds are included in the reference population. When the size of the reference population is very large, it is not necessary to use a reference population that combines the two breeds to impute the genotypes of purebred animals because a within-breed reference population can provide a very high level of imputation accuracy (correct rate ≥ 0.99, correlation ≥ 0.95). However, to ensure that similar imputation accuracies are obtained for crossbred animals, a reference population that combines both parental purebred animals is required. Imputation accuracies are higher when a larger proportion of haplotypes are shared between the reference population and the validation (imputed) populations.
conclusionsThe results from both real data and pedigree-based simulated data demonstrate that genotype imputation from low-density panels to medium-density panels is highly accurate in both purebred and crossbred pigs. In crossbred pigs, combining the parental purebred animals in the reference population is necessary to obtain high imputation accuracy.
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