ArticleAnimal bioscience2025
Evaluation of imputation performance based on the single nucleotide polymorphism panel density and the reference population size in Korean native chicken.
Article in Animal bioscience, 2025. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Not yet cited in PubMed.
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Abstract
objectiveThis study aimed to identify the optimal single nucleotide polymorphism (SNP) panel density for accurate imputation in the Korean native chicken (KNC) and Yeonsan Ogye (YO) populations. The primary focus was on evaluating how the reference population size and SNP density influence imputation performance and accuracy.
methodsData were collected from five purebred lines of KNC and the YO population, comprising a total of 256 KNC and 199 YO chickens. Imputed genotype ratio and accuracy were evaluated across various scenarios using SNP densities of 2.5K, 5K, 10K, and 50K in both populations. Additionally, for the YO dataset, reference population sizes of 50, 100, and 150 were analyzed to assess their impact on imputation outcomes.
resultsHigher SNP densities notably improved imputation performance. Specifically, when SNP panel density reached 10K or greater, the ratio of imputed SNPs exceeded 70% and the accuracy increased substantially, regardless of the reference population size. However, imputation efficiency decreased markedly when either the reference or test population size was around 50 individuals.
conclusionA test SNP density of at least 10K was determined to be essential for accurate genotype imputation. Additionally, imputation efficiency was observed to decline when either the reference or test population included around 50 individuals. These findings provide important data that can guide the genetic improvement of indigenous livestock populations.
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