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Evaluation of imputation performance based on the SNP panel density and the reference population size in Korean native chicken(R) |
Minjun Kim1 
, Hyo Jun Choo2
, Sunghyun Cho3
, Doo Ho Lee4
, Jun Heon Lee1,*
, Dongwon Seo5,*
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1Department of Animal Science, Chungnam National University, Daejeon, Korea
2Poultry Research Institute, National Institute of Animal Science, Rural Development Administration, Pyeongchang, Korea
3Research and Development Center, Insilicogen Inc., Yongin, Korea
4Quantomic research & solution, Daejeon, Korea
5Research Institute TNT Research Company, Jeonju, Korea |
Correspondence:
Jun Heon Lee, Tel: : +82-42-821-5779, Email: junheon@cnu.ac.kr
Dongwon Seo, Tel: : +82-42-821-5779, Email: junheon@cnu.ac.kr
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Received: 19 November 2024 • Revised: 13 February 2025 • Accepted: 20 March 2025 |
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| Abstract |
Objective
This 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.
Methods
Data 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.
Results
Higher 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.
Conclusion
A 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. |
| Keywords:
Imputation; Korean native chicken; Reference population size; SNP density |
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