Animal Bioscience

Asian Australasian Association of Animal Production Societies (아세아태평양축산학회)
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Development and validation of a dual-purpose 60K single nucleotide polymorphism chip for simultaneous genotyping of chicken and duck

  • Jinhyeong Kim (Department of Animal Science, Chungnam National University) ;
  • Eunjin Cho (Department of Bio-AI Convergence, Chungnam National University) ;
  • Minjun Kim (Poultry Research Center, National Institute of Animal Science, Rural Development Administration) ;
  • Jaewon Kim (Department of Animal Science, Chungnam National University) ;
  • Dongwon Seo (Research Institute TNT Research Company) ;
  • Jung-Woo Choi (Department of Animal Science, College of Animal Life Sciences, Kangwon National University) ;
  • Won-Hyong Chung (Department of Animal Science, College of Animal Life Sciences, Kangwon National University) ;
  • Yeongkuk Kim (Quantomic Research & Solution Co.) ;
  • Hyojun Choo (Poultry Research Center, National Institute of Animal Science, Rural Development Administration) ;
  • Jun Heon Lee (Department of Animal Science, Chungnam National University)
  • Received : 2025.10.24
  • Accepted : 2025.12.08
  • Published : 2026.05.01
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Abstract

Objective: Chickens and ducks represent the most important poultry species within the livestock industry. However, the availability of single nucleotide polymorphism (SNP) chips for these species is limited, and development of separate chips for each species requires considerable expense. To address this limitation, we developed the first poultry SNP chip applicable to both species simultaneously. The 60K SNP chip comprises 30,816 SNPs for chickens and 35,209 SNPs for ducks. The performance of the chip was evaluated using non-pooled datasets (chicken only and duck only) and a pooled dataset combining chicken and duck DNA to verify that genotyping accuracy was maintained without cross-species interference. Methods: DNA was extracted from 28 Korean native chickens and 28 Korean native ducks. Genotyping was performed using the Illumina platform, employing chicken-only, duck-only, and pooled chicken-duck SNP panels. Genotype accuracy and concordance were evaluated with PLINK. Sample and SNP quality were assessed in accordance with the Illumina genotyping protocol. Principal component analysis (PCA) was conducted to evaluate and compare the chicken-duck pooled dataset with the non-pooled datasets. Results: The mean genotype concordance of non-pooled (chicken only and duck only) datasets exceeded 99%, while concordance between non-pooled and chicken-duck pooled datasets surpassed 97.8%. All datasets satisfied quality thresholds for call rate, GenCall score, 10% GenCall score, and cluster separation. PCA revealed consistent clustering patterns, with no significant differences observed between non-pooled and pooled datasets. Conclusion: The first, at the best of our knowledge, poultry SNP chip incorporating chicken-duck pooled samples, has been successfully developed and validated. This chip provides reliable genotyping performance for both species and presents a cost-effective option for large-scale SNP chip development in the livestock industry.

Keywords

Acknowledgement

This study was funded by the research project (No. RS-2023-00225185) and (No. RS-2025-00512602) of the Rural Development Administration, Korea.

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