Sequencing & Pangenomes

Performance evaluation of a chicken-duck pooled 60K SNP chip

---

Abstract

Chickens and ducks are important genetic resources in the livestock industry. To achieve genome-based selection, obtaining accurate genotype data is essential. Among the available methods for acquiring genomic information, the single nucleotide polymorphism (SNP) chip offers a reliable and efficient approach. However, due to the high cost of SNP chips, genotyping a large number of samples remains challenging. To overcome this limitation, we developed a dual-species pooled SNP chip by pooling chicken and duck DNA, thereby reducing production costs by half. This study aimed to evaluate the feasibility of this pooled DNA approach for SNP chip analysis. We further examined whether the pooled design introduces any interference between the genotype data of the two species. In this study, 28 Korean native chickens (30,816 SNPs) and 28 Korean native ducks (35,209 SNPs) were used. Hybridization was conducted using two approaches to compare the applicability of pooled and individual genomic DNA on a single Illumina SNP chip. In the pooled approach, chicken and duck DNA were mixed at a 1:1 ratio, while in the individual approach, each species was hybridized separately. Validation was performed by comparing genotypes between the separate and pooled datasets using PLINK v1.9 (--bmerge and --merge). Quality control (QC) was assessed using Illumina QC metrics, including sample-level parameters such as call rate ( >0.95) and 10% GenCall (p10 GC) score ( >0.15), and SNP-level parameters such as cluster separation ( >0.3) and GenCall score ( >0.15). After QC filtering, principal component analysis (PCA) was conducted to evaluate the suitability of the pooled dataset for further analyses. Genotype concordance between the separate and pooled datasets was 99.2% for chickens and 97.8% for ducks. All sample types exceeded the Illumina QC thresholds for call rate and 10% GC score, and all SNPs also satisfied the criteria for cluster separation and GenCall score. These results indicate that the SNP chip was successfully hybridized and produced reliable genotyping data. In the PCA, the pooled chicken dataset showed identical principal component values and clustering patterns to the separate chicken dataset. For ducks, a slight variation was observed, but the overall cluster structure remained consistent. We developed a pooled SNP chip combining chicken and duck DNA, validated through genotype concordance, QC thresholds, and PCA. The results confirm that the pooled dataset can be effectively used for further genomic analyses. However, validation was performed with a limited number of SNPs and samples, and slight differences in the duck datasets require further investigation. This study demonstrates that a pooled chicken-duck SNP chip can provide reliable genotype data comparable to individual hybridization. The pooled approach offers a cost-effective strategy for large-scale genotyping in poultry species.

Keywords: 2026

How to Cite:

Seo, D., Choi, J., Chung, W., Kim, Y., Choo, H. & Lee, J., (2026) “Performance evaluation of a chicken-duck pooled 60K SNP chip”, World Congress on Genetics Applied to Livestock Production Digital Archive 2026(1): 2286430. doi: https://doi.org/10.31274/wcgalp.24002

Rights: 1