Desarrollo y validación de un chip SNP dual de 60K para genotipado simultáneo de pollo y pato

Chickens and ducks are among the most important poultry species in the livestock industry. However, the availability of SNP chips for these species is limited, and developing separate chips for each species requires considerable cost. To overcome this limitation, we developed the first poultry SNP chip that can be applied to both species simultaneously. The 60K SNP chip was designed to include 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 in which chicken and duck DNA were mixed to verify that genotyping accuracy was maintained without cross-species interference.

DNA was extracted from 28 Korean native chickens and 28 Korean native ducks. Genotyping was performed on the Illumina platform with chicken-only, duck-only, and pooled chicken-duck SNP panels. Genotype accuracy and concordance were evaluated with PLINK. Sample and SNP quality were assessed according to the Illumina genotyping protocol. Principal component analysis (PCA) was conducted to assess and compare the chicken-duck pooled dataset with the non-pooled datasets.

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 was higher than 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.

We successfully developed and validated the first poultry SNP chip incorporating chicken-duck pooled samples. This chip provides reliable genotyping performance for both species and offers a cost-effective solution for large-scale SNP chip development in the livestock industry.