Genotype_file

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. </p><p dir="ltr"><b>Results:</b> 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.</p><p dir="ltr"><b>Conclusion:</b> 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.</p>