Development and Characterization of a Single Nucleotide Polymorphism Genotyping Panel for Duck Populations

Single nucleotide polymorphism (SNP) genotyping panels for domesticated ducks are currently lacking, despite their importance for genetic diversity studies and genomic selection. We analyzed whole-genome sequencing data from 74 ducks. To obtain a 40K SNP marker set, we performed SNP calling and applied minor allele frequency (MAF) and linkage disequilibrium (LD) criteria. SNPs from 33 genes associated with Quantitative Trait Loci (QTL) were manually selected and added to the panel. The performance of the resulting SNP panel was validated using genotyping data from 28 additional duck samples. We developed a 40K SNP genotyping panel for ducks. Applying criteria of call rate, MAF, and LD, 37,386 SNP markers were selected. After excluding SNPs near repeats and indels, and incorporating 591 SNPs from 33 duck QTL-associated genes, the final set consisted of 35,613 SNP markers. When evaluating the performance of the SNP panel, genotypes were successfully called for 35,209 out of 35,613 SNPs, achieving a call rate of 98.9%. After applying QC filters, 33,870 SNPs were confirmed to be usable. Our SNP panel design process successfully generated a dataset at a 40K scale without compromising the genetic distances of the whole genome. By minimizing variation at the SNP probe alignment sites, we achieved a high call rate. The panel demonstrated reasonable robustness and suitability for further genomic studies, making it a valuable tool for genetic improvement and trait selection in duck populations.