Genetic Diversity Analysis of Colored and White Feathered Native Duck Population

This study was conducted to analyze the genetic diversity and population structure of native duck populations with colored and white plumage phenotypes. The objective of this research was to identify the genetic diversity and structure of native duck populations with colored and white plumage phenotypes using a 30K SNP chip specifically designed for ducks. For this purpose, native duck samples were provided by the Poultry Research Institute of the National Institute of Animal Science. A total of 300 native ducks (150 colored and 150 white) were genotyped using the 30K SNP chip data. The results showed that the Minor Allele Frequency (MAF) distributions of the two populations were generally similar. However, a sharp decline in the number of SNPs was observed when the MAF exceeded 0.48, with only approximately 2,000 SNPs detected above this threshold. Principal component analysis (PCA) using the identified SNPs revealed a clear separation between the colored and white groups along the first principal component (PC1), which explained 33.6% of the genetic variation. Analysis of Linkage Disequilibrium (LD) and Effective Population Size (Ne) suggested that the colored group exhibited slightly greater genetic diversity compared to the white group. The findings confirmed distinct genetic structures between the two populations. Further research is needed to identify genes associated with feather coloration in native ducks.