Development of Breed-Specific Markers using Single Nucleotide Polymorphisms in Feather Color of Korean Native Chicken, Korean Ogye, and White Leghorn

Korean Ogye (KO) is a valuable genetic resource in Korea for its complete black pigmentation (including feathers, muscles, and bones), which contributes to livestock biodiversity and scientific research on genes related to coloration. Although this unique physical characteristic of KO enables its distinction from other chicken breeds, markers that can distinguish KO from Korean Native Chicken (KNC) breeds of other colors at the molecular level provide versatility of identification across developmental stages and sample types. Therefore, this study aimed to identify single nucleotide polymorphisms (SNPs) in three genes associated with chicken feather coloration—melanocortin 1 receptor (<i>MC1R</i>), tyrosinase (<i>TYR</i>), and agouti-signaling protein (<i>ASIP</i>)—to develop breed-specific markers capable of differentiating White Leghorn (WL), KO, and a Korean Native Chicken Red Brown (KNC_Rb) line. While no SNPs in <i>TYR</i> and <i>ASIP</i> were found to be completely specific, those in the <i>MC1R</i> region showed complete breed specificity, making this locus a unique molecular marker for discriminating each breed through one-step PCR analysis. These breed-specific markers not only enable genetic authentication and traceability of Korean breeds (KNC_Rb, KO) relative to foreign breeds but also provide a crucial molecular framework for verifying donor-recipient relationships in primordial germ cell (PGC)-based germline chimera production.