They comprised 140 Rhode Island Red (RIR) chickens, 82 Cornish chickens, 28 black Korean native chickens (BKNC), 30 red Korean native chickens (RKNC), 30 yellow Korean native chickens (YKNC), 26 parent stocks (PS1) of CCP1, 19 parent stocks (PS2) of CCP2, 191 CCP1 chickens and 172 CCP2 chickens.
To calculate the identification probabilities between CCP1 and CCP2, allele frequencies of these two populations were investigated by PCR-restriction fragment length polymorphism (PCR-RFLP).
In the D-loop region, three polymorphic positions, 225, 239 and 243, were considered for breed discrimination markers because of the large differences in allele frequencies between the CCP1 and CCP2.
In each population, seven RIR, eleven Cornish, nine BKNC, six RKNC, four YKNC, one PS1, five PS2, one CCP1 and five CCP2 haplotypes were identified.
Polymorphisms and repetitive sequences were identified for the LEI0258 alleles in CCP1 and CCP2 populations by sequencing for homozygous animals.
Three mtDNA markers (SNP225, SNP239 and SNP243) and the LEI0258 marker were evaluated for discriminating CCP1 and CCP2 populations.