¹Burdur Mehmet Akif Ersoy University, Faculty of Veterinary Medicine, Department of Genetics, TR-15030 Burdur - TÜRKİYE
²Siirt University, Faculty of Veterinary Medicine, Department of Animal Science, TR-56100 Siirt - TÜRKİYE DOI : 10.9775/kvfd.2025.35434 This study examined polymorphisms of nine genes (ADFP, AGPAT6, FOLR1, LHX3, PITX1, PITX2, PRLR, PROP1, and STAT5A) in Honamlı and Hair goats and compared allele and genotype frequencies with those reported in other breeds. A total of 200 goats (100 Honamlı, 100 Hair) were genotyped using PCR–RFLP. Allele and genotype frequencies were calculated, and deviations from Hardy–Weinberg equilibrium (HWE) were tested. Polymorphisms were identified in ADFP, AGPAT6, FOLR1, LHX3-1, LHX3-3, PITX1, PITX2-1, PRLR, and PROP1, whereas LHX3-2, PITX2-2, and STAT5A were monomorphic. ADFP showed C-allele/CC predominance with significant HWE deviation in both breeds. AGPAT6 (C-allele/CC) conformed to HWE, while FOLR1 (C-allele/CC) deviated only in pooled data. LHX3-1 (A-allele) was in HWE, whereas LHX3-3 (C-allele) deviated in both breeds. PITX1 (G-allele) was in HWE, while PITX2-1 (T-allele) was in HWE in Honamlı but deviated in Hair and pooled populations. PRLR (T-allele/TT) was in HWE, while PROP1 (C-allele/CC) deviated in Hair and pooled groups. STAT5A was fixed for CC. Turkish goats reveals allele predominance patterns and HWE deviations, suggesting effects of selection and population structure. These results enrich global goat genetic resources and support marker-assisted selection for milk traits. Keywords : Candidate genes, Goat, Honamlı, Hair, Milk yield traits, Polymorphism