Amplification of CHD-1 gene fragment in Z and W sex chromosomes of Cemani chicken using a different set of PCR primers

Abstract

Abstract Cemani chicken is a local breed of Indonesian chicken known for its mystical appearance. Selecting sex earlier is essential for the breeding program to determine the population structure. Instead of using phenotype, sexing in birds can be done molecularly by employing the variation of the CHD-1 gene, which belongs to the Z chromosome. Five primers (pair), namely AVP2 and AVP8; CHD1F and CHD1R; AV1237L and AV1272H; CHDZ and CHDW, then AV2550F and AV2718R, were employed to amplify the CHD-1 gene in PCR reaction followed with electrophoresis analysis. Cemani chicken blood was collected from the Bracial vein, followed by DNA extraction. Two primers set, CHD1F and CHD1R, and AV2550F and AV2718R, were able to amplify the CHD-1 gene and distinguish the difference between male (ZZ) vs. female (ZW) chromosome by showing two clear DNA bands in the female source sample and one band in the male sample. Meanwhile, the AVP2 and AVP8, AV1237L, and AV1272H, only show one clear band in both female and male source samples, and no bands resulted from using CHDZ and CHDW primer. Two sets of primers were able to amplify the CHD-1 gene fragment using PCR and amplified for further molecular sex determination in Cemani chicken.