Identification of variation inFibromelanosisregion on chromosome 20 for determining the purity of Indonesian Cemani chicken

Abstract

ABSTRACTAyam Cemani is a local Indonesian chicken with heavy pigmentation in plumage colour, skin, eyes, and inner body organs. This trait with dermal hyperpigmentation is identical toFibromelanosis(Fm) mutation in a Silkie chicken. The causal mutation of theFmtrait is due to an inverted duplication and junction of two genomic regions involving the Endothelin3 (EDN3) gene on chromosome 20. There are two duplication boundaries; one is specific to theFmallele, the other is common for bothFmandfm+allele. Determining birds that are homozygous or heterozygous at this locus is useful for unifying theFmtrait of Cemani populations. This study develops a method for determining the presence or absence ofFmmutation by PCR amplification using the inverted sequences specific to theFmallele. Further, it develops the restriction fragment length polymorphism (RFLP) method in regions common to theFmand wild-typefm+allele. We aim to establish a simple method for detecting homozygous (Fm/Fm) and heterozygous (Fm/fm+) individuals withFmmutation and to clarify the degree of fixation of theFmtrait in the Ayam Cemani populations and the association between the phenotype and genotype. The result showed that mostly, the phenotype for Cemani withFm/fm+genotype is reddish black in their comb; meanwhile, the Cemani with (Fm/Fm) genotype showed heavy black pigmentation. Our study concluded that using the PCR-RFLP method. We can discriminate betweenFmhomozygous and heterozygous birds in the Cemani population. Thus, this briefly genotyping method effectively maintains and protects the pure line of Cemani chicken.