The origin and evolution of fibromelanosis in domesticated chickens: Genomic comparison of Indonesian Cemani and Chinese Silkie breeds

Like Chinese Silkie, Indonesian Ayam Cemani exhibits fibromelanosis or dermal hyperpigmentation and possesses complex segmental duplications on chromosome 20 that involvethe endothelin 3 gene, EDN3. A genomic region, DR1 of 127 kb, together with anotherregion, DR2 of 171 kb, was duplicated by unequal crossing over, accompanied by inversionof one DR2. Quantitative PCR and copy number variation analyses on the Cemani genomesequence confirmed the duplication of EDN3. These genetic arrangements are identical inCemani and Silkie, indicating a single origin of the genetic cause of Fm. The two DR1s harbor two distinct EDN3 haplotypes in a form of permanent heterozygosity, although theyremain allelic in the ancestral Red Jungle Fowl population and some domesticated chickenbreeds, with their allelic divergence time being as recent as 0.3 million years ago. In Cemaniand Silkie breeds, artificial selection favoring the Fm phenotype has left an unambiguousrecord for selective sweep that extends in both directions from tandemly duplicated EDN3loci. This highly homozygous tract is different in length between Cemani and Silkie, reflecting their distinct breeding histories. It is estimated that the Fm phenotype came into existence at least 6600–9100 years ago, prior to domestication of Cemani and Silkie, and thatthroughout domestication there has been intense artificial selection with strength s > 50 persen ineach breed. Plos One : http://doi.org/10.1371/journal.pone.0173147