title: The origin and evolution of fibromelanosis in domesticated chickens: Genomic comparison of Indonesian Cemani and Chinese Silkie breeds.
abstract: Like Chinese Silkie, Indonesian Ayam Cemani exhibits fibromelanosis or dermal hyperpigmentation and possesses complex segmental duplications on chromosome 20 that involve the endothelin 3 gene, EDN3. A genomic region, DR1 of 127 kb, together with another region, DR2 of 171 kb, was duplicated by unequal crossing over, accompanied by inversion of one DR2. Quantitative PCR and copy number variation analyses on the Cemani genome sequence confirmed the duplication of EDN3. These genetic arrangements are identical in Cemani 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 they remain allelic in the ancestral Red Jungle Fowl population and some domesticated chicken breeds, with their allelic divergence time being as recent as 0.3 million years ago. In Cemani and Silkie breeds, artificial selection favoring the Fm phenotype has left an unambiguous record for selective sweep that extends in both directions from tandemly duplicated EDN3 loci. 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 that throughout domestication there has been intense artificial selection with strength s > 50% in each breed.
authors.affiliation: Department of Evolutionary Studies of Biosystems, SOKENDAI (The Graduate University for Advanced Studies), Kanagawa, Japan.|Museum Zoologicum Bogoriense, Research Center for Biology, Indonesian Institute of Science (LIPI), Cibinong, Indonesia.
authors.forename: Anik Budhi
authors.initials: AB
authors.lastname: Dharmayanthi
authors.affiliation: Department of Evolutionary Studies of Biosystems, SOKENDAI (The Graduate University for Advanced Studies), Kanagawa, Japan.
authors.forename: Yohei
authors.initials: Y
authors.lastname: Terai
authors.affiliation: Museum Zoologicum Bogoriense, Research Center for Biology, Indonesian Institute of Science (LIPI), Cibinong, Indonesia.
authors.forename: Sri
authors.initials: S
authors.lastname: Sulandari
authors.affiliation: Museum Zoologicum Bogoriense, Research Center for Biology, Indonesian Institute of Science (LIPI), Cibinong, Indonesia.
authors.forename: M Syamsul Arifin
authors.initials: MS
authors.lastname: Zein
authors.affiliation: Department of Biology, Keio University, Yokohama, Japan.
authors.forename: Toyoko
authors.identifier: http://orcid.org/0000-0002-8233-2943
authors.initials: T
authors.lastname: Akiyama
authors.affiliation: Department of Evolutionary Studies of Biosystems, SOKENDAI (The Graduate University for Advanced Studies), Kanagawa, Japan.
authors.forename: Yoko
authors.initials: Y
authors.lastname: Satta
mesh_terms: D000483:Alleles; D000818:Animals; D005075:Biological Evolution; D001947:Breeding / Q000379:methods; D002645:Chickens / Q000235:genetics*; D002681:China; D002874:Chromosome Mapping / Q000379:methods; D003433:Crosses, Genetic; D056915:DNA Copy Number Variations / Q000235:genetics; D019334:Endothelin-3 / Q000235:genetics; D023281:Genomics / Q000379:methods; D006239:Haplotypes / Q000235:genetics; D017495:Hyperpigmentation / Q000235:genetics*; D007214:Indonesia; D010641:Phenotype
chemical_list: D019334:Endothelin-3