Categories: Pigmentation phene

Links to possible relevant human trait(s) and/or gene(s) in OMIM: 131242 (gene)

Single-gene trait/disorder: yes

Mode of inheritance: Autosomal dominant

Disease-related: no

Key variant known: yes

Year key variant first reported: 2011

Cross-species summary: also called Silky/Silkie hyperpigmentation, black bone

Species-specific name: Also known as Dermal hyperpigmentation

Species-specific symbol: FM

Inheritance: The mutant allele (*FM) is dominant to the wild-type, recessive (*N) allele. The locus symbol is FM.

Mapping: Dorshorst et al. (2010) were the first to map this locus, reporting its location as "10.3–13.1 Mb on chromosome [GGA]20". This mapping was slightly narrowed by Shinomiya et al. (2011) to "10.2-11.7 Mb of chicken chromosome [GGA]20".

Molecular basis: Two studies identified the molecular basis of hyperpigmentation in chickens: Shinomiya (2012; accepted Nov 16, 2011; electronic publication Nov 30, 2011) and Dorshorst et al. (2011, accepted Oct 22, 2011; electronic publication Dec 22, 2011). 
Shinomiya et al. (2012) reported that the characteristic hyperpigmentation in “Silky” chickens is associated with a 130kb duplication of a segment of chicken chromosome 20 that contains five genes and showed that at least four of these genes, including EDN3, show two-fold upregulated gene expression in whole embryos. Dorshorst et al. (2011) showed that the FM mutation involves two large duplications, DUP1 (129kb) and DUP2 (172kb), located on chicken chromosome 20. These two duplicated regions are separated by 417 kb on wild-type [GGA20] chromosomes. Dorshorst et al. showed that the fibromelanosis locus involved a complex rearrangement where at least one of the duplicated copies had an inverted orientation to the other copies. They presented three possible scenarios based on PCR analysis: FM_1, FM_2 and FM_3. Genetic evidence based on a single recombinant from a pedigree strongly supported the FM_2 scenario in which an inverted copy of DUP2 is located between the two copies of DUP1 followed by the 417kb nonduplicated region and the second copy of DUP2. They also reported that DUP1 contains the endothelin 3 (EDN3) gene which encodes a potent mitogen for melanoblasts/melanocytes, that EDN3 shows a 10-fold upregulated expression in skin from FM chickens compared with wild-type, and that this is the likely causal mechanism for the fibromelanosis phenotype. Their analysis of a range of breeds strongly suggested that the mutation giving rise to this double duplication is the cause of FM in all breeds of chickens, and hence is an old mutation, predating the divergence of breeds. Dharmayanthi et al. (2017): "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 (called DUP1 above), together with another region, DR2 of 171 kb (called DUP2 above), was duplicated by unequal crossing over, accompanied by inversion of one DR2. … These genetic arrangements are identical in Cemani and Silkie, indicating a single origin of the genetic cause of Fm as shown by Dorshorst et al. (2011). The two DR1s harbour 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 favouring 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." 
Studies based on long read sequencing as well as genome assemblies have given conflicting results regarding which of the three possible scenarios (FM_1, FM_2 and FM_3) for the order and orientation of DUP1 and DUP2 copies proposed by Dorshorst et al. (2011) is correct. Zhu et al. (2023) presented a chromosome-level assembly for Silkie chickens in which they claim that the FM_1 scenario is the correct one. This conclusion was questioned by Sharma and Vijay (2025) who reanalysed the data by Zhu et al. (2023) and came to the conclusion that the data in fact supported the FM_2 scenario. In a reply to this paper, Zhao et al. (2025) persisted that their data support the FM_1 scenario. However, in a population genetic analysis by Dharmayanthi et al. (2017) it was concluded that the data “clearly showed that the patterns and degrees of polymorphism exhibited by Cemani and Silkie [chickens] are consistent with FM2, but inconsistent with FM1 and FM3”. Thus, this analysis supported the conclusion by Dorshorst et al. (2011) based on a recombination event inconsistent with the FM1 and FM3 scenarios. This conclusion is further supported by a comprehensive genomic survey of 517 FM chickens representing 44 different populations (Ma and Andersson, 2025). Thus, the consensus strongly supports the FM2 scenario that can be represented as DUP1|invertedDUP2|DUP1|413kb|DUP2. Ma and Andersson (2025) also "show that the birth of this complex structural variant must have involved an interchromosomal rearrangement creating fixed heterozygosity due to sequence differences between the two copies of the 127.4 kb [DUP1] duplication".

Breeds: Bohuslän - Dals svarthöna, Sweden (Chicken) (VBO_0007792), Chinese Xingyi bantam, China (Chicken) (VBO_0016856), Dulong chicken, China (Chicken) (VBO_0006673), Emei Black, China (Chicken) (VBO_0006675), Guangxi Black-bone chicken, China (Chicken) (VBO_0006678), H'mong, Viet Nam (Chicken) (VBO_0007907), Jiuyuan Black, China (Chicken) (VBO_0006709), Kadaknath, India (Chicken) (VBO_0007349), Kedu, Indonesia (Chicken) (VBO_0007320), Luning, China (Chicken) (VBO_0006724), Miyi, China (Chicken) (VBO_0006730), Muchuan Silkies Black, China (Chicken) (VBO_0006731), Nunukan, Indonesia (Chicken) (VBO_0007325), Pengxian Buff, China (Chicken) (VBO_0006738), Piao chicken, China (Chicken) (VBO_0006739), Qiandongnan Xiao Xiang, China (Chicken) (VBO_0006741), Silkie (Chicken) (VBO_0000619), Sumatra (Chicken) (VBO_0000629), Taliu Black-bone chicken, China (Chicken) (VBO_0006754), Tibetan, China (Chicken) (VBO_0006759), Weining, China (Chicken) (VBO_0006762), Wuding, China (Chicken) (VBO_0006765), Wuliangshang Black –bone chicken, China (Chicken) (VBO_0006767), Wumeng Silkies, China (Chicken) (VBO_0006768), Xichuan black-bone chicken, China (Chicken) (VBO_0006774), Xishuangbanna Fighting, China (Chicken) (VBO_0006780), Yeonsan Ogye, Republic of Korea (Chicken) (VBO_0007447), Yimeng Blue, China (Chicken) (VBO_0016867).
Breeds in which the phene or likely causal variants have been documented. If a likely causal variant has been documented, see variant-specific breed information in the variant table. (Breed information may be incomplete).

Associated gene: