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Journal of molecular evolution
Feb, 2025;93 (1): 163-180.

Common Ancestry of the Id Locus: Chromosomal Rearrangement and Polygenic Possibilities.

Ashutosh Sharma, Nagarjun Vijay
Author Information
  1. Ashutosh Sharma: Computational Evolutionary Genomics Lab, Department of Biological Sciences, IISER Bhopal, Bhauri, Madhya Pradesh, India.
  2. Nagarjun Vijay: Computational Evolutionary Genomics Lab, Department of Biological Sciences, IISER Bhopal, Bhauri, Madhya Pradesh, India. nagarjun@iiserb.ac.in. ORCID
PMID: 39821315 DOI: 10.1007/s00239-025-10233-z

Abstract

The diversity in dermal pigmentation and plumage color among domestic chickens is striking, with Black Bone Chickens (BBC) particularly notable for their intense melanin hyperpigmentation. This unique trait is driven by a complex chromosomal rearrangement on chromosome 20 at the Fm locus, resulting in the overexpression of the EDN3 (a gene central to melanocyte regulation). In contrast, the inhibition of dermal pigmentation is regulated by the Id locus. Although prior studies using genetic crosses, GWAS, and gene expression analysis have investigated the genetic underpinnings of the Id locus, its precise location and functional details remain elusive. Our study aims to precisely locate the Id locus, identify associated chromosomal rearrangements and candidate genes influencing dermal pigmentation, and examine the ancestral status of the Id locus in BBC breeds. Using public genomic data from BBC and non-BBC breeds, we refined the Id locus to a���~1.6 Mb region that co-localizes with Z amplicon repeat units at the distal end of the q-arm of chromosome Z within a 10.36 Mb inversion in Silkie BBC. Phylogenetic and population structure analyses reveal that the Id locus shares a common ancestry across all BBC breeds, much like the Fm locus. Selection signatures and highly differentiated BBC-specific SNPs within the MTAP gene position it as the prime candidate for the Id locus with CCDC112 and additional genes, suggesting a possible polygenic nature. Our results suggest that the Id locus is shared among BBC breeds and may function as a supergene cluster in shank and dermal pigmentation variation.

Keywords

Id locus Black bone chickens Chromosome Z Dermal pigmentation Genomic variants Inversion

References

  1. Agarwal V, Bell GW, Nam JW, Bartel DP (2015) Predicting effective microRNA target sites in mammalian mRNAs. Elife. https://doi.org/10.7554/ELIFE.05005 [DOI: 10.7554/ELIFE.05005]
  2. Ainger SA, Jagirdar K, Lee KJ et al (2017) Skin pigmentation genetics for the clinic. Dermatology. https://doi.org/10.1159/000468538 [DOI: 10.1159/000468538]
  3. Altschul SF, Gish W, Miller W et al (1990) Basic local alignment search tool. J Mol Biol 215:403���410. https://doi.org/10.1016/S0022-2836(05)80360-2 [DOI: 10.1016/S0022-2836(05)80360-2]
  4. Apopo S, Liu H, Jing L et al (2015) Identification and profiling of microRNAs associated with white and black plumage pigmentation in the white and black feather bulbs of ducks by RNA sequencing. Anim Genet 46:627���635. https://doi.org/10.1111/AGE.12343 [DOI: 10.1111/AGE.12343]
  5. Arora G, Mishra SK, Nautiyal B et al (2011) Genetics of hyperpigmentation associated with the Fibromelanosis gene (Fm) and analysis of growth and meat quality traits in crosses of native Indian Kadaknath chickens and non-indigenous breeds. Br Poult Sci 52:675���685. https://doi.org/10.1080/00071668.2011.635637 [DOI: 10.1080/00071668.2011.635637]
  6. Barrett RDH, Schluter D (2008) Adaptation from standing genetic variation. Trends Ecol Evol 23:38���44. https://doi.org/10.1016/J.TREE.2007.09.008 [DOI: 10.1016/J.TREE.2007.09.008]
  7. Bateson BW, Punnett RC (1911) The inheritance of the peculiar pigmentation of the silky fowl. J Genet 13(1):185���203. https://doi.org/10.1007/BF02981551 [DOI: 10.1007/BF02981551]
  8. Baynash AG, Hosoda K, Giaid A et al (1994) Interaction of endothelin-3 with endothelin-B receptor is essential for development of epidermal melanocytes and enteric neurons. Cell 79:1277���1285. https://doi.org/10.1016/0092-8674(94)90018-3 [DOI: 10.1016/0092-8674(94)90018-3]
  9. Behrmann I, Wallner S, Komyod W et al (2003) Characterization of methylthioadenosin phosphorylase (MTAP) expression in Malignant Melanoma. Am J Pathol 163:683���690. https://doi.org/10.1016/S0002-9440(10)63695-4 [DOI: 10.1016/S0002-9440(10)63695-4]
  10. Bellott DW, Skaletsky H, Pyntikova T et al (2010) Convergent evolution of chicken Z and human X chromosomes by expansion and gene acquisition. Nature 466:612���616. https://doi.org/10.1038/nature09172 [DOI: 10.1038/nature09172]
  11. Bitgood JJ (1985) Additional linkage relationships within the Z chromosome of the chicken. Poult Sci 64:2234���2238. https://doi.org/10.3382/PS.0642234 [DOI: 10.3382/PS.0642234]
  12. Bitgood JJ (1988) Linear relationship of the loci for barring, dermal melanin inhibitor, and recessive white skin on the chicken Z chromosome. Poult Sci 67:530���533. https://doi.org/10.3382/ps.0670530 [DOI: 10.3382/ps.0670530]
  13. Bogdanowicz D, Giaro K, Wr��bel B (2012) TreeCmp: comparison of trees in polynomial time. Evol Bioinform Online 8:475. https://doi.org/10.4137/EBO.S9657 [DOI: 10.4137/EBO.S9657]
  14. Cha J, Jin D, Kim JH et al (2023) Genome-wide association study revealed the genomic regions associated with skin pigmentation in an Ogye x White Leghorn F2 chicken population. Poult Sci. https://doi.org/10.1016/J.PSJ.2023.102720 [DOI: 10.1016/J.PSJ.2023.102720]
  15. Cingolani P, Platts A, Wang LL et al (2012) A program for annotating and predicting the effects of single nucleotide polymorphisms, SnpEff: SNPs in the genome of Drosophila melanogaster strain w1118; iso-2; iso-3. Fly (Austin) 6:80. https://doi.org/10.4161/FLY.19695 [DOI: 10.4161/FLY.19695]
  16. Danecek P, Auton A, Abecasis G et al (2011) The variant call format and VCFtools. Bioinformatics 27:2156���2158. https://doi.org/10.1093/BIOINFORMATICS/BTR330 [DOI: 10.1093/BIOINFORMATICS/BTR330]
  17. Danecek P, Bonfield JK, Liddle J et al (2021) Twelve years of SAMtools and BCFtools. Gigascience 10:1���4. https://doi.org/10.1093/GIGASCIENCE/GIAB008 [DOI: 10.1093/GIGASCIENCE/GIAB008]
  18. Darlington GJ, Ross SE, MacDougald OA (1998) The role of C/EBP genes in adipocyte differentiation. J Biol Chem 273:30057���30060. https://doi.org/10.1074/jbc.273.46.30057 [DOI: 10.1074/jbc.273.46.30057]
  19. DePristo MA, Banks E, Poplin R et al (2011) A framework for variation discovery and genotyping using next-generation DNA sequencing data. Nat Genet 43:491���498. https://doi.org/10.1038/ng.806 [DOI: 10.1038/ng.806]
  20. Dharmayanthi AB, Terai Y, Sulandari S et al (2017) The origin and evolution of fibromelanosis in domesticated chickens: genomic comparison of Indonesian Cemani and Chinese Silkie breeds. PLoS ONE. https://doi.org/10.1371/JOURNAL.PONE.0173147 [DOI: 10.1371/JOURNAL.PONE.0173147]
  21. Dorshorst BJ, Ashwell CM (2009) Genetic mapping of the sex-linked barring gene in the chicken. Poult Sci 88:1811���1817. https://doi.org/10.3382/PS.2009-00134 [DOI: 10.3382/PS.2009-00134]
  22. Dorshorst B, Okimoto R, Ashwell C (2010) Genomic regions associated with dermal hyperpigmentation, polydactyly and other morphological traits in the silkie chicken. J Hered. https://doi.org/10.1093/jhered/esp120 [DOI: 10.1093/jhered/esp120]
  23. Dorshorst B, Molin AM, Rubin CJ et al (2011) A complex genomic rearrangement involving the Endothelin 3 locus causes dermal hyperpigmentation in the chicken. PLoS Genet. https://doi.org/10.1371/journal.pgen.1002412 [DOI: 10.1371/journal.pgen.1002412]
  24. Dunn LC, Jull MA (1927) On the inheritance of some characters op the silky fowl. J Genet. https://doi.org/10.1007/BF02983116 [DOI: 10.1007/BF02983116]
  25. Edeen FC (1985) Truncated repeated sequences generated by recombination in a specific region. Biochemistry 24:229���233. https://doi.org/10.1021/BI00322A033 [DOI: 10.1021/BI00322A033]
  26. Eden FC, Musti AM, Sobieski DA (1981) Clusters of repeated sequences of chicken DNA are extensively methylated but contain specific undermethylated regions. J Mol Biol 148:129���151. https://doi.org/10.1016/0022-2836(81)90509-X [DOI: 10.1016/0022-2836(81)90509-X]
  27. Ellegren H (2011) (2011) Sex-chromosome evolution: recent progress and the influence of male and female heterogamety. Nat Rev Genet 123(12):157���166. https://doi.org/10.1038/nrg2948 [DOI: 10.1038/nrg2948]
  28. Evanno G, Regnaut S, Goudet J (2005) Detecting the number of clusters of individuals using the software STRUCTURE: a simulation study. Mol Ecol 14:2611���2620. https://doi.org/10.1111/J.1365-294X.2005.02553.X [DOI: 10.1111/J.1365-294X.2005.02553.X]
  29. Faraco CD, So S, Vaz SAS et al (2001) Hyperpigmentation in the silkie fowl correlates with abnormal migration of fate-restricted melanoblasts and loss of environmental barrier molecules. Dev Dyn 220:212���222. https://doi.org/10.1002/1097-0177 [DOI: 10.1002/1097-0177]
  30. Farr�� D, Roset R, Huerta M et al (2003) Identification of patterns in biological sequences at the ALGGEN server: PROMO and MALGEN. Nucleic Acids Res 31:3651���3653. https://doi.org/10.1093/NAR/GKG605 [DOI: 10.1093/NAR/GKG605]
  31. Fujita PA, Rhead B, Zweig AS et al (2011) The UCSC Genome Browser database: update 2011. Nucleic Acids Res 39:D876���D882. https://doi.org/10.1093/NAR/GKQ963 [DOI: 10.1093/NAR/GKQ963]
  32. Garrison E, Marth G (2012) Haplotype-based variant detection from short-read sequencing
  33. Ge SX, Jung D, Jung D, Yao R (2020) ShinyGO: A graphical gene-set enrichment tool for animals and plants. Bioinformatics 36:2628���2629. https://doi.org/10.1093/bioinformatics/btz931 [DOI: 10.1093/bioinformatics/btz931]
  34. Glun��i�� M, Vlahovi�� I, Mr��i�� L, Paar V (2022) Global repeat map (GRM) application: finding All DNA tandem repeat units. Algorithms 15:458. https://doi.org/10.3390/A15120458/S1 [DOI: 10.3390/A15120458/S1]
  35. Goel M, Schneeberger K (2022) plotsr: visualizing structural similarities and rearrangements between multiple genomes. Bioinformatics 38:2922���2926. https://doi.org/10.1093/BIOINFORMATICS/BTAC196 [DOI: 10.1093/BIOINFORMATICS/BTAC196]
  36. Goel M, Sun H, Jiao WB, Schneeberger K (2019) SyRI: finding genomic rearrangements and local sequence differences from whole-genome assemblies. Genome Biol 20:1���13. https://doi.org/10.1186/S13059-019-1911-0/FIGURES/5 [DOI: 10.1186/S13059-019-1911-0/FIGURES/5]
  37. Graf J, Voisey J, Hughes I, Van Daal A (2007) Promoter polymorphisms in the MATP (SLC45A2) gene are associated with normal human skin color variation. Hum Mutat 28:710���717. https://doi.org/10.1002/HUMU.20504 [DOI: 10.1002/HUMU.20504]
  38. Hellstr��m AR, Sundstr��m E, Gunnarsson U et al (2010) Sex-linked barring in chickens is controlled by the CDKN2A /B tumour suppressor locus. Pigment Cell Melanoma Res 23:521���530. https://doi.org/10.1111/J.1755-148X.2010.00700.X [DOI: 10.1111/J.1755-148X.2010.00700.X]
  39. Heo S, Cho S, Dinh PTN et al (2023) A genome-wide association study for eumelanin pigmentation in chicken plumage using a computer vision approach. Anim Genet 54:355���362. https://doi.org/10.1111/AGE.13303 [DOI: 10.1111/AGE.13303]
  40. Huang X, Weng Z, He Y et al (2021) Mitochondrial DNA diversity and demographic history of Black-boned chickens in China. Mitochondrial DNA Part B, Resour 6:1462���1467. https://doi.org/10.1080/23802359.2021.1912668 [DOI: 10.1080/23802359.2021.1912668]
  41. Ihaka R, Gentleman R (1996) R: a language for data analysis and graphics. J Comput Graph Stat 5:299���314. https://doi.org/10.1080/10618600.1996.10474713 [DOI: 10.1080/10618600.1996.10474713]
  42. Il SJ, Nam K, Hong H et al (2018) Whole genome and transcriptome maps of the entirely black native Korean chicken breed Yeonsan Ogye. Gigascience 7:1���14. https://doi.org/10.1093/GIGASCIENCE/GIY086 [DOI: 10.1093/GIGASCIENCE/GIY086]
  43. Imsland F, Feng C, Boije H et al (2012) The Rose-comb mutation in chickens constitutes a structural rearrangement causing both altered comb morphology and defective sperm motility. PLoS Genet. https://doi.org/10.1371/journal.pgen.1002775 [DOI: 10.1371/journal.pgen.1002775]
  44. Kanehisa M, Goto S (2000) KEGG: kyoto encyclopedia of genes and genomes. Nucleic Acids Res 28:27. https://doi.org/10.1093/NAR/28.1.27 [DOI: 10.1093/NAR/28.1.27]
  45. Karolchik D, Baertsch R, Diekhans M et al (2003) The UCSC genome browser database. Nucleic Acids Res 31:51���54. https://doi.org/10.1093/NAR/GKG129 [DOI: 10.1093/NAR/GKG129]
  46. Khanna A, Larson DE, Srivatsan SN, et al (2022) Bam-readcount - rapid generation of basepair-resolution sequence metrics. ArXiv 7:3722. https://doi.org/10.21105/joss.03722
  47. Kirkpatrick M, Barton N (2006) Chromosome inversions, local adaptation and speciation. Genetics 173:419���434. https://doi.org/10.1534/GENETICS.105.047985 [DOI: 10.1534/GENETICS.105.047985]
  48. Knief U, Hemmrich-Stanisak G, Wittig M et al (2016) Fitness consequences of polymorphic inversions in the zebra finch genome. Genome Biol 17:1���22. https://doi.org/10.1186/S13059-016-1056-3/FIGURES/6 [DOI: 10.1186/S13059-016-1056-3/FIGURES/6]
  49. Koboldt DC (2020) Best practices for variant calling in clinical sequencing. Genome Med 121(12):1���13. https://doi.org/10.1186/S13073-020-00791-W [DOI: 10.1186/S13073-020-00791-W]
  50. Kopelman NM, Mayzel J, Jakobsson M et al (2015) Clumpak: a program for identifying clustering modes and packaging population structure inferences across K. Mol Ecol Resour 15:1179���1191. https://doi.org/10.1111/1755-0998.12387 [DOI: 10.1111/1755-0998.12387]
  51. Korneliussen TS, Albrechtsen A, Nielsen R (2014) ANGSD: analysis of next generation sequencing data. BMC Bioinform. https://doi.org/10.1186/S12859-014-0356-4 [DOI: 10.1186/S12859-014-0356-4]
  52. Kozomara A, Griffiths-Jones S (2014) miRBase: annotating high confidence microRNAs using deep sequencing data. Nucleic Acids Res. https://doi.org/10.1093/NAR/GKT1181 [DOI: 10.1093/NAR/GKT1181]
  53. K��pper C, Stocks M, Risse JE et al (2015) A supergene determines highly divergent male reproductive morphs in the ruff. Nat Genet 481(48):79���83. https://doi.org/10.1038/ng.3443 [DOI: 10.1038/ng.3443]
  54. Kvaskoff M, Whiteman DC, Zhao ZZ et al (2011) Polymorphisms in nevus-associated genes MTAP, PLA2G6, and IRF4 and the risk of invasive cutaneous melanoma. Twin Res Hum Genet 14:422���432. https://doi.org/10.1375/TWIN.14.5.422 [DOI: 10.1375/TWIN.14.5.422]
  55. Lamichhaney S, Fan G, Widemo F et al (2015) Structural genomic changes underlie alternative reproductive strategies in the ruff (Philomachus pugnax). Nat Genet 481(48):84���88. https://doi.org/10.1038/ng.3430 [DOI: 10.1038/ng.3430]
  56. Larney C, Bailey TL, Koopman P (2014) Switching on sex: transcriptional regulation of the testis-determining gene Sry. Development 141:2195���2205. https://doi.org/10.1242/DEV.107052 [DOI: 10.1242/DEV.107052]
  57. Li H, Durbin R (2009) Fast and accurate short read alignment with Burrows-Wheeler transform. Bioinformatics 25:1754���1760. https://doi.org/10.1093/BIOINFORMATICS/BTP324 [DOI: 10.1093/BIOINFORMATICS/BTP324]
  58. Li G, Li D, Yang N et al (2014) A genome-wide association study identifies novel single nucleotide polymorphisms associated with dermal shank pigmentation in chickens. Poult Sci 93:2983���2987. https://doi.org/10.3382/PS.2014-04164 [DOI: 10.3382/PS.2014-04164]
  59. Li D, Sun G, Zhang M et al (2020) Breeding history and candidate genes responsible for black skin of Xichuan black-bone chicken. BMC Genomics 21:1���15. https://doi.org/10.1186/S12864-020-06900-8/FIGURES/8 [DOI: 10.1186/S12864-020-06900-8/FIGURES/8]
  60. Li J, Lee MO, Chen J et al (2021) Cis-acting mutation affecting GJA5 transcription is underlying the Melanotic within-feather pigmentation pattern in chickens. Proc Natl Acad Sci USA 118:e2109363118. https://doi.org/10.1073/PNAS.2109363118/SUPPL_FILE/PNAS.2109363118.SAPP.PDF [DOI: 10.1073/PNAS.2109363118/SUPPL_FILE/PNAS.2109363118.SAPP.PDF]
  61. Liu H, Xi Y, Tang Q et al (2023) Genetic fine-mapping reveals single nucleotide polymorphism mutations in the MC1R regulatory region associated with duck melanism. Mol Ecol 32:3076���3088. https://doi.org/10.1111/MEC.16924 [DOI: 10.1111/MEC.16924]
  62. Lorenzo PI, Ju��rez-Vicente F, Cobo-Vuilleumier N et al (2017) The diabetes-linked transcription factor PAX4: from gene to functional consequences. Genes 8:101. https://doi.org/10.3390/GENES8030101 [DOI: 10.3390/GENES8030101]
  63. Madrigal G, Minhas BF, Catchen J (2024) Klumpy: a tool to evaluate the integrity of long-read genome assemblies and illusive sequence motifs. Mol Ecol Resour. https://doi.org/10.1111/1755-0998.13982 [DOI: 10.1111/1755-0998.13982]
  64. McGeary SE, Lin KS, Shi CY et al (2019) The biochemical basis of microRNA targeting efficacy. Science 80:366. https://doi.org/10.1126/SCIENCE.AAV1741 [DOI: 10.1126/SCIENCE.AAV1741]
  65. Mcgibbon WH (1978) The genetics of green spotting on shanks of Ancona chickens. J Hered 69:97���100. https://doi.org/10.1093/OXFORDJOURNALS.JHERED.A108912 [DOI: 10.1093/OXFORDJOURNALS.JHERED.A108912]
  66. McKenna A, Hanna M, Banks E et al (2010) The genome analysis toolkit: a MapReduce framework for analyzing next-generation DNA sequencing data. Genome Res 20:1297���1303. https://doi.org/10.1101/gr.107524.110 [DOI: 10.1101/gr.107524.110]
  67. Meisner J, Albrechtsen A (2018) Inferring population structure and admixture proportions in low-depth NGS data. Genetics 210:719���731. https://doi.org/10.1534/GENETICS.118.301336 [DOI: 10.1534/GENETICS.118.301336]
  68. Minh BQ, Schmidt HA, Chernomor O et al (2020) IQ-TREE 2: new models and efficient methods for phylogenetic inference in the genomic era. Mol Biol Evol 37:1530���1534. https://doi.org/10.1093/MOLBEV/MSAA015 [DOI: 10.1093/MOLBEV/MSAA015]
  69. Minto MS, Sotelo-Fonseca JE, Ramesh V, West AE (2024) Genome binding properties of Zic transcription factors underlie their changing functions during neuronal maturation. BMC Biol 22:1���20. https://doi.org/10.1186/S12915-024-01989-9/FIGURES/1 [DOI: 10.1186/S12915-024-01989-9/FIGURES/1]
  70. Mione M, Bosserhoff A (2015) MicroRNAs in melanocyte and melanoma biology. Pigment Cell Melanoma Res 28:340���354. https://doi.org/10.1111/PCMR.12346 [DOI: 10.1111/PCMR.12346]
  71. Mukherjee TK, Jerome FN, Reinhart BS (1969) The inhibition of dermal melanin in the shanks of the domestic fowl. Poult Sci 48:2137���2142. https://doi.org/10.3382/PS.0482137 [DOI: 10.3382/PS.0482137]
  72. Quinlan AR, Hall IM (2010) BEDTools: a flexible suite of utilities for comparing genomic features. Bioinformatics 26:841���842 [DOI: 10.1093/bioinformatics/btq033]
  73. Rambaut A (2014) FigTree v1.4.2., A Graphical Viewer of Phylogenetic Trees. In: http://tree.bio.ed.ac.uk/software/figtree/
  74. Recuerda M, Campagna L (2024) How structural variants shape avian phenotypes: lessons from model systems. Mol Ecol 33:e17364. https://doi.org/10.1111/MEC.17364 [DOI: 10.1111/MEC.17364]
  75. Reedy MV, Faraco CD, Erickson CA (1998) Specification and migration of melanoblasts at the vagal level and in hyperpigmented silkie chickens. Dev Dyn 213:476���485. https://doi.org/10.1002/(SICI)1097-0177(199812)213:4%3c476 [DOI: 10.1002/(SICI)1097-0177(199812)213]
  76. Ren S, Lyu G, Irwin DM et al (2021) Pooled sequencing analysis of geese (Anser cygnoides) reveals genomic variations associated with feather color. Front Genet 12:650013. https://doi.org/10.3389/FGENE.2021.650013/BIBTEX [DOI: 10.3389/FGENE.2021.650013/BIBTEX]
  77. Sanchez-Donoso I, Ravagni S, Rodr��guez-Teijeiro JD et al (2022) Massive genome inversion drives coexistence of divergent morphs in common quails. Curr Biol 32:462-469.e6. https://doi.org/10.1016/J.CUB.2021.11.019 [DOI: 10.1016/J.CUB.2021.11.019]
  78. Sharma A, Vijay N (2024) What is the correct genomic structure of the complex chromosomal rearrangement at the Fm locus in Silkie chicken? bioRxiv 2024.02.05.578760. https://doi.org/10.1101/2024.02.05.578760
  79. Shinde SS, Sharma A, Vijay N (2023) Decoding the fibromelanosis locus complex chromosomal rearrangement of black-bone chicken: genetic differentiation, selective sweeps and protein-coding changes in Kadaknath chicken. Front Genet 14:1180658. https://doi.org/10.3389/FGENE.2023.1180658/BIBTEX [DOI: 10.3389/FGENE.2023.1180658/BIBTEX]
  80. Shinomiya A, Kayashima Y, Kinoshita K, et al (2012) Gene duplication of endothelin 3 is closely correlated with the hyperpigmentation of the internal organs (fibromelanosis) in silky chickens. Genetics
  81. Siwek M, Wragg D, S��awi��ska A et al (2013) Insights into the genetic history of Green-legged Partridgelike fowl: mtDNA and genome-wide SNP analysis. Anim Genet 44:522. https://doi.org/10.1111/AGE.12046 [DOI: 10.1111/AGE.12046]
  82. Skotte L, Korneliussen TS, Albrechtsen A (2013) Estimating individual admixture proportions from next generation sequencing data. Genetics 195:693���702. https://doi.org/10.1534/GENETICS.113.154138 [DOI: 10.1534/GENETICS.113.154138]
  83. Smeds L, Warmuth V, Bolivar P et al (2015) Evolutionary analysis of the female-specific avian W chromosome. Nat Commun. https://doi.org/10.1038/NCOMMS8330 [DOI: 10.1038/NCOMMS8330]
  84. Sohn J, Nam K, Hong H et al (2018) Whole genome and transcriptome maps of the entirely black native Korean chicken breed Yeonsan Ogye. GigaScience 7:giy086.  https://doi.org/10.1093/gigascience/giy086 [DOI: 10.1093/gigascience/giy086]
  85. Tian M, Fang S, Wang Y et al (2014a) Inverted duplication including Endothelin 3 closely related to dermal hyperpigmentation in Silkie chickens. Front Agric Sci Eng 1:121���129. https://doi.org/10.15302/J-FASE-2014026 [DOI: 10.15302/J-FASE-2014026]
  86. Tian M, Hao R, Fang S et al (2014b) Genomic regions associated with the sex-linked inhibitor of dermal melanin in Silkie chicken. Front Agric Sci Eng 1:242���249. https://doi.org/10.15302/J-FASE-2014018 [DOI: 10.15302/J-FASE-2014018]
  87. Tian X, Pang X, Wang L et al (2018) Dynamic regulation of mRNA and miRNA associated with the developmental stages of skin pigmentation in Japanese ornamental carp. Gene 666:32���43. https://doi.org/10.1016/J.GENE.2018.04.054 [DOI: 10.1016/J.GENE.2018.04.054]
  88. Tixier-Boichard M (2002) From phenotype to genotype: major genes in chickens. Worlds Poult Sci J 58:65���75. https://doi.org/10.1079/WPS20020008 [DOI: 10.1079/WPS20020008]
  89. Tsukada J, Yoshida Y, Kominato Y, Auron PE (2011) The CCAAT/enhancer (C/EBP) family of basic-leucine zipper (bZIP) transcription factors is a multifaceted highly-regulated system for gene regulation. Cytokine 54:6���19. https://doi.org/10.1016/J.CYTO.2010.12.019 [DOI: 10.1016/J.CYTO.2010.12.019]
  90. Villarino AV, Kanno Y, Ferdinand JR, O���Shea JJ (2015) Mechanisms of Jak/STAT Signaling in Immunity and Disease. J Immunol 194:21���27. https://doi.org/10.4049/JIMMUNOL.1401867 [DOI: 10.4049/JIMMUNOL.1401867]
  91. Wang Y, Li J, Feng C et al (2017) Transcriptome analysis of comb and testis from Rose-comb Silky chicken (R1/R1) and Beijing Fatty wild type chicken (r/r). Poult Sci. https://doi.org/10.3382/ps/pew447 [DOI: 10.3382/ps/pew447]
  92. Wang G, Liao J, Tang M, Yu S (2018) Genetic variation in the MITF promoter affects skin colour and transcriptional activity in black-boned chickens. Br Poult Sci 59:21���27. https://doi.org/10.1080/00071668.2017.1379053 [DOI: 10.1080/00071668.2017.1379053]
  93. Wellenreuther M, Bernatchez L (2018) Eco-evolutionary genomics of chromosomal inversions. Trends Ecol Evol 33:427���440. https://doi.org/10.1016/J.TREE.2018.04.002 [DOI: 10.1016/J.TREE.2018.04.002]
  94. Xu J, Lin S, Gao X et al (2017) Mapping of Id locus for dermal shank melanin in a Chinese indigenous chicken breed. J Genet. https://doi.org/10.1007/s12041-017-0862-z [DOI: 10.1007/s12041-017-0862-z]
  95. Yan L, Liqing Z, Dexiang Z et al (2010) Faster evolution of Z-linked duplicate genes in chicken. J Genet Genomics 37:695���702. https://doi.org/10.1016/S1673-8527(09)60087-4 [DOI: 10.1016/S1673-8527(09)60087-4]
  96. Yu S, Liao J, Tang M et al (2017) A functional single nucleotide polymorphism in the tyrosinase gene promoter affects skin color and transcription activity in the black-boned chicken. Poult Sci 96:4061���4067. https://doi.org/10.3382/PS/PEX217 [DOI: 10.3382/PS/PEX217]
  97. Yu S, Wang G, Liao J (2019) Association of a novel SNP in the ASIP gene with skin color in black-bone chicken. Anim Genet 50:283���286. https://doi.org/10.1111/AGE.12768 [DOI: 10.1111/AGE.12768]
  98. Yu S, Wang G, Liao J et al (2020) Identification of key microRNAs affecting melanogenesis of breast muscle in Muchuan black-boned chickens by RNA sequencing. Br Poult Sci 61:225���231. https://doi.org/10.1080/00071668.2019.1709619 [DOI: 10.1080/00071668.2019.1709619]
  99. Yuan W, Qin H, Bi H et al (2023) Ssc-mir-221-3p regulates melanin production in Xiang pigs melanocytes by targeting the TYRP1 gene. BMC Genomics 24:1���14. https://doi.org/10.1186/S12864-023-09451-W/FIGURES/6 [DOI: 10.1186/S12864-023-09451-W/FIGURES/6]
  100. Zhang T, Du W, Lu H, Wang L (2018) Genetic Diversity of Mitochondrial DNA of Chinese Black-bone Chicken. Brazilian J Poult Sci 20:565���572. https://doi.org/10.1590/1806-9061-2018-0739 [DOI: 10.1590/1806-9061-2018-0739]
  101. Zhu Z, Ma Y, Li Y et al (2019) Comparison of miRNA-101a-3p and miRNA-144a-3p regulation with the key genes of alpaca melanocyte pigmentation. BMC Mol Biol 20:1���11. https://doi.org/10.1186/S12867-019-0137-8/FIGURES/8 [DOI: 10.1186/S12867-019-0137-8/FIGURES/8]
  102. Zhu F, Yin Z-T, Zhao Q-S et al (2023) A chromosome-level genome assembly for the Silkie chicken resolves complete sequences for key chicken metabolic, reproductive, and immunity genes. Commun Biol 61(6):1���15. https://doi.org/10.1038/s42003-023-05619-y [DOI: 10.1038/s42003-023-05619-y]

Grants

  1. BT/11/IYBA/2018/03/Department of Biotechnology
  2. ECR/2017/001430/Science and Engineering Research Board

MeSH Term

Animals
Chickens
Multifactorial Inheritance
Phylogeny
Polymorphism, Single Nucleotide
Pigmentation
Quantitative Trait Loci
Skin Pigmentation
Gene Rearrangement
Journal Article
Article has an altmetric score of 9

Word Cloud

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