A copy number variant is associated with a spectrum of pigmentation patterns in the rock pigeon (Columba livia)
Autoři:
Rebecca Bruders aff001; Hannah Van Hollebeke aff001; Edward J. Osborne aff002; Zev Kronenberg aff002; Emily Maclary aff001; Mark Yandell aff002; Michael D. Shapiro aff001
Působiště autorů:
School of Biological Sciences, University of Utah, Salt Lake City, Utah, United States of America
aff001; Department of Human Genetics, University of Utah, Salt Lake City, Utah, United States of America
aff002
Vyšlo v časopise:
A copy number variant is associated with a spectrum of pigmentation patterns in the rock pigeon (Columba livia). PLoS Genet 16(5): e32767. doi:10.1371/journal.pgen.1008274
Kategorie:
Research Article
doi:
https://doi.org/10.1371/journal.pgen.1008274
Souhrn
Rock pigeons (Columba livia) display an extraordinary array of pigment pattern variation. One such pattern, Almond, is characterized by a variegated patchwork of plumage colors that are distributed in an apparently random manner. Almond is a sex-linked, semi-dominant trait controlled by the classical Stipper (St) locus. Heterozygous males (ZStZ+ sex chromosomes) and hemizygous Almond females (ZStW) are favored by breeders for their attractive plumage. In contrast, homozygous Almond males (ZStZSt) develop severe eye defects and often lack plumage pigmentation, suggesting that higher dosage of the mutant allele is deleterious. To determine the molecular basis of Almond, we compared the genomes of Almond pigeons to non-Almond pigeons and identified a candidate St locus on the Z chromosome. We found a copy number variant (CNV) within the differentiated region that captures complete or partial coding sequences of four genes, including the melanosome maturation gene Mlana. We did not find fixed coding changes in genes within the CNV, but all genes are misexpressed in regenerating feather bud collar cells of Almond birds. Notably, six other alleles at the St locus are associated with depigmentation phenotypes, and all exhibit expansion of the same CNV. Structural variation at St is linked to diversity in plumage pigmentation and gene expression, and thus provides a potential mode of rapid phenotypic evolution in pigeons.
Klíčová slova:
Alleles – Bird genetics – Bird genomics – Copy number variation – Feathers – Gene expression – Melanocytes – Pigeons
Zdroje
1. Protas ME, Patel NH. (2008) Evolution of Coloration Patterns. Annual Review of Cell and Developmental Biology 24:425–471. doi: 10.1146/annurev.cellbio.24.110707.175302 18593352
2. Roberts NW, Mappes J, Arbuckle K, et al. (2017) The biology of color. Science 357:eaan0221. doi: 10.1126/science.aan0221 28774901
3. Bennett DC, Lamoreux ML. (2003) The color loci of mice—A genetic century. Pigment Cell Research 16:333–344. doi: 10.1034/j.1600-0749.2003.00067.x 12859616
4. Singh AP, Nüsslein-Volhard C. (2015) Zebrafish stripes as a model for vertebrate colour pattern formation. Current Biology. doi: 10.1016/j.cub.2014.11.013 25602311
5. Seo K, Mohanty TR, Choi T, Hwang I. (2007) Biology of epidermal and hair pigmentation in cattle: a mini-review. Veterinary Dermatology 18:392–400. doi: 10.1111/j.1365-3164.2007.00634.x 17991156
6. Kaelin CB, Barsh GS. (2013) Genetics of Pigmentation in Dogs and Cats. Annual Review of Animal Biosciences 1:125–156. doi: 10.1146/annurev-animal-031412-103659 25387014
7. Andersson L. (2001) Genetic dissection of phenotypic diversity in farm animals. Nature Reviews Genetics 2:130–138. doi: 10.1038/35052563 11253052
8. Linderholm A, Larson G. (2013) The role of humans in facilitating and sustaining coat colour variation in domestic animals. Seminars in Cell and Developmental Biology 24:587–593. doi: 10.1016/j.semcdb.2013.03.015 23567209
9. Andersson L. (2016) Domestic animals as models for biomedical research. Upsala Journal of Medical Sciences 121:1–11. doi: 10.3109/03009734.2015.1091522 26479863
10. Domyan ET, Shapiro MD. (2017) Pigeonetics takes flight: Evolution, development, and genetics of intraspecific variation. Developmental Biology 427:241–250. doi: 10.1016/j.ydbio.2016.11.008 27847323
11. Domyan ET, Guernsey MW, Kronenberg Z, et al. (2014) Epistatic and combinatorial effects of pigmentary gene mutations in the domestic pigeon. Current Biology 24:459–464. doi: 10.1016/j.cub.2014.01.020 24508169
12. Guernsey MW, Ritscher L, Miller MA, Smith DA, Schöneberg T, Shapiro MD. (2013) A Val85Met Mutation in Melanocortin-1 Receptor Is Associated with Reductions in Eumelanic Pigmentation and Cell Surface Expression in Domestic Rock Pigeons (Columba livia). PLoS ONE 8:1–9. doi: 10.1371/journal.pone.0074475 23977400
13. Vickrey AI, Bruders R, Kronenberg Z, et al. (2018) Introgression of regulatory alleles and a missense coding mutation drive plumage pattern diversity in the rock pigeon. eLife 7:e34803. doi: 10.7554/eLife.34803 30014848
14. Manceau M, Domingues VS, Linnen CR, Rosenblum EB, Hoekstra HE. (2010) Convergence in pigmentation at multiple levels: mutations, genes and function. Philosophical Transactions of the Royal Society B 365:2439–2450. doi: 10.1098/rstb.2010.0104 20643733
15. Rosenblum EB, Parent CE, Brandt EE. (2014) The Molecular Basis of Phenotypic Convergence. Annual Review of Ecology, Evolution, and Systematics 45:203–226. doi: 10.1146/annurev-ecolsys-120213-091851
16. Cieslak M, Reissmann M, Hofreiter M, Ludwig A. (2011) Colours of domestication. Biological Reviews 86:885–899. doi: 10.1111/j.1469-185X.2011.00177.x 21443614
17. Hoekstra HE. (2006) Genetics, development and evolution of adaptive pigmentation in vertebrates. Heredity 97:222–234. doi: 10.1038/sj.hdy.6800861 16823403
18. Mallarino R, Henegar C, Mirasierra M, Manceau M, Schradin C, Vallejo M, Beronja S, Barsh GS, Hoekstra HE. (2016) Developmental mechanisms of stripe patterns in rodents. Nature 539:518–523. doi: 10.1038/nature20109 27806375
19. Parichy DM. (2003) Pigment patterns: fish in stripes and spots. Current Biology 13:R947–50. doi: 10.1016/j.cub.2003.11.038 14680649
20. Brunberg E, Andersson L, Cothran G, Sandberg K, Mikko S, Lindgren G. (2006) A missense mutation in PMEL17 is associated with the Silver coat color in the horse. BMC Genetics 7:46. doi: 10.1186/1471-2156-7-46 17029645
21. Parichy DM, Spiewak JE. (2015) Origins of adult pigmentation: diversity in pigment stem cell lineages and implications for pattern evolution. Pigment Cell and Melanoma Research Melanoma Research 28:31–50. doi: 10.1111/pcmr.12332 25421288
22. Schmutz SM, Berryere TG, Dreger DL. (2009) MITF and white spotting in dogs: A population study. Journal of Heredity 100:S66–S74. doi: 10.1093/jhered/esp029
23. Karlsson EK, Baranowska I, Wade CM, et al. (2007) Efficient mapping of mendelian traits in dogs through genome-wide association. Nature Genetics 39:1321–1328. doi: 10.1038/ng.2007.10 17906626
24. Wriedt C, Christie W. (1925) Zur Genetik der gesprenkelten Haustaube. Induktive Abstammungs- und Vererbungslehre 38:271–306. doi: 10.1007/BF02118234
25. Sell A. (2012) Pigeon genetics: applied genetics in the domestic pigeon. Sell Publishing, Achim, Germany.
26. Hollander WF, Cole LJ. (1940) Somatic Mosaics in the Domestic Pigeon. Genetics 25:16–40. 17246956
27. Hollander WF. (1942) Auto-sexing in the domestic pigeon. Journal of Heredity 33:135–140. doi: 10.1093/oxfordjournals.jhered.a105150
28. Quinn JW. (1971) The Pigeon Breeders Notebook An Introduction to Pigeon Science. Published by Author, Atwater, Ohio.
29. Ghigi A. (1908) Sviluppo e comparsa di caratteri sessuli secondari in alcuni ucelli. Reale Accademia delle Scienze dell’Istituto di Bologna 15 Mar:3–23.
30. Moore J. (1735) Columbarium: or, the pigeon-house; being an introduction to a natural history of tame pigeons. J. Wilford, London.
31. Ezzedine K, Eleftheriadou V, Whitton M, Van Geel N. (2015) Vitiligo. The Lancet 386:74–84. doi: 10.1016/S0140-6736(14)60763-7
32. Yaghoobi R, Omidian M, Bagherani N. (2011) Vitiligo: A review of the published work. Journal of Dermatology 38:419–431. doi: 10.1111/j.1346-8138.2010.01139.x 21667529
33. Njoo MD, Westerhof W. (2001) Vitiligo Pathogenesis and treatment. American Journal of Clinical Dermatology 2:167–81. doi: 10.2165/00128071-200102030-00006 11705094
34. Tobin DJ, Paus R. (2001) Graying: Gerontobiology of the hair follicle pigmentary unit. Experimental Gerontology 36:29–54. doi: 10.1016/s0531-5565(00)00210-2 11162910
35. Endou M, Aoki H, Kobayashi T, Kunisada T. (2014) Prevention of hair graying by factors that promote the growth and differentiation of melanocytes. The Journal of Dermatology 41:716–723. doi: 10.1111/1346-8138.12570 25099157
36. Peter J, Rodgers R. (2015) The Pigeon Genetics Newsletter. The Pigeon Genetics Newsletter 10:1–25.
37. Hollander WF. (1944) Mosaic Effects in Domestic Birds. The Quarterly Review of Biology 19:285–307.
38. Wright L, Lumley RW, Ludlow JW, Lydon AF. (1895) Fulton’s Book of Pigeons. Cassel & Co. Ltd, London.
39. Bellone RR. (2010) Pleiotropic effects of pigmentation genes in horses. Animal Genetics 41:100–110. doi: 10.1111/j.1365-2052.2010.02116.x 21070283
40. Andersson LS, Wilbe M, Viluma A, Cothran G, Ekesten B, Ewart S, Lindgren G. (2013) Equine Multiple Congenital Ocular Anomalies and Silver Coat Colour Result from the Pleiotropic Effects of Mutant PMEL. PLoS ONE 8:e75639. doi: 10.1371/journal.pone.0075639 24086599
41. Osinchuk S, Grahn B. (2018) Diagnostic ophthalmology. Canadian Veterinary Journal 59:315–316. 29599564
42. Ségard EM, Depecker MC, Lang J, Gemperli A, Cadoré J-L. (2013) Ultrasonographic features of PMEL17 (Silver) mutant gene-associated multiple congenital ocular anomalies (MCOA) in Comtois and Rocky Mountain horses. Veterinary Ophthalmology 16:429–435. doi: 10.1111/vop.12021 23278951
43. Ramsey DT, Ewart SL, Render JA, Cook CS, Latimer CA. (1999) Congenital ocular abnormalities of Rocky Mountain Horses. Veterinary Ophthalmology 2:47–59. doi: 10.1046/j.1463-5224.1999.00050.x 11397242
44. Clark LA, Wahl JM, Rees CA, Murphy KE. (2006) Retrotransposon insertion in SILV is responsible for merle patterning of the domestic dog. PNAS 103:1376–81. doi: 10.1073/pnas.0506940103 16407134
45. Domyan ET, Kronenberg Z, Infante CR, et al. (2016) Molecular shifts in limb identity underlie development of feathered feet in two domestic avian species. eLife 5:e12115. doi: 10.7554/eLife.12115 26977633
46. Hu H, Huff CD, Moore B, Flygare S, Reese MG, Yandell M. (2013) VAAST 2.0: Improved Variant Classification and Disease-Gene Identification Using a Conservation-Controlled Amino Acid Substitution Matrix. Genetic Epidemiology 37:622–634. doi: 10.1002/gepi.21743 23836555
47. Kent WJ. (2002) BLAT—The BLAST-like alignment tool. Genome Research 12:656–664. doi: 10.1101/gr.229202 11932250
48. Widlund HR, Fisher DE, Ramaswamy S, Miller AJ, Du J, Horstmann MA. (2011) MLANA/MART1 and SILV/PMEL17/GP100 Are Transcriptionally Regulated by MITF in Melanocytes and Melanoma. The American Journal of Pathology 163:333–343. doi: 10.1016/s0002-9440(10)63657-7 12819038
49. Hoashi T, Watabe H, Muller J, Yamaguchi Y, Vieira WD, Hearing VJ. (2005) MART-1 is required for the function of the melanosomal matrix protein PMEL17/GP100 and the maturation of melanosomes. Journal of Biological Chemistry 280:14006–14016. doi: 10.1074/jbc.M413692200 15695812
50. De Mazie AM, Van Donselaar, Salvi S, Davoust J, Cerottini J, Slot JW. (2002) The Melanocytic Protein Melan-A / MART-1 Has a Subcellular Localization Distinct from Typical Melanosomal Proteins. Traffic 3:678–693. doi: 10.1034/j.1600-0854.2002.30909.x 12191019
51. Meredith D, Christian HC. (2008) The SLC16 monocaboxylate transporter family. Xenobiotica 38(7–8):1072–1106. doi: 10.1080/00498250802010868 18668440
52. Halestrap AP. (2012) The monocarboxylate transporter family—Structure and functional characterization. IUBMB Life 64:1–9. doi: 10.1002/iub.573 22131303
53. Halestrap AP, Meredith D. (2004) The SLC16 gene family—From monocarboxylate transporters (MCTs) to aromatic amino acid transporters and beyond. Pflugers Archiv European Journal of Physiology 447:619–628. doi: 10.1007/s00424-003-1067-2 12739169
54. Imamura M, Takahashi A, Yamauchi T, et al. (2016) Genome-wide association studies in the Japanese population identify seven novel loci for type 2 diabetes. Nature Communications 7:10531. doi: 10.1038/ncomms10531 26818947
55. Williams Amy AL, Jacobs Suzanne SBR, Moreno-Macías H, et al. (2014) Sequence variants in SLC16A11 are a common risk factor for type 2 diabetes in Mexico. Nature 506:97–101. doi: 10.1038/nature12828 24390345
56. Hara K, Fujita H, Johnson TA, et al. (2014) Genome-wide association study identifies three novel loci for type 2 diabetes. Human Molecular Genetics 23:239–246. doi: 10.1093/hmg/ddt399 23945395
57. Letunic I, Bork P. (2017) 20 years of the SMART protein domain annotation resource. Nucleic Acids Research 46:D493–D496. doi: 10.1093/nar/gkx922 29040681
58. Price ER, Horstmann MA, Wells AG, Weilbaecher KN, Takemoto CM, Landis MW, Fisher DE. (1998) α-melanocyte-stimulating hormone signaling regulates expression of Microphthalmia, a gene deficient in Waardenburg syndrome. Journal of Biological Chemistry 273:33042–33047. doi: 10.1074/jbc.273.49.33042 9830058
59. Aberdam E, Bertolotto C, Sviderskaya EV, de Thillot V, Hemesath TJ, Fisher DE, Bennett DC, Ortonne JP, Ballotti R. (1998) Involvement of microphthalmia in the inhibition of melanocyte lineage differentiation and of melanogenesis by agouti signal protein. Journal of Biological Chemistry 273:19560–19565. doi: 10.1074/jbc.273.31.19560 9677380
60. Dunn KJ, Brady M, Ochsenbauer-Jambor C, Snyder S, Incao A, Pavan WJ. (2005) WNT1 and WNT3a promote expansion of melanocytes through distinct modes of action. Pigment Cell Research 18:167–180. doi: 10.1111/j.1600-0749.2005.00226.x 15892713
61. Takeda K, Yasumoto K, Takada R, Takada S, Watanabe K, Udono T, Saito H, Takahashi K, Shibahara S. (2000) Induction of melanocyte-specific microphthalmia-associated transcription factor by Wnt-3a. Journal of Biological Chemistry 275:14013–14016. doi: 10.1074/jbc.c000113200 10747853
62. Levy C, Khaled M, Fisher DE. (2006) MITF: master regulator of melanocyte development and melanoma oncogene. Trends in Molecular Medicine 12:406–414. doi: 10.1016/j.molmed.2006.07.008 16899407
63. Haase E, Ito S, Sell A, Wakamatsu K. (1992) Feathers from Wild and Domestic Pigeons. The Journal of Heredity 83:4–7. doi: 10.1093/oxfordjournals.jhered.a111160
64. Harris ML, Baxter LL, Loftus SK, Pavan WJ. (2010) Sox proteins in melanocyte development and melanoma. Pigment Cell and Melanoma Research 23:496–513. doi: 10.1111/j.1755-148X.2010.00711.x 20444197
65. Steingrímsson E, Copeland NG, Jenkins NA. (2004) Melanocytes and the Microphthalmia Transcription Factor Network. Annual Review of Genetics 38:365–411. doi: 10.1146/annurev.genet.38.072902.092717 15568981
66. Yasumoto K, Yokoyama K, Takahashi K, Tomita Y, Shibahara S. (1997) Functional analysis of microphthalmia-associated transcription factor in pigment cell-specific transcription of the human tyrosinase family genes. Journal of Biological Chemistry 272:503–9. doi: 10.1074/jbc.272.1.503 8995290
67. Yu M, Yue Z, Wu P, Wu DY, Mayer JA, Medina M, Widelitz RB, Jiang TX, Chuong CM. (2004) The developmental biology of feather follicles. International Journal of Developmental Biology 48:181–191. doi: 10.1387/ijdb.031776my 15272383
68. Wu CC, Klaesson A, Buskas J, Ranefall P, Mirzazadeh R, Söderberg O, Wolf JBW. (2019) In situ quantification of individual mRNA transcripts in melanocytes discloses gene regulation of relevance to speciation. Journal of Experimental Biology. doi: 10.1242/jeb.194431 30718374
69. Mountjoy KG, Robbins LS, Mortrud MT, Cone RD. (1992) The cloning of a family of genes that encode the melanocortin receptors. Science 257:1248–1251. doi: 10.1126/science.1325670 1325670
70. Zdarsky E, Favor J, Jackson IJ. (1990) The molecular basis of brown, an old mouse mutation, and of an induced revertant to wild type. Genetics 126:443–449. 2245916
71. Hellström AR, Watt B, Fard SS, et al. (2011) Inactivation of PMEL alters melanosome shape but has only a subtle effect on visible pigmentation. PLoS Genetics 7:e1002285. doi: 10.1371/journal.pgen.1002285 21949658
72. Watt B, Van Niel G, Raposo G, Marks MS. (2013) PMEL: A pigment cell-specific model for functional amyloid formation. Pigment Cell and Melanoma Research 26:300–315. doi: 10.1111/pcmr.12067 23350640
73. Kobayashi T, Urabe K, Orlow SJ, Higashi K, Imokawa G, Kwon BS, Potterf B, Hearing VJ. (1994) The Pmel 17/silver locus protein. Characterization and investigation of its melanogenic function. Journal of Biological Chemistry 269:29198–29205. 7961886
74. Huntley R. (1999) The Almond Family. http://www.angelfire.com/ga/huntleyloft/qualmond.html. Accessed 1 Jan 2017.
75. Hollander WF. (1975) Sectorial Mosaics in the Domestic Pigeon: 25 More Years. Journal of Heredity 66:177–202. 1172514
76. Colnaghi R, Carpenter G, Volker M, O’Driscoll M. (2011) The consequences of structural genomic alterations in humans: Genomic Disorders, genomic instability and cancer. Seminars in Cell and Developmental Biology 22:875–885. doi: 10.1016/j.semcdb.2011.07.010 21802523
77. Du J, Miller AJ, Widlund HR, Horstmann MA, Ramaswamy S, Fisher DE. (2003) MLANA/MART1 and SILV/PMEL17/GP100 Are Transcriptionally Regulated by MITF in Melanocytes and Melanoma. American Journal of Pathology 163:333–343. doi: 10.1016/S0002-9440(10)63657-7 12819038
78. Mover FH. (1966) Genetic variations in the fine structure and ontogeny of mouse melanin granules. Integrative and Comparative Biology 6:43–66. doi: 10.1093/icb/6.1.43 5902512
79. Kobayashi T, Vieira WD, Potterf B, Sakai C, Imokawa G, Hearing VJ. (1995) Modulation of melanogenic protein expression during the switch from eu- to pheomelanogenesis. Journal of Cell Science 108:2301–2309. 7673350
80. Furumura M, Sakai C, Potterf SB, Vieira WD, Barsh GS, Hearing VJ. (1998) Characterization of genes modulated during pheomelanogenesis using differential display. Proceedings of the National Academy of Sciences of the United States of America 95:7374–7378. doi: 10.1073/pnas.95.13.7374 9636156
81. Kerje S, Sharma P, Gunnarsson U, et al. (2004) The Dominant white, Dun and Smoky color variants in chicken are associated with insertion/deletion polymorphisms in the PMEL17 gene. Genetics 168:1507–18. doi: 10.1534/genetics.104.027995 15579702
82. Kuehn C, Weikard R. (2007) Multiple splice variants within the bovine silver homologue (SILV) gene affecting coat color in cattle indicate a function additional to fibril formation in melanophores. BMC Genomics 8:335. doi: 10.1186/1471-2164-8-335 17892572
83. Schmutz SM, Dreger DL. (2013) Interaction of MC1R and PMEL alleles on solid coat colors in Highland cattle. Animal Genetics 44:9–13. doi: 10.1111/j.1365-2052.2012.02361.x 22524257
84. Kwon BS, Halaban R, Ponnazhagan S, Kim K, Chintamaneni C, Bennett D, Pickard RT. (1995) Mouse silver mutation is caused by a single base insertion in the putative cytoplasmic domain of Pmel 17. Nucleic Acids Research 23:154–8. doi: 10.1093/nar/23.1.154 7870580
85. Lahola-Chomiak AA, Footz T, Nguyen-Phuoc K, et al. (2019) Non-Synonymous variants in premelanosome protein (PMEL) cause ocular pigment dispersion and pigmentary glaucoma. Human Molecular Genetics 28:1298–1311. doi: 10.1093/hmg/ddy429 30561643
86. Schonthaler HB, Lampert JM, Von Lintig J, Schwarz H, Geisler R, Neuhauss SCF. (2005) A mutation in the silver gene leads to defects in melanosome biogenesis and alterations in the visual system in the zebrafish mutant fading vision. Developmental Biology 284:421–436. doi: 10.1016/j.ydbio.2005.06.001 16024012
87. Murphy SC, Evans JM, Tsai KL, Clark LA. (2018) Length variations within the Merle retrotransposon of canine PMEL: Correlating genotype with phenotype. Mobile DNA 9:26. doi: 10.1186/s13100-018-0131-6 30123327
88. Brunberg E, Andersson L, Cothran G, Sandberg K, Mikko S, Lindgren G. (2006) A missense mutation in PMEL17 is associated with the Silver coat color in the horse. BMC Genetics 7:46. doi: 10.1186/1471-2156-7-46 17029645
89. Komáromy AM, Rowlan JS, La Croix NC, Mangan BG. (2011) Equine Multiple Congenital Ocular Anomalies (MCOA) syndrome in PMEL17 (Silver) mutant ponies: Five cases. Veterinary Ophthalmology 14:313–320. doi: 10.1111/j.1463-5224.2011.00878.x 21929608
90. Hellström AR, Watt B, Fard SS, et al. (2011) Inactivation of PMEL alters melanosome shape but has only a subtle effect on visible pigmentation. PLoS Genetics 7:e1002285. doi: 10.1371/journal.pgen.1002285 21949658
91. Gelatt KN, Powell NG, Huston K. (1981) Inheritance of microphthalmia with coloboma in the Australian shepherd dog. American Journal of Veterinary Research 42:1686–1690. 7325429
92. Vogel P, Read RW, Vance RB, Platt KA, Troughton K, Rice DS. (2008) Ocular albinism and hypopigmentation defects in Slc24a5-/- mice. Veterinary Pathology 45:264–279. doi: 10.1354/vp.45-2-264 18424845
93. Brooks BP, Larson DM, Chan C-C, et al. (2007) Analysis of Ocular Hypopigmentation in Rab38 cht/cht Mice. Investigative Opthalmology & Visual Science 48:3905. doi: 10.1167/iovs.06-1464 17724166
94. Gronskov K, Ek J, Brondum-Nielsen K. (2007) Oculocutaneous albinism. Orphanet Journal of Rare Diseases 2:43. doi: 10.1186/1750-1172-2-43 17980020
95. Hirai T, Fukui Y, Motojima K. (2007) PPARα Agonists Positively and Negatively Regulate the Expression of Several Nutrient/Drug Transporters in Mouse Small Intestine. Biological & Pharmaceutical Bulletin 30:2185–2190. doi: 10.1248/bpb.30.2185 17978498
96. Krishnan S. (2019) Nested tandem duplications of the gene Melanoma antigen recognized by T-cells (Mlana) underlie the sexual dimorphism locus in domestic pigeons. bioRxiv Genetics. doi: 10.1101/754986
97. Marchant TW, Johnson EJ, McTeir L, et al. (2017) Canine Brachycephaly Is Associated with a Retrotransposon-Mediated Missplicing of SMOC2. Current Biology 27:1573–1584.e6. doi: 10.1016/j.cub.2017.04.057 28552356
98. Stranger BE, Forrest MS, Dunning M, et al. (2007) Relative Impact of Nucleotide and Copy Number Variation on Gene Expression Phenotypes. Science 315:848–853. doi: 10.1126/science.1136678 17289997
99. Zhou J, Lemos B, Dopman EB, Hartl DL. (2011) Copy-number variation: The balance between gene dosage and expression in Drosophila melanogaster. Genome Biology and Evolution 3:1014–1024. doi: 10.1093/gbe/evr023 21979154
100. Freeman JL, Perry GH, Feuk L, et al. (2006) Copy number variation: New insights in genome diversity. Genome Research 949–961. doi: 10.1101/gr.3677206 16809666
101. Cruz C, Houseley J. (2014) Endogenous RNA interference is driven by copy number. eLife 3:e01581. doi: 10.7554/eLife.01581 24520161
102. Dorer DR, Henikoff S. (1994) Expansions of transgene repeats cause heterochromatin formation and gene silencing in Drosophila. Cell 77:993–1002. doi: 10.1016/0092-8674(94)90439-1 8020105
103. Assaad FF, Tucker KL, Signer ER. (1993) Epigenetic repeat-induced gene silencing (RIGS) in Arabidopsis. Plant Molecular Biology 22:1067–1085. doi: 10.1007/BF00028978 8400126
104. Garrick D, Fiering S, Martin DIK, Whitelaw E. (1998) Repeat-induced gene silencing in mammals. Nature Genetics 18:56–59. doi: 10.1038/ng0198-56 9425901
105. Henikoff S. (1998) Conspiracy of silence among repeated transgenes. BioEssays 20:532–535. doi: 10.1002/(SICI)1521-1878(199807)20:7<532::AID-BIES3>3.0.CO;2-M 9723001
106. Girirajan S, Campbell CD, Eichler EE. (2011) Human Copy Number Variation and Complex Genetic Disease. Annual Review of Genetics 45:203–226. doi: 10.1146/annurev-genet-102209-163544 21854229
107. Wain LV., Armour J AL, Tobin MD. (2009) Genomic copy number variation, human health, and disease. The Lancet 374:340–350. doi: 10.1016/S0140-6736(09)60249-X
108. Zhang F, Gu W, Hurles ME, Lupski JR. (2009) Copy Number Variation in Human Health, Disease, and Evolution. Annual Review of Genomics and Human Genetics 10:451–81. doi: 10.1146/annurev.genom.9.081307.164217 19715442
109. Sopko R, Huang D, Preston N, et al. (2006) Mapping Pathways and Phenotypes by Systematic Gene Overexpression. Molecular Cell 21:319–330. doi: 10.1016/j.molcel.2005.12.011 16455487
110. Lang KS, Muhm A, Moris A, Stevanovic S, Rammensee H-G, Caroli CC, Wernet D, Schittek B, Knauss-Scherwitz E, Garbe C. (2001) HLA-A2 Restricted, Melanocyte-Specific CD8+ T Lymphocytes Detected in Vitiligo Patients are Related to Disease Activity and are Predominantly Directed Against MelanA/MART1. Journal of Investigative Dermatology 116:891–897. doi: 10.1046/j.1523-1747.2001.01363.x 11407977
111. Byrne KT, Turk MJ. (2011) New perspectives on the role of vitiligo in immune responses to melanoma. Oncotarget 2:684–94. doi: 10.18632/oncotarget.323 21911918
112. Shi F, Kong B-W, Song J, Lee J, Dienglewicz RL, Erf GF. (2012) Understanding mechanisms of vitiligo development in Smyth line of chickens by transcriptomic microarray analysis of evolving autoimmune lesions. BMC Immunology 13:18. doi: 10.1186/1471-2172-13-18 22500953
113. Wright D, Boije H, Meadows JRS, et al. (2009) Copy Number Variation in Intron 1 of SOX5 Causes the Pea-comb Phenotype in Chickens. PLoS Genetics 5:e1000512. doi: 10.1371/journal.pgen.1000512 19521496
114. Hollander WF. (1982) Origins and excursions in pigeon genetics—flecks and sex. The Ink Spot INC, Burton, Kansas.
115. Sponenberg DP. (1984) Germinal reversion of the merle allele in Australian shepherd dogs. Journal of Heredity 75:78–78. doi: 10.1093/oxfordjournals.jhered.a109874 6323572
116. Farslow JC, Lipinski KJ, Packard LB, Edgley ML, Taylor J, Flibotte S, Moerman DG, Katju V, Bergthorsson U. (2015) Rapid Increase in frequency of gene copy-number variants during experimental evolution in Caenorhabditis elegans. BMC Genomics 16:1044. doi: 10.1186/s12864-015-2253-2 26645535
117. Bryk J, Tautz D. (2014) Copy number variants and selective sweeps in natural populations of the house mouse (Mus musculus domesticus). Frontiers in Genetics 5:153. doi: 10.3389/fgene.2014.00153 24917877
118. Axelsson E, Ratnakumar A, Arendt ML, Maqbool K, Webster MT, Perloski M, Liberg O, Arnemo JM, Hedhammar Å, Lindblad-Toh K. (2013) The genomic signature of dog domestication reveals adaptation to a starch-rich diet. Nature 495:360–364. doi: 10.1038/nature11837 23354050
119. Cone KR, Kronenberg ZN, Yandell M, Elde NC. (2017) Emergence of a Viral RNA Polymerase Variant during Gene Copy Number Amplification Promotes Rapid Evolution of Vaccinia Virus. Journal of Virology 91:e01428–16. doi: 10.1128/jvi.01428-16 27928012
120. Holt C, Campbell M, Keays DA, et al. (2018) Improved Genome Assembly and Annotation for the Rock Pigeon (Columba livia). G3 8:1391–1398. doi: 10.1534/g3.117.300443 29519939
121. McKenna A, Hanna M, Banks E, et al. (2010) The Genome Analysis Toolkit: A MapReduce framework for analyzing next-generation DNA sequencing data. Genome Research 20:1297–1303. doi: 10.1101/gr.107524.110 20644199
122. Li H. (2011) A statistical framework for SNP calling, mutation discovery, association mapping and population genetical parameter estimation from sequencing data. Bioinformatics 27:2987–2993. doi: 10.1093/bioinformatics/btr509 21903627
123. Gene Codes Corporation. Sequencher version 5.4.6 DNA sequence analysis software. Ann Arbor, MI, USA. http://www.genecodes.com.
124. Danecek P, Auton A, Abecasis G, et al. (2011) The variant call format and VCFtools. Bioinformatics 27:2156–2158. doi: 10.1093/bioinformatics/btr330 21653522
125. Robinson JT, Thorvaldsdóttir H, Winckler W, Guttman M, Lander ES, Getz G, Mesirov JP. (2011) Integrative genomics viewer. Nature Biotechnology 29:24–26. doi: 10.1038/nbt.1754 21221095
126. Camacho C, Coulouris G, Avagyan V, Ma N, Papadopoulos J, Bealer K, Madden TL. (2009) BLAST+: architecture and applications. BMC Bioinformatics 10:421. doi: 10.1186/1471-2105-10-421 20003500
127. R Core Team. (2019) R: A language and environment for statistical computing. R Foundation for Statistical Computing, Vienna. https://www.r-project.org.
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