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Illumina-sequencing based transcriptome study of coat color phenotypes in domestic goats

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Abstract

This study performed a comprehensive expression profiling of genes expressed in the skin of goats with three different coat colors by Illumina Sequencing. A total of 91 significantly expressed genes were detected when comparing gray skin to white skin library and these included 74 up-regulated and 17 down-regulated genes in gray skin. There were 67 differentially expressed genes between brown skin and white skin libraries, 23 of which were up-regulated and 44 were down-regulated in brown skin. When we compared brown and gray libraries, 154 differentially expressed genes were found, of which 33 showed higher expression and 121 showed lower expression in brown skin. To our surprise, MC1R, MITF, TYR and KIT showed no significant difference in expression between the goats with three skin colors, whereas ASIP was detected in white skin but not in dark skins. In this study, PMEL, TRPM1, TYRP1 and DCT were significantly up-regulated in brown goat skin compare with gray and white skins. PMEL showed higher expression in gray goat skin compared with white goat skin, whereas there were no significant differences in the expression of TYRP1, TRPM1 and DCT between gray and white skin samples. In addition, ELOVL3 showed higher expression in gray goat skin than in brown and white skins, whereas there was no significant differences in the expression of ELOVL3 between brown and white skin samples. These results expand our understanding of the complex molecular mechanisms of skin physiology and melanogenesis in goat and provide a foundation for future studies.

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References

  • Abitbol M, Legrand R, Tiret L (2015) A missense mutation in the agouti signaling protein gene (ASIP) is associated with the no light points coat phenotype in donkeys. Genet Sel Evol 47:28

    Article  PubMed  PubMed Central  Google Scholar 

  • Barsh G, Cotsarelis G (2007) How hair gets its pigment. Cell 130:779–781

    Article  CAS  PubMed  Google Scholar 

  • Bauer GL, Praetorius C, Bergsteinsdottir K, Hallsson JH, Gisladottir BK, Schepsky A, Swing DA, O’Sullivan TN, Arnheiter H, Bismuth K et al (2009) The role of MITF phosphorylation sites during coat color and eye development in mice analyzed by bacterial artificial chromosome transgene rescue. Genetics 183:581–594

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Becker D, Otto M, Ammann P, Keller I, Drogemuller C, Leeb T (2015) The brown coat colour of Coppernecked goats is associated with a non-synonymous variant at the TYRP1 locus on chromosome 8. Anim Genet 46:50–54

    Article  CAS  PubMed  Google Scholar 

  • Bellone RR, Brooks SA, Sandmeyer L, Murphy BA, Forsyth G, Archer S, Bailey E, Grahn B (2008) Differential gene expression of TRPM1, the potential cause of congenital stationary night blindness and coat spotting patterns (LP) in the Appaloosa horse (Equus caballus). Genetics 179:1861–1870

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Berryere TG, Schmutz SM, Schimpf RJ, Cowan CM, Potter J (2003) TYRP1 is associated with dun coat colour in Dexter cattle or how now brown cow? Anim Genet 34:169–175

    Article  CAS  PubMed  Google Scholar 

  • 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 Genet 7:46

    Article  PubMed  PubMed Central  Google Scholar 

  • Budd PS, Jackson IJ (1995) Structure of the mouse tyrosinase-related protein-2/dopachrome tautomerase (Tyrp2/Dct) gene and sequence of two novel slaty alleles. Genomics 29:35–43

    Article  CAS  PubMed  Google Scholar 

  • Bunge R, Thomas DL, Nash TG, Lupton CJ (1996) Performance of hair breeds and prolific wool breeds of sheep in southern Illinois: wool production and fleece quality. J Anim Sci 74:25–30

    Article  CAS  PubMed  Google Scholar 

  • Ciampolini R, Cecchi F, Spaterna A, Bramante A, Bardet SM, Oulmouden A (2013) Characterization of different 5′-untranslated exons of the ASIP gene in black-and-tan Doberman Pinscher and brindle Boxer dogs. Anim Genet 44:114–117

    Article  CAS  PubMed  Google Scholar 

  • Cieslak M, Reissmann M, Hofreiter M, Ludwig A (2011) Colours of domestication. Biol Rev Camb Philos Soc 86:885–899

    Article  PubMed  Google Scholar 

  • Clark LA, Wahl JM, Rees CA, Murphy KE (2006) Retrotransposon insertion in SILV is responsible for merle patterning of the domestic dog. Proc Natl Acad Sci USA 103:1376–1381

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Deng W, Tan Y, Wang X, Xi D, He Y, Yang S, Mao H, Gao S (2009) Molecular cloning, sequence characteristics, and polymorphism analyses of the tyrosinase-related protein 2/DOPAchrome tautomerase gene of black-boned sheep (Ovis aries). Genome 52:1001–1011

    Article  CAS  PubMed  Google Scholar 

  • Dereure O (2001) Drug-induced skin pigmentation. Epidemiology, diagnosis and treatment. Am J Clin Dermatol 2:253–262

    Article  CAS  PubMed  Google Scholar 

  • Drogemuller C, Giese A, Martins-Wess F, Wiedemann S, Andersson L, Brenig B, Fries R, Leeb T (2006) The mutation causing the black-and-tan pigmentation phenotype of Mangalitza pigs maps to the porcine ASIP locus but does not affect its coding sequence. Mamm Genome 17:58–66

    Article  PubMed  Google Scholar 

  • Fontanesi L, Tazzoli M, Beretti F, Russo V (2006) Mutations in the melanocortin 1 receptor (MC1R) gene are associated with coat colours in the domestic rabbit (Oryctolagus cuniculus). Anim Genet 37:489–493

    Article  CAS  PubMed  Google Scholar 

  • Gratten J, Beraldi D, Lowder BV, McRae AF, Visscher PM, Pemberton JM, Slate J (2007) Compelling evidence that a single nucleotide substitution in TYRP1 is responsible for coat-colour polymorphism in a free-living population of Soay sheep. Proc Biol Sci 274:619–626

    Article  CAS  PubMed  Google Scholar 

  • Gutierrez-Gil B, Wiener P, Williams JL (2007) Genetic effects on coat colour in cattle: dilution of eumelanin and phaeomelanin pigments in an F2-Backcross Charolais x Holstein population. BMC Genet 8:56

    Article  PubMed  PubMed Central  Google Scholar 

  • Guyonneau L, Murisier F, Rossier A, Moulin A, Beermann F (2004) Melanocytes and pigmentation are affected in dopachrome tautomerase knockout mice. Mol Cell Biol 24:3396–3403

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Han JL, Yang M, Yue YJ, Guo TT, Liu JB, Niu CE, Yang BH (2015) Analysis of agouti signaling protein (ASIP) gene polymorphisms and association with coat color in Tibetan sheep (Ovis aries). Genet Mol Res 14:1200–1209

    Article  CAS  PubMed  Google Scholar 

  • Hellstrom AR, Watt B, Fard SS, Tenza D, Mannstrom P, Narfstrom K, Ekesten B, Ito S, Wakamatsu K, Larsson J et al (2011) Inactivation of Pmel alters melanosome shape but has only a subtle effect on visible pigmentation. PLoS Genet 7:e1002285

    Article  PubMed  PubMed Central  Google Scholar 

  • Ito S, Wakamatsu K (2008) Chemistry of mixed melanogenesis–pivotal roles of dopaquinone. Photochem Photobiol 84:582–592

    Article  CAS  PubMed  Google Scholar 

  • Ito S, Wakamatsu K, Ozeki H (2000) Chemical analysis of melanins and its application to the study of the regulation of melanogenesis. Pigment Cell Res 13(Suppl 8):103–109

    Article  PubMed  Google Scholar 

  • Jablonski NG, Chaplin G (2010) Colloquium paper: human skin pigmentation as an adaptation to UV radiation. Proc Natl Acad Sci USA 107(Suppl 2):8962–8968

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Jackson IJ, Chambers DM, Tsukamoto K, Copeland NG, Gilbert DJ, Jenkins NA, Hearing V (1992) A second tyrosinase-related protein, TRP-2, maps to and is mutated at the mouse slaty locus. EMBO J 11:527–535

    CAS  PubMed  PubMed Central  Google Scholar 

  • Joerg H, Fries HR, Meijerink E, Stranzinger GF (1996) Red coat color in Holstein cattle is associated with a deletion in the MSHR gene. Mamm Genome 7:317–318

    Article  CAS  PubMed  Google Scholar 

  • Kerje S, Sharma P, Gunnarsson U, Kim H, Bagchi S, Fredriksson R, Schutz K, Jensen P, von Heijne G, Okimoto R et al (2004) The Dominant white, Dun and Smoky color variants in chicken are associated with insertion/deletion polymorphisms in the PMEL17 gene. Genetics 168:1507–1518

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Kidson SH, Fabian BC (1981) The effect of temperature on tyrosinase activity in Himalayan mouse skin. J Exp Zool 215:91–97

    Article  CAS  PubMed  Google Scholar 

  • Kijas JM, Wales R, Tornsten A, Chardon P, Moller M, Andersson L (1998) Melanocortin receptor 1 (MC1R) mutations and coat color in pigs. Genetics 150:1177–1185

    CAS  PubMed  PubMed Central  Google Scholar 

  • Kuhn C, Weikard R (2007) An investigation into the genetic background of coat colour dilution in a Charolais× German Holstein F2 resource population. Anim Genet 38:109–113

    Article  PubMed  Google Scholar 

  • Lamoreux ML, Wakamatsu K, Ito S (2001) Interaction of major coat color gene functions in mice as studied by chemical analysis of eumelanin and pheomelanin. Pigment Cell Res 14:23–31

    Article  CAS  PubMed  Google Scholar 

  • Lyons LA, Foe IT, Rah HC, Grahn RA (2005) Chocolate coated cats: TYRP1 mutations for brown color in domestic cats. Mamm Genome 16:356–366

    Article  CAS  PubMed  Google Scholar 

  • Marklund L, Moller MJ, Sandberg K, Andersson L (1996) A missense mutation in the gene for melanocyte-stimulating hormone receptor (MC1R) is associated with the chestnut coat color in horses. Mamm Genome 7:895–899

    Article  CAS  PubMed  Google Scholar 

  • Marklund S, Moller M, Sandberg K, Andersson L (1999) Close association between sequence polymorphism in the KIT gene and the roan coat color in horses. Mamm Genome 10:283–288

    Article  CAS  PubMed  Google Scholar 

  • Mundy NI, Kelly J (2006) Investigation of the role of the agouti signaling protein gene (ASIP) in coat color evolution in primates. Mamm Genome 17:1205–1213

    Article  CAS  PubMed  Google Scholar 

  • Nadeau NJ, Minvielle F, Mundy NI (2006) Association of a Glu92Lys substitution in MC1R with extended brown in Japanese quail (Coturnix japonica). Anim Genet 37:287–289

    Article  CAS  PubMed  Google Scholar 

  • Nadeau NJ, Mundy NI, Gourichon D, Minvielle F (2007) Association of a single-nucleotide substitution in TYRP1 with roux in Japanese quail (Coturnix japonica). Anim Genet 38:609–613

    Article  CAS  PubMed  Google Scholar 

  • Newton JM, Wilkie AL, He L, Jordan SA, Metallinos DL, Holmes NG, Jackson IJ, Barsh GS (2000) Melanocortin 1 receptor variation in the domestic dog. Mamm Genome 11:24–30

    Article  CAS  PubMed  Google Scholar 

  • Nicoloso L, Negrini R, Ajmone-Marsan P, Crepaldi P (2012) On the way to functional agro biodiversity: coat colour gene variability in goats. Animal 6:41–49

    Article  CAS  PubMed  Google Scholar 

  • Norris BJ, Whan VA (2008) A gene duplication affecting expression of the ovine ASIP gene is responsible for white and black sheep. Genome Res 18:1282–1293

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Oancea E, Vriens J, Brauchi S, Jun J, Splawski I, Clapham DE (2009) TRPM1 forms ion channels associated with melanin content in melanocytes. Sci Signal 2:ra21

    PubMed  PubMed Central  Google Scholar 

  • Paterson EK, Fielder TJ, MacGregor GR, Ito S, Wakamatsu K, Gillen DL, Eby V, Boissy RE, Ganesan AK (2015) Tyrosinase depletion prevents the maturation of melanosomes in the mouse hair follicle. PLoS ONE 10:e0143702

    Article  PubMed  PubMed Central  Google Scholar 

  • Penagaricano F, Zorrilla P, Naya H, Robello C, Urioste JI (2012) Gene expression analysis identifies new candidate genes associated with the development of black skin spots in Corriedale sheep. J Appl Genet 53:99–106

    Article  CAS  PubMed  Google Scholar 

  • Philipp U, Hamann H, Mecklenburg L, Nishino S, Mignot E, Gunzel-Apel AR, Schmutz SM, Leeb T (2005) Polymorphisms within the canine MLPH gene are associated with dilute coat color in dogs. BMC Genet 6:34

    Article  PubMed  PubMed Central  Google Scholar 

  • Prasolova LA, Os’kina IN, Pliusnina IZ, Trut LN (2009) Methyl-containing diet of mothers affects the AGOUTI gene expression in the offspring of rats with various behavioral types. Genetika 45:670–676

    CAS  PubMed  Google Scholar 

  • Rieder S, Taourit S, Mariat D, Langlois B, Guerin G (2001) Mutations in the agouti (ASIP), the extension (MC1R), and the brown (TYRP1) loci and their association to coat color phenotypes in horses (Equus caballus). Mamm Genome 12:450–455

    Article  CAS  PubMed  Google Scholar 

  • Schmutz SM, Berryere TG, Goldfinch AD (2002) TYRP1 and MC1R genotypes and their effects on coat color in dogs. Mamm Genome 13:380–387

    Article  CAS  PubMed  Google Scholar 

  • Schmutz SM, Berryere TG, Ellinwood NM, Kerns JA, Barsh GS (2003) MC1R studies in dogs with melanistic mask or brindle patterns. J Hered 94:69–73

    Article  CAS  PubMed  Google Scholar 

  • Slominski A, Tobin DJ, Shibahara S, Wortsman J (2004) Melanin pigmentation in mammalian skin and its hormonal regulation. Physiol Rev 84:1155–1228

    Article  CAS  PubMed  Google Scholar 

  • Steingrimsson E, Copeland NG, Jenkins NA (2006) Mouse coat color mutations: from fancy mice to functional genomics. Dev Dyn 235:2401–2411

    Article  PubMed  Google Scholar 

  • Sturm RA, Duffy DL (2012) Human pigmentation genes under environmental selection. Genome Biol 13:248

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Theos AC, Truschel ST, Raposo G, Marks MS (2005) The Silver locus product Pmel17/gp100/Silv/ME20: controversial in name and in function. Pigment Cell Res 18:322–336

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Vage DI, Klungland H, Lu D, Cone RD (1999) Molecular and pharmacological characterization of dominant black coat color in sheep. Mamm Genome 10:39–43

    Article  CAS  PubMed  Google Scholar 

  • Wade CM, Giulotto E, Sigurdsson S, Zoli M, Gnerre S, Imsland F, Lear TL, Adelson DL, Bailey E, Bellone RR et al (2009) Genome sequence, comparative analysis, and population genetics of the domestic horse. Science 326:865–867

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Wang L, Fan J, Yu M, Zheng S, Zhao Y (2011a) Association of goat (Capra hircus) CD4 gene exon 6 polymorphisms with ability of sperm internalizing exogenous DNA. Mol Biol Rep 38:1621–1628

    Article  CAS  PubMed  Google Scholar 

  • Wang PQ, Deng LM, Zhang BY, Chu MX, Hou JZ (2011b) Polymorphisms of the cocaine-amphetamine-regulated transcript (CART) gene and their association with reproductive traits in Chinese goats. Genet Mol Res 10:731–738

    Article  CAS  PubMed  Google Scholar 

  • Westerberg R, Tvrdik P, Unden AB, Mansson JE, Norlen L, Jakobsson A, Holleran WH, Elias PM, Asadi A, Flodby P et al (2004) Role for ELOVL3 and fatty acid chain length in development of hair and skin function. J Biol Chem 279:5621–5629

    Article  CAS  PubMed  Google Scholar 

  • Xu T, Guo X, Wang H, Hao F, Du X, Gao X, Liu D (2013) Differential gene expression analysis between anagen and telogen of Capra hircus skin based on the de novo assembled transcriptome sequence. Gene 520:30–38

    Article  CAS  PubMed  Google Scholar 

  • Zhang J, Liu F, Cao J, Liu X (2015) Skin transcriptome profiles associated with skin color in chickens. PLoS ONE 10:e0127301

    Article  PubMed  PubMed Central  Google Scholar 

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Acknowledgements

We are grateful to members of our laboratories for critical reading of the manuscript and helpful discussion. This work was supported by the National Natural Science Foundation of China (Nos. 31172196, 31501940), the Applied Basic Research Programs of Hebei Province (No. 15962901D), College Innovation Team Leader Training Programme of Hebei Province (No. LJRC004), Program for the Top Young-aged Innovative Talents of Higher Learning Institutions of Hebei Province (No. BJ2016026), the Science and Technology Pillar Program of Qinhuangdao (No. 201502A058) and PhD Research Start Fund of Hebei Normal University of Science and Technology (2014). We kindly thank members from Novogene Bioinformatics Institute for their assistance with original data processing and related bioinformatic analysis.

Author contributions

Yongdong Peng and Xianglong Li conceived and designed the experiments; Xiaohui Liu, Liying Geng, Zhengzhu Liu and Yuanfang Gong performed the experiments; Yongdong Peng, Ruxue Ma and Chuansheng Zhang analyzed the data; Lisha Li and Jingshi Li contributed reagents/materials/analysis tools; Yongdong Peng and Xianglong Li contributed to write the manuscript.

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  1. College of Animal Science and Technology, Hebei Normal University of Science and Technology, Qinhuangdao, 066004, Hebei, People’s Republic of China

    Yongdong Peng, Ruxue Ma, Chuansheng Zhang, Zhengzhu Liu, Yuanfang Gong & Xianglong Li

  2. College of Animal Science and Technology, Agricultural University of Hebei Province, Baoding, 071001, Hebei, People’s Republic of China

    Xiaohui Liu, Lisha Li & Xianglong Li

  3. College of Life Science and Technology, Hebei Normal University of Science and Technology, Qinhuangdao, 066004, Hebei, People’s Republic of China

    Liying Geng & Jingshi Li

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  1. Yongdong Peng
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  2. Xiaohui Liu
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  3. Liying Geng
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Correspondence to Xianglong Li.

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Yongdong Peng, Xiaohui Liu, Liying Geng, Ruxue Ma, Lisha Li, Jingshi Li, Chuansheng Zhang, Zhengzhu Liu, Yuanfang Gong and Xianglong Li declare that they have no conflict of interest.

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This article does not contain any studies with human participants or animals performed by any of the authors. All animal experiments were reviewed and approved by the Institutional Animal Care and Use Committee of Hebei Normal University of Science and Technology, China. Procedures were performed in accordance with the Regulations for the Administration of Affairs Concerning Experimental Animals (The State Council of the People’s Republic of China, 2011).

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Peng, Y., Liu, X., Geng, L. et al. Illumina-sequencing based transcriptome study of coat color phenotypes in domestic goats. Genes Genom 39, 817–830 (2017). https://doi.org/10.1007/s13258-017-0543-6

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