Advertisement

Avian Genomics in Animal Breeding and the End of the Model Organism

Chapter

Abstract

Avian genomics have long benefited from chicken being not only an important agricultural species but also a model organism for various fields of research including genetics, immunology, embryology and more recently vertebrate genome organisation and function. Thanks to this, chicken was in 2004 amongst the first vertebrates sequenced, and its genome annotation still benefits from a large community of users. Hundreds of quantitative trait loci (QTLs) have been mapped in chicken, and genome-wide information is now used in breeding programmes in agriculture. The chicken genome sequence was soon followed by the zebra finch sequencing, a model for the biology of learned vocalisation. Shortly after, the advent of new sequencing technologies, reducing cost and increasing speed of sequencing, allowed the turkey and duck genomes to follow. Now, close to 50 bird genomes are published, and with the ever-decreasing cost of sequencing and most recent genome assembly techniques, many more are expected soon. In the new era of genomics technologies, will model organisms remain essential?

Keywords

Chicken Animal breeding Model organism Genomics Avian Genome Sequence Bird Genomics 

References

  1. Abasht B, Dekkers JCM, Lamont SJ (2006) Review of quantitative trait loci identified in the chicken. Poult Sci 85:2079–2096PubMedCrossRefGoogle Scholar
  2. Abzhanov A, Protas M, Grant BR, Grant PR, Tabin CJ (2004) Bmp4 and morphological variation of beaks in Darwin’s finches. Science 305:1462–1465.  https://doi.org/10.1126/science.1098095 CrossRefPubMedGoogle Scholar
  3. Agnvall B, Bélteky J, Jensen P (2017) Brain size is reduced by selection for tameness in Red Junglefowl? Correlated effects in vital organs. Sci Rep 7:645.  https://doi.org/10.1016/j.applanim.2008.04.003 CrossRefGoogle Scholar
  4. Anderson TM, Vonholdt BM, Candille SI, Musiani M, Greco C, Stahler DR, Smith DW, Padhukasahasram B, Randi E, Leonard JA, Bustamante CD, Ostrander EA, Tang H, Wayne RK, Barsh GS (2009) Molecular and evolutionary history of melanism in North American gray wolves. Science 323:1339–1343.  https://doi.org/10.1126/science.1165448 CrossRefPubMedPubMedCentralGoogle Scholar
  5. Andersson L, Archibald AL, Bottema CD, Brauning R, Burgess SC, Burt DW, Casas E, Cheng HH, Clarke L, Couldrey C, Dalrymple BP, Elsik CG, Foissac S, Giuffra E, Groenen MA, Hayes BJ, Huang LS, Khatib H, Kijas JW, Kim H, Lunney JK, Mccarthy FM, McEwan JC, Moore S, Nanduri B, Notredame C, Palti Y, Plastow GS, Reecy JM, Rohrer GA, Sarropoulou E, Schmidt CJ, Silverstein J, Tellam RL, Tixier-Boichard M, Tosser-Klopp G, Tuggle CK, Vilkki J, White SN, Zhao S, Zhou H, FAANG Consortium (2015) Coordinated international action to accelerate genome-to-phenome with FAANG, the Functional Annotation of Animal Genomes project. Genome Biol 16:57PubMedPubMedCentralCrossRefGoogle Scholar
  6. Aparicio S, Chapman J, Stupka E, Putnam N, Chia J-M, Dehal P, Christoffels A, Rash S, Hoon S, Smit A, Gelpke MDS, Roach J, Oh T, Ho IY, Wong M, Detter C, Verhoef F, Predki P, Tay A, Lucas S, Richardson P, Smith SF, Clark MS, Edwards YJK, Doggett N, Zharkikh A, Tavtigian SV, Pruss D, Barnstead M, Evans C, Baden H, Powell J, Glusman G, Rowen L, Hood L, Tan YH, Elgar G, Hawkins T, Venkatesh B, Rokhsar D, Brenner S (2002) Whole-genome shotgun assembly and analysis of the genome of Fugu rubripes. Science 297:1301–1310PubMedCrossRefGoogle Scholar
  7. Auer H, Mayr B, Lambrou M, Schleger W (1987) An extended chicken karyotype, including the NOR chromosome. Cytogenet Cell Genet 45:218–221PubMedCrossRefGoogle Scholar
  8. Augui S, Nora EP, Heard E (2011) Regulation of X-chromosome inactivation by the X-inactivation centre. Nat Rev Genet 12:429–442.  https://doi.org/10.1038/nrg2987 CrossRefPubMedGoogle Scholar
  9. Avery OT (1944) Studies on the chemical nature of the substance inducing chemical transformation of pneumococcal types: induction of transformation by a desoxyribonucleic acid fraction isolated from pneumococcus type III. J Exp Med 79:137–158PubMedPubMedCentralCrossRefGoogle Scholar
  10. Axelsson E, Webster MT, Smith NGC, Burt DW, Ellegren H (2005) Comparison of the chicken and turkey genomes reveals a higher rate of nucleotide divergence on microchromosomes than macrochromosomes. Genome Res 15:120–125PubMedPubMedCentralCrossRefGoogle Scholar
  11. Baker Z, Schumer M, Haba Y, Bashkirova L, Holland C, Rosenthal GG, Przeworski M (2017) Repeated losses of PRDM9-directed recombination despite the conservation of PRDM9 across vertebrates. eLife 6:e24133.  https://doi.org/10.7554/eLife.24133 CrossRefPubMedPubMedCentralGoogle Scholar
  12. Barbosa-Morais NL, Irimia M, Pan Q, Xiong HY, Gueroussov S, Lee LJ, Slobodeniuc V, Kutter C, Watt S, Colak R, Kim T, Misquitta-Ali CM, Wilson MD, Kim PM, Odom DT, Frey BJ, Blencowe BJ (2012) The evolutionary landscape of alternative splicing in vertebrate species. Science 338:1587–1593.  https://doi.org/10.1126/science.1230612 CrossRefPubMedGoogle Scholar
  13. Bay RA, Harrigan RJ, Underwood VL, Gibbs HL, Smith TB, Ruegg K (2018) Genomic signals of selection predict climate-driven population declines in a migratory bird. Science 359:83–86.  https://doi.org/10.1126/science.aan4380 CrossRefPubMedGoogle Scholar
  14. Bed’hom B, Vaez M, Coville J-L, Gourichon D, Chastel O, Follett S, Burke T, Minvielle F (2012) The lavender plumage colour in Japanese quail is associated with a complex mutation in the region of MLPH that is related to differences in growth, feed consumption and body temperature. BMC Genomics 13:442PubMedPubMedCentralCrossRefGoogle Scholar
  15. Bellott DW, Skaletsky H, Pyntikova T, Mardis ER, Graves T, Kremitzki C, Brown LG, Rozen S, Warren WC, Wilson RK, Page DC (2010) Convergent evolution of chicken Z and human X chromosomes by expansion and gene acquisition. Nature 466:612–616PubMedPubMedCentralCrossRefGoogle Scholar
  16. Bellott DW, Skaletsky H, Cho T-J, Brown L, Locke D, Chen N, Galkina S, Pyntikova T, Koutseva N, Graves T, Kremitzki C, Warren WC, Clark AG, Gaginskaya E, Wilson RK, Page DC (2017) Avian W and mammalian Y chromosomes convergently retained dosage-sensitive regulators. Nat Genet 49:387–394.  https://doi.org/10.1038/ng.3778 CrossRefPubMedPubMedCentralGoogle Scholar
  17. Bitgood JJ (1993) Manipulation of the avian genome, Chapter 5. CRC Press, Guelph, ONGoogle Scholar
  18. Blanchette M, Green ED, Miller W, Haussler D (2004) Reconstructing large regions of an ancestral mammalian genome in silico. Genome Res 14(12):2412–2423PubMedPubMedCentralCrossRefGoogle Scholar
  19. Boardman PE, Sanz-Ezquerro J, Overton IM, Burt DW, Bosch E, Fong WT, Tickle C, Brown WRA, Wilson SA, Hubbard SJ (2002) A comprehensive collection of chicken cDNAs. Curr Biol 12:1965–1969PubMedCrossRefGoogle Scholar
  20. Boije H, Harun-Or-Rashid M, Lee Y-J, Imsland F, Bruneau N, Vieaud A, Gourichon D, Tixier-Boichard M, Bed’hom B, Andersson L, Hallböök F (2012) Sonic hedgehog-signalling patterns the developing chicken comb as revealed by exploration of the pea-comb mutation. PLoS One 7:e50890PubMedPubMedCentralCrossRefGoogle Scholar
  21. Bornelöv S, Seroussi E, Yosefi S, Pendavis K, Burgess SC, Grabherr M, Friedman-Einat M, Andersson L (2017) Correspondence on Lovell et al.: identification of chicken genes previously assumed to be evolutionarily lost. Genome Biol 18:112.  https://doi.org/10.1186/s13059-017-1231-1 CrossRefPubMedPubMedCentralGoogle Scholar
  22. Bourque G, Zdobnov EM, Bork P, Pevzner PA, Tesler G (2005) Comparative architectures of mammalian and chicken genomes reveal highly variable rates of genomic rearrangements across different lineages. Genome Res 15:98–110PubMedPubMedCentralCrossRefGoogle Scholar
  23. Buenrostro JD, Giresi PG, Zaba LC, Chang HY, Greenleaf WJ (2013) Transposition of native chromatin for fast and sensitive epigenomic profiling of open chromatin, DNA-binding proteins and nucleosome position. Nat Methods 10:1213–1218.  https://doi.org/10.1073/pnas.95.25.14863 CrossRefPubMedPubMedCentralGoogle Scholar
  24. Bumstead N, Palyga J (1992) A preliminary linkage map of the chicken genome. Genomics 13:690–697PubMedCrossRefGoogle Scholar
  25. Burt DW (2007) Emergence of the chicken as a model organism: implications for agriculture and biology. Poult Sci 86(7):1460–1471PubMedCrossRefGoogle Scholar
  26. Burt DW, Bruley C, Dunn IC, Jones CT, Ramage A, Law AS, Morrice DR, Paton IR, Smith J, Windsor D, Sazanov A, Fries R, Waddington D (1999) The dynamics of chromosome evolution in birds and mammals. Nature 402:411–413PubMedCrossRefGoogle Scholar
  27. Cao W, Edery I (2017) Mid-day siesta in natural populations of D. melanogaster from Africa exhibits an altitudinal cline and is regulated by splicing of a thermosensitive intron in the period clock gene. BMC Evol Biol:1–17.  https://doi.org/10.1186/s12862-017-0880-8
  28. Chang C-M, Coville J-L, Coquerelle G, Gourichon D, Oulmouden A, Tixier-Boichard M (2006) Complete association between a retroviral insertion in the tyrosinase gene and the recessive white mutation in chickens. BMC Genomics 7:19.  https://doi.org/10.1186/1471-2164-7-19 CrossRefPubMedPubMedCentralGoogle Scholar
  29. Christidis L (1990) Animal cytogenetics. Chordata 3. B. Aves. Gebruder Borntraeger Verlagsbuchhandlung, BerlinGoogle Scholar
  30. Church DM, Schneider VA, Graves T, Auger K, Cunningham F, Bouk N, Chen H-C, Agarwala R, McLaren WM, Ritchie GRS, Albracht D, Kremitzki M, Rock S, Kotkiewicz H, Kremitzki C, Wollam A, Trani L, Fulton L, Fulton R, Matthews L, Whitehead S, Chow W, Torrance J, Dunn M, Harden G, Threadgold G, Wood J, Collins J, Heath P, Griffiths G, Pelan S, Grafham D, Eichler EE, Weinstock G, Mardis ER, Wilson RK, Howe K, Flicek P, Hubbard T (2011) Modernizing reference genome assemblies. PLoS Biol 9:e1001091PubMedPubMedCentralCrossRefGoogle Scholar
  31. Claussnitzer M, Dankel SN, Kim K-H, Quon G, Meuleman W, Haugen C, Glunk V, Sousa IS, Beaudry JL, Puviindran V, Abdennur NA, Liu J, Svensson P-A, Hsu Y-H, Drucker DJ, Mellgren G, Hui C-C, Hauner H, Kellis M (2015) FTO obesity variant circuitry and adipocyte browning in humans. N Engl J Med 373:895–907PubMedPubMedCentralCrossRefGoogle Scholar
  32. Consortium MGS, Waterston RH, Lindblad-Toh K, Birney E, Rogers J, Abril JF, Agarwal P, Agarwala R, Ainscough R, Alexandersson M, An P, Antonarakis SE, Attwood J, Baertsch R, Bailey J, Barlow K, Beck S, Berry E, Birren B, Bloom T, Bork P, Botcherby M, Bray N, Brent MR, Brown DG, Brown SD, Bult C, Burton J, Butler J, Campbell RD, Carninci P, Cawley S, Chiaromonte F, Chinwalla AT, Church DM, Clamp M, Clee C, Collins FS, Cook LL, Copley RR, Coulson A, Couronne O, Cuff J, Curwen V, Cutts T, Daly M, David R, Davies J, Delehaunty KD, Deri J, Dermitzakis ET, Dewey C, Dickens NJ, Diekhans M, Dodge S, Dubchak I, Dunn DM, Eddy SR, Elnitski L, Emes RD, Eswara P, Eyras E, Felsenfeld A, Fewell GA, Flicek P, Foley K, Frankel WN, Fulton LA, Fulton RS, Furey TS, Gage D, Gibbs RA, Glusman G, Gnerre S, Goldman N, Goodstadt L, Grafham D, Graves TA, Green ED, Gregory S, Guigó R, Guyer M, Hardison RC, Haussler D, Hayashizaki Y, Hillier LW, Hinrichs A, Hlavina W, Holzer T, Hsu F, Hua A, Hubbard T, Hunt A, Jackson I, Jaffe DB, Johnson LS, Jones M, Jones TA, Joy A, Kamal M, Karlsson EK, Karolchik D, Kasprzyk A, Kawai J, Keibler E, Kells C, Kent WJ, Kirby A, Kolbe DL, Korf I, Kucherlapati RS, Kulbokas EJ, Kulp D, Landers T, Leger JP, Leonard S, Letunic I, Levine R, Li J, Li M, Lloyd C, Lucas S, Ma B, Maglott DR, Mardis ER, Matthews L, Mauceli E, Mayer JH, McCarthy M, McCombie WR, McLaren S, McLay K, McPherson JD, Meldrim J, Meredith B, Mesirov JP, Miller W, Miner TL, Mongin E, Montgomery KT, Morgan M, Mott R, Mullikin JC, Muzny DM, Nash WE, Nelson JO, Nhan MN, Nicol R, Ning Z, Nusbaum C, O’Connor MJ, Okazaki Y, Oliver K, Overton-Larty E, Pachter L, Parra G, Pepin KH, Peterson J, Pevzner P, Plumb R, Pohl CS, Poliakov A, Ponce TC, Ponting CP, Potter S, Quail M, Reymond A, Roe BA, Roskin KM, Rubin EM, Rust AG, Santos R, Sapojnikov V, Schultz B, Schultz J, Schwartz MS, Schwartz S, Scott C, Seaman S, Searle S, Sharpe T, Sheridan A, Shownkeen R, Sims S, Singer JB, Slater G, Smit A, Smith DR, Spencer B, Stabenau A, Stange-Thomann N, Sugnet C, Suyama M, Tesler G, Thompson J, Torrents D, Trevaskis E, Tromp J, Ucla C, Ureta-Vidal A, Vinson JP, Von Niederhausern AC, Wade CM, Wall M, Weber RJ, Weiss RB, Wendl MC, West AP, Wetterstrand K, Wheeler R, Whelan S, Wierzbowski J, Willey D, Williams S, Wilson RK, Winter E, Worley KC, Wyman D, Yang S, Yang S-P, Zdobnov EM, Zody MC, Lander ES (2002) Initial sequencing and comparative analysis of the mouse genome. Nature 420:520–562CrossRefGoogle Scholar
  33. Cooper MD, Peterson RDA, Good RA (1965) Delineation of the thymic and bursal lymphoid systems in the chicken. Nature 205:143–146PubMedCrossRefGoogle Scholar
  34. Crooijmans RP, Vrebalov J, Dijkhof RJ, Van Der Poel JJ, Groenen MA (2000) Two-dimensional screening of the Wageningen chicken BAC library. Mamm Genome 11:360–363PubMedCrossRefGoogle Scholar
  35. Dalloul RA, Long JA, Zimin AV, Aslam L, Beal K, Blomberg LA, Bouffard P, Burt DW, Crasta O, Crooijmans RPMA, Cooper K, Coulombe RA, De S, Delany ME, Dodgson JB, Dong JJ, Evans C, Frederickson KM, Flicek P, Florea L, Folkerts O, Groenen MAM, Harkins TT, Herrero J, Hoffmann S, Megens H-J, Jiang A, de Jong P, Kaiser P, Kim H, Kim K-W, Kim S, Langenberger D, Lee M-K, Lee T, Mane S, Marçais G, Marz M, McElroy AP, Modise T, Nefedov M, Notredame C, Paton IR, Payne WS, Pertea G, Prickett D, Puiu D, Qioa D, Raineri E, Ruffier M, Salzberg SL, Schatz MC, Scheuring C, Schmidt CJ, Schroeder S, Searle SMJ, Smith EJ, Smith J, Sonstegard TS, Stadler PF, Tafer H, Tu ZJ, Van Tassell CP, Vilella AJ, Williams KP, Yorke JA, Zhang L, Zhang H-B, Zhang X, Zhang Y, Reed KM (2010) Multi-platform next-generation sequencing of the domestic turkey (Meleagris gallopavo): genome assembly and analysis. PLoS Biol 8:e1000475PubMedPubMedCentralCrossRefGoogle Scholar
  36. Davies B, Hatton E, Altemose N, Hussin JG, Pratto F, Zhang G, Hinch AG, Moralli D, Biggs D, Diaz R, Preece C, Li R, Bitoun E, Brick K, Green CM, Camerini-Otero RD, Myers SR, Donnelly P (2016) Re-engineering the zinc fingers of PRDM9 reverses hybrid sterility in mice. Nature 530(7589):171–176PubMedPubMedCentralCrossRefGoogle Scholar
  37. Davydov EV, Goode DL, Sirota M, Cooper GM, Sidow A, Batzoglou S (2010) Identifying a high fraction of the human genome to be under selective constraint using GERP++. PLoS Comput Biol 6:e1001025.  https://doi.org/10.1371/journal.pcbi.1001025 CrossRefPubMedPubMedCentralGoogle Scholar
  38. de Magalhaes JP (2015) The big, the bad and the ugly: extreme animals as inspiration for biomedical research. EMBO Rep 16:771–776.  https://doi.org/10.15252/embr.201540606 CrossRefPubMedPubMedCentralGoogle Scholar
  39. Delany ME (2004) Genetic variants for chick biology research: from breeds to mutants. Mech Dev 121:1169–1177.  https://doi.org/10.1016/j.mod.2004.05.018 CrossRefPubMedGoogle Scholar
  40. Dong Y, Xie M, Jiang Y, Xiao N, Du X, Zhang W, Tosser-Klopp G, Wang J, Yang S, Liang J, Chen W, Chen J, Zeng P, Hou Y, Bian C, Pan S, Li Y, Liu X, Wang W, Servin B, Sayre B, Zhu B, Sweeney D, Moore R, Nie W, Shen Y, Zhao R, Zhang G, Li J, Faraut T, Womack J, Zhang Y, Kijas J, Cockett N, Xu X, Zhao S, Wang J, Wang W (2013) Sequencing and automated whole-genome optical mapping of the genome of a domestic goat (Capra hircus). Nat Biotechnol 31:135–141PubMedCrossRefGoogle Scholar
  41. Donis-Keller H, Green P, Helms C, Cartinhour S, Weiffenbach B, Stephens K, Keith TP, Bowden DW, Smith DR, Lander ES (1987) A genetic linkage map of the human genome. Cell 51:319–337PubMedCrossRefGoogle Scholar
  42. Dorshorst B, Harun-Or-Rashid M, Bagherpoor AJ, Rubin C-J, Ashwell C, Gourichon D, Tixier-Boichard M, Hallböök F, Andersson L (2015) A genomic duplication is associated with ectopic eomesodermin expression in the embryonic chicken comb and two duplex-comb phenotypes. PLoS Genet 11:e1004947.  https://doi.org/10.1371/journal.pgen.1004947 CrossRefPubMedPubMedCentralGoogle Scholar
  43. Douaud M, Feve K, Gerus M, Fillon V, Bardes S, Gourichon D, Dawson DA, Hanotte O, Burke T, Vignoles F, Morisson M, Tixier-Boichard M, Vignal A, Pitel F (2008) Addition of the microchromosome GGA25 to the chicken genome sequence assembly through radiation hybrid and genetic mapping. BMC Genomics 9:129PubMedPubMedCentralCrossRefGoogle Scholar
  44. Dunn IC, Paton IR, Clelland AK, Sebastian S, Johnson EJ, McTeir L, Windsor D, Sherman A, Sang H, Burt DW, Tickle C, Davey MG (2011) The chicken polydactyly (Po) locus causes allelic imbalance and ectopic expression of Shh during limb development. Dev Dyn 240:1163–1172.  https://doi.org/10.1002/dvdy.22623 CrossRefPubMedGoogle Scholar
  45. Dunn IC, Meddle SL, Wilson PW, Wardle CA, Law AS, Bishop VR, Hindar C, Robertson GW, Burt DW, Ellison SJH, Morrice DM, Hocking PM (2013) Decreased expression of the satiety signal receptor CCKAR is responsible for increased growth and body weight during the domestication of chickens. Am J Physiol Endocrinol Metab 304:E909–E921PubMedPubMedCentralCrossRefGoogle Scholar
  46. Eory L, Halligan DL, Keightley PD (2010) Distributions of selectively constrained sites and deleterious mutation rates in the hominid and murid genomes. Mol Biol Evol 27(1):177–192PubMedCrossRefGoogle Scholar
  47. ENCODE Project Consortium, Dunham I, Kundaje A, Aldred SF, Collins PJ, Davis CA, Doyle F, Epstein CB, Frietze S, Harrow J, Kaul R, Khatun J, Lajoie BR, Landt SG, Lee B-K, Pauli F, Rosenbloom KR, Sabo P, Safi A, Sanyal A, Shoresh N, Simon JM, Song L, Trinklein ND, Altshuler RC, Birney E, Brown JB, Cheng C, Djebali S, Dong X, Dunham I, Ernst J, Furey TS, Gerstein M, Giardine B, Greven M, Hardison RC, Harris RS, Herrero J, Hoffman MM, Iyer S, Kelllis M, Khatun J, Kheradpour P, Kundaje A, Lassman T, Li Q, Lin X, Marinov GK, Merkel A, Mortazavi A, Parker SCJ, Reddy TE, Rozowsky J, Schlesinger F, Thurman RE, Wang J, Ward LD, Whitfield TW, Wilder SP, Wu W, Xi HS, Yip KY, Zhuang J, Bernstein BE, Birney E, Dunham I, Green ED, Gunter C, Snyder M, Pazin MJ, Lowdon RF, Dillon LAL, Adams LB, Kelly CJ, Zhang J, Wexler JR, Green ED, Good PJ, Feingold EA, Bernstein BE, Birney E, Crawford GE, Dekker J, Elinitski L, Farnham PJ, Gerstein M, Giddings MC, Gingeras TR, Green ED, Guigo R, Hardison RC, Hubbard TJ, Kellis M, Kent WJ, Lieb JD, Margulies EH, Myers RM, Snyder M, Starnatoyannopoulos JA, Tennebaum SA, Weng Z, White KP, Wold B, Khatun J, Yu Y, Wrobel J, Risk BA, Gunawardena HP, Kuiper HC, Maier CW, Xie L, Chen X, Giddings MC, Bernstein BE, Epstein CB, Shoresh N, Ernst J, Kheradpour P, Mikkelsen TS, Gillespie S, Goren A, Ram O, Zhang X, Wang L, Issner R, Coyne MJ, Durham T, Ku M, Truong T, Ward LD, Altshuler RC, Eaton ML, Kellis M, Djebali S, Davis CA, Merkel A, Dobin A, Lassmann T, Mortazavi A, Tanzer A, Lagarde J, Lin W, Schlesinger F, Xue C, Marinov GK, Khatun J, Williams BA, Zaleski C, Rozowsky J, Röder M, Kokocinski F, Abdelhamid RF, Alioto T, Antoshechkin I, Baer MT, Batut P, Bell I, Bell K, Chakrabortty S, Chen X, Chrast J, Curado J, Derrien T, Drenkow J, Dumais E, Dumais J, Duttagupta R, Fastuca M, Fejes-Toth K, Ferreira P, Foissac S, Fullwood MJ, Gao H, Gonzalez D, Gordon A, Gunawardena HP, Howald C, Jha S, Johnson R, Kapranov P, King B, Kingswood C, Li G, Luo OJ, Park E, Preall JB, Presaud K, Ribeca P, Risk BA, Robyr D, Ruan X, Sammeth M, Sandu KS, Schaeffer L, See L-H, Shahab A, Skancke J, Suzuki AM, Takahashi H, Tilgner H, Trout D, Walters N, Wang H, Wrobel J, Yu Y, Hayashizaki Y, Harrow J, Gerstein M, Hubbard TJ, Reymond A, Antonarakis SE, Hannon GJ, Giddings MC, Ruan Y, Wold B, Carninci P, Guigo R, Gingeras TR, Rosenbloom KR, Sloan CA, Learned K, Malladi VS, Wong MC, Barber GP, Cline MS, Dreszer TR, Heitner SG, Karolchik D, Kent WJ, Kirkup VM, Meyer LR, Long JC, Maddren M, Raney BJ, Furey TS, Song L, Grasfeder LL et al (2012) An integrated encyclopedia of DNA elements in the human genome. Nature 489:57–74CrossRefGoogle Scholar
  48. Engström PG, Steijger T, Sipos B, Grant GR, Kahles A, Rätsch G, Goldman N, Hubbard TJ, Harrow J, Guigo R, Bertone P, RGASP Consortium (2013) Systematic evaluation of spliced alignment programs for RNA-seq data. Nat Methods 10:1185–1191.  https://doi.org/10.1038/nmeth.2722 CrossRefPubMedPubMedCentralGoogle Scholar
  49. Eriksson J, Larson G, Gunnarsson U, Bed’hom B, Tixier-Boichard M, Strömstedt L, Wright D, Jungerius A, Vereijken A, Randi E, Jensen P, Andersson L (2008) Identification of the yellow skin gene reveals a hybrid origin of the domestic chicken. PLoS Genet 4:e1000010.  https://doi.org/10.1371/journal.pgen.1000010 CrossRefPubMedPubMedCentralGoogle Scholar
  50. Ernst J, Kellis M (2012) ChromHMM: automating chromatin-state discovery and characterization. Nat Methods 9:215–216.  https://doi.org/10.1101/gr.229102 CrossRefPubMedPubMedCentralGoogle Scholar
  51. Feng C, Gao Y, Dorshorst B, Song C, Gu X, Li Q, Li J, Liu T, Rubin C-J, Zhao Y, Wang Y, Fei J, Li H, Chen K, Qu H, Shu D, Ashwell C, Da Y, Andersson L, Hu X, Li N (2014) A cis-regulatory mutation of PDSS2 causes silky-feather in chickens. PLoS Genet 10:e1004576PubMedPubMedCentralCrossRefGoogle Scholar
  52. Fillon V, Zoorob R, Yerle M, Auffray C, Vignal A (1996) Mapping of the genetically independent chicken major histocompatibility complexes B@ and RFP-Y@ to the same microchromosome by two-color fluorescent in situ hybridization. Cytogenet Cell Genet 75:7–9PubMedCrossRefGoogle Scholar
  53. Fillon V, Morisson M, Zoorob R, Auffray C, Douaire M, Gellin J, Vignal A (1998) Identification of 16 chicken microchromosomes by molecular markers using two-colour fluorescence in situ hybridization (FISH). Chromosom Res 6:307–313CrossRefGoogle Scholar
  54. Flink LG, Allen R, Barnett R, Malmström H, Peters J, Eriksson J, Andersson L, Dobney K, Larson G (2014) Establishing the validity of domestication genes using DNA from ancient chickens. Proc Natl Acad Sci USA 111:6184–6189.  https://doi.org/10.1073/pnas.1308939110 CrossRefGoogle Scholar
  55. Fresard L, Leroux S, Servin B, Gourichon D, Dehais P, Cristobal MS, Marsaud N, Vignoles F, Bed’hom B, Coville J-L, Hormozdiari F, Beaumont C, Zerjal T, Vignal A, Morisson M, Lagarrigue S, Pitel F (2014) Transcriptome-wide investigation of genomic imprinting in chicken. Nucleic Acids Res 42:3768–3782PubMedPubMedCentralCrossRefGoogle Scholar
  56. Galkina S, Fillon V, Saifitdinova A, Daks A, Kulak M, Dyomin A, Koshel E, Gaginskaya ER (2017) Chicken microchromosomes in the lampbrush phase: a cytogenetic description. Cytogenet Genome Res 152(1):46–54.  https://doi.org/10.1159/000475563 CrossRefPubMedGoogle Scholar
  57. Gibbs RA, Weinstock GM, Metzker ML, Muzny DM, Sodergren EJ, Scherer S, Scott G, Steffen D, Worley KC, Burch PE, Okwuonu G, Hines S, Lewis L, DeRamo C, Delgado O, Dugan-Rocha S, Miner G, Morgan M, Hawes A, Gill R, Celera, Holt RA, Adams MD, Amanatides PG, Baden-Tillson H, Barnstead M, Chin S, Evans CA, Ferriera S, Fosler C, Glodek A, Gu Z, Jennings D, Kraft CL, Nguyen T, Pfannkoch CM, Sitter C, Sutton GG, Venter JC, Woodage T, Smith D, Lee H-M, Gustafson E, Cahill P, Kana A, Doucette-Stamm L, Weinstock K, Fechtel K, Weiss RB, Dunn DM, Green ED, Blakesley RW, Bouffard GG, De Jong PJ, Osoegawa K, Zhu B, Marra M, Schein J, Bosdet I, Fjell C, Jones S, Krzywinski M, Mathewson C, Siddiqui A, Wye N, McPherson J, Zhao S, Fraser CM, Shetty J, Shatsman S, Geer K, Chen Y, Abramzon S, Nierman WC, Havlak PH, Chen R, Durbin KJ, Egan A, Ren Y, Song X-Z, Li B, Liu Y, Qin X, Cawley S, Worley KC, Cooney AJ, D’Souza LM, Martin K, Wu JQ, Gonzalez-Garay ML, Jackson AR, Kalafus KJ, McLeod MP, Milosavljevic A, Virk D, Volkov A, Wheeler DA, Zhang Z, Bailey JA, Eichler EE, Tuzun E, Birney E, Mongin E, Ureta-Vidal A, Woodwark C, Zdobnov E, Bork P, Suyama M, Torrents D, Alexandersson M, Trask BJ, Young JM, Huang H, Wang H, Xing H, Daniels S, Gietzen D, Schmidt J, Stevens K, Vitt U, Wingrove J, Camara F, Mar Albà M, Abril JF, Guigo R, Smit A, Dubchak I, Rubin EM, Couronne O, Poliakov A, Hübner N, Ganten D, Goesele C, Hummel O, Kreitler T, Lee Y-A, Monti J, Schulz H, Zimdahl H, Himmelbauer H, Lehrach H, Jacob HJ, Bromberg S, Gullings-Handley J, Jensen-Seaman MI, Kwitek AE, Lazar J, Pasko D, Tonellato PJ, Twigger S, Ponting CP, Duarte JM, Rice S, Goodstadt L, Beatson SA, Emes RD, Winter EE, Webber C, Brandt P, Nyakatura G, Adetobi M, Chiaromonte F, Elnitski L, Eswara P, Hardison RC, Hou M, Kolbe D, Makova K, Miller W, Nekrutenko A, Riemer C, Schwartz S, Taylor J, Yang S, Zhang Y, Lindpaintner K, Andrews TD, Caccamo M, Clamp M, Clarke L, Curwen V, Durbin R, Eyras E, Searle SM, Cooper GM, Batzoglou S, Brudno M, Sidow A, Stone EA, Venter JC, Payseur BA, Bourque G, López-Otín C, Puente XS, Chakrabarti K, Chatterji S, Dewey C, Pachter L, Bray N, Yap VB, Caspi A, Tesler G, Pevzner PA, Haussler D, Roskin KM, Baertsch R, Clawson H, Furey TS, Hinrichs AS, Karolchik D, Kent WJ, Rosenbloom KR, Trumbower H, Weirauch M, Cooper DN, Stenson PD, Ma B, Brent M, Arumugam M, Shteynberg D, Copley RR, Taylor MS, Riethman H, Mudunuri U, Peterson J, Guyer M, Felsenfeld A, Old S, Mockrin S, Collins F, Consortium RGSP (2004) Genome sequence of the Brown Norway rat yields insights into mammalian evolution. Nature 428:493–521PubMedCrossRefGoogle Scholar
  58. Goddard ME, Hayes BJ (2007) Genomic selection. J Anim Breed Genet 124:323–330.  https://doi.org/10.1111/j.1439-0388.2007.00702.x CrossRefPubMedGoogle Scholar
  59. Groenen MA, Cheng HH, Bumstead N, Benkel BF, Briles WE, Burke T, Burt DW, Crittenden LB, Dodgson J, Hillel J, Lamont S, de Leon AP, Soller M, Takahashi H, Vignal A (2000) A consensus linkage map of the chicken genome. Genome Res 10:137–147PubMedPubMedCentralGoogle Scholar
  60. Groenen MAM, Wahlberg P, Foglio M, Cheng HH, Megens H-J, Crooijmans RPMA, Besnier F, Lathrop M, Muir WM, Wong GK-S, Andersson L (2009) A high-density SNP-based linkage map of the chicken genome reveals sequence features correlated with recombination rate. Genome Res 19:510–519PubMedPubMedCentralCrossRefGoogle Scholar
  61. Gross JB, Borowsky R, Tabin CJ (2009) A novel role for Mc1r in the parallel evolution of depigmentation in independent populations of the cavefish Astyanax mexicanus. PLoS Genet 5:e1000326.  https://doi.org/10.1371/journal.pgen.1000326 CrossRefPubMedPubMedCentralGoogle Scholar
  62. Gunnarsson U, Hellström AR, Tixier-Boichard M, Minvielle F, Bed’hom B, Ito S, Jensen P, Rattink A, Vereijken A, Andersson L (2007) Mutations in SLC45A2 cause plumage color variation in chicken and Japanese quail. Genetics 175:867–877PubMedPubMedCentralCrossRefGoogle Scholar
  63. Gunnarsson U, Kerje S, Bed’hom B, Sahlqvist A-S, Ekwall O, Tixier-Boichard M, Kämpe O, Andersson L (2011) The Dark brown plumage color in chickens is caused by an 8.3-kb deletion upstream of SOX10. Pigment Cell Melanoma Res 24:268–274.  https://doi.org/10.1111/j.1755-148X.2011.00825.x CrossRefPubMedGoogle Scholar
  64. Haig D (2014) Coadaptation and conflict, misconception and muddle, in the evolution of genomic imprinting. Heredity 113:96–103.  https://doi.org/10.1038/hdy.2013.97 CrossRefPubMedGoogle Scholar
  65. Halaas JL, Gajiwala KS, Maffei M, Cohen SL, Chait BT, Rabinowitz D, Lallone RL, Burley SK, Friedman JM (1995) Weight-reducing effects of the plasma protein encoded by the obese gene. Science 269:543–546PubMedCrossRefGoogle Scholar
  66. Hamburger V, Hamilton HL (1992) A series of normal stages in the development of the chick embryo. 1951. Dev Dyn 195(4):231–272. Department of Zoology, Washington University, St. Louis, MissouriPubMedCrossRefGoogle Scholar
  67. Hickey G, Paten B, Earl D, Zerbino D, Haussler D (2013) HAL: a hierarchical format for storing and analyzing multiple genome alignments. Bioinformatics 29:1341–1342.  https://doi.org/10.1093/bioinformatics/btt128 CrossRefPubMedPubMedCentralGoogle Scholar
  68. Hillier LW, Miller W, Birney E, Warren W, Hardison RC, Ponting CP, Bork P, Burt DW, Groenen MAM, Delany ME, Dodgson JB, Genome Fingerprint Map Sequence, Assembly, Chinwalla AT, Cliften PF, Clifton SW, Delehaunty KD, Fronick C, Fulton RS, Graves TA, Kremitzki C, Layman D, Magrini V, McPherson JD, Miner TL, Minx P, Nash WE, Nhan MN, Nelson JO, Oddy LG, Pohl CS, Randall-Maher J, Smith SM, Wallis JW, Yang S-P, Mapping, Romanov MN, Rondelli CM, Paton B, Smith J, Morrice D, Daniels L, Tempest HG, Robertson L, Masabanda JS, Griffin DK, Vignal A, Fillon V, Jacobbson L, Kerje S, Andersson L, Crooijmans RPM, Aerts J, van der Poel JJ, Ellegren H, sequencing cDNA, Caldwell RB, Hubbard SJ, Grafham DV, Kierzek AM, McLaren SR, Overton IM, Arakawa H, Beattie KJ, Bezzubov Y, Boardman PE, Bonfield JK, Croning MDR, Davies RM, Francis MD, Humphray SJ, Scott CE, Taylor RG, Tickle C, Brown WRA, Rogers J, Buerstedde J-M, Wilson SA, sequencing O, libraries, Stubbs L, Ovcharenko I, Gordon L, Lucas S, Miller MM, Inoko H, Shiina T, Kaufman J, Salomonsen J, Skjoedt K, Wong GK-S, Wang J, Liu B, Wang J, Yu J, Yang H, Nefedov M, Koriabine M, Dejong PJ, Analysis, annotation, Goodstadt L, Webber C, Dickens NJ, Letunic I, Suyama M, Torrents D, von Mering C, Zdobnov EM, Makova K, Nekrutenko A, Elnitski L, Eswara P, King DC, Yang S, Tyekucheva S, Radakrishnan A, Harris RS, Chiaromonte F, Taylor J, He J, Rijnkels M, Griffiths-Jones S, Ureta-Vidal A, Hoffman MM, Severin J, Searle SMJ, Law AS, Speed D, Waddington D, Cheng Z, Tuzun E, Eichler E, Bao Z, Flicek P, Shteynberg DD, Brent MR, Bye JM, Huckle EJ, Chatterji S, Dewey C, Pachter L, Kouranov A, Mourelatos Z, Hatzigeorgiou AG, Paterson AH, Ivarie R, Brandström M, Axelsson E, Backström N, Berlin S, Webster MT, Pourquié O, Reymond A, Ucla C, Antonarakis SE, Long M, Emerson JJ, Betrán E, Dupanloup I, Kaessmann H, Hinrichs AS, Bejerano G, Furey TS, Harte RA, Raney B, Siepel A, Kent WJ, Haussler D, Eyras E, Castelo R, Abril JF, Castellano S, Camara F, Parra G, Guigo R, Bourque G, Tesler G, Pevzner PA, Smit A, management P, Fulton LA, Mardis ER, Wilson RK (2004) Sequence and comparative analysis of the chicken genome provide unique perspectives on vertebrate evolution. Nature 432:695–716CrossRefGoogle Scholar
  69. Huang Y, Li Y, Burt DW, Chen H, Zhang Y, Qian W, Kim H, Gan S, Zhao Y, Li J, Yi K, Feng H, Zhu P, Li B, Liu Q, Fairley S, Magor KE, Du Z, Hu X, Goodman L, Tafer H, Vignal A, Lee T, Kim K-W, Sheng Z, An Y, Searle S, Herrero J, Groenen MAM, Crooijmans RPMA, Faraut T, Cai Q, Webster RG, Aldridge JR, Warren WC, Bartschat S, Kehr S, Marz M, Stadler PF, Smith J, Kraus RHS, Zhao Y, Ren L, Fei J, Morisson M, Kaiser P, Griffin DK, Rao M, Pitel F, Wang J, Li N (2013) The duck genome and transcriptome provide insight into an avian influenza virus reservoir species. Nat Genet 45:776–783.  https://doi.org/10.1038/ng.2657 CrossRefPubMedPubMedCentralGoogle Scholar
  70. Huss D, Lansford R (2017) Fluorescent quail: a transgenic model system for the dynamic study of avian development. Methods Mol Biol 1650:125–147.  https://doi.org/10.1007/978-1-4939-7216-6_8 CrossRefPubMedGoogle Scholar
  71. Hutt FB (1933) Genetics of the fowl. II. A four-gene autosomal linkage group. Genetics 18:82–94PubMedPubMedCentralGoogle Scholar
  72. Imsland F, Feng C, Boije H, Bed’hom B, Fillon V, Dorshorst B, Rubin C-J, Liu R, Gao Y, Gu X, Wang Y, Gourichon D, Zody MC, Zecchin W, Vieaud A, Tixier-Boichard M, Hu X, Hallböök F, Li N, Andersson L (2012) The rose-comb mutation in chickens constitutes a structural rearrangement causing both altered comb morphology and defective sperm motility. PLoS Genet 8:e1002775.  https://doi.org/10.1371/journal.pgen.1002775 CrossRefPubMedPubMedCentralGoogle Scholar
  73. Itoh Y, Melamed E, Yang X, Kampf K, Wang S, Yehya N, Van Nas A, Replogle K, Band MR, Clayton DF, Schadt EE, Lusis AJ, Arnold AP (2007) Dosage compensation is less effective in birds than in mammals. J Biol 6:2.  https://doi.org/10.1186/jbiol53 CrossRefPubMedPubMedCentralGoogle Scholar
  74. Jarvis ED, Mirarab S, Aberer AJ, Li B, Houde P, Li C, Ho SYW, Faircloth BC, Nabholz B, Howard JT, Suh A, Weber CC, da Fonseca RR, Li J, Zhang F, Li H, Zhou L, Narula N, Liu L, Ganapathy G, Boussau B, Bayzid MS, Zavidovych V, Subramanian S, Gabaldón T, Capella-Gutiérrez S, Huerta-Cepas J, Rekepalli B, Munch K, Schierup M, Lindow B, Warren WC, Ray D, Green RE, Bruford MW, Zhan X, Dixon A, Li S, Li N, Huang Y, Derryberry EP, Bertelsen MF, Sheldon FH, Brumfield RT, Mello CV, Lovell PV, Wirthlin M, Schneider MPC, Prosdocimi F, Samaniego JA, Vargas Velazquez AM, Alfaro-Núñez A, Campos PF, Petersen B, Sicheritz-Ponten T, Pas A, Bailey T, Scofield P, Bunce M, Lambert DM, Zhou Q, Perelman P, Driskell AC, Shapiro B, Xiong Z, Zeng Y, Liu S, Li Z, Liu B, Wu K, Xiao J, Yinqi X, Zheng Q, Zhang Y, Yang H, Wang J, Smeds L, Rheindt FE, Braun M, Fjeldså J, Orlando L, Barker FK, Jønsson KA, Johnson W, Koepfli K-P, O’Brien S, Haussler D, Ryder OA, Rahbek C, Willerslev E, Graves GR, Glenn TC, McCormack J, Burt D, Ellegren H, Alström P, Edwards SV, Stamatakis A, Mindell DP, Cracraft J, Braun EL, Warnow T, Jun W, Gilbert MTP, Zhang G (2014) Whole-genome analyses resolve early branches in the tree of life of modern birds. Science 346:1320–1331PubMedPubMedCentralCrossRefGoogle Scholar
  75. Jax E, Wink M, Kraus RHS (2018) Avian transcriptomics: opportunities and challenges. J Ornithol 159(3):599–629CrossRefGoogle Scholar
  76. Kain KH, Miller JWI, Jones-Paris CR, Thomason RT, Lewis JD, Bader DM, Barnett JV, Zijlstra A (2014) The chick embryo as an expanding experimental model for cancer and cardiovascular research. Dev Dyn 243:216–228.  https://doi.org/10.1002/dvdy.24093 CrossRefPubMedGoogle Scholar
  77. Karlsson A-C, Svemer F, Eriksson J, Darras VM, Andersson L, Jensen P (2015) The effect of a mutation in the thyroid stimulating hormone receptor (TSHR) on development, behaviour and TH levels in domesticated chickens. PLoS One 10:e0129040.  https://doi.org/10.1371/journal.pone.0129040 CrossRefPubMedPubMedCentralGoogle Scholar
  78. Karlsson A-C, Fallahshahroudi A, Johnsen H, Hagenblad J, Wright D, Andersson L, Jensen P (2016) A domestication related mutation in the thyroid stimulating hormone receptor gene (TSHR) modulates photoperiodic response and reproduction in chickens. Gen Comp Endocrinol 228:69–78PubMedCrossRefGoogle Scholar
  79. Kerje S, Lind J, Schütz K, Jensen P, Andersson L (2003) Melanocortin 1-receptor (MC1R) mutations are associated with plumage colour in chicken. Anim Genet 34:241–248PubMedCrossRefGoogle Scholar
  80. Kerje S, Sharma P, Gunnarsson U, Kim H, Bagchi S, Fredriksson R, Schütz K, Jensen P, von Heijne G, Okimoto R, Andersson L (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.  https://doi.org/10.1534/genetics.104.027995 CrossRefPubMedPubMedCentralGoogle Scholar
  81. Korlach J, Gedman G, Kingan SB, Chin C-S, Howard JT, Audet J-N, Cantin L, Jarvis ED (2017) De novo PacBio long-read and phased avian genome assemblies correct and add to reference genes generated with intermediate and short reads. Gigascience 6:1–16.  https://doi.org/10.1093/gigascience/gix085 CrossRefPubMedPubMedCentralGoogle Scholar
  82. Kranis A, Gheyas AA, Boschiero C, Turner F, Yu L, Smith S, Talbot R, Pirani A, Brew F, Kaiser P, Hocking PM, Fife M, Salmon N, Fulton J, Strom TM, Haberer G, Weigend S, Preisinger R, Gholami M, Qanbari S, Simianer H, Watson KA, Woolliams JA, Burt DW (2013) Development of a high density 600K SNP genotyping array for chicken. BMC Genomics 14:59PubMedPubMedCentralCrossRefGoogle Scholar
  83. Kraus RHS, Wink M (2015) Avian genomics: fledging into the wild! J Ornithol 156:851–865.  https://doi.org/10.1007/s10336-015-1253-y CrossRefGoogle Scholar
  84. Kuo RI, Tseng E, Eory L, Paton IR, Archibald AL, Burt DW (2017) Normalized long read RNA sequencing in chicken reveals transcriptome complexity similar to human. BMC Genomics 18:323.  https://doi.org/10.1186/s12864-017-3691-9 CrossRefPubMedPubMedCentralGoogle Scholar
  85. Ladjali K, Tixier-Boichard M, Cribiu EP (1995) High-resolution chromosome preparations for G-and R-banding in Gallus domesticus. J Hered 86:136–139CrossRefGoogle Scholar
  86. Laine VN, Gossmann TI, Schachtschneider KM, Garroway CJ, Madsen O, Verhoeven KJF, de Jager V, Megens H-J, Warren WC, Minx P, Crooijmans RPMA, Corcoran P, Great Tit HapMap Consortium, Sheldon BC, Slate J, Zeng K, van Oers K, Visser ME, Groenen MAM (2016) Evolutionary signals of selection on cognition from the great tit genome and methylome. Nat Commun 7:10474.  https://doi.org/10.1038/ncomms10474 CrossRefPubMedPubMedCentralGoogle Scholar
  87. Lam ET, Hastie A, Lin C, Ehrlich D, Das SK, Austin MD, Deshpande P, Cao H, Nagarajan N, Xiao M, Kwok P-Y (2012) Genome mapping on nanochannel arrays for structural variation analysis and sequence assembly. Nat Biotechnol 30:771–776PubMedCrossRefGoogle Scholar
  88. Lamichhaney S, Fan G, Widemo F, Gunnarsson U, Thalmann DS, Hoeppner MP, Kerje S, Gustafson U, Shi C, Zhang H, Chen W, Liang X, Huang L, Wang J, Liang E, Wu Q, Lee SM-Y, Xu X, Höglund J, Liu X, Andersson L (2016) Structural genomic changes underlie alternative reproductive strategies in the ruff (Philomachus pugnax). Nat Genet 48:84–88PubMedCrossRefPubMedCentralGoogle Scholar
  89. Lander ES, Linton LM, Birren B, Nusbaum C, Zody MC, Baldwin J, Devon K, Dewar K, Doyle M, FitzHugh W, Funke R, Gage D, Harris K, Heaford A, Howland J, Kann L, Lehoczky J, LeVine R, McEwan P, McKernan K, Meldrim J, Mesirov JP, Miranda C, Morris W, Naylor J, Raymond C, Rosetti M, Santos R, Sheridan A, Sougnez C, Stange-Thomann N, Stojanovic N, Subramanian A, Wyman D, Rogers J, Sulston J, Ainscough R, Beck S, Bentley D, Burton J, Clee C, Carter N, Coulson A, Deadman R, Deloukas P, Dunham A, Dunham I, Durbin R, French L, Grafham D, Gregory S, Hubbard T, Humphray S, Hunt A, Jones M, Lloyd C, McMurray A, Matthews L, Mercer S, Milne S, Mullikin JC, Mungall A, Plumb R, Ross M, Shownkeen R, Sims S, Waterston RH, Wilson RK, Hillier LW, McPherson JD, Marra MA, Mardis ER, Fulton LA, Chinwalla AT, Pepin KH, Gish WR, Chissoe SL, Wendl MC, Delehaunty KD, Miner TL, Delehaunty A, Kramer JB, Cook LL, Fulton RS, Johnson DL, Minx PJ, Clifton SW, Hawkins T, Branscomb E, Predki P, Richardson P, Wenning S, Slezak T, Doggett N, Cheng JF, Olsen A, Lucas S, Elkin C, Uberbacher E, Frazier M, Gibbs RA, Muzny DM, Scherer SE, Bouck JB, Sodergren EJ, Worley KC, Rives CM, Gorrell JH, Metzker ML, Naylor SL, Kucherlapati RS, Nelson DL, Weinstock GM, Sakaki Y, Fujiyama A, Hattori M, Yada T, Toyoda A, Itoh T, Kawagoe C, Watanabe H, Totoki Y, Taylor T, Weissenbach J, Heilig R, Saurin W, Artiguenave F, Brottier P, Bruls T, Pelletier E, Robert C, Wincker P, Smith DR, Doucette-Stamm L, Rubenfield M, Weinstock K, Lee HM, Dubois J, Rosenthal A, Platzer M, Nyakatura G, Taudien S, Rump A, Yang H, Yu J, Wang J, Huang G, Gu J, Hood L, Rowen L, Madan A, Qin S, Davis RW, Federspiel NA, Abola AP, Proctor MJ, Myers RM, Schmutz J, Dickson M, Grimwood J, Cox DR, Olson MV, Kaul R, Raymond C, Shimizu N, Kawasaki K, Minoshima S, Evans GA, Athanasiou M, Schultz R, Roe BA, Chen F, Pan H, Ramser J, Lehrach H, Reinhardt R, McCombie WR, de la Bastide M, Dedhia N, Blöcker H, Hornischer K, Nordsiek G, Agarwala R, Aravind L, Bailey JA, Bateman A, Batzoglou S, Birney E, Bork P, Brown DG, Burge CB, Cerutti L, Chen HC, Church D, Clamp M, Copley RR, Doerks T, Eddy SR, Eichler EE, Furey TS, Galagan J, Gilbert JG, Harmon C, Hayashizaki Y, Haussler D, Hermjakob H, Hokamp K, Jang W, Johnson LS, Jones TA, Kasif S, Kaspryzk A, Kennedy S, Kent WJ, Kitts P, Koonin EV, Korf I, Kulp D, Lancet D, Lowe TM, McLysaght A, Mikkelsen T, Moran JV, Mulder N, Pollara VJ, Ponting CP, Schuler G, Schultz J, Slater G, Smit AF, Stupka E, Szustakowski J, Thierry-Mieg D, Thierry-Mieg J, Wagner L, Wallis J, Wheeler R, Williams A, Wolf YI, Wolfe KH, Yang S-P, Yeh RF, Collins F, Guyer MS, Peterson J, Felsenfeld A, Wetterstrand KA, Patrinos A, Morgan MJ, de Jong P, Catanese JJ, Osoegawa K, Shizuya H, Choi S, Chen YJ, Szustakowki J, International Human Genome Sequencing Consortium (2001) Initial sequencing and analysis of the human genome. Nature 409:860–921PubMedCrossRefGoogle Scholar
  90. Laun K, Coggill P, Palmer S, Sims S, Ning Z, Ragoussis J, Volpi E, Wilson N, Beck S, Ziegler A, Volz A (2006) The leukocyte receptor complex in chicken is characterized by massive expansion and diversification of immunoglobulin-like loci. PLoS Genet 2:e73PubMedPubMedCentralCrossRefGoogle Scholar
  91. Laver T, Harrison J, O’Neill PA, Moore K, Farbos A, Paszkiewicz K, Studholme DJ (2015) Assessing the performance of the Oxford nanopore technologies MinION. Biomol Detect Quantif 3:1–8.  https://doi.org/10.1016/j.bdq.2015.02.001 CrossRefPubMedPubMedCentralGoogle Scholar
  92. Le Bihan-Duval E, Nadaf J, Berri C, Pitel F, Graulet B, Godet E, Leroux SY, Demeure O, Lagarrigue S, Duby C, Cogburn LA, Beaumont CM, Duclos MJ (2011) Detection of a cis eQTL controlling BMCO1 gene expression leads to the identification of a QTG for chicken breast meat color. PLoS One 6:e14825PubMedPubMedCentralCrossRefGoogle Scholar
  93. Le Douarin NM, Teillet MA (1974) Experimental analysis of the migration and differentiation of neuroblasts of the autonomic nervous system and of neurectodermal mesenchymal derivatives, using a biological cell marking technique. Dev Biol 41:162–184PubMedCrossRefGoogle Scholar
  94. Lennox J (2017) Aristotle’s biology, Spring 2017 Edition. The Stanford Encyclopedia of PhilosophyGoogle Scholar
  95. Levin I, Santangelo L, Cheng H, Crittenden LB, Dodgson JB (1994) An autosomal genetic linkage map of the chicken. J Hered 85:79–85PubMedCrossRefGoogle Scholar
  96. Lin MF, Jungreis I, Kellis M (2011) PhyloCSF: a comparative genomics method to distinguish protein coding and non-coding regions. Bioinformatics 27:i275–i282.  https://doi.org/10.1093/bioinformatics/btr209 CrossRefPubMedPubMedCentralGoogle Scholar
  97. Lindblad-Toh K, Garber M, Zuk O, Lin MF, Parker BJ, Washietl S, Kheradpour P, Ernst J, Jordan G, Mauceli E, Ward LD, Lowe CB, Holloway AK, Clamp M, Gnerre S, Alföldi J, Beal K, Chang J, Clawson H, Cuff J, Di Palma F, Fitzgerald S, Flicek P, Guttman M, Hubisz MJ, Jaffe DB, Jungreis I, Kent WJ, Kostka D, Lara M, Martins AL, Massingham T, Moltke I, Raney BJ, Rasmussen MD, Robinson J, Stark A, Vilella AJ, Wen J, Xie X, Zody MC, Broad Institute Sequencing Platform and Whole Genome Assembly Team, Baldwin J, Bloom T, Chin CW, Heiman D, Nicol R, Nusbaum C, Young S, Wilkinson J, Worley KC, Kovar CL, Muzny DM, Gibbs RA, Baylor College of Medicine Human Genome Sequencing Center Sequencing Team, Cree A, Dihn HH, Fowler G, Jhangiani S, Joshi V, Lee S, Lewis LR, Nazareth LV, Okwuonu G, Santibanez J, Warren WC, Mardis ER, Weinstock GM, Wilson RK, Genome Institute at Washington University, Delehaunty K, Dooling D, Fronik C, Fulton L, Fulton B, Graves T, Minx P, Sodergren E, Birney E, Margulies EH, Herrero J, Green ED, Haussler D, Siepel A, Goldman N, Pollard KS, Pedersen JS, Lander ES, Kellis M (2011) A high-resolution map of human evolutionary constraint using 29 mammals. Nature 478:476–482.  https://doi.org/10.1038/nature10530 CrossRefPubMedPubMedCentralGoogle Scholar
  98. Litt M, Luty JA (1989) A hypervariable microsatellite revealed by in vitro amplification of a dinucleotide repeat within the cardiac muscle actin gene. Am J Hum Genet 44:397–401PubMedPubMedCentralGoogle Scholar
  99. Loog L, Thomas MG, Barnett R, Allen R, Sykes N, Paxinos PD, Lebrasseur O, Dobney K, Peters J, Manica A, Larson G, Eriksson A (2017) Inferring allele frequency trajectories from ancient DNA indicates that selection on a chicken gene coincided with changes in medieval husbandry practices. Mol Biol Evol 34(8):1981–1990.  https://doi.org/10.1093/molbev/msx142 CrossRefPubMedPubMedCentralGoogle Scholar
  100. Lovell PV, Wirthlin M, Wilhelm L, Minx P, Lazar NH, Carbone L, Warren WC, Mello CV (2014) Conserved syntenic clusters of protein coding genes are missing in birds. Genome Biol 15(12):565PubMedPubMedCentralCrossRefGoogle Scholar
  101. Lowe CB, Clarke JA, Baker AJ, Haussler D, Edwards SV (2015) Feather development genes and associated regulatory innovation predate the origin of Dinosauria. Mol Biol Evol 32:23–28.  https://doi.org/10.1093/molbev/msu309 CrossRefPubMedGoogle Scholar
  102. Mack KL, Nachman MW (2017) Gene regulation and speciation. Trends Genet 33:68–80.  https://doi.org/10.1016/j.tig.2016.11.003 CrossRefPubMedGoogle Scholar
  103. Margulies EH (2003) Identification and characterization of multi-species conserved sequences. Genome Res 13:2507–2518PubMedPubMedCentralCrossRefGoogle Scholar
  104. Mariani P, Barrow PA, Cheng HH, Groenen MM, Negrini R, Bumstead N (2001) Localization to chicken chromosome 5 of a novel locus determining salmonellosis resistance. Immunogenetics 53:786–791PubMedCrossRefGoogle Scholar
  105. Masabanda JS, Burt DW, O’Brien PCM, Vignal A, Fillon V, Walsh PS, Cox H, Tempest HG, Smith J, Habermann F, Schmid M, Matsuda Y, Ferguson-Smith MA, Crooijmans RPMA, Groenen MAM, Griffin DK (2004) Molecular cytogenetic definition of the chicken genome: the first complete avian karyotype. Genetics 166:1367–1373PubMedPubMedCentralCrossRefGoogle Scholar
  106. McQueen HA, Fantes J, Cross SH, Clark VH, Archibald AL, Bird AP (1996) CpG islands of chicken are concentrated on microchromosomes. Nat Genet 12:321–324.  https://doi.org/10.1038/ng0396-321 CrossRefPubMedGoogle Scholar
  107. McQueen HA, Siriaco G, Bird AP (1998) Chicken microchromosomes are hyperacetylated, early replicating, and gene rich. Genome Res 8:621–630PubMedPubMedCentralCrossRefGoogle Scholar
  108. Melamed E, Arnold AP (2007) Regional differences in dosage compensation on the chicken Z chromosome. Genome Biol 8:R202PubMedPubMedCentralCrossRefGoogle Scholar
  109. Mello CV (2014) The zebra finch, Taeniopygia guttata: an avian model for investigating the neurobiological basis of vocal learning. Cold Spring Harb Protoc 2014:1237–1242PubMedPubMedCentralCrossRefGoogle Scholar
  110. Mihola O, Trachtulec Z, Vlcek C, Schimenti JC, Forejt J (2009) A mouse speciation gene encodes a meiotic histone H3 methyltransferase. Science 323:373–375PubMedCrossRefGoogle Scholar
  111. Miller MM, Taylor RL (2016) Brief review of the chicken major histocompatibility complex: the genes, their distribution on chromosome 16, and their contributions to disease resistance. Poult Sci 95:375–392.  https://doi.org/10.3382/ps/pev379 CrossRefPubMedPubMedCentralGoogle Scholar
  112. Minvielle F, Bed’hom B, Coville J-L, Ito S, Inoue-Murayama M, Gourichon D (2010) The “silver” Japanese quail and the MITF gene: causal mutation, associated traits and homology with the “blue” chicken plumage. BMC Genet 11:15PubMedPubMedCentralCrossRefGoogle Scholar
  113. Morisson M, Denis M, Milan D, Klopp C, Leroux S, Bardes S, Pitel F, Vignoles F, Gérus M, Fillon V, Douaud M, Vignal A (2007) The chicken RH map: current state of progress and microchromosome mapping. Cytogenet Genome Res 117:14–21.  https://doi.org/10.1159/000103160 CrossRefPubMedGoogle Scholar
  114. Morris K, Hindle M, Boitard S et al (2019) The quail as an avian model system: its genome provides insights into social behaviour, seasonal biology and infectious disease response. bioRxiv. doi: http://dx.doi.org/10.1101/575332Google Scholar
  115. Mou C, Pitel F, Gourichon D, Vignoles F, Tzika A, Tato P, Yu L, Burt DW, Bed’hom B, Tixier-Boichard M, Painter KJ, Headon DJ (2011) Cryptic patterning of avian skin confers a developmental facility for loss of neck feathering. PLoS Biol 9:e1001028.  https://doi.org/10.1371/journal.pbio.1001028 CrossRefPubMedPubMedCentralGoogle Scholar
  116. Mullikin JC, McMurray AA (1999) DNA sequencing – sequencing the genome, fast. Science 283:1867–1868PubMedCrossRefGoogle Scholar
  117. Muret K, Klopp C, Wucher V, Esquerré D, Legeai F, Lecerf F, Désert C, Boutin M, Jehl F, Acloque H, Giuffra E, Djebali S, Foissac S, Derrien T, Lagarrigue S (2017) Long noncoding RNA repertoire in chicken liver and adipose tissue. Genet Sel Evol 49:6.  https://doi.org/10.1186/s12711-016-0275-0 CrossRefPubMedPubMedCentralGoogle Scholar
  118. Nadaf J, Gilbert H, Pitel F, Berri CM, Feve K, Beaumont C, Duclos MJ, Vignal A, Porter TE, Simon J, Aggrey SE, Cogburn LA, Le Bihan-Duval E (2007) Identification of QTL controlling meat quality traits in an F2 cross between two chicken lines selected for either low or high growth rate. BMC Genomics 8:155PubMedPubMedCentralCrossRefGoogle Scholar
  119. NCBI Resource Coordinators (2017) Database resources of the national center for biotechnology information. Nucleic Acids Res 45:D12–D17.  https://doi.org/10.1093/nar/gkw1071 CrossRefGoogle Scholar
  120. Ng CS, Wu P, Foley J, Foley A, McDonald M-L, Juan W-T, Huang C-J, Lai Y-T, Lo W-S, Chen C-F, Leal SM, Zhang H, Widelitz RB, Patel PI, Li W-H, Chuong C-M (2012) The chicken frizzle feather is due to an α-keratin (KRT75) mutation that causes a defective rachis. PLoS Genet 8:e1002748.  https://doi.org/10.1371/journal.pgen.1002748 CrossRefPubMedPubMedCentralGoogle Scholar
  121. Nguyen N, Hickey G, Raney BJ, Armstrong J, Clawson H, Zweig A, Karolchik D, Kent WJ, Haussler D, Paten B (2014) Comparative assembly hubs: web-accessible browsers for comparative genomics. Bioinformatics 30:3293–3301.  https://doi.org/10.1093/bioinformatics/btu534 CrossRefPubMedPubMedCentralGoogle Scholar
  122. Ohta T (1995) Synonymous and nonsynonymous substitutions in mammalian genes and the nearly neutral theory. J Mol Evol 40:56–63PubMedCrossRefGoogle Scholar
  123. Oliva R, Dixon GH (1989) Chicken protamine genes are intronless. The complete genomic sequence and organization of the two loci. J Biol Chem 264:12472–12481PubMedGoogle Scholar
  124. Ottenburghs J (2019) Avian species concepts in the light of genomics. In: Kraus RHS (ed) Avian genomics in ecology and evolution. Springer, ChamGoogle Scholar
  125. Ovcharenko I (2005) Evolution and functional classification of vertebrate gene deserts. Genome Res 15:137–145PubMedPubMedCentralCrossRefGoogle Scholar
  126. Park PJ (2009) ChIP-seq: advantages and challenges of a maturing technology. Nat Rev Genet 10:669–680.  https://doi.org/10.1038/nbt717 CrossRefPubMedPubMedCentralGoogle Scholar
  127. Paten B, Earl D, Nguyen N, Diekhans M, Zerbino D, Haussler D (2011) Cactus: algorithms for genome multiple sequence alignment. Genome Res 21:1512–1528.  https://doi.org/10.1101/gr.123356.111 CrossRefPubMedPubMedCentralGoogle Scholar
  128. Pertea M, Shumate A, Pertea G, Varabyou A, Chang Y-C, Madugundu AK, Pandey A, Salzberg S (2018) Thousands of large-scale RNA sequencing experiments yield a comprehensive new human gene list and reveal extensive transcriptional noise. BioRxiv:332825.  https://doi.org/10.1101/332825
  129. Pichugin AM, Galkina SA, Potekhin AA, Punina EO, Rautian MS, Rodionov AV (2001) Determination of the minimum size of Gallus gallus domesticus chicken microchromosome by a pulse electrophoresis method. Genetika 37:657–660PubMedGoogle Scholar
  130. Pitel F, Bergé R, Coquerelle G, Crooijmans RP, Groenen MA, Vignal A, Tixier-Boichard M (2000) Mapping the naked neck (NA) and polydactyly (PO) mutants of the chicken with microsatellite molecular markers. Genet Sel Evol 32:73–86PubMedPubMedCentralCrossRefGoogle Scholar
  131. Pitel F, Faraut T, Bruneau G, Monget P (2010) Is there a leptin gene in the chicken genome? Lessons from phylogenetics, bioinformatics and genomics. Gen Comp Endocrinol 167:1–5PubMedCrossRefGoogle Scholar
  132. Putnam NH, O’Connell BL, Stites JC, Rice BJ, Blanchette M, Calef R, Troll CJ, Fields A, Hartley PD, Sugnet CW, Haussler D, Rokhsar DS, Green RE (2016) Chromosome-scale shotgun assembly using an in vitro method for long-range linkage. Genome Res 26:342–350PubMedPubMedCentralCrossRefGoogle Scholar
  133. Ren C, Lee M-K, Yan B, Ding K, Cox B, Romanov MN, Price JA, Dodgson JB, Zhang H-B (2003) A BAC-based physical map of the chicken genome. Genome Res 13:2754–2758PubMedPubMedCentralCrossRefGoogle Scholar
  134. Roadmap Epigenomics Consortium, Kundaje A, Meuleman W, Ernst J, Bilenky M, Yen A, Heravi-Moussavi A, Kheradpour P, Zhang Z, Wang J, Ziller MJ, Amin V, Whitaker JW, Schultz MD, Ward LD, Sarkar A, Quon G, Sandstrom RS, Eaton ML, Wu Y-C, Pfenning AR, Wang X, Claussnitzer M, Liu Y, Coarfa C, Harris RA, Shoresh N, Epstein CB, Gjoneska E, Leung D, Xie W, Hawkins RD, Lister R, Hong C, Gascard P, Mungall AJ, Moore R, Chuah E, Tam A, Canfield TK, Hansen RS, Kaul R, Sabo PJ, Bansal MS, Carles A, Dixon JR, Farh K-H, Feizi S, Karlic R, Kim A-R, Kulkarni A, Li D, Lowdon R, Elliott G, Mercer TR, Neph SJ, Onuchic V, Polak P, Rajagopal N, Ray P, Sallari RC, Siebenthall KT, Sinnott-Armstrong NA, Stevens M, Thurman RE, Wu J, Zhang B, Zhou X, Beaudet AE, Boyer LA, De Jager PL, Farnham PJ, Fisher SJ, Haussler D, Jones SJM, Li W, Marra MA, McManus MT, Sunyaev S, Thomson JA, Tlsty TD, Tsai L-H, Wang W, Waterland RA, Zhang MQ, Chadwick LH, Bernstein BE, Costello JF, Ecker JR, Hirst M, Meissner A, Milosavljevic A, Ren B, Stamatoyannopoulos JA, Wang T, Kellis M (2015) Integrative analysis of 111 reference human epigenomes. Nature 518:317–330PubMedCentralCrossRefPubMedGoogle Scholar
  135. Roberts RJ, Carneiro MO, Schatz MC (2013) The advantages of SMRT sequencing. Genome Biol 14:405.  https://doi.org/10.1186/gb-2013-14-6-405 CrossRefPubMedPubMedCentralGoogle Scholar
  136. Roest Crollius H, Jaillon O, Bernot A, Dasilva C, Bouneau L, Fischer C, Fizames C, Wincker P, Brottier P, Quétier F, Saurin W, Weissenbach J (2000) Estimate of human gene number provided by genome-wide analysis using Tetraodon nigroviridis DNA sequence. Nat Genet 25:235–238PubMedCrossRefGoogle Scholar
  137. Romanov MN, Price JA, Dodgson JB (2003) Integration of animal linkage and BAC contig maps using overgo hybridization. Cytogenet Genome Res 102:277–281PubMedCrossRefGoogle Scholar
  138. Romé H, Varenne A, Hérault F, Chapuis H, Alleno C, Dehais P, Vignal A, Burlot T, Le Roy P (2015) GWAS analyses reveal QTL in egg layers that differ in response to diet differences. Genet Sel Evol 47:83PubMedPubMedCentralCrossRefGoogle Scholar
  139. Rous P (1911) A sarcoma of the fowl transmissible by an agent separable from the tumor cells. J Exp Med 13:397–411PubMedPubMedCentralCrossRefGoogle Scholar
  140. Rubin C-J, Zody MC, Eriksson J, Meadows JRS, Sherwood E, Webster MT, Jiang L, Ingman M, Sharpe T, Ka S, Hallböök F, Besnier F, Carlborg O, Bed’hom B, Tixier-Boichard M, Jensen P, Siegel P, Lindblad-Toh K, Andersson L (2010) Whole-genome resequencing reveals loci under selection during chicken domestication. Nature 464(7288):587–591PubMedCrossRefGoogle Scholar
  141. Schmidt D, Wilson MD, Ballester B, Schwalie PC, Brown GD, Marshall A, Kutter C, Watt S, Martinez-Jimenez CP, Mackay S, Talianidis I, Flicek P, Odom DT (2010) Five-vertebrate ChIP-seq reveals the evolutionary dynamics of transcription factor binding. Science 328:1036–1040.  https://doi.org/10.1126/science.1186176 CrossRefPubMedPubMedCentralGoogle Scholar
  142. Schmutz J, Grimwood J (2004) Fowl sequence. Nature 432:679–680.  https://doi.org/10.1038/432679a CrossRefPubMedGoogle Scholar
  143. Schoffner A, Kristan WB (1965) Karyotype of Gallus Domesticus with evidence for a W chromosome. Genetics 52:474Google Scholar
  144. Schwochow Thalmann D, Ring H, Sundström E, Cao X, Larsson M, Kerje S, Höglund A, Fogelholm J, Wright D, Jemth P, Hallböök F, Bed’hom B, Dorshorst B, Tixier-Boichard M, Andersson L (2017) The evolution of sex-linked barring alleles in chickens involves both regulatory and coding changes in CDKN2A. PLoS Genet 13:e1006665.  https://doi.org/10.1371/journal.pgen.1006665 CrossRefPubMedPubMedCentralGoogle Scholar
  145. Seroussi E, Pitel F, Leroux S, Morisson M, Bornelöv S, Miyara S, Yosefi S, Cogburn LA, Burt DW, Anderson L, Friedman-Einat M (2017) Mapping of leptin and its syntenic genes to chicken chromosome 1p. BMC Genet 18:77.  https://doi.org/10.1186/s12863-017-0543-1 CrossRefPubMedPubMedCentralGoogle Scholar
  146. Shendure J, Balasubramanian S, Church GM, Gilbert W, Rogers J, Schloss JA, Waterston RH (2017) DNA sequencing at 40: past, present and future. Nature 550:345–353.  https://doi.org/10.1038/nature24286 CrossRefPubMedGoogle Scholar
  147. Singhal S, Leffler EM, Sannareddy K, Turner I, Venn O, Hooper DM, Strand AI, Li Q, Raney B, Balakrishnan CN, Griffith SC, McVean G, Przeworski M (2015) Stable recombination hotspots in birds. Science 350:928–932.  https://doi.org/10.1126/science.aad0843 CrossRefPubMedPubMedCentralGoogle Scholar
  148. Soller M, Beckmann JS (1986) Restriction-fragment-length-polymorphisms in poultry breeding. Poult Sci 65:1474–1488CrossRefGoogle Scholar
  149. Steijger T, Abril JF, Engström PG, Kokocinski F, RGASP Consortium, Hubbard TJ, Guigo R, Harrow J, Bertone P (2013) Assessment of transcript reconstruction methods for RNA-seq. Nat Methods 10:1177–1184.  https://doi.org/10.1038/nmeth.2714 CrossRefPubMedGoogle Scholar
  150. Stevison LS, Woerner AE, Kidd JM, Kelley JL, Veeramah KR, McManus KF, Great Ape Genome Project, Bustamante CD, Hammer MF, Wall JD (2016) The time scale of recombination rate evolution in great apes. Mol Biol Evol 33:928–945.  https://doi.org/10.1093/molbev/msv331 CrossRefPubMedGoogle Scholar
  151. Théveneau E, Mayor R (2012) Neural crest delamination and migration: from epithelium-to-mesenchyme transition to collective cell migration. Dev Biol 366:34–54.  https://doi.org/10.1016/j.ydbio.2011.12.041 CrossRefPubMedGoogle Scholar
  152. Tixier-Boichard M (2007) From phenotype to genotype: major genes in chickens. Worlds Poult Sci J 58:65–75.  https://doi.org/10.1079/WPS20020008 CrossRefGoogle Scholar
  153. Tixier-Boichard M, Bed’hom B, Rognon X (2011) Chicken domestication: from archeology to genomics. C R Biol 334:197–204.  https://doi.org/10.1016/j.crvi.2010.12.012 CrossRefPubMedGoogle Scholar
  154. Tobita-Teramoto T, Jang GY, Kino K, Salter DW, Brumbaugh J, Akiyama T (2000) Autosomal albino chicken mutation (ca/ca) deletes hexanucleotide (-deltaGACTGG817) at a copper-binding site of the tyrosinase gene. Poult Sci 79:46–50PubMedCrossRefGoogle Scholar
  155. Ulitsky I, Bartel DP (2013) lincRNAs: genomics, evolution, and mechanisms. Cell 154:26–46.  https://doi.org/10.1016/j.cell.2013.06.020 CrossRefPubMedPubMedCentralGoogle Scholar
  156. Vaez M, Follett SA, Bed’hom B, Gourichon D, Tixier-Boichard M, Burke T (2008) A single point-mutation within the melanophilin gene causes the lavender plumage colour dilution phenotype in the chicken. BMC Genet 9:7PubMedPubMedCentralCrossRefGoogle Scholar
  157. Venter JC, Adams MD, Myers EW, Li PW, Mural RJ, Sutton GG, Smith HO, Yandell M, Evans CA, Holt RA, Gocayne JD, Amanatides P, Ballew RM, Huson DH, Wortman JR, Zhang Q, Kodira CD, Zheng XH, Chen L, Skupski M, Subramanian G, Thomas PD, Zhang J, Gabor Miklos GL, Nelson C, Broder S, Clark AG, Nadeau J, McKusick VA, Zinder N, Levine AJ, Roberts RJ, Simon M, Slayman C, Hunkapiller M, Bolanos R, Delcher A, Dew I, Fasulo D, Flanigan M, Florea L, Halpern A, Hannenhalli S, Kravitz S, Levy S, Mobarry C, Reinert K, Remington K, Abu-Threideh J, Beasley E, Biddick K, Bonazzi V, Brandon R, Cargill M, Chandramouliswaran I, Charlab R, Chaturvedi K, Deng Z, Di Francesco V, Dunn P, Eilbeck K, Evangelista C, Gabrielian AE, Gan W, Ge W, Gong F, Gu Z, Guan P, Heiman TJ, Higgins ME, Ji RR, Ke Z, Ketchum KA, Lai Z, Lei Y, Li Z, Li J, Liang Y, Lin X, Lu F, Merkulov GV, Milshina N, Moore HM, Naik AK, Narayan VA, Neelam B, Nusskern D, Rusch DB, Salzberg S, Shao W, Shue B, Sun J, Wang Z, Wang A, Wang X, Wang J, Wei M, Wides R, Xiao C, Yan C, Yao A, Ye J, Zhan M, Zhang W, Zhang H, Zhao Q, Zheng L, Zhong F, Zhong W, Zhu S, Zhao S, Gilbert D, Baumhueter S, Spier G, Carter C, Cravchik A, Woodage T, Ali F, An H, Awe A, Baldwin D, Baden H, Barnstead M, Barrow I, Beeson K, Busam D, Carver A, Center A, Cheng ML, Curry L, Danaher S, Davenport L, Desilets R, Dietz S, Dodson K, Doup L, Ferriera S, Garg N, Gluecksmann A, Hart B, Haynes J, Haynes C, Heiner C, Hladun S, Hostin D, Houck J, Howland T, Ibegwam C, Johnson J, Kalush F, Kline L, Koduru S, Love A, Mann F, May D, McCawley S, McIntosh T, McMullen I, Moy M, Moy L, Murphy B, Nelson K, Pfannkoch C, Pratts E, Puri V, Qureshi H, Reardon M, Rodriguez R, Rogers YH, Romblad D, Ruhfel B, Scott R, Sitter C, Smallwood M, Stewart E, Strong R, Suh E, Thomas R, Tint NN, Tse S, Vech C, Wang G, Wetter J, Williams S, Williams M, Windsor S, Winn-Deen E, Wolfe K, Zaveri J, Zaveri K, Abril JF, Guigó R, Campbell MJ, Sjolander KV, Karlak B, Kejariwal A, Mi H, Lazareva B, Hatton T, Narechania A, Diemer K, Muruganujan A, Guo N, Sato S, Bafna V, Istrail S, Lippert R, Schwartz R, Walenz B, Yooseph S, Allen D, Basu A, Baxendale J, Blick L, Caminha M, Carnes-Stine J, Caulk P, Chiang YH, Coyne M, Dahlke C, Mays A, Dombroski M, Donnelly M, Ely D, Esparham S, Fosler C, Gire H, Glanowski S, Glasser K, Glodek A, Gorokhov M, Graham K, Gropman B, Harris M, Heil J, Henderson S, Hoover J, Jennings D, Jordan C, Jordan J, Kasha J, Kagan L, Kraft C, Levitsky A, Lewis M, Liu X, Lopez J, Ma D, Majoros W, McDaniel J, Murphy S, Newman M, Nguyen T, Nguyen N, Nodell M, Pan S, Peck J, Peterson M, Rowe W, Sanders R, Scott J, Simpson M, Smith T, Sprague A, Stockwell T, Turner R, Venter E, Wang M, Wen M, Wu D, Wu M, Xia A, Zandieh A, Zhu X (2001) The sequence of the human genome. Science 291:1304–1351PubMedCrossRefGoogle Scholar
  158. Vignal A, Boitard S, Thebault N, Dayo G-K, Yapi-Gnaore V, Youssao I, Berthouly-Salazar C, Pálinkás-Bodzsár N, Guémené D, Thibaud-Nissen F, Warren WC, Tixier-Boichard M, Rognon X (2019) A guinea fowl genome assembly provides new evidence on evolution following domestication and selection in galliformes. Mol Ecol Resour [Internet]. [cited 2019 Apr 17];0(ja). Available from: https://onlinelibrary.wiley.com/doi/abs/10.1111/1755-0998.13017
  159. Villar D, Berthelot C, Aldridge S, Rayner TF, Lukk M, Pignatelli M, Park TJ, Deaville R, Erichsen JT, Jasinska AJ, Turner JMA, Bertelsen MF, Murchison EP, Flicek P, Odom DT (2015) Enhancer evolution across 20 mammalian species. Cell 160:554–566.  https://doi.org/10.1016/j.cell.2015.01.006 CrossRefPubMedPubMedCentralGoogle Scholar
  160. Wallis JW, Aerts J, Groenen MAM, Crooijmans RPMA, Layman D, Graves TA, Scheer DE, Kremitzki C, Fedele MJ, Mudd NK, Cardenas M, Higginbotham J, Carter J, McGrane R, Gaige T, Mead K, Walker J, Albracht D, Davito J, Yang S-P, Leong S, Chinwalla A, Sekhon M, Wylie K, Dodgson J, Romanov MN, Cheng H, De Jong PJ, Osoegawa K, Nefedov M, Zhang H, McPherson JD, Krzywinski M, Schein J, Hillier L, Mardis ER, Wilson RK, Warren WC (2004) A physical map of the chicken genome. Nature 432:761–764PubMedCrossRefGoogle Scholar
  161. Wang Z, Gerstein M, Snyder M (2009) RNA-Seq: a revolutionary tool for transcriptomics. Nat Rev Genet 10:57–63.  https://doi.org/10.1038/nrg2484 CrossRefPubMedPubMedCentralGoogle Scholar
  162. Wang Y, Gao Y, Imsland F, Gu X, Feng C, Liu R, Song C, Tixier-Boichard M, Gourichon D, Li Q, Chen K, Li H, Andersson L, Hu X, Li N (2012) The crest phenotype in chicken is associated with ectopic expression of HOXC8 in cranial skin. PLoS One 7:e34012.  https://doi.org/10.1371/journal.pone.0034012 CrossRefPubMedPubMedCentralGoogle Scholar
  163. Wang Z, Qu L, Yao J, Yang X, Li G, Zhang Y, Li J, Wang X, Bai J, Xu G, Deng X, Yang N, Wu C (2013) An EAV-HP insertion in 5′ flanking region of SLCO1B3 causes blue eggshell in the chicken. PLoS Genet 9:e1003183.  https://doi.org/10.1371/journal.pgen.1003183 PubMedPubMedCentralCrossRefGoogle Scholar
  164. Wang Q, Li K, Zhang D, Li J, Xu G, Zheng J, Yang N, Qu L (2015) Next-generation sequencing techniques reveal that genomic imprinting is absent in day-old Gallus gallus domesticus brains. PLoS One 10:e0132345.  https://doi.org/10.1371/journal.pone.0132345 CrossRefPubMedPubMedCentralGoogle Scholar
  165. Wang Q, Mank JE, Li J, Yang N, Qu L (2017) Allele-specific expression analysis does not support sex chromosome inactivation on the chicken Z chromosome. Genome Biol Evol 9:619–626.  https://doi.org/10.1093/gbe/evx031 CrossRefPubMedPubMedCentralGoogle Scholar
  166. Warren WC, Clayton DF, Ellegren H, Arnold AP, Hillier LW, Künstner A, Searle S, White S, Vilella AJ, Fairley S, Heger A, Kong L, Ponting CP, Jarvis ED, Mello CV, Minx P, Lovell P, Velho TAF, Ferris M, Balakrishnan CN, Sinha S, Blatti C, London SE, Li Y, Lin Y-C, George J, Sweedler J, Southey B, Gunaratne P, Watson M, Nam K, Backström N, Smeds L, Nabholz B, Itoh Y, Whitney O, Pfenning AR, Howard J, Völker M, Skinner BM, Griffin DK, Ye L, McLaren WM, Flicek P, Quesada V, Velasco G, López-Otín C, Puente XS, Olender T, Lancet D, Smit AFA, Hubley R, Konkel MK, Walker JA, Batzer MA, Gu W, Pollock DD, Chen L, Cheng Z, Eichler EE, Stapley J, Slate J, Ekblom R, Birkhead T, Burke T, Burt D, Scharff C, Adam I, Richard H, Sultan M, Soldatov A, Lehrach H, Edwards SV, Yang S-P, Li X, Graves T, Fulton L, Nelson J, Chinwalla A, Hou S, Mardis ER, Wilson RK (2010) The genome of a songbird. Nature 464:757–762PubMedPubMedCentralCrossRefGoogle Scholar
  167. Warren WC, Hillier LW, Tomlinson C, Minx P, Kremitzki M, Graves T, Markovic C, Bouk N, Pruitt KD, Thibaud-Nissen F, Schneider V, Mansour TA, Brown CT, Zimin A, Hawken R, Abrahamsen M, Pyrkosz AB, Morisson M, Fillon V, Vignal A, Chow W, Howe K, Fulton JE, Miller MM, Lovell P, Mello CV, Wirthlin M, Mason AS, Kuo R, Burt DW, Dodgson JB, Cheng HH (2017) A new chicken genome assembly provides insight into avian genome structure. G3 (Bethesda) 7:109–117.  https://doi.org/10.1534/g3.116.035923 CrossRefGoogle Scholar
  168. Weber JL, May PE (1989) Abundant class of human DNA polymorphisms which can be typed using the polymerase chain reaction. Am J Hum Genet 44:388–396PubMedPubMedCentralGoogle Scholar
  169. Weissensteiner M, Suh A, Repetitive DNA (2019) The dark matter of avian genomics. In: Kraus RHS (ed) Avian genomics in ecology and evolution. Springer, ChamGoogle Scholar
  170. Wilkins AS, Wrangham RW, Fitch WT (2014) The “domestication syndrome” in mammals: a unified explanation based on neural crest cell behavior and genetics. Genetics 197:795–808.  https://doi.org/10.1534/genetics.114.165423 CrossRefPubMedPubMedCentralGoogle Scholar
  171. Wragg D, Mwacharo JM, Alcalde JA, Wang C, Han J-L, Gongora J, Gourichon D, Tixier-Boichard M, Hanotte O (2013) Endogenous retrovirus EAV-HP linked to blue egg phenotype in Mapuche fowl. PLoS One 8:e71393PubMedPubMedCentralCrossRefGoogle Scholar
  172. Wright D, Boije H, Meadows JRS, Bed’hom B, Gourichon D, Vieaud A, Tixier-Boichard M, Rubin C-J, Imsland F, Hallböök F, Andersson L (2009) Copy number variation in intron 1 of SOX5 causes the pea-comb phenotype in chickens. PLoS Genet 5:e1000512.  https://doi.org/10.1371/journal.pgen.1000512 CrossRefPubMedPubMedCentralGoogle Scholar
  173. Xiang H, Gao J, Yu B, Zhou H, Cai D, Zhang Y, Chen X, Wang X, Hofreiter M, Zhao X (2014) Early Holocene chicken domestication in Northern China. Proc Natl Acad Sci USA 111:17564–17569PubMedCrossRefGoogle Scholar
  174. Xiang H, Gao J, Yu B, Hofreiter M, Zhao X (2015) Reply to Peters et al.: further discussions confirm early Holocene chicken domestication in Northern China. Proc Natl Acad Sci USA 112:E2416PubMedCrossRefGoogle Scholar
  175. Yandell M, Ence D (2012) A beginner’s guide to eukaryotic genome annotation. Nat Rev Genet 13:329–342PubMedCrossRefGoogle Scholar
  176. Yates A, Akanni W, Amode MR, Barrell D, Billis K, Carvalho-Silva D, Cummins C, Clapham P, Fitzgerald S, Gil L, Girón CG, Gordon L, Hourlier T, Hunt SE, Janacek SH, Johnson N, Juettemann T, Keenan S, Lavidas I, Martin FJ, Maurel T, McLaren W, Murphy DN, Nag R, Nuhn M, Parker A, Patricio M, Pignatelli M, Rahtz M, Riat HS, Sheppard D, Taylor K, Thormann A, Vullo A, Wilder SP, Zadissa A, Birney E, Harrow J, Muffato M, Perry E, Ruffier M, Spudich G, Trevanion SJ, Cunningham F, Aken BL, Zerbino DR, Flicek P (2016) Ensembl 2016. Nucleic Acids Res 44:D710–D716PubMedCrossRefGoogle Scholar
  177. Zhang F, Wen Y, Guo X (2014a) CRISPR/Cas9 for genome editing: progress, implications and challenges. Hum Mol Genet 23:R40–R46.  https://doi.org/10.1093/hmg/ddu125 CrossRefPubMedGoogle Scholar
  178. Zhang G, Jarvis ED, Gilbert MTP (2014b) A flock of genomes. Science 346(6215):1308–1309PubMedPubMedCentralCrossRefGoogle Scholar
  179. Zhang G, Li C, Li Q, Li B, Larkin DM, Lee C, Storz JF, Antunes A, Greenwold MJ, Meredith RW, Ödeen A, Cui J, Zhou Q, Xu L, Pan H, Wang Z, Jin L, Zhang P, Hu H, Yang W, Hu J, Xiao J, Yang Z, Liu Y, Xie Q, Yu H, Lian J, Wen P, Zhang F, Li H, Zeng Y, Xiong Z, Liu S, Zhou L, Huang Z, An N, Wang J, Zheng Q, Xiong Y, Wang G, Wang B, Wang J, Fan Y, da Fonseca RR, Alfaro-Núñez A, Schubert M, Orlando L, Mourier T, Howard JT, Ganapathy G, Pfenning A, Whitney O, Rivas MV, Hara E, Smith J, Farré M, Narayan J, Slavov G, Romanov MN, Borges R, Machado JP, Khan I, Springer MS, Gatesy J, Hoffmann FG, Opazo JC, Håstad O, Sawyer RH, Kim H, Kim K-W, Kim HJ, Cho S, Li N, Huang Y, Bruford MW, Zhan X, Dixon A, Bertelsen MF, Derryberry E, Warren W, Wilson RK, Li S, Ray DA, Green RE, O’Brien SJ, Griffin D, Johnson WE, Haussler D, Ryder OA, Willerslev E, Graves GR, Alström P, Fjeldså J, Mindell DP, Edwards SV, Braun EL, Rahbek C, Burt DW, Houde P, Zhang Y, Yang H, Wang J, Avian Genome Consortium, Jarvis ED, Gilbert MTP, Wang J (2014c) Comparative genomics reveals insights into avian genome evolution and adaptation. Science 346:1311–1320PubMedPubMedCentralCrossRefGoogle Scholar
  180. Zhang T, Zhang X, Han K, Zhang G, Wang J, Xie K, Xue Q, Fan X (2017) Analysis of long noncoding RNA and mRNA using RNA sequencing during the differentiation of intramuscular preadipocytes in chicken. PLoS One 12:e0172389.  https://doi.org/10.1371/journal.pone.0172389 CrossRefPubMedPubMedCentralGoogle Scholar

Copyright information

© Springer Nature Switzerland AG 2019

Authors and Affiliations

  1. 1.GenPhySEUniversité de Toulouse, INRA, INPT, INP-ENVTCastanet TolosanFrance
  2. 2.Royal (Dick) School of Veterinary Studies, The Roslin Institute, University of Edinburgh, Easter BushMidlothianUK

Personalised recommendations