Progress from chicken genetics to the chicken genome

Poultry Science

Volumn 85, Issue 12, 2006, Pages 2050-2060

  Siegel, P B ^a   Dodgson, J B ^b   Andersson, L ^c,d  

^a VIRGINIA POLYTECHNIC INSTITUTE AND STATE UNIVERSITY   (United States)

^b Michigan State University ^*  (United States)

^c UPPSALA UNIVERSITY   (Sweden)

^d SWEDISH UNIVERSITY OF AGRICULTURAL SCIENCES   (Sweden)

Author keywords

Animal model; Domestication; Genome mapping; Genome sequence; Quantitative trait loci

Indexed keywords

ANIMALIA;

EID: 33846044696     PISSN: 00325791     EISSN: 15253171     Source Type: Journal    
DOI: 10.1093/ps/85.12.2050     Document Type: Review

References (99)

1. Abplanalp, H. 1992. Inbred lines as genetic resources of chickens. Poult. Sci. Rev. 4:29-39.
2. Abril, J. F., R. Castelo, and R. Guigo. 2005. Comparison of splice sites in mammals and chicken. Genome Res. 15:111-119.
3. Aerts, J., R. Crooijmans, S. Cornelissen, K. Hemmatian, T. Veenendaal, A. Jaadar, J. van der Poel, V. Fillon, A. Vignal, and M. Groenen. 2003. Integration of chicken genomic resources to enable whole-genome sequencing. Cytogenet. Genome Res. 102:297-303.
4. Andersson, L., and M. Georges. 2004. Domestic animal genomics: Deciphering the genetics of complex traits. Nat. Rev. Genet. 5:202-212.
5. Axelsson, E., M. T. Webster, N. G. Smith, D. W. Burt, and H. Ellegren. 2005. Comparison of the chicken and turkey genomes reveals a higher rate of nucleotide divergence on microchromosomes than macrochromosomes. Genome Res. 15:120-125.
6. Bateson, W. 1902. Experiments with poultry. Repts. Evol. Comm. Roy. Soc. 1:87-124.
7. Bateson, W., and R. C. Punnett. 1905-1908. Experimental studies in the physiology of heredity. Pages 42-59 in Classic Papers in Genetics. J. A. Peters, ed. Prentice-Hall, Englewood Cliffs, NJ.
8. Beebe, W. 1926. Pheasants: Their Lives and Homes. Vol. 1. Doubleday, Garden City, NJ.
9. Botstein, D., R. L. White, M. Skolnick, and R. W. Davis. 1980. Construction of a genetic linkage map in man using restriction fragment length polymorphisms. Am. J. Hum. Genet. 32:314-331.
10. Bourque, G., E. M. Zdobnov, P. Bork, P. A. Pevzner, and G. Tesler. 2005. Comparative architectures of mammalian and chicken genomes reveal highly variable rates of genomic rearrangements across different lineages. Genome Res. 15:98-110.
11. Brown, W. R. A., S. J. Hubbard, C. Tickle, and S. A. Wilson. 2003. The chicken as a model for large-scale analysis of vertebrate gene function. Nat. Rev. Genet. 4:87-98.
12. Bumstead, N., and J. Palyga. 1992. A preliminary linkage map of the chicken genome. Genomics 13:690-697.
13. Bumstead, N., J. R. Young, C. Tregaskes, J. Palyga, and P. P. Dunn. 1994. Linkage mapping and partial sequencing of 10 cDNA loci in the chicken. Anim. Genet. 25:337-341.
14. Burnside, J., S. S. Liou, and L. A. Cogburn. 1991. Molecular cloning of the chicken growth hormone receptor complementary deoxyribonucleic acid: Mutation of the gene in sex-linked dwarf chickens. Endocrinology 128:3183-3192.
15. Carlborg, O., L. Jacobsson, P. Ahgren, P. Siegel, and L. Andersson. 2006. Epistasis and the release of genetic variation during long-term selection. Nat. Genet. 38:418-420.
16. Cheng, H. H., and L. B. Crittenden. 1994. Microsatellite markers for genetic mapping in the chicken. Poult. Sci. 73:539-546.
17. Church, G. M. 2006. Genomes for all. Sci. Am. 294:46-54.
18. Clayton, G. A. 1972. Selection plateau in poultry. Ann. Genet. Sel. Anim. 4:561-568.
19. Cohen, S., and R. Levi-Montalcini. 1956. A nerve growth-stimulating factor isolated from snake venom. Proc. Natl. Acad. Sci. USA 42:571-574.
20. Cole, R. K. 1966. Hereditary hypothyroidism in the domestic fowl. Genetics 53:1021-1033.
21. Cooper, M. D., D. A. Raymond, R. D. Peterson, M. A. South, and R. A. Good. 1966. The functions of the thymus system and the bursa system in the chicken. J. Exp. Med. 123:75-102.
22. Copeland, N. G., and N. A. Jenkins. 1991. Development and applications of a molecular genetic linkage map of the mouse genome. Trends Genet. 7:113-118.
23. Crawford, R. D. 1990. Poultry Breeding and Genetics. Elsevier, New York.
24. Crittenden, L. B., L. Provencher, L. Santangelo, I. Levin, H. Abplanalp, R. W. Briles, W. E. Briles, and J. B. Dodgson. 1993. Characterization of a Red Jungle Fowl by White Leghorn backcross reference population for molecular mapping of the chicken genome. Poult. Sci. 72:334-348.
25. Crooijmans, R. P. M. A., A. J. van Kampen, J. J. van der Poel, and M. A. M. Groenen. 1993. Highly polymorphic microsatellite markers in poultry. Anim. Genet. 24:441-443.
26. Crooijmans, R. P. M. A., J. Vrebalov, R. J. M. Dijkhof, J. J. van der Poel, and M. A. M. Groenen. 2000. Two-dimensional screening of the Wageningen chicken BAC library. Mamm. Genome 11:360-363.
27. Cummings, I. W., A. Y. Liu, and W. A. Salser. 1978. Identification of a new chicken α-globin structural gene by complementary DNA cloning. Nature 276:418-419.
28. Darvasi, A. 1998. Experimental strategies for the genetic dissection of complex traits in animal models. Nat. Genet. 18:19-24.
29. Delany, M. 2006. Avian genetic stocks: The high and low points from an academia researcher. Poult. Sci. 85:223-226.
30. Dickerson, G. E. 1955. Genetic slippage in response to selection for multiple objectives. Cold Spring Harb. Symp. Quant. Biol. 20:213-224.
31. Dodgson, J. B. 2003. Chicken genome sequence: A centennial gift to poultry genetics. Cytogenet. Genome Res. 102:291-296.
32. Dodgson, J. B., H. H. Cheng, and R. Okimoto. 1997. DNA marker technology: A revolution in animal genetics. Poult. Sci. 76:1108-1114.
33. Dodgson, J. B., J. Strommer, and J. D. Engel. 1979. The isolation of the chicken β-globin gene and a linked embryonic β-like globin gene from a chicken DNA recombinant library. Cell 17:879-887.
34. Dohner, J. V. 2001. The Encyclopedia of Endangered Livestock and Poultry Breeds. Yale Univ. Press, New Haven, CT.
35. Dunnington, E. A., and P. B. Siegel. 1996. Long-term divergent selection for eight-week body weight in White Plymouth Rock chickens. Poult. Sci. 75:1168-1179.
36. Eitan, Y., and M. Soller. 2004. Selection induced genetic variation. Pages 153-176 in Evolutionary Theory and Processes: Modern Horizons. Papers in Honor of Eviatar Nevo. S. P. Wasser, ed. Kluwer Acad. Pub., The Netherlands.
37. Falconer, D. S. 1992. Early selection experiments. Annu. Rev. Genet. 26:1-14.
38. Groenen, M. A. M., H. H. Cheng, N. Bumstead, B. Benkel, E. Briles, D. W. Burt, T. Burke, J. Dodgson, J. Hillel, S. Lamont, F. A. Ponce de Leon, G. Smith, M. Soller, H. Takahashi, and A. Vignal. 2000. A consensus linkage map of the chicken genome. Genome Res. 10:137-147.
39. Haberfeld, A., A. Cahaner, O. Yoffe, Y. Plotsky, and J. Hillel. 1991. DNA fingerprints of farm animals generated by microsatellite and minisatellite DNA probes. Anim. Genet. 22:299-305.
40. Hale, E. B. 1969. Domestication and the evolution of behavior. Pages 22-42 in The Behavior of Domestic Animals. 2nd ed. E. S. E. Hafez, ed. Lippincott Williams and Wilkins, Baltimore, MD.
41. Herbergs, J., M. Siwek, R. P. M. A. Crooijmans, J. J. van der Poel, and M. A. M. Groenen. 1999. Multicolor fluorescent detection and mapping of AFLP markers in chicken (Gallus domesticus). Anim. Genet. 30:274-285.
42. Hill, W. G. 2005.Acentury of corn selection. Science 307:683-684.
43. Hubbard, S. J., D. V. Grafham, K. J. Beattie, I. M. Overton, S. R. McLaren, M. D. Croning, P. E. Boardman, J. K. Bonfield, J. Burnside, R. M. Davies, E. R. Farrell, M. D. Francis, S. Griffiths-Jones, S. J. Humphray, C. Hyland, C. E. Scott, H. Tang, R. G. Taylor, C. Tickle, W. R. Brown, E. Birney, J. Rogers, and S. A. Wilson. 2005. Transcriptome analysis for the chicken based on 19,626 finished cDNA sequences and 485,337 expressed sequence tags. Genome Res. 15:174-183.
44. Humphries, P., M. Cochet, A. Krust, P. Gerlinger, P. Kourilsky, and P. Chambon. 1977. Molecular cloning of extensive sequences of the in vitro synthesized chicken ovalbumin structural gene. Nucleic Acids Res. 4:2389-2406.
45. Hutt, F. B. 1949. Genetics of the Fowl. McGraw-Hill, New York.
46. International Chicken Genome Sequencing Consortium. 2004. Sequence and comparative analysis of the chicken genome provide unique perspectives on vertebrate evolution. Nature 432:695-716.
47. International Chicken Polymorphism Map Consortium. 2004. A genetic variation map for chicken with 2.8 million singlenucleotide polymorphisms. Nature 432:717-722.
48. International Human Genome Sequencing Consortium. 2001. Initial sequencing and analysis of the human genome. Nature 409:860-921.
49. Jacobsson, L., H.-B. Park, P. Wahlberg, R. Fredriksson, M. Perez-Enciso, P. B. Siegel, and L. Andersson. 2005. Many QTLs with minor additive effects are associated with a large difference in growth between two selection lines in chickens. Genet. Res. 86:115-125.
50. Jull, M. A. 1927. The races of the domestic fowl. Natl. Geogr. Mag. 51:379-452.
51. Kellner, W. A., R. T. Sullivan, B. H. Carlson, and J. W. Thomas. 2005. Uprobe: A genome-wide universal probe resource for comparative physical mapping in vertebrates. Genome Res. 15:166-173.
52. Kerje, S., P. Sharma, U. Gunnarsson, H. Kim, S. Bagchi, R. Fredriksson, K. Schütz, P. Jensen, G. von Heijne, R. Okimoto, and L. Andersson. 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.
53. Khatib, H., E. Genislav, L. B. Crittenden, N. Bumstead, and M. Soller. 1993. Sequence-tagged microsatellite sites as markers in chicken reference and resource populations. Anim. Genet. 24:355-362.
54. Knorr, C., H. H. Cheng, and J. B. Dodgson. 1999. Application of AFLP markers to genome mapping in poultry. Anim. Genet. 30:28-35.
55. Lamon, H. M., and R. R. Slocum. 1927. The Mating and Breeding of Poultry. Orange-Judd Pub., New York.
56. Lee, M.-K., C. W. Ren, B. Yan, B. Cox, H.-B. Zhang, M. N. Romanov, F. G. Sizemore, S. P. Suchyta, E. Peters, and J. B. Dodgson. 2003. Construction and characterization of three BAC libraries for analysis of the chicken genome. Anim. Genet. 34:151-152.
57. Lehrach, H., A. M. Frischauf, D. Hanahan, J. Wozney, F. Fuller, R. Crkvenjakov, H. Boedtker, and P. Doty. 1978. Construction and characterization of a 2.5-kilobase procollagen clone. Proc. Natl. Acad. Sci. USA 75:5417-5421.
58. Lerner, I. A. 1958. The Genetic Basis of Selection. John Wiley & Sons Inc., New York.
59. Levin, I., L. B. Crittenden, and J. B. Dodgson. 1994a. Mapping DNA polymorphisms using PCR primers derived from the sequence of an avian CR1 element. J. Hered. 85:73-78.
60. Levin, I., L. Santangelo, H. Cheng, L. B. Crittenden, and J. B. Dodgson. 1994b. An autosomal genetic linkage map of the chicken. J. Hered. 85:79-85.
61. Lewis, H. R. 1977. America's debt to the hen. Natl. Geogr. Mag. 51:453-468.
62. Maniatis, T., R. C. Hardison, E. Lacy, J. Lauer, C. O'Connell, D. Quon, G. K. Sim, and A. Efstratiadis. 1978. The isolation of structural genes from libraries of eukaryotic DNA. Cell 15:687-701.
63. McBride, G., I. P. Parer, and F. Foenander. 1969. The social organization and behaviour of feral domestic fowl. Anim. Behav. Monogr. 2:127-181.
64. McClements, W., and A. M. Skalka. 1977. Analysis of chicken ribosomal RNA genes and construction of λ hybrids containing gene fragments. Science 196:195-197.
65. McPherson, J. D., J. Dodgson, R. Krumlauf, and O. Pourquie. 2002. Proposal to sequence the genome of the chicken. http://www.genome.gov/Pages/ Research/Sequencing/SeqProposals/Chicken_Genome.pdf Accessed March 30, 2006.
66. McReynolds, L. A., J. J. Monahan, D. W. Bendure, S. L. Woo, G. V. Paddock, W. Salser, J. Dorson, R. E. Moses, and B. W. O'Malley. 1977. The ovalbumin gene. Insertion of ovalbumin gene sequences in chimeric bacterial plasmids. J. Biol. Chem. 252:1840-1843.
67. Meuwissen, T., B. Hayes, and M. Goddard. 2001. Prediction of total genetic value using genome-wide dense marker maps. Genetics 157:1819-1829.
68. Moran, C. 1993. Microsatellite repeats in pig (Sus domestica) and chicken (Gallus domesticus) genomes. J. Hered. 84:274-280.
69. Morisson, M., A. Lemière, S. Bosc, M. Galan, F. Plisson-Petit, P. Pinton, C. Delcros, K. Fève, F. Pitel, V. Fillon, M. Yerle, and A. Vignal. 2002. ChickRH6: A chicken whole-genome radiation hybrid panel. Genet. Sel. Evol. 34:521-533.
70. Morisson, M., F. Pitel, V. Fillon, A. Pouzadoux, R. Berge, J. P. Vit, R. Zoorob, C. Auffray, J. Gellin, and A. Vignal. 1998. Integration of chicken cytogenetic and genetic maps: 18 new polymorphic markers isolated from BAC and PAC clones. Anim. Genet. 29:348-355.
71. Muir, W. M., and S. E. Aggrey. 2003. Poultry Genetics, Breeding and Biotechnology. CABI Pub., Cambridge, MA.
72. Murayama, H. 1927. Fowl of the the old and new world. Natl. Geogr. Mag. 51:I-XVI.
73. Ovcharenko, I., G. G. Loots, B. M. Giardine, M. Hou, J. Ma, R. C. Hardison, L. Stubbs, and W. Miller. 2005a. Mulan: Multiple-sequence local alignment and visualization for studying function and evolution. Genome Res. 15:184-194.
74. Ovcharenko, I., G. G. Loots, M. A. Nobrega, R. C. Hardison, W. Miller, and L. Stubbs. 2005b. Evolution and functional classification of vertebrate gene deserts. Genome Res. 15:137-145.
75. Park, H.-B., L. Jacobsson, P. Wahlberg, P. B. Siegel, and L. Andersson. 2006. QTL analysis of body composition and metabolic traits in an intercross between chicken lines divergently selected for growth. Physiol. Genomics. 25:216-223.
76. Paulsen, M., T. Khare, C. Burgard, S. Tierling, and J. Walter. 2005. Evolution of the Beckwith-Wiedemann syndrome region in vertebrates. Genome Res. 15:146-153.
77. Pennisi, E. 2001. So many choices, so little money. Science 294:82-85.
78. Perler, F., A. Efstratiadis, P. Lomedico, W. Gilbert, R. Kolodner, and J. B. Dodgson. 1980. The evolution of genes: The chicken preproinsulin gene. Cell 20:555-566.
79. Punnett, R. G. 1923. Heredity in Poultry. MacMillan and Co., London, UK.
80. Ren, C., M. K. Lee, B. Yan, K. Ding, B. Cox, M. N. Romanov, J. A. Price, J. B. Dodgson, and H.-B. Zhang. 2003. A BAC-based physical map of the chicken genome. Genome Res. 13:2754-2758.
81. Ross, M. T., S. LaBrie, J. McPherson, and V. P. Stanton. 1999. Screening large-insert libraries by hybridization. Pages 5.6.1-5.6.52 in Current Protocols in Human Genetics. N. C. Dracopoli, J. L. Haines, B. R. Korf, D. T. Moir, C. C. Morton, C. E. Seidman, J. G. Seidman, and D. R. Smith, ed. John Wiley & Sons Inc., New York.
82. Rous, P. 1911. A sarcoma of the fowl transmissible by an agent separable from the tumor cells. J. Exp. Med. 13:397-411.
83. Sippel, A. E., H. Land, W. Lindenmaier, M. C. Nguyen-Huu, T. Wurtz, K. N. Timmis, K. Giesecke, and G. Schütz. 1978. Cloning of chicken lysozyme structural gene sequences synthesized in vitro. Nucleic Acids Res. 5:3275-3294.
84. Smith, P., and C. Daniel. 1975. The Chicken Book. Little Brown, New York.
85. Smith, E. J., L. A. Lyons, H. H. Cheng, and S. P. Suchyta. 1997. Comparative mapping of the chicken genome using the East Lansing reference population. Poult. Sci. 76:743-747.
86. Smyth, J. R. 1996. Genetics of plumage, skin and pigmentation in chickens. Pages 109-167 in Poultry Breeding and Genetics, R. D. Crawford, ed. Elsevier, New York, NY.
87. Soller, M., S. Weigend, M. N. Romanov, J. C. M. Dekkers, and S. J. Lamont. Strategies to assess structural variation in the chicken genome and its associations with biodiversity and biological performance. Poult. Sci. 85:2061-2078
88. Spencer, J. L., J. S. Gavora, and R. S. Gowe. 1979. Effects of selection for high egg production in chickens on shedding of lymphoid leucosis virus and gs antigen into eggs. Poult. Sci. 58:279-284.
89. Stéhelin, D., H. E. Varmus, J. M. Bishop, and P. K. Vogt. 1976. DNA related to the transforming gene(s) of avian sarcoma virus is present in normal avian DNA. Nature 260:170-173.
90. Stevens, L. 1991. Genetics and Evolution of the Domestic Fowl. Cambridge Univ. Press, New York.
91. Theos, A., S. Truschel, G. Raposo, and M. Marks. 2005. The Silver locus product Pmel17/gp100/Silv/ME20: Controversial in name and in function. Pigment Cell Res. 18:322-336.
92. Van Laere, A. S., M. Nguyen, M. Braunschweig, C. Nezer, C. Collette, L. Moreau, A. L. Archibald, C. S. Haley, N. Buys, G. Andersson, M. Georges, and L. Andersson. 2003. Positional identification of a regulatory mutation in IGF2 causing a major QTL effect on muscle growth in the pig. Nature 425:832-836.
93. Vogt, P. K. 1997. Historical introduction to the general properties of retroviruses. Pages 1-25 in Retroviruses. J. M. Coffin, S. H. Hughes, and H. E. Varmus, ed. Cold Spring Harbor Laboratory Press, NY.
94. Wallis, J. W., J. Aerts, M. Groenen, R. Crooijmans, D. Layman, T. Graves, D. Scheer, C. Kremitzki, J. Higgenbotham, T. Gaige, K. Mead, J. Walker, D. Albracht, J. Divito, S.-P. Yang, S. Leong, A. Chinwalla, L. Hillier, M. Sekhon, J. Dodgson, M. N. Romanov, H. Cheng, P. J. de Jong, H. Zhang, J. D. McPherson, M. Krzywinski, J. Schein, E. Mardis, R. Wilson, and W. C. Warren. 2004. A physical map of the chicken genome. Nature 432:761-764.
95. Warren, W., L. Hillier, E. Mardis, and R. Wilson. 2005. Additional sequencing of the chicken genome. http://www.genome.gov/Pages/Research/ Sequencing/SeqProposals/ChickenFinishingSeq.pdf Accessed March 30, 2006.
96. West, B., and B. X. Zhou. 1989. Did the chickens go North? New evidence for domestication. World's Poult. Sci. J. 45:205-218.
97. Wick, G., L. Andersson, K. Hala, M. E. Gershwin, C. F. Selmi, G. F. Erf, S. J. Lamont, and R. Sgonc. 2006. Avian models with spontaneous autoimmune diseases. Adv. Immunol. (in press).
98. Wicker, T., J. S. Robertson, S. R. Schulze, F. A. Feltus, V. Magrini, J. A. Morrison, E. R. Mardis, R. K. Wilson, D. G. Peterson, A. H. Paterson, and R. Ivarie. 2005. The repetitive landscape of the chicken genome. Genome Res. 15:126-136.
99. Yokomine, T., H. Shirohzu, W. Purbowasito, A. Toyoda, H. Iwama, K. Ikeo, T. Hori, S. Mizuno, M. Tsudzuki, Y. Matsuda, M. Hattori, Y. Sakaki, and H. Sasaki. 2005. Structural and functional analysis of a 0.5-Mb chicken region orthologous to the imprinted mammalian Ascl2/Mash2-Igf2-H19 region. Genome Res. 15:154-165.