Poultry genome sequences: Progress and outstanding challenges

Cytogenetic and Genome Research

Volumn 134, Issue 1, 2011, Pages 19-26

  Dodgson, J B ^a   Delany, M E ^b   Cheng, H H ^c  

^a 2209 Biomedical and Physical Sciences Bldg ^*  (United States)

^b UNIVERSITY OF CALIFORNIA   (United States)

^c AGRICULTURAL RESEARCH SERVICE   (United States)

Author keywords

BAC contig map; Comparative genome map; Copy number variation; Genome sequence; Genome wide marker assisted selection; Single nucleotide polymorphism

Indexed keywords

CONTIG;

ANIMAL GENETICS; BACTERIAL ARTIFICIAL CHROMOSOME; CHICKEN; CHROMOSOME; FOWL; GENE LINKAGE DISEQUILIBRIUM; GENE MAPPING; GENE SEQUENCE; GENETIC ASSOCIATION; GENETIC CORRELATION; GENETIC GAIN; GENETIC LINKAGE; GENOME; HUMAN; MICROCHROMOSOME; NONHUMAN; PHENOTYPE; POULTRY; PRIORITY JOURNAL; PROTEOMICS; REVIEW; SELECTIVE SWEEP; SEX CHROMOSOME; SINGLE NUCLEOTIDE POLYMORPHISM; TRANSCRIPTOMICS; TURKEY (BIRD);

ANIMALS; BASE SEQUENCE; EVOLUTION, MOLECULAR; GENETIC LINKAGE; GENETIC TECHNIQUES; GENOME; HUMANS; POULTRY;

ANIMALIA; GALLIFORMES;

EID: 79955481394     PISSN: 14248581     EISSN: None     Source Type: Journal    
DOI: 10.1159/000324413     Document Type: Review

References (47)

1. Abplanalp H: Inbred lines as genetic resources of chickens. Poult Sci Rev 4: 29-39 (1992)
2. Abril JF, Castelo R, Guigo R: Comparison of splice sites in mammals and chicken. Genome Res 15: 111-119 (2005)
3. Axelsson E, Webster MT, Smith NG, Burt DW, Ellegren H: Comparison of the chicken and turkey genomes reveals a higher rate of nucleotide divergence on microchromosomes than macrochromosomes. Genome Res 15: 120-125 (2005)
4. Bellott DW, Skeletsky H, Pyntikova T, Mardis ER, Graves T, et al: Convergent evolution of chicken Z and human X chromosomes by expansion and gene acquistion. Nature 466: 612-616 (2010)
5. Bourque G, Zdobnov EM, Bork P, Pevzner PA, Tesler G: Comparative architectures of mammalian and chicken genomes reveal highly variable rates of genomic rearrangements across different lineages. Genome Res 15: 98-110 (2005)
6. Burnside J, Ouyang M, Anderson A, Bernberg E, Lu C, et al: Deep sequencing of chicken microRNAs. BMC Genomics 9: 185 (2008)
7. Burt DW, Bruley C, Dunn IC, Jones CT, Ramage A, et al: The dynamics of chromosome evolution in birds and mammals. Nature 402: 411-413 (1999) (Pubitemid 129544828)
8. Buza TJ, McCarthy FM, Burgess SC: Experimental- confirmation and functional-annotation of predicted proteins in the chicken genome. BMC Genomics 8: 425 (2007)
9. Chaves LD, Harry DE, Reed KM: Genome-wide genetic diversity of 'Nici', the DNA source for the CHORI-260 turkey BAC library and candidate for whole genome sequencing. Anim Genet 40: 348-352 (2009)
10. Chen M, Payne WS, Dunn JR, Chang S, Hunt H, et al: Retroviral delivery of RNA interference against Marek's Disease virus in vivo. Poult Sci 88: 1373-1380 (2009)
11. Dalloul RA, Long JA, Zimin AV, Aslam L, Beal K, et al: Multi-platform next-generation sequencing of the domestic turkey (Meleagris gallopavo) : genome assembly and analysis. PloS Biol 8:e1000475 (2010)
12. Dohner JV: The Encyclopedia of Endangered Livestock and Poultry Breeds (Yale University Press, New Haven 2001)
13. Dorshorst B, Okimoto R, Ashwell C: Genomic regions associated with dermal hyperpigmentation, polydactyly and other morphological traits in the Silkie chicken. J Hered 101: 339-350 (2010)
14. Dorshorst BJ, Ashwell CM: Genetic mapping of the sex-linked barring gene in the chicken. Poult Sci 88: 1811-1817 (2009)
15. Eid J, Fehr A, Gray J, Luong K, Lyle J, et al: Realtime DNA sequencing from single polymerase molecules. Science 323: 133-138 (2009)
16. Elferink MG, Vallée AA, Jungerius AP, Crooijmans RP, Groenen MA: Partial duplication of the PRLR and SPEF2 genes at the late feathering locus in chicken. BMC Genomics 9: 391 (2008)
17. Eriksson J, Larson G, Gunnarsson U, Bed'hom B, Tixier-Boichard M, et al: Identification of the yellow skin gene reveals a hybrid origin of the domestic chicken. PLoS Genet 4:e1000010 (2008)
18. Eriksson J, Rubin CJ, Zody MC, Meadows JRS, Sherwood E, et al: Identification of loci under selection during chicken domestication through whole genome sequencing. Proceedings, Plant and Animal Genomes XVIII, abstract (2010)
19. Genome 10K Community of Scientists: Genome 10K: a proposal to obtain whole-genome sequence for 10,000 vertebrate species. J Hered 100: 659-674 (2009)
20. Geurts AM, Cost GJ, Freyvert Y, Zeitler B, Miller JC, et al: Knockout rats via embryo microinjection of zinc-finger nucleases. Science 325: 433 (2009)
21. Groenen MA, Wahlberg P, Foglio M, Cheng HH, Megens HJ, et al: A high-density SNP-based linkage map of the chicken genome reveals sequence features correlated with recombination rate. Genome Res 19: 510-519 (2009)
22. Gunnarsson U, Hellström AR, Tixier-Boichard M, Minvielle F, Bed'hom B, et al: Mutations in SLC45A2 cause plumage color variation in chicken and Japanese quail. Genetics 175: 867-877 (2007) (Pubitemid 46798283)
23. Heidari M, Huebner M, Kireev D, Silva RF: Transcriptional profiling of Marek's disease virus genes during cytolytic and latent infection. Virus Genes 36: 383-392 (2008)
24. Hubbard SJ, Grafham DV, Beattie KJ, Overton IM, McLaren SR, et al: Transcriptome analysis for the chicken based on 19,626 finished cDNA sequences and 485,337 expressed sequence tags. Genome Res 15: 174-183 (2005
25. International Chicken Genome Sequencing Consortium: Sequence and comparative analysis of the chicken genome provide unique perspectives on vertebrate evolution. Nature 432: 695-716 (2004)
26. International Chicken Polymorphism Map Consortium: a genetic variation map for chicken with 2.8 million single-nucleotide polymorphisms. Nature 432: 717-722 (2004)
27. Kellner WA, Sullivan RT, Carlson BH, Thomas JW: Uprobe: a genome-wide universal probe resource for comparative physical mapping in vertebrates. Genome Res 15: 166-173 (2005)
28. Kerje S, Sharma P, Gunnarsson U, Kim H, Bagchi S, et al: The Dominant white , Dun and Smoky color variants in chicken are associated with insertion/deletion polymorphisms in the PMEL17 gene. Genetics 168: 1507-1518 (2004) (Pubitemid 40007364)
29. Lee MK, Ren CW, Yan B, Cox B, Zhang H-B, et al: Construction and characterization of three BAC libraries for analysis of the chicken genome. Anim Genet 34: 151-152 (2003) (Pubitemid 36412901)
30. Li X, Chiang HI, Zhu J, Dowd SE, Zhou H: Characterization of a newly developed chicken 44K Agilent microarray. BMC Genomics 9: 60 (2008)
31. Lipson D, Raz T, Kieu A, Jones DR, Giladi E, et al: Quantification of the yeast transcriptome by single-molecule sequencing. Nat Biotechnol 27: 652-658 (2009)
32. Liu HC, Soderblom EJ, Goshe MB: A mass spectrometry-based proteomic approach to study Marek's Disease Virus gene expression. J Virol Methods 135: 66-75 (2006) (Pubitemid 43728852)
33. Meuwissen T, Hayes B, Goddard M: Prediction of total genetic value using genome-wide dense marker maps. Genetics 157: 1819-1829 (2001) (Pubitemid 32298846)
34. Muir WM, Wong GK, Zhang Y, Wang J, Groenen MA, et al: Genome-wide assessment of worldwide chicken SNP genetic diversity indicates significant absence of rare alleles in commercial breeds. Proc Natl Acad Sci USA 105: 17312-17317 (2008)
35. Ovcharenko I, Loots GG, Giardine BM, Hou M, Ma J, et al: Mulan: multiple-sequence local alignment and visualization for studying function and evolution. Genome Res 15: 184-194 (2005a)
36. Ovcharenko I, Loots GG, Nobrega MA, Hardison RC, Miller W, Stubbs L: Evolution and functional classification of vertebrate gene deserts. Genome Res 15: 137-145 (2005b)
37. Paulsen M, Khare T, Burgard C, Tierling S, Walter J: Evolution of the Beckwith-Wiedemann syndrome region in vertebrates. Genome Res 15: 146-153 (2005)
38. Rubin CJ, Eriksson J, Ingman M, Jiang L, Meadows J, et al: Whole genome resequencing - a major leap forward in chicken genomics. Proceedings, Plant and Animal Genomes XVII, abstract (2009)
39. Siegel PB, Dodgson JB, Andersson L: Progress from chicken genetics to the chicken genome. Poult Sci 85: 2050-2060 (2006) (Pubitemid 46063976)
40. Suchyta SP, Cheng HH, Burnside J, Dodgson JB: Comparative mapping of chicken anchor loci orthologous to genes on human chromosomes 1, 4 and 9. Anim Genet 32: 12-18 (2001) (Pubitemid 32540300)
41. Velculescu VE, Zhang L, Vogelstein B, Kinzler KW: Serial analysis of gene expression. Science 270: 484-487 (1995)
42. Wallis JW, Aerts J, Groenen M, Crooijmans R, Layman D, et al: A physical map of the chicken genome. Nature 432: 761-764 (2004) (Pubitemid 39656296)
43. Warren WC, Clayton DF, Ellegren H, Arnold AP, Hillier LW, et al: The genome of a songbird. Nature 464: 757-762 (2010)
44. Wicker T, Robertson JS, Schulze SR, Feltus FA, Magrini V, et al: The repetitive landscape of the chicken genome. Genome Res 15: 126-136 (2005)
45. Wold B, Myers RM: Sequence census methods for functional genomics. Nat Methods 5: 19-21 (2008)
46. Wright D, Boije H, Meadows JR, Bed'hom B, Gourichon D, et al: Copy number variation in intron 1 of SOX5 causes the Pea-comb phenotype in chickens. PLoS Genet 5:e1000512 (2009)
47. Yokomine T, Shirohzu H, Purbowasito W, Toyoda A, Iwama H, et al: 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 (2005