Skip to main content
NCBI home page
Genetics logoLink to Genetics
. 2004 Mar;166(3):1367–1373. doi: 10.1534/genetics.166.3.1367

Molecular cytogenetic definition of the chicken genome: the first complete avian karyotype.

Julio S Masabanda 1, Dave W Burt 1, Patricia C M O'Brien 1, Alain Vignal 1, Valerie Fillon 1, Philippa S Walsh 1, Helen Cox 1, Helen G Tempest 1, Jacqueline Smith 1, Felix Habermann 1, Michael Schmid 1, Yoichi Matsuda 1, Malcolm A Ferguson-Smith 1, Richard P M A Crooijmans 1, Martien A M Groenen 1, Darren K Griffin 1
PMCID: PMC1470793  PMID: 15082555

Abstract

Chicken genome mapping is important for a range of scientific disciplines. The ability to distinguish chromosomes of the chicken and other birds is thus a priority. Here we describe the molecular cytogenetic characterization of each chicken chromosome using chromosome painting and mapping of individual clones by FISH. Where possible, we have assigned the chromosomes to known linkage groups. We propose, on the basis of size, that the NOR chromosome is approximately the size of chromosome 22; however, we suggest that its original assignment of 16 should be retained. We also suggest a definitive chromosome classification system and propose that the probes developed here will find wide utility in the fields of developmental biology, DT40 studies, agriculture, vertebrate genome organization, and comparative mapping of avian species.

Full Text

The Full Text of this article is available as a PDF (201.9 KB).

Selected References

These references are in PubMed. This may not be the complete list of references from this article.

  1. Ahlroth M. K., Kola E. H., Ewald D., Masabanda J., Sazanov A., Fries R., Kulomaa M. S. Characterization and chromosomal localization of the chicken avidin gene family. Anim Genet. 2000 Dec;31(6):367–375. doi: 10.1046/j.1365-2052.2000.00681.x. [DOI] [PubMed] [Google Scholar]
  2. Auer H., Mayr B., Lambrou M., Schleger W. An extended chicken karyotype, including the NOR chromosome. Cytogenet Cell Genet. 1987;45(3-4):218–221. doi: 10.1159/000132457. [DOI] [PubMed] [Google Scholar]
  3. Buitenhuis A. J., Crooijmans R. P. M. A., Bruijnesteijn van Coppenraet E. S., Veenendaal A., Groenen M. A. M., van der Poel J. J. Improvement of the comparative map of chicken chromosome 13. Anim Genet. 2002 Aug;33(4):249–254. doi: 10.1046/j.1365-2052.2002.00861.x. [DOI] [PubMed] [Google Scholar]
  4. Burt D. W., Bruley C., Dunn I. C., Jones C. T., Ramage A., Law A. S., Morrice D. R., Paton I. R., Smith J., Windsor D. The dynamics of chromosome evolution in birds and mammals. Nature. 1999 Nov 25;402(6760):411–413. doi: 10.1038/46555. [DOI] [PubMed] [Google Scholar]
  5. Burt Dave, Pourquie Olivier. Genetics. Chicken genome--science nuggets to come soon. Science. 2003 Jun 13;300(5626):1669–1669. doi: 10.1126/science.1086231. [DOI] [PubMed] [Google Scholar]
  6. Carter N. P., Ferguson-Smith M. A., Perryman M. T., Telenius H., Pelmear A. H., Leversha M. A., Glancy M. T., Wood S. L., Cook K., Dyson H. M. Reverse chromosome painting: a method for the rapid analysis of aberrant chromosomes in clinical cytogenetics. J Med Genet. 1992 May;29(5):299–307. doi: 10.1136/jmg.29.5.299. [DOI] [PMC free article] [PubMed] [Google Scholar]
  7. Cogburn L. A., Wang X., Carre W., Rejto L., Porter T. E., Aggrey S. E., Simon J. Systems-wide chicken DNA microarrays, gene expression profiling, and discovery of functional genes. Poult Sci. 2003 Jun;82(6):939–951. doi: 10.1093/ps/82.6.939. [DOI] [PubMed] [Google Scholar]
  8. Crooijmans R. P., Dijkhof R. J., Veenendaal T., van der Poel J. J., Nicholls R. D., Bovenhuis H., Groenen M. A. The gene orders on human chromosome 15 and chicken chromosome 10 reveal multiple inter- and intrachromosomal rearrangements. Mol Biol Evol. 2001 Nov;18(11):2102–2109. doi: 10.1093/oxfordjournals.molbev.a003751. [DOI] [PubMed] [Google Scholar]
  9. Crooijmans R. P., Vrebalov J., Dijkhof R. J., van der Poel J. J., Groenen M. A. Two-dimensional screening of the Wageningen chicken BAC library. Mamm Genome. 2000 May;11(5):360–363. doi: 10.1007/s003350010068. [DOI] [PubMed] [Google Scholar]
  10. Dhar P. K., Sonoda E., Fujimori A., Yamashita Y. M., Takeda S. DNA repair studies: experimental evidence in support of chicken DT40 cell line as a unique model. J Environ Pathol Toxicol Oncol. 2001;20(4):273–283. [PubMed] [Google Scholar]
  11. Emara M. G., Kim H. Genetic markers and their application in poultry breeding. Poult Sci. 2003 Jun;82(6):952–957. doi: 10.1093/ps/82.6.952. [DOI] [PubMed] [Google Scholar]
  12. Fillon V., Morisson M., Zoorob R., Auffray C., Douaire M., Gellin J., Vignal A. Identification of 16 chicken microchromosomes by molecular markers using two-colour fluorescence in situ hybridization (FISH). Chromosome Res. 1998 Jun;6(4):307–313. doi: 10.1023/a:1009274925051. [DOI] [PubMed] [Google Scholar]
  13. Fukagawa T., Hayward N., Yang J., Azzalin C., Griffin D., Stewart A. F., Brown W. The chicken HPRT gene: a counter selectable marker for the DT40 cell line. Nucleic Acids Res. 1999 May 1;27(9):1966–1969. doi: 10.1093/nar/27.9.1966. [DOI] [PMC free article] [PubMed] [Google Scholar]
  14. Griffin D. K., Haberman F., Masabanda J., O'Brien P., Bagga M., Sazanov A., Smith J., Burt D. W., Ferguson-Smith M., Wienberg J. Micro- and macrochromosome paints generated by flow cytometry and microdissection: tools for mapping the chicken genome. Cytogenet Cell Genet. 1999;87(3-4):278–281. doi: 10.1159/000015449. [DOI] [PubMed] [Google Scholar]
  15. Habermann F. A., Cremer M., Walter J., Kreth G., von Hase J., Bauer K., Wienberg J., Cremer C., Cremer T., Solovei I. Arrangements of macro- and microchromosomes in chicken cells. Chromosome Res. 2001;9(7):569–584. doi: 10.1023/a:1012447318535. [DOI] [PubMed] [Google Scholar]
  16. Hudson Damien F., Morrison Ciaran, Ruchaud Sandrine, Earnshaw William C. Reverse genetics of essential genes in tissue-culture cells: 'dead cells talking'. Trends Cell Biol. 2002 Jun;12(6):281–287. doi: 10.1016/s0962-8924(02)02281-x. [DOI] [PubMed] [Google Scholar]
  17. Jennen D. G. J., Crooijmans R. P. M. A., Kamps B., Açar R., Veenendaal A., van der Poel J. J., Groenen M. A. M. A comparative map of chicken chromosome 24 and human chromosome 11. Anim Genet. 2002 Jun;33(3):205–210. doi: 10.1046/j.1365-2052.2002.00860.x. [DOI] [PubMed] [Google Scholar]
  18. Jeurissen S. H., Boonstra-Blom A. G., Al-Garib S. O., Hartog L., Koch G. Defence mechanisms against viral infection in poultry: a review. Vet Q. 2000 Oct;22(4):204–208. doi: 10.1080/01652176.2000.9695059. [DOI] [PubMed] [Google Scholar]
  19. Ladjali-Mohammedi K., Bitgood J. J., Tixier-Boichard M., Ponce De Leon F. A. International system for standardized avian karyotypes (ISSAK): standardized banded karyotypes of the domestic fowl (Gallus domesticus). Cytogenet Cell Genet. 1999;86(3-4):271–276. doi: 10.1159/000015318. [DOI] [PubMed] [Google Scholar]
  20. Le Bihan-Duval E., Berri C., Baeza E., Millet N., Beaumont C. Estimation of the genetic parameters of meat characteristics and of their genetic correlations with growth and body composition in an experimental broiler line. Poult Sci. 2001 Jul;80(7):839–843. doi: 10.1093/ps/80.7.839. [DOI] [PubMed] [Google Scholar]
  21. Ledur M. C., Fairfull R. W., McMillan I., Asseltine L. Genetic effects of aging on egg production traits in the first laying cycle of White Leghorn strains and strain crosses. Poult Sci. 2000 Mar;79(3):296–304. doi: 10.1093/ps/79.3.296. [DOI] [PubMed] [Google Scholar]
  22. Liu H. C., Cheng H. H., Tirunagaru V., Sofer L., Burnside J. A strategy to identify positional candidate genes conferring Marek's disease resistance by integrating DNA microarrays and genetic mapping. Anim Genet. 2001 Dec;32(6):351–359. doi: 10.1046/j.1365-2052.2001.00798.x. [DOI] [PubMed] [Google Scholar]
  23. Mariani P., Barrow P. A., Cheng H. H., Groenen M. M., Negrini R., Bumstead N. Localization to chicken chromosome 5 of a novel locus determining salmonellosis resistance. Immunogenetics. 2001 Nov 17;53(9):786–791. doi: 10.1007/s00251-001-0387-7. [DOI] [PubMed] [Google Scholar]
  24. Masabanda J., Friedl R., Sazanov A., Lahti J. M., Li H., Kidd V. J., Fries R. Mapping of five members of the cyclin gene family on chicken chromosomes by FISH. Chromosome Res. 1998 Apr;6(3):231–233. doi: 10.1023/b:chro.0000010409.06615.3f. [DOI] [PubMed] [Google Scholar]
  25. Masabanda Julio S., Griffin Darren K. Generation of chromosome paints: approach for increasing specificity and intensity of signals. Biotechniques. 2003 Mar;34(3):530-2, 534, 536. doi: 10.2144/03343st05. [DOI] [PubMed] [Google Scholar]
  26. Nanda I., Zend-Ajusch E., Shan Z., Grützner F., Schartl M., Burt D. W., Koehler M., Fowler V. M., Goodwin G., Schneider W. J. Conserved synteny between the chicken Z sex chromosome and human chromosome 9 includes the male regulatory gene DMRT1: a comparative (re)view on avian sex determination. Cytogenet Cell Genet. 2000;89(1-2):67–78. doi: 10.1159/000015567. [DOI] [PubMed] [Google Scholar]
  27. Pekarik Vladimir, Bourikas Dimitris, Miglino Nicola, Joset Pascal, Preiswerk Stephan, Stoeckli Esther T. Screening for gene function in chicken embryo using RNAi and electroporation. Nat Biotechnol. 2002 Dec 23;21(1):93–96. doi: 10.1038/nbt770. [DOI] [PubMed] [Google Scholar]
  28. Schmid M., Nanda I., Guttenbach M., Steinlein C., Hoehn M., Schartl M., Haaf T., Weigend S., Fries R., Buerstedde J. M. First report on chicken genes and chromosomes 2000. Cytogenet Cell Genet. 2000;90(3-4):169–218. doi: 10.1159/000056772. [DOI] [PubMed] [Google Scholar]
  29. Shetty S., Griffin D. K., Graves J. A. Comparative painting reveals strong chromosome homology over 80 million years of bird evolution. Chromosome Res. 1999;7(4):289–295. doi: 10.1023/a:1009278914829. [DOI] [PubMed] [Google Scholar]
  30. Smith J., Bruley C. K., Paton I. R., Dunn I., Jones C. T., Windsor D., Morrice D. R., Law A. S., Masabanda J., Sazanov A. Differences in gene density on chicken macrochromosomes and microchromosomes. Anim Genet. 2000 Apr;31(2):96–103. doi: 10.1046/j.1365-2052.2000.00565.x. [DOI] [PubMed] [Google Scholar]
  31. Smith J., Burt D. W. Parameters of the chicken genome (Gallus gallus). Anim Genet. 1998 Aug;29(4):290–294. doi: 10.1046/j.1365-2052.1998.00334.x. [DOI] [PubMed] [Google Scholar]
  32. Suchyta S. P., Cheng H. H., Burnside J., Dodgson J. B. Comparative mapping of chicken anchor loci orthologous to genes on human chromosomes 1, 4 and 9. Anim Genet. 2001 Feb;32(1):12–18. doi: 10.1046/j.1365-2052.2001.00717.x. [DOI] [PubMed] [Google Scholar]
  33. Tatsuda K., Fujinaka K. Genetic mapping of the QTL affecting body weight in chickens using a F2 family. Br Poult Sci. 2001 Jul;42(3):333–337. doi: 10.1080/00071660120055296. [DOI] [PubMed] [Google Scholar]
  34. Telenius H., Carter N. P., Bebb C. E., Nordenskjöld M., Ponder B. A., Tunnacliffe A. Degenerate oligonucleotide-primed PCR: general amplification of target DNA by a single degenerate primer. Genomics. 1992 Jul;13(3):718–725. doi: 10.1016/0888-7543(92)90147-k. [DOI] [PubMed] [Google Scholar]
  35. Wain H. M., Toye A. A., Hughes S., Bumstead N. Targeting of marker loci to chicken chromosome 16 by representational difference analysis. Anim Genet. 1998 Dec;29(6):446–452. doi: 10.1046/j.1365-2052.1998.296374.x. [DOI] [PubMed] [Google Scholar]
  36. Warren Madhuri, Smith Amanda, Partridge Natalie, Masabanda Julio, Griffin Darren, Ashworth Alan. Structural analysis of the chicken BRCA2 gene facilitates identification of functional domains and disease causing mutations. Hum Mol Genet. 2002 Apr 1;11(7):841–851. doi: 10.1093/hmg/11.7.841. [DOI] [PubMed] [Google Scholar]

Articles from Genetics are provided here courtesy of Oxford University Press

RESOURCES