The Application of Zoo-Fish Technique for Analysis of Chromosomal Rearrangements in the Equidae Family

Klaudia Pawlina 1  and Monika Bugno-Poniewierska
  • 1 National Research Institute of Animal Production, Laboratory of Genomics, 32-083 Balice n. Kraków, Poland
  • 2 Department of Genetics, University of Rzeszów, Sokołowska 26, 36-100 Kolbuszowa, Poland

The Application of Zoo-Fish Technique for Analysis of Chromosomal Rearrangements in the Equidae Family

Genome analysis is necessary to trace evolutionary rearrangements and relationships between species. Initially, to this end, the tools of classical cytogenetics were used but along with the development of molecular cytogenetics methods it became possible to analyse the genome more thoroughly. One of the widely used methods is fluorescence in situ hybridization (FISH) and its different types. Zoo-FISH, or cross-species chromosome painting, which uses painting probes specific for whole chromosomes, enables detecting homologous synteny blocks, the occurrence of which is evidence that species share a common ancestry and are related. Zoo-FISH technique is complemented by FISH with probes specific to chromosome arms or repetitive sequences (telomeres, centromeres), which provide additional information about karyotype organization, as well as karyotype polymorphism and conservation. Another method used is FISH with gene-specific probes, which enable the localization of single loci, thus making it possible to determine linkages between genes and verify data obtained after using painting probes in Zoo-FISH technique. Because of its diverse karyotype and rapid karyotypic evolution, the Equidae family is an ideal object of study using a number of methods based on in situ hybridization, which, in turn, enables information to be obtained at many levels of DNA organization.

If the inline PDF is not rendering correctly, you can download the PDF file here.

  • Brinkmeyer - Langford C., Raudsepp T., Gustafson - Seabury A., Chowdhary B. P. (2008). A BAC contig map over the proximal approximately 3.3 Mb region of horse chromosome 21. Cytogenet. Genome Res., 120: 164-172.

  • Bugno M., Klukowka - Rotzler J., Słota E., Witarski W., Gerber V., Leeb T. (2007). Fluorescent in situ hybridization mapping of the epidermal growth factor receptor gene in donkey. J. Anim. Breed. Genet., 124: 172-174.

  • Bugno M., Słota E., Witarski W., Gerber V., Klukowska - Roetzler J. (2009). Interleukin 4 receptor alpha (IL4R) and calcium-activated chloride channel 1 (CLCA1) genes map to donkey chromosome. Hereditas, 146 (3): 118-121.

  • Bugno - Poniewierska M., WnukM., Witarski W., Słota E. (2009). The fluorescence in situ study of highly repeated DNA sequences in domestic horse (Equus caballus) and domestic donkey (Equus asinus) - Advantages and limits of usefulness in phylogenetic analyses. J. Anim. Feed. Sci., 18: 723-732.

  • Bugno - Poniewierska M., Pawlina K., Dardzińska A., ZąbekT., Słota E. Klu - kowka - Rötzler J. (2010). FISH mapping of six genes responsible for development of the nervous and skeletal systems on donkey (Equus asinus) chromosomes. Hereditas, 147: 132-135.

  • Bush G. L., Case S. M., Wilson A. C., Paton J. L. (1977). Rapid speciation and chromosomal evolution in mammals. Proc. Natl Acad. Sci. USA, 74: 3942-3946.

  • Chowdhary B. P., Raudsepp P. (2001). Chromosome painting in farm, pet and wild animals. Meth. Cell Sci., 23: 37-55.

  • Chowdhary B. P., Fronicke L., Gustavsson I., Scherthan H. (1996). Comparative analysis of the cattle and human genomes: detection of ZOO-FISH and gene mapping-based chromosomal homologies. Mamm. Genome, 7: 297-302.

  • Davis B. W., Raudsepp T., Pearks Wilkerson A. J., Agarwala R., Schäffer A. A., Houck M., Chowdhary B. P., Murphy W. J. (2009). A high-resolution cat radiation hybrid and integrated FISH mapping resource for phylogenomic studies across Felidae. Genomics, 93: 299-304.

  • Dobigny G., Ducroz J. F., Robinson T. J., Volobouev V. (2004). Cytogenetics and cladistics. Syst. Biol., 53: 470-484.

  • Dranchak P. K., Ekenstedt K. J., Valberg S. J., Chowdhary B. P., Raudsepp T., Mickelson J. R. (2006). Chromosomal assignments for the equine AMPK family genes. Anim. Genet., 37: 293-294.

  • Faraut T. (2008). Addressing chromosome evolution in the whole-genome sequence era. Chromosome Res., 16: 5-16.

  • Ferguson - Smith M. A., Trifonov V. (2007). Mammalian karyotype evolution. Nat. Rev. Genet., 8: 950-962.

  • Glas R., Marshall Graves J. A., Toder R., Ferguson - Smith M., O'Brien P. C. (1999). Cross-species chromosome painting between human and marsupial directly demonstrates the ancient region of the mammalian X. Mamm. Genome, 10: 1115-1116.

  • Gomez - Fabre P. M., Helou K., Stahl F. (2002). Predictions based on the rat-mouse comparative map provide mapping information on over 6000 new rat genes. Mamm. Genome, 13: 189-193.

  • Graphodatsky A. S., Yang F., O'Brien P. C. M., Serdukova N., Milne B. S., Trifo - nov V., Ferguson - Smith M. A. (2000). A comparative chromosome map of the Arctic fox, red fox and dog defined by chromosome painting and high resolution G banding. Chromosome Res., 8: 253-263.

  • Graphodatsky S. A., Perelman P. L., Sokolovskaya N. V., Beklemisheva V. R., Serdukova N. A., Dobigny G., O'Brien S. J., Ferguson - Smith M. A., Yang F. (2008). Phylogenomics of the dog and fox family (Canidae, Carnivora) revealed by chromosome painting. Chromosome Res., 16: 129-143.

  • Hameister H., Klett C., Bruch J., Dixkens C., Vogel W., Christensen K. (1997). Zoo-FISH analysis: the American mink (Mustela vison) closely resembles the cat karyotype. Chromosome Res., 5: 5-11.

  • Hardison R. C. (2003). Comparative genomics. PLoS Biology, 1, p. E58.

  • Helou K., Walentinsson A., Levan G., Ståhl F. (2001). Between rat and mouse zoo-FISH reveals 49 chromosomal segments that have been conserved in evolution. Mamm. Genome, 12: 765-771.

  • Hu Z., Rohrer G. A., Stone R. T., Murtaugh M. P., Beattie C. W. (1997). Genomic mapping of chemokine and transforming growth factor genes in swine. Mamm. Genome, 8: 246-249.

  • Jauch A., Wienberg J., Stanyon R., Arnold N., Tofanelli S., Ishida T., Cremer T. (1992). Reconstruction of genomic rearrangements in great apes and gibbons by chromosome painting. Proc. Natl. Acad. Sci. USA, 89: 8611-8615.

  • Kemkemer C., Kohn M., Cooper D. N., Froenicke L., Högel J., Hameister H., Kehrer - Sawatzki H. (2009). Gene synteny comparisons between different vertebrates provide new insights into breakage and fusion events during mammalian karyotype evolution. BMC Evol. Biol., 9, p. 84.

  • Mäkinen A., Gustavsson I. (1982). A comparative chromosome-banding study in the silver fox, the blue fox, and their hybrids. Hereditas, 97: 289-297.

  • Milenkovic D., Oustry - Vaiman A., Lear T. L., Billault A., Mariat D., Piumi F., Schibler L., Cribiu E., Guerin G. (2002). Cytogenetic localization of 136 genes in the horse: comparative mapping with the human genome. Mamm. Genome, 13: 524-534.

  • Murphy W. J., Larkin D. M., Everts - van der Wind A., Bourque G., Tesler G., Auvil L., Beever J. E., Chowdhary B. P., Galibert F., Gatzke L., Hitte C., Meyers S. N., Milan D., Ostrander E. A., Pape G., Parker H. G., Raudsepp T., Rogatcheva M. B., Schook L. B., Skow L. C. (2005). Dynamics of mammalian chromosome evolution inferred from multispecies comparative maps. Science, 309: 613-617.

  • Musilova P., Kubickova S., Zrnova E., Horin P., Vahala J., Rubes J. (2007). Karyotypic relationships among Equus grevyi, Equus burchelli and domestic horse defined using horse chromosome arm-specific probes. Chromosome Res., 15: 807-813.

  • Musilova P., Kubickova S., Horin P., Vodička R., Rubes J. (2009). Karyotypic relationships in Asiatic asses (kulan and kiang) as defined using horse chromosome arm-specific and region-specific probes. Chromosome Res., 17: 783-790.

  • Myka J. L., Lear T. L., Houck M. L., Ryder O. A., Bailey E. (2003 a). FISH analysis comparing genome organization in the domestic horse (Equus caballus) to that of the Mongolian wild horse (E. przewalskii). Cytogenet. Genome Res., 102: 222-225.

  • Myka J. L., Lear T. L., Houck M. L., Ryder O. A., Bailey E. (2003b). Homologous fission event(s) implicated for chromosomal polymorphisms among five species in the genus Equus. Cytogenet. Genome Res., 102: 217-221.

  • Nash W. G., Menninger J. C., Wienberg J., Padilla - Nash H. M., O'Brien S. J. (2001). The pattern of phylogenomic evolution of the Canidae. Cytogenet. Cell Genet., 95: 210-224.

  • Ng M. P., Vergara I. A., Frech C., Chen Q., Zeng X., Pei J., Chen N. (2009). OrthoClusterDB: an online platform for synteny blocks. BMC Bioinformatics, 10, p. 192.

  • Nie W., Wang J., Perelman P., Graphodatsky A. S., Yang F. (2003). Comparative chromosome painting defines the karyotypic relationships among the domestic dog, Chinese raccoon dog and Japanese raccoon dog. Chromosome Res., 11: 735-740.

  • Passarge E., Horsthemke B., Farber R. A. (1999). Incorrect use of the term synteny. Nat. Genet., 23, p. 387.

  • Perelman P. L., Graphodatsky A. S., Serdukova N. A., Nie W., Alkalaeva E. Z., Fu B., Robinson T. J., Yang F. (2005). Karyotypic conservatism in the suborder Feliformia (Order Carnivora). Cytogenet. Genome Res., 108: 348-354.

  • Pevzner P., Tesler G. (2003). Genome rearrangements in mammalian evolution: lessons from human and mouse genomes. Genome Res., 13: 37-45.

  • Power M. M. (1984). Comparative R banding in the horse, donkey and zebra. Proc. of the 6th European Colloquium on Cytogenetics of Domestic Animals, July 16-20, Zurich, Switzerland, pp. 145-155.

  • Prakash B., Olsaker I., Gustavsson I., Chowdhary B. P. (1997). FISH mapping of three bovine cosmids to cattle, goat, sheep and buffalo X chromosomes. Hereditas, 126: 115-119.

  • Raudsepp T., Chowdhary B. P. (1999). Construction of chromosome-specific paints for metaand submetacentric autosomes and the sex chromosomes in the horse and their use to detect homologous chromosomal segments in the donkey. Chromosome Res., 6: 103-114.

  • Raudsepp T., Chowdhary B. P. (2001). Correspondence of human chromosomes 9, 12, 15, 16, 19 and 20 with donkey chromosomes refines homology between horse and donkey karyotypes. Chromosome Res., 9: 623-629.

  • Raudsepp T., Fronicke L., Scherthan H., Gustavsson I., Chowdhary B. P. (1996). Zoo-FISH delineates conserved chromosomal segments in horse and man. Chromosome Res., 4: 218-225.

  • Raudsepp T., Otte K., Rozell B., Chowdhary B. P. (1997). FISH mapping of the IGF2 gene in horse and donkey - detection of homoeology with HSA11. Mamm. Genome, 8: 569-572.

  • Raudsepp T., Kijas J., Godard S., Guerin G., Andersson L., Chowdhary B. P. (1999). Comparison of horse chromosome 3 with donkey and human chromosomes using cross-species painting and heterologous FISH mapping. Mamm. Genome, 10: 277-282.

  • Raudsepp T., Mariat D., Guerin G., Chowdhary B. P. (2001). Comparative FISH mapping of 32 loci reveals new homologous regions between donkey and horse karyotypes. Cytogenet. Cell Genet., 94: 180-185.

  • Raudsepp T., Lear T. L., Chowdhary B. P. (2002). Comparative mapping in equids: the asine X chromosome is rearranged compared to horse and Hartmann's mountain zebra. Cytogenet. Genome Res., 96: 206-209.

  • Raudsepp T., Lee E-J., Kata S. R., Brinkmeyer C., Mickelson J. R., Skow L. C., Womack J. E., Chowdhary B. P. (2004). Exceptional conservation of horse-human gene order on X chromosome revealed by high-resolution radiation hybrid mapping. Proc. Natl. Acad. Sci. USA, 101: 2386-2391.

  • Richard F., Messaoudi C., Bonnet - Garnier A., Lombard M., Dutrillaux B. (2003). Highly conserved chromosomes in an Asian squirrel (Menetes berdmorei, Rodentia: Sciuridae) as demonstrated by ZOO-FISH with human probes. Chromosome Res., 11: 597-603.

  • Ropiquet A., Hassanin A., Pagacova E., Gerbault - Sereau M., Cernohorska H., Kubickova S., Bonillo C., Rubes J., Robinson T. J. (2010). A paradox revealed: karyo-type evolution in the four-horned antelope occurs by tandem fusion (Mammalia, Bovidae, Tetracerus quadricornis). Chromosome Res., 18: 277-286.

  • Ryder O. A., Epel N. C., Benirschke K. (1978). Chromosome banding studies of the Equidae. Cytogenet. Cell Genet., 20: 323-350.

  • Santani A., Raudsepp T., Chowdhary B. P. (2002). Interstitial telomeric sites and NORs in Hartmann's zebra (Equus zebra hartmannae) chromosomes. Chromosome Res., 10: 527-534.

  • Scherthan H., Cremer T., Arnason U., Weier H. U., Lima - de - Faria A., Frönicke L. (1994). Comparative chromosome painting discloses homologous segments in distantly related mammals. Nat. Genet., 6: 342-347.

  • Sun H. F., Ernst C. W., Yerle M., Pinton P., Rothschild M. F., Chardon P., Roger - Gaillard C., Tuggle C. K. (1999). Human chromosome 3 and pig chromosome 13 show complete synteny conservation but extensive gene-order differences. Cytogenet. Cell Genet., 85: 273-278.

  • Szczerbal I., Chmurzyńska A., Switonski M. (2007). Cytogenetic mapping of eight genes encoding fatty acid binding proteins (FABPs) in the pig genome. Cytogenet. Genome Res., 118: 63-66.

  • Thomas R., Breen M., Langford C. F., Binns M. M. (1999). Zoo-FISH analysis of dog chromosome 5: identification of conserved synteny with human and cat chromosomes. Cytogenet. Cell Genet., 87: 4-10.

  • Trifonov V., Yang F., Ferguson - Smith M. A., Robinson T. J. (2003). Cross-species chromosome painting in the Perissodactyla: delimitation of homologous regions in Burchell's zebra (Equus burchellii) and the white (Ceratotherium simum) and black rhinoceros (Diceros bicornis). Cytogenet. Genome Res., 103: 104-110.

  • Wichman H. A., Payne C. T., Ryder O. A., Hamilton M. J., Maltbie M., Baker R. J. (1991). Genomic distribution of heterochromatin sequences in Equids: Implications in rapid chromosomal evolution. J. Hered., 82: 369-377.

  • Yang F., FuB., O'Brien P. C., Robinson T. J., Ryder O. A., Ferguson - Smith M. A. (2003). Karyotypic relationships of horses and zebras: results of crossspecies chromosome painting. Cytogenet. Genome Res., 102: 235-243.

  • Yang F., Fu B., O'Brien P. C. M., Nie W., Ryder O. A., Ferguson - Smith M. A. (2004). Refined genome-wide comparative map of the domestic horse, donkey and human based on cross species chromosome painting: insight into the occasional fertility of mules. Chromosome Res., 12: 65-76.


Journal + Issues