Chromosome Research

, Volume 19, Issue 4, pp 493–506 | Cite as

Comparative FISH mapping of Daucus species (Apiaceae family)

  • Marina Iovene
  • Pablo F. Cavagnaro
  • Douglas Senalik
  • C. Robin Buell
  • Jiming Jiang
  • Philipp W. SimonEmail author


The cytogenetic characterization of the carrot genome (Daucus carota L., 2n = 18) has been limited so far, partly because of its somatic chromosome morphology and scant of chromosome markers. Here, we integrate the carrot linkage groups with pachytene chromosomes by fluorescent in situ hybridization (FISH) mapping genetically anchored bacterial artificial chromosomes (BACs). We isolated a satellite repeat from the centromeric regions of the carrot chromosomes, which facilitated the study of the pachytene-based karyotype and demonstrated that heterochromatic domains were mainly confined to the pericentromeric regions of each chromosome. Chromosome-specific BACs were used to: (1) physically locate genetically unanchored DNA sequences, (2) reveal relationships between genetic and physical distances, and (3) address chromosome evolution in Daucus. Most carrot BACs generated distinct FISH signals in 22-chromosome Daucus species, providing evidence for syntenic chromosome segments and rearrangements among them. These results provide a foundation for further cytogenetic characterization and chromosome evolution studies in Daucus.


Carrot wild Daucus species integration map comparative FISH mapping chromosome evolution 



Bacterial artificial chromosome




Fluorescent in situ hybridization


Linkage group


Sequence-tagged site marker


Simple sequence repeats


Sequence-characterized amplified region



We thank Dr. Jiri Macas for his invaluable help in the analysis of the BAC sequences generated in this work.

Supplementary material

10577_2011_9202_MOESM1_ESM.ppt (9.3 mb)
ESM 1 (ppt 9515 kb)
10577_2011_9202_MOESM2_ESM.txt (142 kb)
ESM 2 (TXT 141 kb)


  1. Arumuganathan K, Earle ED (1991) Nuclear DNA content of some important plant species. Plant Mol Biol Rep 9:208–218CrossRefGoogle Scholar
  2. Barton DW (1950) Pachytene morphology of the tomato chromosome complement. Am J Bot 37:639–643CrossRefGoogle Scholar
  3. Boiteux LS, Belter JG, Roberts PA, Simon PW (2000) RAPD linkage map of the genomic region encompassing the root-knot nematode (Meloidogyne javanica) resistance locus in carrot. Theor Appl Genet 100:439–446CrossRefGoogle Scholar
  4. Bowman M, Senalik D, Matvienko M, Van Deynze A, Simon PW (2010) Developing genomic resources for the Apiaceae. In: Plant & Animal Genomes XVIII Conference, San Diego, CA, 9–13 January 2010. P037.Google Scholar
  5. Cavagnaro PF, Chung SM, Szklarczyk M et al (2009) Characterization of a deep-coverage carrot (Daucus carota L.) BAC library and initial analysis of BAC-end sequences. Mol Genet Genomics 281:273–288PubMedCrossRefGoogle Scholar
  6. Cavagnaro PF, Chung SM, Manin S, Atkins AE, Simon PW (2010) New carrot microsatellites—linkage mapping, diversity analysis and transferability to other Apiaceae. In: Plant & Animal Genomes XVIII Conference, San Diego, CA, 9–13 January 2010. P038.Google Scholar
  7. Cheng Z, Presting GG, Buell CR, Wing RA, Jiang J (2001a) High-resolution pachytene chromosome mapping of bacterial artificial chromosomes anchored by genetic markers reveals the centromere location and the distribution of genetic recombination along chromosome 10 of rice. Genetics 157:1749–1757PubMedGoogle Scholar
  8. Cheng Z, Buell CR, Wing RA, Gu M, Jiang J (2001b) Toward a cytological characterization of the rice genome. Genome Res 11:2133–2141PubMedCrossRefGoogle Scholar
  9. Dempsey E (1994) Traditional analysis of maize pachytene chromosomes. In: Freeling M, Walbot V (eds) The maize handbook. Springer, New York, pp 432–441Google Scholar
  10. Dong F, Song J, Naess SK, Helgeson JP, Gebhardt G, Jiang J (2000) Development and applications of a set of chromosome specific cytogenetic DNA markers in potato. Theor Appl Genet 101:1001–1007CrossRefGoogle Scholar
  11. Dubcovsky J, Dvořák J (1995) Ribosomal RNA multigene loci: Nomads of the Triticeae genomes. Genetics 140:1367–1377PubMedGoogle Scholar
  12. Figueroa DM, Bass HW (2010) A historical and modern perspective on plant cytogenetics. Brief Funct Genomics 9:92–105Google Scholar
  13. Fonsêca A, Ferreira J, Barros R, dos Santos T et al (2010) Cytogenetic map of common bean (Phaseolus vulgaris L.). Chromosome Res 18:487–502PubMedCrossRefGoogle Scholar
  14. Fransz P, Armstrong A, Alonso-Blanco C, Fischer TC, Torres-Ruiz RA, Jones G (1998) Cytogenetics for the model system Arabidopsis thaliana. Plant J 13:867–876PubMedCrossRefGoogle Scholar
  15. Gerlach WL, Bedrock JR (1979) Cloning and characterization of ribosomal RNA genes from wheat and barley. Nucleic Acids Res 109:1346–1352Google Scholar
  16. Gerlach WL, Dyer TA (1980) Sequence organization of the repeating units in the nucleus of wheat which contain 5S rRNA genes. Nucleic Acids Res 8:4851–4865PubMedCrossRefGoogle Scholar
  17. Grzebelus D, Jagosz B, Simon PW (2007) The DcMaster transposon display maps polymorphic insertion sites in the carrot (Daucus carota L.) genome. Gene 390:67–74PubMedCrossRefGoogle Scholar
  18. Han YH, Zhang ZH, Liu CX et al (2009) Centromere repositioning in cucurbit species: implication of the genomic impact from centromere activation and inactivation. Proc Nat Acad Sci USA 106:14937–14941PubMedCrossRefGoogle Scholar
  19. Iovene M, Grzebelus E, Carputo D, Jiang J, Simon PW (2008a) Major cytogenetic landmarks and karyotype analysis in Daucus carota and other Apiaceae. Am J Bot 95:793–804CrossRefGoogle Scholar
  20. Iovene M, Wielgus SM, Simon PW, Buell CR, Jiang J (2008b) Chromatin structure and physical mapping of chromosome 6 of potato and comparative analyses with tomato. Genetics 180:1307–1317PubMedCrossRefGoogle Scholar
  21. Islam-Faridi MN, Childs KL, Klein PE et al (2002) A molecular cytogenetic map of sorghum chromosome 1: fluorescence in situ hybridization analysis with mapped bacterial artificial chromosomes. Genetics 161:345–353PubMedGoogle Scholar
  22. Jiang J, Gill BS (2006) Current status and the future of fluorescence in situ hybridization (FISH) in plant genome research. Genome 49:1057–1068PubMedCrossRefGoogle Scholar
  23. Jiang J, Birchler JA, Parrott WA, Dawe RK (2003) A molecular view of plant centromeres. Trends Plant Sci 8:570–575PubMedCrossRefGoogle Scholar
  24. Just BJ, Santos CAF, Fonseca MEN, Boiteux LS, Oloizia BB, Simon PW (2007) Carotenoid biosynthesis structural genes in carrot (Daucus carota): isolation, sequence-characterization, single nucleotide polymorphism (SNP) markers and genome mapping. Theor Appl Genet 114:693–704PubMedCrossRefGoogle Scholar
  25. Kim JS, Islam-Faridi MN, Klein PE et al (2005) Comprehensive molecular cytogenetic analysis of sorghum genome architecture: distribution of euchromatin, heterochromatin, genes and recombination in comparison to rice. Genetics 171:1963–1976PubMedCrossRefGoogle Scholar
  26. Koo D-H, Jiang J (2009) Super-stretched pachytene chromosomes for fluorescence in situ hybridization mapping and immunodetection of DNA methylation. Plant J 59:509–516PubMedCrossRefGoogle Scholar
  27. Koo D-H, Choi H-W, Cho J, Hur Y, Bang J-W (2005) A high-resolution karyotype of cucumber (Cucumis sativus L. ‘Winter Long’) revealed by C-banding, pachytene analysis, and RAPD-aided fluorescence in situ hybridization. Genome 48:534–540PubMedCrossRefGoogle Scholar
  28. Kulikova O, Gualtieri G, Geurts R et al (2001) Integration of the FISH pachytene and genetic maps of Medicago truncatula. Plant J 27:49–58PubMedCrossRefGoogle Scholar
  29. Lee B-Y, Downie SR (1999) A molecular phylogeny of Apiaceae tribe Caucalideae and related taxa: inferences based on ITS sequence data. Syst Bot 24:461–479CrossRefGoogle Scholar
  30. Lee B-Y, Levin A, Downie SR (2001) Relationships within the spiny-fruited umbellifers (Scandiceae subtribes Daucinae and Torilidinae) as assessed by phylogenetic analysis of morphological characters. Syst Bot 26:622–642Google Scholar
  31. Li J, Hsia A-P, Schnable PS (2007) Recent advances in plant recombination. Curr Opin Plant Biol 10:131–135PubMedCrossRefGoogle Scholar
  32. Lou Q, Iovene M, Spooner DM, Buell CR, Jiang J (2010) Evolution of chromosome 6 of Solanum species revealed by comparative fluorescence in situ hybridization mapping. Chromosoma 119:435–442PubMedCrossRefGoogle Scholar
  33. Lu S, Van Eck J, Zhou X et al (2006) The cauliflower Or gene encodes a DnaJ cysteine-rich domain-containing protein that mediates high levels of beta-carotene accumulation. Plant Cell 18:3594–3605PubMedCrossRefGoogle Scholar
  34. Lysak MA, Berr A, Pecinka A, Schmidt R, McBreen K, Schubert I (2006) Mechanisms of chromosome number reduction in Arabidopsis thaliana and related Brassicaceae species. Proc Natl Acad Sci USA 103:5224–5229PubMedCrossRefGoogle Scholar
  35. Mandakova T, Lysak MA (2008) Chromosomal phylogeny and karyotype evolution in x = 7 crucifer species (Brassicaceae). Plant Cell 20:2559–2570PubMedCrossRefGoogle Scholar
  36. Mézard C (2006) Meiotic recombination hotspots in plants. Biochem Soc Trans 34:531–534PubMedCrossRefGoogle Scholar
  37. Moore DM (1971) Chromosome studies in the Umbelliferae. In: Heywood VH (ed) The biology and chemistry of the Umbelliferae. Academic, London, UK, pp 233–255Google Scholar
  38. Ohmido N, Ishimaru A, Kato S, Sato S, Tabata S, Fukui K (2010) Integration of cytogenetic and genetic linkage maps of Lotus japonicus, a model plant for legumes. Chromosome Res 18:287–299PubMedCrossRefGoogle Scholar
  39. Pedrosa-Harand A, Kami J, Gepts P, Geffroy V, Schweizer D (2009) Cytogenetic mapping of common bean chromosomes reveals a less compartmentalized small-genome plant species. Chromosome Res 17:405–417PubMedCrossRefGoogle Scholar
  40. Rubatzky VE, Quiros CF, Simon PW (1999) Carrots and related vegetable Umbelliferae. CABI Publishing, New YorkGoogle Scholar
  41. Sáenz Laín C (1981) Research on Daucus L. (Umbelliferae). An Inst Botanico AJ Cavanilles 37:481–533Google Scholar
  42. Santos CAF, Simon PW (2002) QTL analyses reveal clustered loci for accumulation of major provitamin A carotenes and lycopene in carrot roots. Mol Genet Genomics 268:122–129PubMedCrossRefGoogle Scholar
  43. Santos CAF, Simon PW (2004) Merging carrot linkage groups based on conserved dominant AFLP markers in F2 populations. J Amer Soc Hort Sci 129:211–217Google Scholar
  44. Schrader O, Ahne R, Fuchs J (2003) Karyoptype analysis of Daucus carota L. using Giemsa C-Banding and FISH of 5S and 18S–25S rRNA specific genes. Caryologia 56:149–154Google Scholar
  45. Sharma AK, Ghosh C (1954) Cytogenetics of some of the Indian umbellifers. Genetica 27:17–44PubMedCrossRefGoogle Scholar
  46. Simon PW (2000) Domestication, historical development, and modern breeding of carrot. Plant Breed Rev 19:157–189Google Scholar
  47. Simon PW, Freeman RE, Vieira JV (2008) Carrot. In: Prohens J, Nuez F (eds) Handbook of Plant Breeding, Vegetables II: Fabaceae, Liliaceae, Solanaceae, and Umbelliferae, vol 2. Springer, Berlin, pp 327–357Google Scholar
  48. Sutton GG, White O, Adams MD, Kerlavage AR (1995) TIGR assembler: a new tool for assembling large shotgun sequencing projects. Genome 1:9–19Google Scholar
  49. Tang X, de Boer JM, vanEck HJ, Bachem CWB, Visser RGF, de Jong H (2009) Assignment of genetic linkage maps to diploid Solanum tuberosum pachytene chromosomes by BAC-FISH technology. Chromosome Res 17:899–915PubMedCrossRefGoogle Scholar
  50. Vivek BS, Simon PW (1999) Linkage relationships among molecular markers and storage root traits of carrot (Daucus carota L. ssp. sativus). Theor Appl Genet 99:58–64CrossRefGoogle Scholar
  51. Walling JG, Shoemaker RC, Young ND, Mudge J, Jackson SA (2006) Chromosome level homeology in paleopolyploid soybean (Glycine max) revealed through integration of genetic and chromosome maps. Genetics 172:1893–1900PubMedCrossRefGoogle Scholar
  52. Wang C-JR, Harper L, Cande ZW (2006) High-resolution single-copy gene fluorescence in situ hybridization and its use in the construction of a cytogenetic map of maize chromosome 9. Plant Cell 18:529–544PubMedCrossRefGoogle Scholar
  53. Wang K, Yang Z, Shu C et al (2009) Higher axial-resolution and sensitivity pachytene fluorescence in situ hybridization protocol in tetraploid cotton. Chromosome Res 17:1041–1050PubMedCrossRefGoogle Scholar
  54. Yan HH, Jin W, Nagaki K et al (2005) Transcription and histone modifications in the recombination-free region spanning a rice centromere. Plant Cell 17:3227–3238PubMedCrossRefGoogle Scholar
  55. Yan HH, Ito H, Nobuta K et al (2006) Genomic and genetic characterization of rice Cen3 reveals extensive transcription and evolutionary implications of a complex centromere. Plant Cell 18:2123–2133PubMedCrossRefGoogle Scholar
  56. Zhang D, Yang Q, Bao W et al (2005) Molecular cytogenetic characterization of the Antirrhinum majus genome. Genetics 169:325–335PubMedCrossRefGoogle Scholar
  57. Zhu W, Ouyang S, Iovene M et al (2008) Analysis of 90 Mb of the potato genome reveals conservation of gene structures and order with tomato but divergence in repetitive sequence composition. BMC Genomics 9:286PubMedCrossRefGoogle Scholar
  58. Zwick MS, Hanson RE, Mcknight TD et al (1997) A rapid procedure for the isolation of Cot-1 DNA from plants. Genome 40:138–142PubMedCrossRefGoogle Scholar

Copyright information

© Springer Science+Business Media B.V. (outside the USA) 2011

Authors and Affiliations

  • Marina Iovene
    • 1
    • 4
  • Pablo F. Cavagnaro
    • 1
    • 5
  • Douglas Senalik
    • 2
  • C. Robin Buell
    • 3
  • Jiming Jiang
    • 1
  • Philipp W. Simon
    • 1
    • 2
    Email author
  1. 1.Department of HorticultureUniversity of WisconsinMadisonUSA
  2. 2.USDA-ARS, Vegetable Crops Research Unit, Department of HorticultureUniversity of WisconsinMadisonUSA
  3. 3.Department of Plant BiologyMichigan State UniversityEast LansingUSA
  4. 4.CNR-Institute of Plant GeneticsBariItaly
  5. 5.CONICET and INTA-EEA La Consulta CC8San CarlosArgentina

Personalised recommendations