Skip to main content
SpringerLink
Log in

Macromolecular organization and genetic mapping of a rapidly evolving chromosome-specific tandem repeat family (B77) in cotton (Gossypium)

  • Published:
Plant Molecular Biology Aims and scope Submit manuscript

Abstract

Isolation and characterization of the most prominent repetitive element families in the genome of tetraploid cotton (Gossypium barbadense L; [39]) revealed a small subset of families that showed very different properties in tetraploids than in their diploid progenitors, separated by 1-2 million years. One element, B77, was characterized in detail, and compared to the well-conserved 5S and 45S rRNA genes. The 572 bp B77 repeat was found to be concentrated in several discontinuous tandem arrays confined to a single 550 kb SalI fragment in tetraploid cotton. Genetic mapping based on the absence of the pentameric ‘rung’ in the G. barbadense ‘ladder’ showed that B77 maps to a D-subgenome chromosome. In situ hybridization supports the contention that the array is confined largely to a single chromosomal site in the D-subgenome. The B77 repeat has undergone a substantial increase in copy number since formation of tetraploid cotton from its diploid relatives. RFLPs observed among tetraploid cotton species suggest that amplification and/or rearrangement of the repeat may have continued after divergence of the five tetraploid cotton species. B77 contains many short direct repeats and shares significant DNA sequence homology with a Nicotiana alata retrotransposon Tna1-2 integrase motif. The recent amplification of B77 on linkage group D04 suggests that the D-subgenome of tetraploid cotton may be subject to different evolutionary constraints than the D-genome diploid chromosomes, which exhibit few genome-specific elements. Further, the abundance of B77 in G. gossypioides supports independent evidence that it may be the closest extant relative of the D-genome ancestor of cotton.

This is a preview of subscription content, log in via an institution to check access.

Access this article

Log in via an institution

Price excludes VAT (USA)
Tax calculation will be finalised during checkout.

Instant access to the full article PDF.

Institutional subscriptions

Similar content being viewed by others

References

  1. Arumuganathan K, Martin GB, Telenius H, Tanksley SD, Earle ED: Chromosome 2-specific DNA clones from flowsorted chromosomes of tomato. Mol Gen Genet 242: 551–558 (1994).

    Google Scholar 

  2. Awgulewitsch A, Bunemann H: Isolation of Y-chromosomal repetitive DNA sequences of Drosophila hydei via enrichment of chromosome-specific sequences by heterogeneous hybridization between female and male DNA. J Biochem Biophys Meth 12: 37–50 (1986).

    Google Scholar 

  3. Beasley JO: Meiotic chromosome behavior in species hybrids, haploids, and induced polyploids ofGossypium. Genetics 27: 25–54 (1942).

    Google Scholar 

  4. Burk RD, Stamberg J, Young KE, Smith KD: Use of repetitive DNA for diagnosis of chromosomal rearrangements. Hum Genet 64: 339–342 (1983).

    Google Scholar 

  5. Chittenden LM, Schertz KF, Lin Y-R, Wing RA, Paterson AH: A detailed RFLP map of Sorghum bicolor × S. propinquum suitable for high-density mapping suggests ancestral duplication of chromosome or chromosomal segments. Theor Appl Genet 87: 925–933 (1994).

    Google Scholar 

  6. Crane CF, Price HJ, Stelly DM, Czeshin DG: Identification of a homoeologous chromosome pair by in situ DNA hybridization to ribosomal RNA loci in meiotic chromosomes of cotton (Gossypium hirsutum). Genome 35: 1015–1022 (1993).

    Google Scholar 

  7. Cronn EC, Zhao X, Paterson AH, Wendel JF: Polymorphism and concerted evolution in a tandemly repeated gene family: 5S ribosomal DNA in diploid and allopolyploid cottons. J Mol Evol 42: 685–705 (1996).

    Google Scholar 

  8. Disteche C, Luthy D, Haslam DB, Hoar D: Prenatal identification of a deleted Y chromosome by cytogenetics and a Y-specific repetitive DNA probe. Hum Genet 67: 222–224 (1984).

    Google Scholar 

  9. Edwards GA, Endrizzi JE: Cell size, nuclear size, and DNA content relationships in Gossypium. Can J Genet Cytol 17: 181–186 (1976).

    Google Scholar 

  10. Endrizzi JE, Turcotte RJ, Kohel RJ: Qualitative genetics, cytology, and cytogenetics. ASA/CSSA/SSSA Publishers, Madison, WI (1984).

    Google Scholar 

  11. Endrizzi JE, Turcotte RJ, Kohel RJ: Genetics, cytology, and evolution of Gossypium. Adv Genet 23: 271–375 (1985).

    Google Scholar 

  12. Feinberg AP, Vogelstein B: A technique for radiolabeling DNA restriction endonuclease fragments to high specific activity. Anal Biochem 132: 6–13 (1983).

    Google Scholar 

  13. Fryxell PA: A revised taxonomic interpretation of Gossypium L. (Malvaceae). Rheedea 2: 108–165 (1992).

    Google Scholar 

  14. Fryxell PA: The natural history of the cotton tribe. Texas A & M University Press, College Station, TX (1979).

    Google Scholar 

  15. Ganal MW, Broun P, Tanksley SD: Genetic mapping of tandemly repeated telomeric DNA sequences in tomato (Lycopersicon esculentum). Genomics 14: 444–448 (1992).

    Google Scholar 

  16. Hall KJ, Parker JS, Ellis THN: The relationship between genetic and cytogenetic map of pea. I. Standard and translocation karyotypes. Genome 40: 744–754 (1997).

    Google Scholar 

  17. Hall KJ, Parker JS, Ellis THN, Turner T, Knox MR, Hofer JMI, Lu J, Ferrandiz C, Hunter PJ, Taylor JD, Baird K: The relationship between genetic and cytogenetic map of pea. II. Physical maps of linkage mapping populations. Genome 40: 755–769 (1997).

    Google Scholar 

  18. Hanson RE, Islam-Faridi MN, Percival EA, Crane CF, Ji Y, McKnight TD, Stelly DM, Price HJ: Distributions of 5S and 18S-28S rDNA loci in a tetraploid cotton (Gossypium hirsutum L.) and its putative diploid ancestors. Chromosoma 105: 55–61 (1996).

    Google Scholar 

  19. Heslop-Harrison JS, Harrison GE, Leitch IJ: Reprobing of DNA:DNA in situ hybridization preparations. Technical Tips 8: 372–373 (1992).

    Google Scholar 

  20. Islam-Faridi MN, Mujeeb-Kazi A: Visualization of Secale cereale DNA in wheat germplasm by fluorescent in situ hybridization. Theor Appl Genet 90: 595–600 (1995).

    Google Scholar 

  21. Jewell DC, Islam-Faridi MN: Details of a technique for somatic chromosome preparation and C-banding of maize. In: Freeling M, Walbot W (eds) The Maize Handbook, pp. 484–493. Springer-Verlag, New York (1994).

    Google Scholar 

  22. Kimber G: Basis of the diploid-like meiotic behavior of polyploid cotton. Nature 191: 98–99 (1961).

    Google Scholar 

  23. Kohler MR, Vogt PH: Interstitial deletions of repetitive DNA blocks in dicentric human Y chromosomes. Chromosoma 103: 324–330 (1994).

    Google Scholar 

  24. Nickrent DL, Soltis DE: A comparision of angiosperm phylogenies from nuclear 18S rRNA and rbcL sequences. Ann MO Bot Gard 82: 208–234 (1995).

    Google Scholar 

  25. Nishioka Y, Dolan BM, Zahed L: Molecular characterization of a mouse Y chromosomal repetitive sequence amplified in distantly related species in the genus Mus. Genome 36: 588–593 (1993).

    Google Scholar 

  26. Nishioka Y, Lamothe E: Isolation and characterization of a mouse Y chromosomal repetitive sequence. Genetics 113: 417–432 (1986).

    Google Scholar 

  27. Nishioka Y, Lamothe E: Isolation of human Y chromosomal major repetitive sequences from a flow-sorted Y chromosomal library. Am J Med Genet 27: 711–717 (1987).

    Google Scholar 

  28. Paterson AH, Brubaker CL, Wendel JF: A rapid method for extraction of cotton (Gossypium spp.) genomic DNA suitable for RFLP or PCR analysis. Plant Mol Biol Rep 11: 122–127 (1993).

    Google Scholar 

  29. Reinisch AJ, Dong J-M, Brubaker CL, Stelly DM, Wendel JF, Paterson AH: A detailed RFLP map of cotton, Gossypium hirsutum × Gossypiumbarbadens: chromosome organization and evolution in a disomic polyploid genome. Genetics 138: 829–847 (1994).

    Google Scholar 

  30. Roder MS, Lapitan NL, Sorrells ME, Tanksley SD: Genetic and physical mapping of barley telomeres. Mol Gen Genet 238: 294–303 (1993).

    Google Scholar 

  31. Royo J, Nass N, Matton DP, Okamoto S, Clarke AE, Newbigin E: A retrotransposon-like sequence linked to the S-locus of Nicotiana alata is expressed in styles in response to touch. Mol Gen Genet 250: 180–188 (1996).

    Google Scholar 

  32. Sanger F, Nicklen S, Coulson AR: DNA sequencing with chain-terminating inhibitors. Proc Natl Acad Sci USA 74: 5363–5367 (1977).

    Google Scholar 

  33. Stallings RL, Whitmore SA, Doggett NA, Callen DF: Refined physical mapping of chromosome 16-specific low-abundance repetitive DNA sequences. Cytogenet Cell Genet 63: 97–101 (1993).

    Google Scholar 

  34. Wendel JF: New World cottons contain Old World cytoplasm. Proc Natl Acad Sci USA 86: 4132–4136 (1989).

    Google Scholar 

  35. Wendel JF, Albert VA: Phylogenetis of the cotton genus (Gossypium): character-state weighted parsimony analysis of chloroplast-DNA restriction site data and its systematic and biogeographic implications. Syst Bot 17: 115–143 (1992).

    Google Scholar 

  36. Wendel JF, Schnabel A, Seelanan T: Bi-directional interlocus concerted evolution following allopolyploid speciation in cotton (Gossypium). Proc Natl Acad Sci USA 92: 280–284 (1995).

    Google Scholar 

  37. Wendel JF, Schnabel A, Seelanan T: An unusual ribosomal DNA sequence from Gossypium gossypioides reveals ancient, cryptic, intergenomic introgression. Mol Phyl Evol 4: 298–313 (1995).

    Google Scholar 

  38. Wu KS, Tanksley SD: Genetic and physical mapping of telomeres and macrosatellites of rice. Plant Mol Biol 22: 861–872 (1993).

    Google Scholar 

  39. Zhao X, Wing RA, Paterson AH: Cloning and characterization of the majority of repetitive DNA in cotton (Gossypium L.). Genome 38: 1177–1188 (1995).

    Google Scholar 

  40. Zhao X, Wu T, Xie Y, Wu R: Genome-specific repetitive sequences in the genus Oryza. Theor Appl Genet 78: 201–209 (1989).

    Google Scholar 

  41. Zhao X, Zhang H-B, Wing RA, Paterson AH: A simple method for isolation of megabase DNA from cotton. Plant Mol Biol Rep 12: 110–115 (1994).

    Google Scholar 

  42. Zhao X, Si Y, Hansen RE, Crane CF, Rice HJ, Stelly DM, Wendel JF, Paterson AH: Dispersed repetative DNA has spread to new genomes in cotton. Genome Res 8: 479–492 (1998).

    Google Scholar 

Download references

Author information

Authors and Affiliations

  1. Department of Soil and Crop Sciences, Texas A& M University, College Station, TX, 77843-2474, USA

    Xinping Zhao, Yuanfu Ji & Xiaoling Ding

  2. University of Michigan Medical Center, 5110 CCGC, 1500 E. Medical Center Dr., Ann Arbor, MI, 48109-0940, USA

    David M. Stelly & Andrew H. Paterson

Authors
  1. Xinping Zhao
    View author publications

    You can also search for this author in PubMed Google Scholar

  2. Yuanfu Ji
    View author publications

    You can also search for this author in PubMed Google Scholar

  3. Xiaoling Ding
    View author publications

    You can also search for this author in PubMed Google Scholar

  4. David M. Stelly
    View author publications

    You can also search for this author in PubMed Google Scholar

  5. Andrew H. Paterson
    View author publications

    You can also search for this author in PubMed Google Scholar

Rights and permissions

Reprints and permissions

About this article

Cite this article

Zhao, X., Ji, Y., Ding, X. et al. Macromolecular organization and genetic mapping of a rapidly evolving chromosome-specific tandem repeat family (B77) in cotton (Gossypium). Plant Mol Biol 38, 1031–1041 (1998). https://doi.org/10.1023/A:1006073116627

Download citation

  • Issue Date:

  • DOI: https://doi.org/10.1023/A:1006073116627

Search

Navigation