Molecular and General Genetics MGG

, Volume 244, Issue 6, pp 638–645

Hypomethylated sequences: Characterization of the duplicate soybean genome

  • Tong Zhu
  • James M. Schupp
  • Arnold Oliphant
  • Paul Keim
Original Paper

Abstract

Soybean is believed to be a diploidized tetraploid generated from an allotetraploid ancestor. In this study, we used hypomethylated genomic DNA as a source of probes to investigate the genomic structure and methylation patterns of duplicated sequences. Forty-five genomic clones from Phaseolus vulgaris and 664 genomic clones from Glycine max were used to examine the duplicated regions in the soybean genome. Southern analysis of genomic DNA using probes from both sources revealed that greater than 15% of the hypomethylated genomic regions were only present once in the soybean genome. The remaining ca. 85% of the hypomethylated regions comprise duplicated or middle repetitive DNA sequences. If only the ratio of single to duplicate probe patterns is considered, it appears that 25% of the single-copy sequences have been lost. By using a subset of probes that only detected duplicated sequences, we examined the methylation status of the homeologous genomes with the restriction enzymes MspI and HpaII. We found that in all cases both copies of these regions were hypomethylated, although there were examples of low-level methylation. It appears that duplicate sequences are being eliminated in the diploidization process. Our data reveal no evidence that duplicated sequences are being “silenced” by inactivation correlated with methylation patterns.

Key words

DNA methylation Gene duplication Glycine max Phaseolus vulgaris Tetraploidy 

Preview

Unable to display preview. Download preview PDF.

Unable to display preview. Download preview PDF.

References

  1. Apuya N, Frazier B, Keim P, Roth EJ, Lark KG (1988) The development of RFLP markers for genetic studies in soybeans. Theor Appl Genet 75: 889–901Google Scholar
  2. Arumuganatheum K, Earle ED (1991) Nuclear DNA content of some important plant species. Plant Mot Biol Rep 9: 208–218Google Scholar
  3. Bird AP (1986) CpG-rich islands and the function of DNA methylation. Nature 321: 209–213Google Scholar
  4. Brettell RIS, Dennis ES (1991) Reactivation of a silent Ac following tissue culture is associated with heritable alterations in its methylation pattern. Mot Gen Genet 229: 369–375Google Scholar
  5. Burr B, Burr FA, Thompson KH, Albertson MC, Stuber C (1988) Gene mapping with recombinant inbreds in maize. Genetics 118: 519–526Google Scholar
  6. Chase CD, Ortega VM, Vallejos CE (1991) DNA restriction fragment length polymorphisms correlate with isozyme diversity in Phaseolus vulgaris L. Theor Appl Genet 81: 806–811Google Scholar
  7. Doyle JJ, Doyle JL (1993) Chloroplast DNA phylogeny of the papilionoid legume tribe Phaseoleae. Syst Bot 18: 309–327Google Scholar
  8. Ellis THN, Delseny M, Lee D, Burcham WG (1989) Methylated and undermethylated rDNA repeats are interspersed at random in two higher plant species. Plant Mot Biol 14: 73–80Google Scholar
  9. Flavell RB, O'Dell M, Thompson WF (1988) Regulation of cytosine methylation in ribosomal DNA and nucleolus organizer expression in wheat. J Mot Biol 204: 523–534Google Scholar
  10. Funke RP, Kolchinsky A, Gresshoff PM (1993) Physical mapping of a region in the soybean (Glycine max) genome containing duplicated sequences. Plant Mot Biol 22: 437–446Google Scholar
  11. Gastony GJ (1991) Gene silencing in a polyploid homosporous fern: paleopolyploidy revisited. Proc Natl Acad Sci USA 88: 1602–1605Google Scholar
  12. Goldberg RB (1978) DNA sequence organization in the soybean plant. Biochem Genet 16: 45–68Google Scholar
  13. Grandbastein MA, Berry-Lowe S, Shirley BW, Meagher RB (1986) Two soybean ribulose-1,5-biphosphate carboxylase small subunit genes share extensive homology even in distant flank sequences. Plant Mot Biol 7: 451–465Google Scholar
  14. Gruenbaum Y, Naveh-Mary T, Cedar H, Razin A (1981) Sequence specificity of methylation in higher plant DNA. Nature 292: 860–862Google Scholar
  15. Gurley WB, Hepburn AG, Key JL (1979) Sequence organization of the soybean genome. Biochim Biophys Acta 561: 167–183Google Scholar
  16. Haufler CH (1987) Electrophoresis is modifying our concepts of evolution in Homosporous pteridophytes. Am J Bot 74: 953–966Google Scholar
  17. Hepburn AG, Belanger FC, Mattheis JR (1987) DNA methylation in plants. Dev Genet 8: 475–493Google Scholar
  18. Hightower RC, Meagher RB (1985) Divergence and differential expression of soybean actin genes. EMBO J 4: 1–8Google Scholar
  19. Hymowitz T, Singh RJ (1987) Taxonomy and speciation. In: Wilcox JR (ed) Soybeans: improvement, production, and uses, 2nd edn (Agron Monogr 16) ASA, CSSA, and SSSA, Madison, Wis, pp 23–48Google Scholar
  20. Jupe ER, Zimmer EA (1993) DNasel-sensitive and undermethylated rDNA is preferentially expressed in a maize hybrid. Plant Mot Bio1 21: 805–822Google Scholar
  21. Keim P, Shoemaker RC (1988) Construction of a random recombinant DNA library that is primarily single-copy sequence. Soybean Genet Newslett 15: 147–148Google Scholar
  22. Keim P, Olson TC, Shoemaker RC (1988) A rapid protocol for isolating soybean DNA. Soybean Genet Newslett 15: 150–152Google Scholar
  23. Keim P, Diers BW, Olson T, Shoemaker RC (1990) RFLP mapping in soybean: association between marker loci and variation in quantitative traits. Genetics 126: 735–742Google Scholar
  24. Keim P, Beavis W, Schupp J, Freestone R (1992) Evaluation of soybean RFLP marker diversity in adapted germ plasm. Theor Appl Genet 85: 205–212Google Scholar
  25. Kessler C, Manta V (1990) Specificity of restriction endonucleases and DNA modification methytransferase — a review. Gene 92: 1–248Google Scholar
  26. Kumar PS, Hymowitz T (1989) Where are the diploid (2n = 2x = 20) genome donors of Glycine Wild. (Leguminosa, Papilionoideae)? Euphytica 40: 221–226Google Scholar
  27. Kunze R, Starlinger P, Schwartz D (1988) DNA methylation of the maize transposable element Ac interferes with its transcription. Mot Gen Genet 214: 325–327Google Scholar
  28. Maniatis T, Fritsch EF, Sambrook J (1982) Molecular cloning: a laboratory manual. Cold Spring Harbor Laboratory Press, Cold Spring Harbor. New YorkGoogle Scholar
  29. McClelland M (1983) The frequency and distribution of methylatable DNA sequences in leguminous plant protein coding genes. J Mot Evol 19: 3346–3354Google Scholar
  30. Ohno S (1970) Evolution by gene duplication. Springer-Verlag, New YorkGoogle Scholar
  31. Palmer RG, Kilen TC (1987) Qualitative genetics and cytogenetics. In: Wilcox JR (ed) Soybeans: improvement, production, and uses, 2nd edn. ASA, CSSA, and SSSA, Madison, Wis, pp 135–209Google Scholar
  32. Sardana R, O'Dell M, Flavell R (1993) Correlation between the size of the intergenic regulatory region, the status of cytosine methylation of rRNA genes and nucleolur expression in wheat. Mot Gen Genet 236: 155–162Google Scholar
  33. Shoemaker RC, Gully RD, Lorenzen LL, Specht JE (1992) Molecular genetic mapping of soybean: map utilization. Crop Sci 32: 1091–1098Google Scholar
  34. Vallejos CE, Sakiyama NS, Chase CD (1992) A molecular markerbased linkage map of Phaseolus vulgaris L. Genetics 131: 733–740Google Scholar
  35. Watson JC, Kaufman LS, Thompson WF (1987) Developmental regulation of cytosine methylation in the nuclear ribosomal RNA genes of Pisum satimm. J Mot Biol 193: 15–26Google Scholar
  36. Werth CR, Windham MD (1991) A model for divergent, allopatric speciation of polyploid pteridophytes resulting from silencing of duplicate-gene expression. Am Nat 137: 515–526Google Scholar
  37. Zamir D, Tanksley SD (1988) Tomato genome is comprised largely of fast-evolving low copy-number sequences. Mot Gen Genet 213: 254–261Google Scholar

Copyright information

© Springer-Verlag 1994

Authors and Affiliations

  • Tong Zhu
    • 1
  • James M. Schupp
    • 1
  • Arnold Oliphant
    • 2
  • Paul Keim
    • 1
  1. 1.Department of Biological SciencesNorthern Arizona UniversityFlagstaffUSA
  2. 2.Pioneer Hi-Bred InternationalJohnstonUSA

Personalised recommendations