Hypomethylated sequences: Characterization of the duplicate soybean genome

Tong Zhu, James M. Schupp, Arnold Oliphant, Paul Keim

Research output: Contribution to journalArticlepeer-review

48 Scopus citations


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.

Original languageEnglish (US)
Pages (from-to)638-645
Number of pages8
JournalMGG Molecular & General Genetics
Issue number6
StatePublished - Nov 1994


  • DNA methylation
  • Gene duplication Glycine max
  • Phaseolus vulgaris
  • Tetraploidy

ASJC Scopus subject areas

  • Genetics


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