Features of a 103-kb gene-rich region in soybean include an inverted perfect repat cluster of CHS genes comprising the I locus

Steven J. Clough, Jigyasa H. Tuteja, Min Li, Laura F. Marek, Randy C. Shoemaker, Lila O. Vodkin

Research output: Contribution to journalArticle

Abstract

The I locus in soybean (Glycine max) corresponds to a region of chalcone synthase (CHS) gene duplications affecting seed pigmentation. We sequenced and annotated BAC clone 104J7, which harbors a dominant ii allele from Glycine max 'Williams 82', to gain insight into the genetic structure of this multigenic region in addition to examining its flanking regions. The 103-kb BAC encompasses a gene-rich region with 11 putatively expressed genes. In addition to six copies of CHS, these genes include: a geranylgeranyltransferase type II β subunit (E.C.2.5.1.60), a β-galactosidase, a putative spermine and (or) spermidine synthase (E.C.2.5.1.16), and an unknown expressed gene. Strikingly, sequencing data revealed that the 10.91-kb CHS1, CHS3, CHS4 cluster is present as a perfect inverted repeat separated by 5.87 kb. Contiguous arrangement of CHS paralogs could lead to folding into multiple secondary structures, hypothesized to induce deletions that have previously been shown to effect CHS expression. BAC104J7 also contains several gene fragments representing a cation/hydrogen exchanger, a 40S ribosomal protein, a CBL-interacting protein kinase, and the amino terminus of a subtilisin. Chimeric ESTs were identified that may represent read-through transcription from a flanking truncated gene into a CHS cluster, generating aberrant CHS RNA molecules that could play a role in CHS gene silencing.

Original languageEnglish (US)
Pages (from-to)819-831
Number of pages13
JournalGenome
Volume47
Issue number5
DOIs
StatePublished - Oct 1 2004

Keywords

  • BAC
  • Chalcone synthase
  • Gene duplication
  • Gene silencing
  • Gene-rich region
  • Soybean

ASJC Scopus subject areas

  • Biotechnology
  • Molecular Biology
  • Genetics

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