Aberrant splicing of intron 1 leads to the heterogeneous 5' UTR and decreased expression of waxy gene in rice cultivars of intermediate amylose content

Plant J. 1998 May;14(4):459-65. doi: 10.1046/j.1365-313x.1998.00126.x.


We have previously reported that three distinct patterns of waxy (Wx) gene transcript accumulation were present in 31 rice cultivars. The cultivars with high amylose content (group I) contain a 2.3 kb mature Wx mRNA, cultivars with intermediate amylose content (group II) produce both a 3.3 kb Wx pre-mRNA, which contains intron 1, and the 2.3 kb Wx mature mRNA, and cultivars with no amylose (group III) accumulate only the 3.3 kb Wx pre-mRNA. Analyses of the cDNAs reveals that four splice donor sites and three splice acceptor sites in intron 1 give rise to six splicing patterns in 2.3 kb Wx mRNA of group II cultivars. In addition, aberrant intron 1 excision causes either deletion of 4 or 5 nucleotides, or addition of 7 and 13 nucleotides at the junction of exon 1 and exon 2 of the 2.3 kb mRNA. In contrast, only one normal splicing pattern (one splice donor site and one splice acceptor site) was found in the 2.3 kb mRNA of group I cultivars. Nucleotide sequences of the Wx intron 1 in group I and group II cultivars differ by 16 individual bases. We suggest that these deletions or additions contribute to inefficient splicing of intron 1 from the 3.3 kb Wx pre-mRNA, as well as an aberrant splicing of the Wx intron 1 to produce the 2.3 kb mRNA with a heterogeneous 5' untranslated region (5'-UTR). As a consequence, the total amount of translatable Wx mRNA, and therefore the Wx protein and amylose content, are reduced in the group II cultivars compared with the group I cultivars.

Publication types

  • Comparative Study
  • Research Support, Non-U.S. Gov't

MeSH terms

  • Alternative Splicing*
  • Amylose / metabolism
  • Base Sequence
  • Introns*
  • Molecular Sequence Data
  • Oryza / genetics*
  • Oryza / metabolism
  • Plant Proteins / biosynthesis*
  • Plant Proteins / genetics
  • Polymerase Chain Reaction
  • RNA Precursors / metabolism
  • RNA, Messenger / biosynthesis
  • Sequence Alignment
  • Sequence Homology, Nucleic Acid
  • Species Specificity
  • Starch Synthase / biosynthesis*
  • Starch Synthase / genetics


  • Plant Proteins
  • RNA Precursors
  • RNA, Messenger
  • waxy protein, plant
  • Amylose
  • Starch Synthase

Associated data

  • GENBANK/X53694
  • GENBANK/X64108