An SNP caused loss of seed shattering during rice domestication

Science. 2006 Jun 2;312(5778):1392-6. doi: 10.1126/science.1126410. Epub 2006 Apr 13.


Loss of seed shattering was a key event in the domestication of major cereals. We revealed that the qSH1 gene, a major quantitative trait locus of seed shattering in rice, encodes a BEL1-type homeobox gene and demonstrated that a single-nucleotide polymorphism (SNP) in the 5' regulatory region of the qSH1 gene caused loss of seed shattering owing to the absence of abscission layer formation. Haplotype analysis and association analysis in various rice collections revealed that the SNP was highly associated with shattering among japonica subspecies of rice, implying that it was a target of artificial selection during rice domestication.

Publication types

  • Historical Article
  • Research Support, Non-U.S. Gov't

MeSH terms

  • Agriculture / history*
  • Alleles
  • Chromosome Mapping
  • Chromosomes, Plant
  • Crops, Agricultural / genetics*
  • Crops, Agricultural / history
  • Genes, Plant
  • History, Ancient
  • Humans
  • Molecular Sequence Data
  • Oryza / genetics*
  • Oryza / history
  • Plant Proteins / genetics
  • Polymorphism, Single Nucleotide*
  • Quantitative Trait Loci
  • Seeds*
  • Transcription Factors / genetics


  • Plant Proteins
  • Transcription Factors

Associated data

  • GENBANK/AB071330
  • GENBANK/AB071331
  • GENBANK/AB071332
  • GENBANK/AB071333