Natural variation at the DEP1 locus enhances grain yield in rice

Nat Genet. 2009 Apr;41(4):494-7. doi: 10.1038/ng.352. Epub 2009 Mar 22.


Grain yield is controlled by quantitative trait loci (QTLs) derived from natural variations in many crop plants. Here we report the molecular characterization of a major rice grain yield QTL that acts through the determination of panicle architecture. The dominant allele at the DEP1 locus is a gain-of-function mutation causing truncation of a phosphatidylethanolamine-binding protein-like domain protein. The effect of this allele is to enhance meristematic activity, resulting in a reduced length of the inflorescence internode, an increased number of grains per panicle and a consequent increase in grain yield. This allele is common to many Chinese high-yielding rice varieties and likely represents a relatively recent introduction into the cultivated rice gene pool. We also show that a functionally equivalent allele is present in the temperate cereals and seems to have arisen before the divergence of the wheat and barley lineages.

Publication types

  • Research Support, Non-U.S. Gov't

MeSH terms

  • Gene Expression Regulation, Plant
  • Genetic Markers
  • Genetic Variation*
  • Molecular Sequence Data
  • Mutation
  • Oryza / enzymology
  • Oryza / genetics
  • Oryza / growth & development*
  • Plant Proteins / genetics
  • Quantitative Trait Loci
  • Receptor-Like Protein Tyrosine Phosphatases, Class 3 / genetics*


  • Genetic Markers
  • Plant Proteins
  • Receptor-Like Protein Tyrosine Phosphatases, Class 3

Associated data

  • GENBANK/FJ039902
  • GENBANK/FJ039903
  • GENBANK/FJ039904
  • GENBANK/FJ039905