Variation in NRT1.1B contributes to nitrate-use divergence between rice subspecies

Nat Genet. 2015 Jul;47(7):834-8. doi: 10.1038/ng.3337. Epub 2015 Jun 8.


Asian cultivated rice (Oryza sativa L.) consists of two main subspecies, indica and japonica. Indica has higher nitrate-absorption activity than japonica, but the molecular mechanisms underlying that activity remain elusive. Here we show that variation in a nitrate-transporter gene, NRT1.1B (OsNPF6.5), may contribute to this divergence in nitrate use. Phylogenetic analysis revealed that NRT1.1B diverges between indica and japonica. NRT1.1B-indica variation was associated with enhanced nitrate uptake and root-to-shoot transport and upregulated expression of nitrate-responsive genes. The selection signature of NRT1.1B-indica suggests that nitrate-use divergence occurred during rice domestication. Notably, field tests with near-isogenic and transgenic lines confirmed that the japonica variety carrying the NRT1.1B-indica allele had significantly improved grain yield and nitrogen-use efficiency (NUE) compared to the variety without that allele. Our results show that variation in NRT1.1B largely explains nitrate-use divergence between indica and japonica and that NRT1.1B-indica can potentially improve the NUE of japonica.

Publication types

  • Research Support, Non-U.S. Gov't

MeSH terms

  • Alleles
  • Animals
  • Anion Transport Proteins / genetics*
  • Anion Transport Proteins / metabolism
  • Base Sequence
  • Cells, Cultured
  • Genetic Speciation
  • Genetic Variation
  • Nitrates / metabolism
  • Oryza / genetics*
  • Oryza / metabolism
  • Phylogeny
  • Plant Proteins / genetics*
  • Plant Proteins / metabolism
  • Polymorphism, Single Nucleotide
  • Species Specificity
  • Xenopus laevis


  • Anion Transport Proteins
  • Nitrates
  • Plant Proteins
  • nitrate transporters