Diagnostic kit for rice blight resistance

Nat Biotechnol. 2019 Nov;37(11):1372-1379. doi: 10.1038/s41587-019-0268-y. Epub 2019 Oct 28.


Blight-resistant rice lines are the most effective solution for bacterial blight, caused by Xanthomonas oryzae pv. oryzae (Xoo). Key resistance mechanisms involve SWEET genes as susceptibility factors. Bacterial transcription activator-like (TAL) effectors bind to effector-binding elements (EBEs) in SWEET gene promoters and induce SWEET genes. EBE variants that cannot be recognized by TAL effectors abrogate induction, causing resistance. Here we describe a diagnostic kit to enable analysis of bacterial blight in the field and identification of suitable resistant lines. Specifically, we include a SWEET promoter database, RT-PCR primers for detecting SWEET induction, engineered reporter rice lines to visualize SWEET protein accumulation and knock-out rice lines to identify virulence mechanisms in bacterial isolates. We also developed CRISPR-Cas9 genome-edited Kitaake rice to evaluate the efficacy of EBE mutations in resistance, software to predict the optimal resistance gene set for a specific geographic region, and two resistant 'mega' rice lines that will empower farmers to plant lines that are most likely to resist rice blight.

Publication types

  • Research Support, Non-U.S. Gov't
  • Research Support, U.S. Gov't, Non-P.H.S.

MeSH terms

  • Bacterial Proteins / genetics
  • Binding Sites
  • CRISPR-Cas Systems
  • Databases, Genetic
  • Disease Resistance*
  • Gene Editing
  • Gene Expression Regulation, Plant
  • Membrane Transport Proteins / chemistry
  • Membrane Transport Proteins / genetics*
  • Membrane Transport Proteins / metabolism
  • Mutation
  • Oryza / genetics
  • Oryza / growth & development*
  • Oryza / microbiology
  • Plant Proteins / genetics
  • Promoter Regions, Genetic
  • Sequence Analysis, DNA
  • Transcription Activator-Like Effectors / metabolism*
  • Xanthomonas / metabolism
  • Xanthomonas / pathogenicity*


  • Bacterial Proteins
  • Membrane Transport Proteins
  • Plant Proteins
  • Transcription Activator-Like Effectors

Supplementary concepts

  • Xanthomonas oryzae