High resolution genetic mapping and candidate gene identification at the xa5 locus for bacterial blight resistance in rice ( Oryza sativa L.)

Theor Appl Genet. 2003 Jun;107(1):62-73. doi: 10.1007/s00122-003-1231-2. Epub 2003 Apr 3.


The xa5 resistance gene from rice provides recessive, race-specific resistance to bacterial blight of rice caused by the pathogen Xanthomonas oryzae pv oryzae. A high-resolution genetic map of the chromosomal region surrounding xa5 was developed by placing 44 DNA markers on the distal end of rice chromosome 5. The basis for mapping was a PCR-based screening of 1,016 F(2) individuals derived from a cross between a near-isogenic line (NIL) and its corresponding recurrent parent to identify recombinants in the region. Recombinant F(2) individuals were progeny tested using F(3) families inoculated with the Philippine strain PXO 61 of bacterial blight pathogen. The xa5 gene was mapped to a 0.5-cM interval between the markers RS7 and RM611, which spanned an interval of approximately 70 kb and contained a total of 11 open reading frames. Sequence data for the locus was generated from an Indica (the IR24 isoline, IRBB21) BAC covering part of the region and compared to other overlapping Indica (cv 93-11) and Japonica (cv Nipponbare) sequences. Candidate-gene analysis revealed that a basal transcription factor (TFIIa), an ABC transporter, a tRNA synthase, a MAP kinase and a cysteine protease, as well as four unknown, hypothetical or putative proteins, are encoded at the locus and could be potential candidates for the resistance gene product. The mechanism by which these genes could provide recessive, race-specific resistance will be elucidated by map-based cloning of the xa5 gene.

Publication types

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

MeSH terms

  • Chromosomes, Artificial, Bacterial
  • Cloning, Molecular
  • DNA / metabolism
  • Gene Library
  • Genes, Plant*
  • Genetic Markers
  • Genotype
  • Immunity, Innate / genetics*
  • Oryza / genetics*
  • Oryza / microbiology
  • Physical Chromosome Mapping
  • Plant Diseases / genetics*
  • Recombination, Genetic


  • Genetic Markers
  • DNA