Theoretical and Applied Genetics

, Volume 107, Issue 1, pp 62–73 | Cite as

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

  • Matthew W. Blair
  • Amanda J. Garris
  • Anjali S. Iyer
  • Brad Chapman
  • Stephen Kresovich
  • Susan R. McCouch

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 F2 individuals derived from a cross between a near-isogenic line (NIL) and its corresponding recurrent parent to identify recombinants in the region. Recombinant F2 individuals were progeny tested using F3 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.

Xanthomonas oryzae pv oryzae Recessive resistance gene High-resolution mapping Single nucleotide polymorphism Simple sequence repeat markers 

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Copyright information

© Springer-Verlag 2003

Authors and Affiliations

  • Matthew W. Blair
    • 1
  • Amanda J. Garris
    • 1
  • Anjali S. Iyer
    • 1
  • Brad Chapman
    • 1
  • Stephen Kresovich
    • 2
  • Susan R. McCouch
    • 1
  1. 1., Department of Plant Breeding, 240 Emerson Hall, Cornell University, Ithaca, NY 14853-1901, USA
  2. 2., Institute of Genomic Diversity, Plant Breeding Department, 130 Biotechnology Building, Cornell University, USA
  3. 3., CIAT - International Center for Tropical Agriculture, A. A. 6713, Cali, Colombia, South America
  4. 4., Plant Genome Mapping Laboratory, University of Georgia, Riverbend Research Laboratory, Room 162, Athens, GA 30602, USA

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