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Genetics

Measurement of Haplotypic Variation in Xanthomonas oryzae pv. oryzae Within a Single Field by rep-PCR and RFLP Analyses. C. M. Vera Cruz, Department of Plant Pathology, 4024 Throckmorton Plant Sciences Center, Kansas State University, Manhattan 66506-5502. E. Y. Ardales, D. Z. Skinner, J. Talag, R. J. Nelson, F. J. Louws, H. Leung, T. W. Mew, and J. E. Leach. Ninth authors: Department of Plant Pathology, 4024 Throckmorton Plant Sciences Center, Kansas State University, Manhattan 66506-5502; second, fourth, fifth, and eighth authors: Division of Entomology and Plant Pathology, International Rice Research Institute, P.O. Box 933, 1099 Manila, the Philippines; third author: USDA-ARS and Department of Agronomy, Kansas State University, Manhattan 66506-5502; sixth author: MSU-DOE Plant Research Lab, Michigan Stale University, East Lansing 48824; seventh author: Department of Plant Pathology, Washington State University, Pullman 99164-6430. Phytopathology 86:1352-1359. Accepted for publication 2 September 1996. Copyright 1996 The American Phytopathological Society. DOI: 10.1094/Phyto-86-1352.

The haplotypic variation of Xanlhomonas oryzae pv. oryzae in a farmer's field that had endemic bacterial blight in the Philippines was evaluated at a single time. The genomic structure of the field population was analyzed by repetitive sequence-based polymerase chain reaction with oligonucleotide primers corresponding to interspersed repeated sequences in prokaryotic genomes and restriction fragment length polymorphism (RFLP) with the insertion sequence IS1113. The techniques and specific probes and primers were selected because they grouped consistently into the same lineages a set of 30 selected X. oryzae pv. oryzae strains that represented the four distinct RFLP lineages found in the Philippines did. Strains (155) were systematically collected from a field planted to rice cv. Sinandomeng, which is susceptible to the indigenous pathogen population. Two of the four Philippine lineages, B and C, which included race 2 and races 3 and 9, respectively, were detected in the field. Lineage C was the predominant population (74.8%). The haplotypic diversities of 10 of the 25 blocks were significantly greater than the total haplotypic diversity of the collection in the entire field; however, between individual blocks the haplotypic diversities were not significantly different. Maplo-types from both lineages were distributed randomly across the field. Analysis of genetic diversity at the microgeographic scale provided insights into the finer scale of variation of X oryzae pv. oryzae, which are useful in designing experiments to study effects of host resistance on the population structure of the bacterial blight pathogen.