Analysis of DNA Polymorphism and Virulence in Philippine Strains of Xanthomonas oryzae pv. oryzicola

Abstract

Molecular tools were used to analyze the genetic diversity and population structure of Xanthomonas oryzae pv. oryzicola, the bacterial leaf streak pathogen of rice in the Philippines. Representative pathogen strains were selected and used to assess resistance in rice germplasm. A partial genomic library of X. oryzae pv. oryzicola was constructed, and a 459-bp clone containing the repetitive DNA element R41 was selected as a probe for restriction fragment length polymorphism (RFLP) analysis and sequenced. R41 shared 44% sequence homology with the putative transposase gene of IS1112, an insertion element cloned from X. oryzae pv. oryzae. Using R41 as a probe for RFLP analysis, 26 band profiles were discerned in a collection of 123 strains of X. oryzae pv. oryzicola. Analysis of PstI digestion patterns of DNA from the same collection resolved 36 haplotypes. Several clusters of strains were detected after grouping of data based on either pR41 as a probe or Pst1 digestion patterns. However, based on bootstrap analysis, the clusters were not robust. Genetic diversity was high for the entire collection as well as within spatially and temporally defined subsets of strains. Even a set of strains collected from a single site at a single time was highly diverse. Strains representing the different DNA types were inoculated to a set of diverserice cultivars. Consistent rice varietal groupings were obtained from disease reaction data, but there was no correlation between pathogen isolate cluster and host reaction across inoculation trials. Isozyme group I of rice, representing tropical japonica and javanica germplasm, is a promising source of resistance to bacterial leaf streak.

An operon for production of bioactive gibberellin A4 phytohormone with wide distribution in the bacterial rice leaf streak pathogen Xanthomonas oryzae pv. oryzicola

“…For screening, previously described West African (Wonni et al ., ) and Asian (Raymundo et al ., ) X. oryzae strains were obtained from a collection maintained at Colorado State University (Fort Collins, CO, USA). The presence of the GA biosynthetic operon was directly investigated by PCR amplification of four overlapping fragments that together cover the entire operon (Fig.…”

“…Insertion sequence elements in the vicinity of the GA operon were first found using ISfinder New Phytologist (Siguier et al, 2006), and then more completely elucidated by manual curation. For screening, previously described West African (Wonni et al, 2014) and Asian (Raymundo et al, 1999) X. oryzae strains were obtained from a collection maintained at Colorado State University (Fort Collins, CO, USA). The presence of the GA biosynthetic operon was directly investigated by PCR amplification of four overlapping fragments that together cover the entire operon ( Fig.…”

Xanthomonas oryzae pathovars: model pathogens of a model crop

“…Xoc has not been studied as broadly, but analysis of strains isolated at different times and different locations in the Philippines showed a level of diversity similar to Xoo (Raymundo et al ., 1999). Clusters of isolates were not robust, and there was no correlation between clusters and the reactions of a diverse set of rice varieties.…”

Evaluation of Rice Germplasm against Bacterial Leaf Streak Disease Reveals Sources of Resistance in African Varieties

“…However, most rice germplasm cultivated in Asia is susceptible to BLS. Raymundo et al [13] reported that the African variety Morobereckan (upland japonica) is one of the most resistant to Asian Xoc strains. The wild rice O. meyeriana and O. officinalis showed a high level of resistance to Chinese Xoc strains [14].…”