Phytophthora clandestina, a serious pathogen of subterranean clover (Trifolium subterraneum), has only been recorded in Australia. A rapid method was used to characterise genetic variation among 61 isolates of P. clandestina belonging to eight pathogenic races based on DNA sequencing and single-strand conformation polymorphism (SSCP) analyses of the β-tubulin gene of the pathogen. The β-tubulin gene among those tested displayed a high degree of variability among isolates. Cluster analysis of the SSCP profiles grouped the 61 isolates into two main clusters (A and B). Cluster A with 3 subclusters viz; I (race 177), II (race 000) and III (races 001, 121, 101, 143 and 157) and B with race 173 alone. In addition, SSCP of β-tubulin also successfully differentiated between races 173 and 177, the two most prevalent and most virulent of the races studied. This is the first time that the β-tubulin gene has been used to study intra-species variation in this pathogen. In addition to showing relationship among the strains, it also provides a practical means for rapid monitoring of current and future differences in the distribution of P. clandestina strains, giving subterranean clover breeders and farmers a sound basis for the selection/breeding and deployment of appropriate cultivars to counter the predominant strain populations in specific localities.
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