Bakanae disease of rice in California: Investigations of disease incidence, spread, and pathogen population structure

Bakanae was observed in California in 1999, and by 2001 could be found in the majority of rice production regions of the state. While yield losses have been low thus far in California, it is important to understand the factors that influence incidence and spread of Fusarium fujikuroi throughout the state. Rice seed infested with F. fujikuroi was found to be the primary source of inoculum for Bakanae. A comparison of three seed assay methods on 198 seed lots included seed plating, observation of seedlings on germination boards and in a field grow-out assay. Low Spearman correlations between the assay methods suggested that the grow-out assay was the most suitable seed assay method. In the seed assay, seed sources and cultivars differed significantly in disease incidence. Studies on infested soil, infected crop residue and Bakanae infected Echinochloa spp. showed that infected crop residue, weed species, and infested soil, could serve as reservoirs for F. fujikuroi inoculum. Experiments utilizing established disease foci suggested that secondary spread of Bakanae in the field is not likely.; A population genetics analysis including 174 isolates of F. fujikuroi collected between 2000 and 2003 was initiated to improve understanding of the Bakanae disease cycle. Vegetative Compatibility Groups (VCGs), mating type, and Amplified Fragment Length Polymorphism (AFLP) analyses were used to elucidate the population genetic structure, and determine the importance of sexual recombination in the disease cycle. Three VCGs were detected, along with both mating types. AFLP analysis revealed the presence of 27 unique isolates, with 53% of the isolates representing a single clone. Cluster analysis assigned the isolates to three clusters, by VCG. Analysis of molecular variance indicated that VCG was the most significant contributor to observed AFLP variation, explaining 76.3%. Tests to detect random mating were carried out before and after clone-correction for the entire population, and for two intensively sampled single field populations. Random mating was rejected in all cases except the clone-corrected entire population. Low VCG diversity, predominance of a single clone and random mating test results suggest that though sexual reproduction may be occurring, clonal reproduction of F. fujikuroi predominates in California.