Limited Evidence for Accumulation of Latent Infections of Canker-Causing Pathogens in Shoots of Stone Fruit and Nut Crops in California.

Prevalence of latent infections of the canker-causing fungi and species of , , , , and in young shoots of almond, prune, and walnut trees in California was studied to test the hypotheses that latent infections accumulate from current-season shoots to 1-year-old shoots in the orchard and there are distinct associations among pathogen taxa present as latent infections in the same shoot. Samples of newly emerged and 1-year-old shoots were periodically collected in each almond, prune, and walnut orchard for two growing seasons. A real-time quantitative PCR assay was used to quantify latent infection with three parameters: incidence, molecular severity, and latent infection index. spp. were absent from most samples. For almond, spp. and spp. were detected with a maximum incidence >90%, while and spp. incidence was <20% in most cases. In prune orchards, the incidence levels of were >50% in most cases, while those of spp. and spp. were 30 to 60% and 30 to 100%, respectively. For walnut, many samplings showed higher incidence in 1-year-old (30 to 80%) than in newly emerged shoots (10 to 50%). Accumulation of latent infection between the two shoot age classes was detected in only a few cases. The percentages of samples showing coexistence of two, three, and four pathogen taxa in the same shoot were 20 to 25, <10, and <5%, respectively. Pairwise associations among pathogen taxa in the same shoot were significant in many cases.