Quantification of Cylindrocarpon sp. in roots of almond and peach trees from orchards affected by Prunus replant disease
R. G. BHAT (1), L. S. Schmidt (2), G. T. Browne (2)
(1) University of California, Davis, CA, U.S.A.; (2) USDA ARS, Davis, CA, U.S.A.
Prunus replant disease (PRD) is a poorly understood soilborne complex that suppresses replanted almond and peach orchards in California. Using culture-dependent and culture-independent approaches, we found Cylindrocarpon (Cyl) macrodidymum among microorganisms associated with PRD. We developed a qPCR assay to further examine the Cyl-PRD association; a selective primer pair that amplified a 374-bp rDNA fragment from C. macrodidymum was coupled with a specific hydrolysis probe. The assay was optimized and validated using genomic DNA from the target and 70 non-target microorganisms and rootstocks. The lower detection limit was 100 fg Cyl DNA per 25 µl of PCR mix. The assay was used with root samples from replicate healthy and PRD-affected almond and peach trees (in fumigated and non-fumigated plots, respectively) in five California orchards. All orchards were planted in winter and expressed PRD symptoms the following summer. Root samples were collected on 1 to 5 dates per orchard from Apr.-Sept. of the year trees were planted. In orchards 1-3, Cyl levels were significantly higher in PRD-affected than in healthy roots on some dates (7 of 11 sampling dates), but in orchards 4 and 5 (1 date each) Cyl levels were near the lower detection limit and did not differ in relation to PRD incidence. We conclude that Cyl concentration in roots is positively associated with PRD in some orchards; the relationship may be seasonal, requiring systematic temporal sampling for quantification.
© 2011 by The American
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