Effect of sampling time, quantification method and tree sample pooling on Phytophthora cinnamomi root quantities in South African avocado orchards

Abstract

Phytophthora cinnamomi is a destructive soilborne pathogen causing Phytophthora root rot on avocados worldwide. Little is known about the effect of time of root sampling, root quantification method (quantitative real-time PCR [qPCR]) versus baiting) and tree sample pooling strategies, on the quantification of the pathogen in roots in avocado orchard trees. This was investigated in six avocado orchards in two climatically different production regions (Mooketsi and Letaba) in the Limpopo Province, South Africa, over a two-year period. Two different tree sample pooling strategies, consisting of either a four-pooled-group (four groups each containing five pooled trees) or a single-pooled-group (20 trees pooled) per one-hectare, were both shown to be suitable for quantifying P. cinnamomi in tree roots using qPCR or root baiting. Phytophthora cinnamomi root quantities from the two tree sample pooling strategies were significantly correlated for both quantification methods. Both quantification methods were suitable for quantifying the pathogen in roots, although qPCR was superior to root baiting at identifying significant differences in P. cinnamomi quantities among root sampling time points. The effect of time of sampling was dependent on the investigated year. In 2017, root quantities, which were only evaluated using qPCR, did not reveal a consistent trend of a specific sampling time yielding the highest root quantities for most of the orchards. However, in 2018, five of the orchards, based on the qPCR analyses, contained significantly higher P. cinnamomi root quantities in May (late autumn) than in March (early autumn), August (late winter), and October/November (late spring). In 2018, P. cinnamomi root DNA quantities were significantly positively correlated with the number of soil temperature hours at 20-24°C and 20-29°C two months preceding the root sampling dates, and negatively correlated with the number of hours at 15-19°C two months preceding to root sampling. Our study has identified P. cinnamomi root quantification methods and tree sample pooling strategies which will be useful for understanding the biology of the pathogen and when disease management strategies should be in place.