Identification and characterisation of Phytophthora species associated with New Zealand apple orchards

Abstract

Phytophthora root and crown rot is a destructive and economically important disease of apple worldwide. Several Phytophthora species are implicated but there have been no recent detailed studies to identify and characterise the Phytophthora species associated with New Zealand apple orchards. Soil samples were obtained from apple orchards in Hawke’s Bay (11 orchard blocks), Tasman (13 orchard blocks), Waikato (2 orchard blocks), Otago (2 orchard blocks) and Canterbury (2 orchard blocks), representing different cultivars and age groups. Phytophthora isolates were recovered by baiting using Himalayan cedar needles (Cedrus deodara), lupin radicles and apple cotyledons as baits. Lupin was the most effective bait, recovering 147 Phytophthora spp. isolates compared to apple cotyledons (72 isolates) and cedar needles (52 isolates). The Phytophthora isolates recovered were identified based on morphology and DNA sequencing. Seven species were identified, Phytophthora cactorum, P. cambivora, P. megasperma, P. plurivora, P. rosacearum, P. chamydospora, P. cryptogeae and isolates with unresolved identity (Phytophthora spp.). The most prevalent species was P. cactorum (203 isolates). A higher number of Phytophthora spp. and P. cactorum isolates were recovered from the old (> 20-year-old) and medium (6–19-year-old) orchards compared to the young (2–5-year-old) orchards. The genetic diversity of P. cactorum was determined using random amplified microsatellites (RAMS) and universally primed polymerase chain reaction (UP-PCR) primers and relative virulence of isolates of the recovered Phytophthora species assessed. The 59 P. cactorum isolates were placed into five major groups of 3, 16, 9, 9 and 20 isolates each with two isolates each placed in groups by themselves, with the P. cactorum population in the orchards dispersed in the different groups. From the genetic diversity analysis isolates of P. cactorum and representative isolates of the different species recovered were selected and their virulence assessed on different apple rootstocks using detached root and shoot assays and whole plant experiments. All Phytophthora species and P. cactorum isolates tested were virulent on the apple rootstocks tested, with rootstock MM106 being more susceptible than M9 and M26. There was no correlation between the genetic diversity and virulence. The prevalence and dominance of P. cactorum determined in the study denotes its significance within New Zealand’s apple orchards. The broad diversity of Phytophthora species identified emphasizes the need for continued monitoring to safeguard orchards from these potential threats. These may also represent a reciprocal threat for other ecosystems if these species move from orchards to forest/native ecosystems and vice versa.