Detection and quantification of Cronartium pini from Scots pine bark and wood with Cronartium spp.-specific quantitative PCR

The forest disease, Scots pine blister rust, is caused by the rust fungus Cronartium pini. This pathogen was previously known as the host-alternating type C. flaccidum and non-host-alternating type Peridermium pini. Recent epidemics of this disease in Northern European forests, especially young Scots pine forests in Sweden, caused significant economic and ecological losses. Cronartium pini can be identified based on the typical orange blister-like aecia in Scots pine in summer, but any molecular identification and quantification method has not been available for Cronartium spp. This study developed qPCR primers that are specific to Cronartium spp. and evaluated DNA extraction protocols from pine bark and wood to enable robust qPCR assays. As little as three Cronartium ITS copies can be detected with the protocol. Since only C. pini is known to infect Scots pine in Northern Europe, the protocols were applied to detect C. pini from Scots pine samples without typical symptoms and investigate the C. pini colonization in Scots pine branches from the forest. These results will aid the detection and quantification of C. pini in asymptomatic or symptomatic samples and monitoring Scots pine blister rust in the forest in northern Europe.