2.1 Pathogen sampling and identification in potato fields with blackleg disease symptoms
Pectinolytic bacteria were isolated from symptomatic plant tissues on crystal violet pectate medium (Hélias, Hamon, Huchet, Wolf, & Andrivon, 2012). Isolates were purified on agar plates and characterized at the genus (Dickeya and Pectobacterium ) and species (D. solani and D. dianthicola ) levels using the PCR primers listed in Table S1 . Two sampling strategies were used. From 2004 to 2015, a national inventory was conducted in French potato producing areas. Each year (with the exception of the year 2006), fields exhibiting blackleg symptoms were randomly sampled by collecting diseased plants from which isolates were recovered and characterized. From 541 fields, around 1600 isolates were collected and taxonomically characterized. In parallel, from 2013 to 2016, 19 of the potato fields exhibiting more than 1% of blackleg incidence were deeply sampled. Around 30 plants with blackleg symptoms were collected along a transect in each field, and a single isolate was retained from each of the 548 plants. The resulting 548 isolates were characterized taxonomically.