Long term field sampling in Sweden reveals a shift in occurrence of cytochrome b genotype and amino acid substitution F129L in Alternaria solani, together with a high incidence of the G143A substitution in Alternaria alternata

Abstract

The incidence of the pathogenic fungus Alternaria solani on potato during the years 2009 to 2016 was analysed and the distribution of the two genotypes of cytochrome b (genotype 1, GI and genotype 2, GII) determined. Potato leaflets with lesions resembling early blight were collected in August and September 2009–2016 in the south-eastern part of Sweden and during 2010 and 2012–2014 in the central part of Sweden. In total, 2042 potato leaflet samples were analysed using diagnostic PCR methods. Alternaria solani was more commonly found in the samples collected later in the growing seasons. The occurrence of substitutions in the gene encoding cytochrome b, associated with loss of sensitivity towards strobilurins, was determined by sequencing a segment in the target gene in all confirmed A. solani samples. The proportion of A. solani GI decreased in relation to GII over the years. All except five GI samples were non-mutated. Genotype 2 was already present in the first year of sampling but only one sample possessed the F129 L substitution. A distinct shift from non-mutated GII to GII F129 L was observed between the season of 2011–2012 and a similar shift occurred in the pathogen population from GI to GII between 2012 and 2013. Identification of Alternaria alternata was performed during 2009–2013. The species was most often in co-occurrence with A. solani. Most of the samples investigated possessed the G143A substitution associated with strobilurin resistance.