Genotyping Dickeya dianthicola causing potato blackleg and soft rot associated with inoculum geography in Northeastern America

Authors: GE, TONGLING - University Of Maine; JIANG, HE - University Of Maine; JOHNSON, STEVEN - University Of Maine Cooperative Extension; Larkin, Robert - Bob; CHARKOWSKI, AMY - Colorado State University; SECOR, GARY - North Dakota State University; HAO, JIANJUN - University Of Maine

Submitted to: Plant Disease
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: 11/17/2020
Publication Date: 11/19/2020
Citation: Ge, T., Jiang, H., Johnson, S.B., Larkin, R.P., Charkowski, A.O., Secor, G., Hao, J. 2020. Genotyping Dickeya dianthicola causing potato blackleg and soft rot associated with inoculum geography in Northeastern America. Plant Disease. https://doi.org/10.1094/pdis-10-20-2138-re.
DOI: https://doi.org/10.1094/pdis-10-20-2138-re

Interpretive Summary: A major outbreak of a serious and damaging disease of potato plants, known as blackleg and soft rot of potato, caused primarily by the bacterial pathogen Dickeya dianthicola, has resulted in significant economic losses in the Northeaster United States since 2015. Because this disease is primarily spread by infected seed, it was believed that the pathogen originated from seed tubers. To determine the distribution and potential origin of the epidemic, potato samples were collected from 11 northeastern states from 2015 to 2019 and tested for the presence and genetic characteristics of the pathogen. Potato samples from all states showed the presence of Dickeya dianthicola, with positive tests accounting for 39.8% of all samples. Analysis of genetic diversity indicated three distinct genotypes, designated Types I, II, and III. Type I was the predominant genotype and primarily associated with Maine, whereas Types II and III occurred primarily in other states and appeared to be more closely associated with isolates from other countries. This work indicates that the disease outbreak was caused by multiple strains of D. dianthicola of varying geographic origin. This research is useful for researchers to identify the genetic diversity and origins of the epidemic and can be used to improve control strategies and mitigate disease losses.

Technical Abstract: An outbreak of blackleg and soft rot of potato, caused primarily by the bacterial pathogen Dickeya dianthicola, has resulted in significant economic losses in the Northeastern United States since 2015. The spread of this seedborne disease is highly associated with seed distribution, therefore it was believed that the pathogen originated from seed tubers. To elucidate the epidemics of blackleg and track inoculum origins, a total of 1183 potato samples were collected from 11 northeastern states from 2015 to 2019. Of these samples, 39.8% tested positive for D. dianthicola. Seventeen isolates of Dickeya dianthicola were recovered from these samples and the genetic diversity of these isolates was examined. Fingerprinting with BOX-PCR and phylogenetic analysis based on 16S rDNA and gapA sequences indicated that D. dianthicola isolates were divided into three genotypes, denoted Type I, II, and III. Ninety five percent of samples from Maine were Type I. Type II was found in Maine only in 2015 and 2018. Type II was present throughout the five years in some states at a lower percentage than Type I. Type III was found in Pennsylvania, New Jersey and Massachusetts, but not in Maine. Therefore, Type I appears to be associated with Maine, but Type II appeared to be endemic to the Northeastern United States. The Type II and rarer Type III strain are closer to the D. dianthicola type strain, which was isolated from countries out of USA. This work provides evidence that the outbreak of blackleg of potato in the Northeastern United States was caused by multiple strains of D. dianthicola. Geographic origins of these strains require further investigation.