Population genetic structure of Alternaria species collected from tomato and potato in North Carolina and Wisconsin

Authors: ADHIKARI, TIKA - North Carolina State University; MUZHINJI, NORMAN - Ministry Of Agriculture - Namibia; Halterman, Dennis; LOUWS, FRANK - North Carolina State University

Submitted to: Scientific Reports
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: 8/13/2019
Publication Date: 8/23/2021
Citation: Adhikari, T.B., Muzhinji, N., Halterman, D.A., Louws, F.J. 2021. Population genetic structure of Alternaria species collected from tomato and potato in North Carolina and Wisconsin. Phytopathology. (2021) 11:17024. https://doi.org/10.1038/s41598-021-95486-6.
DOI: https://doi.org/10.1038/s41598-021-95486-6

Interpretive Summary: Fungal plant pathogens belonging to the Genus Alternaria cause diseases of potato and tomato, including early blight, leaf blight, and stem canker. Samples of Alternaria species were collected from potato and tomato fields in North Carolina and Wisconsin in order to study the population diversity. Genetic analyses were done to identify population structures. We found that in three distinct clusters, indicating that population differences were determined by the host and geographic location. The main conclusion is that mixed reproduction is likely contributing to the diversity among Alternaria species and that most populations are distinctly suited to infecting potatoes or tomatoes. The tools developed and methods used in this study will impact future investigations into the differences that exist in evolving populations of Alternaria species from tomato and potato. The results will also impact the development of effective disease management strategies for Alternaria in tomato and potato.

Technical Abstract: Early blight (EB), caused by Alternaria linariae (Neerg.) Simmons and A. solani (Ellis and Martin) Jones and Grout of tomato and potato, and leaf blight and stem canker, caused by A. alternata (Fr.) Keissler of tomato are economically important diseases in the United States. In total, 214 isolates of Alternaria spp. were collected from tomato and potato fields between 2012 and 2015 in North Carolina (NC) and Wisconsin (WI). Polymerase chain reaction (PCR)-based primers were employed to identify these isolates and newly developed 10 microsatellite or simple-sequence repeat (SSR) loci were used to analyze the genetic structure and population differentiation of the three Alternaria spp. SSR analysis indicated high gene diversity (H value = 0.52 to 0.92) and genotypic diversity (Shannon-Weiner’s index = 2.00 to 4.00), and significant population differentiation among three Alternaria spp. Discriminant analysis of principal components (DAPC) revealed genetically three distinct clusters of Alternaria spp. from tomato and potato, indicating that the populations were structured by host preference and geographic locations. Clone-corrected data to test the null hypothesis of random mating indicated an equal distribution of both mating type genes in populations of A. alternata and A. solani but it was significantly deviated from 1:1 ratio in populations of A. linariae. Significant multilocus linkage equilibrium was counted in one population each of A. linariae and A. alternata. Overall, these results suggest that mixed reproduction is likely contributing to develop genetically diverse genotypes and that most populations of Alternaria spp. are genetically differentiated over the tomato and potato fields in NC and WI.