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ARS Home » Pacific West Area » Corvallis, Oregon » Horticultural Crops Research Unit » Research » Publications at this Location » Publication #335439
Title: Genetic variation within clonal lineages of Phytophthora infestans revealed through genotyping-by-sequencing, and implications for late blight epidemiology

Author
item HANSEN, ZACHARIAH - Cornell University
item EVERTS, KATHRYNE - Cornell University
item FRY, WILLIAM - University Of Wisconsin
item GEVENS, AMANDA - University Of Wisconsin
item Grunwald, Niklaus - Nik
item GUGINO, BETH - Pennsylvania State University
item JOHNSON, DENNIS - Washington State University
item JOHNSON, STEVEN - University Of Maine Cooperative Extension
item JUDELSON, HOWARD - University Of California
item Knaus, Brian
item MCGRATH, MARGARET - Cornell University
item MYERS, KEVIN - Cornell University
item RISTAINO, PAMELA - University Of Florida
item ROBERTS, PAMELA - University Of Florida
item SECOR, GARY - North Dakota State University
item SMART, CHRISTINE - Cornell University

Submitted to: PLOS ONE
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: 10/17/2016
Publication Date: 11/3/2016
Citation: Hansen, Z.R., Everts, K.L., Fry, W.E., Gevens, A.J., Grunwald, N.J., Gugino, B.K., Johnson, D.A., Johnson, S.B., Judelson, H.S., Knaus, B.J., McGrath, M.T., Myers, K.L., Ristaino, P.D., Roberts, P.D., Secor, G.A., Smart, C.D. 2016. Genetic variation within clonal lineages of Phytophthora infestans revealed through genotyping-by-sequencing, and implications for late blight epidemiology. PLoS One. 11(11):e0165690. doi:10.1371/journal.pone.0165690.

Interpretive Summary: Phytophthora infestans, the cause of the devastating late blight disease of potato and tomato, reproduces as distinct genetic clones in the US. We evaluated genetic diversity within 4 distinct clones found commonly in the US named US8, US11, US23 and US24. Our results support previous studies that found significant genetic diversity within clones of P. infestans.

Technical Abstract: Genotyping-by-sequencing (GBS) was performed on 257 Phytophthora infestans isolates belonging to four clonal lineages to study within-lineage diversity. The four lineages used in the study included US-8 (n=28), US-11 (n=27), US-23 (n=166), and US-24 (n=36), with isolates originating from 23 of the United States and Ontario, Canada. The majority of isolates were collected between 2010 and 2014 (94%), with the remaining isolates were collected in 1994 to 2009, and 2015. Between 3,774 and 5,070 single-nucleotide polymorphisms (SNPs) were identified within each lineage, and were used to investigate relationships among individuals. K-means hierarchical clustering revealed three clusters within lineage US-23, with US-23 isolates clustering more by collection year than by geographic origin. K-means hierarchical clustering did not reveal significant clustering within the smaller US-8, US-11, and US-24 data sets. Neighbor-joining (NJ) trees were also constructed for each lineage. All four NJ trees revealed evidence for regional pathogen dispersal and overwintering, as well as long distance pathogen transport. In the US-23 NJ tree clustering by year was relatively prominent versus clustering by region, which indicates the importance of long-distance pathogen transport as a source of initial late blight inoculum. Our results support previous studies that found significant genetic diversity within clonal lineages of P. infestans, and show that GBS offers sufficiently high resolution to detect sub-structuring within clonal populations.