Genetic Variation within Clonal Lineages of Phytophthora infestans Revealed through Genotyping-By-Sequencing, and Implications for Late Blight Epidemiology.
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 were 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 collected from 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 pathogen dispersal and overwintering within regions, as well as long-distance pathogen transport across regions. In the US-23 NJ tree, grouping by year was more prominent than grouping 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.
Plant Pathology and Plant-Microbe Biology Section, Cornell University, Geneva, NY, United States of America.
Zachariah R
ZR
Hansen
Department of Plant Science and Landscape Architecture, University of Maryland, Salisbury, MD, United States of America.
Kathryne L
KL
Everts
Plant Pathology and Plant-Microbe Biology Section, Cornell University, Ithaca, NY, United States of America.
William E
WE
Fry
Department of Plant Pathology, University of Wisconsin, Madison, WI, United States of America.
Amanda J
AJ
Gevens
Horticultural Crops Research Laboratory, United States Department of Agriculture-Agricultural Research Service, Corvallis, OR, United States of America.
Niklaus J
NJ
Grünwald
Department of Plant Pathology and Environmental Microbiology, The Pennsylvania State University, University Park, PA, United States of America.
Beth K
BK
Gugino
Department of Plant Pathology, Washington State University, Pullman, WA, United States of America.
Dennis A
DA
Johnson
University of Maine Cooperative Extension, Presque Isle, ME, United States of America.
Steven B
SB
Johnson
Department of Plant Pathology and Microbiology, University of California Riverside, Riverside, CA, United States of America.
Howard S
HS
Judelson
Horticultural Crops Research Laboratory, United States Department of Agriculture-Agricultural Research Service, Corvallis, OR, United States of America.
Brian J
BJ
Knaus
Plant Pathology and Plant-Microbe Biology Section, Cornell University, Riverhead, NY, United States of America.
Margaret T
MT
McGrath
Plant Pathology and Plant-Microbe Biology Section, Cornell University, Ithaca, NY, United States of America.
Kevin L
KL
Myers
Department of Plant Pathology, North Carolina State University, Raleigh, NC, United States of America.
Jean B
JB
Ristaino
Department of Plant Pathology, University of Florida, Immokalee, FL, United States of America.
Pamela D
PD
Roberts
Department of Plant Pathology, North Dakota State University, Fargo, ND, United States of America.
Gary A
GA
Secor
Plant Pathology and Plant-Microbe Biology Section, Cornell University, Geneva, NY, United States of America.
Christine D
CD
Smart
D001483:Base Sequence; D002170:Canada; D016054:DNA, Protozoan / Q000235:genetics*; D008040:Genetic Linkage / Q000235:genetics; D005838:Genotype; D005843:Geography; D018551:Solanum lycopersicum / Q000469:parasitology; D055750:Phytophthora infestans / Q000235:genetics* / Q000302:isolation & purification*; D010935:Plant Diseases / Q000469:parasitology*; D020641:Polymorphism, Single Nucleotide / Q000235:genetics*; D017422:Sequence Analysis, DNA; D011198:Solanum tuberosum / Q000469:parasitology; D014481:United States
D016054:DNA, Protozoan