Genetic variation within clonal lineages of phytophthora infestans revealed through genotyping-by-sequencing, and implications for late blight epidemiology

Zachariah R. Hansen, Kathryne L. Everts, William E. Fry, Amanda J. Gevens, Niklaus J. Grünwald, Beth Krueger Gugino, Dennis A. Johnson, Steven B. Johnson, Howard S. Judelson, Brian J. Knaus, Margaret T. McGrath, Kevin L. Myers, Jean B. Ristaino, Pamela D. Roberts, Gary A. Secor, Christine D. Smart

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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 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. Kmeans 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 substructuring within clonal populations.

Original languageEnglish (US)
Article numbere0165690
JournalPloS one
Volume11
Issue number11
DOIs
StatePublished - Nov 1 2016

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Phytophthora infestans
Epidemiology
Pathogens
Joining
genotyping
Cluster Analysis
epidemiology
genetic variation
pathogens
Polymorphism
overwintering
provenance
single nucleotide polymorphism
Ontario
inoculum
Nucleotides
Canada
Single Nucleotide Polymorphism
Population

All Science Journal Classification (ASJC) codes

  • Biochemistry, Genetics and Molecular Biology(all)
  • Agricultural and Biological Sciences(all)

Cite this

Hansen, Zachariah R. ; Everts, Kathryne L. ; Fry, William E. ; Gevens, Amanda J. ; Grünwald, Niklaus J. ; Gugino, Beth Krueger ; Johnson, Dennis A. ; Johnson, Steven B. ; Judelson, Howard S. ; Knaus, Brian J. ; McGrath, Margaret T. ; Myers, Kevin L. ; Ristaino, Jean B. ; Roberts, Pamela D. ; Secor, Gary A. ; Smart, Christine D. / Genetic variation within clonal lineages of phytophthora infestans revealed through genotyping-by-sequencing, and implications for late blight epidemiology. In: PloS one. 2016 ; Vol. 11, No. 11.
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title = "Genetic variation within clonal lineages of phytophthora infestans revealed through genotyping-by-sequencing, and implications for late blight epidemiology",
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 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. Kmeans 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 substructuring within clonal populations.",
author = "Hansen, {Zachariah R.} and Everts, {Kathryne L.} and Fry, {William E.} and Gevens, {Amanda J.} and Gr{\"u}nwald, {Niklaus J.} and Gugino, {Beth Krueger} and Johnson, {Dennis A.} and Johnson, {Steven B.} and Judelson, {Howard S.} and Knaus, {Brian J.} and McGrath, {Margaret T.} and Myers, {Kevin L.} and Ristaino, {Jean B.} and Roberts, {Pamela D.} and Secor, {Gary A.} and Smart, {Christine D.}",
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Hansen, ZR, Everts, KL, Fry, WE, Gevens, AJ, Grünwald, NJ, Gugino, BK, Johnson, DA, Johnson, SB, Judelson, HS, Knaus, BJ, McGrath, MT, Myers, KL, Ristaino, JB, Roberts, PD, Secor, GA & Smart, CD 2016, 'Genetic variation within clonal lineages of phytophthora infestans revealed through genotyping-by-sequencing, and implications for late blight epidemiology', PloS one, vol. 11, no. 11, e0165690. https://doi.org/10.1371/journal.pone.0165690

Genetic variation within clonal lineages of phytophthora infestans revealed through genotyping-by-sequencing, and implications for late blight epidemiology. / Hansen, Zachariah R.; Everts, Kathryne L.; Fry, William E.; Gevens, Amanda J.; Grünwald, Niklaus J.; Gugino, Beth Krueger; Johnson, Dennis A.; Johnson, Steven B.; Judelson, Howard S.; Knaus, Brian J.; McGrath, Margaret T.; Myers, Kevin L.; Ristaino, Jean B.; Roberts, Pamela D.; Secor, Gary A.; Smart, Christine D.

In: PloS one, Vol. 11, No. 11, e0165690, 01.11.2016.

Research output: Contribution to journalArticle

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T1 - Genetic variation within clonal lineages of phytophthora infestans revealed through genotyping-by-sequencing, and implications for late blight epidemiology

AU - Hansen, Zachariah R.

AU - Everts, Kathryne L.

AU - Fry, William E.

AU - Gevens, Amanda J.

AU - Grünwald, Niklaus J.

AU - Gugino, Beth Krueger

AU - Johnson, Dennis A.

AU - Johnson, Steven B.

AU - Judelson, Howard S.

AU - Knaus, Brian J.

AU - McGrath, Margaret T.

AU - Myers, Kevin L.

AU - Ristaino, Jean B.

AU - Roberts, Pamela D.

AU - Secor, Gary A.

AU - Smart, Christine D.

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N2 - 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. Kmeans 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 substructuring within clonal populations.

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