Comparison of genotyping by sequencing and microsatellite markers for unravelling population structure in the clonal fungus Verticillium dahliae

V. Rafiei, Z. Banihashemi, R. M. Jiménez-Díaz, J. A. Navas-Cortés, B. B. Landa, Maria Del Mar Jimenez Gasco, B. G. Turgeon, M. G. Milgroom

Research output: Contribution to journalArticle

4 Citations (Scopus)

Abstract

Microsatellite genotyping of a large sample of isolates of Verticillium dahliae from diverse locations recently identified seven distinct genotypic clusters. However, these clusters were not put in the context of phenotypes known to be correlated with clonal lineages in V. dahliae. The objective of this study was to compare clusters defined by microsatellite markers with clonal lineages defined by single-nucleotide polymorphisms (SNPs) and vegetative compatibility groups (VCGs). Genotyping isolates known to belong to specific clonal lineages (based on SNPs) with microsatellite markers determined the correspondence of clusters and lineages. All but one cluster corresponded to a known clonal lineage, allowing analysis of correlations of phenotypes with microsatellite genotypes from other studies. As shown previously, most race 1 isolates are in lineage 2A, and most isolates with the defoliating pathotype are in lineage 1A. Phylogenetic incompatibility was used to test for recombination or homoplasy caused by hypervariable microsatellite loci; incompatibility was highly correlated with the number of alleles per locus, suggesting that homoplasy caused by parallel evolution of microsatellite alleles is the cause of incompatibility. Microsatellite genotyping of lineage 1A isolates from cotton and olive in Spain over a 29-year period revealed remarkably little variation; these markers did not mutate enough to provide insight on the spatial and temporal expansion of this clone. Overall, this study showed that microsatellite genotyping can be used to identify clonal lineages in V. dahliae, which has predictive power for inferring phenotypes of phytopathological relevance such as race and pathotype.

Original languageEnglish (US)
Pages (from-to)76-86
Number of pages11
JournalPlant Pathology
Volume67
Issue number1
DOIs
StatePublished - Jan 1 2018

Fingerprint

Verticillium
Verticillium dahliae
Microsatellite Repeats
genotyping
population structure
Fungi
microsatellite repeats
fungi
Population
pathotypes
Phenotype
phenotype
single nucleotide polymorphism
Single Nucleotide Polymorphism
Alleles
alleles
parallel evolution
loci
Olea
Spain

All Science Journal Classification (ASJC) codes

  • Agronomy and Crop Science
  • Genetics
  • Plant Science
  • Horticulture

Cite this

Rafiei, V. ; Banihashemi, Z. ; Jiménez-Díaz, R. M. ; Navas-Cortés, J. A. ; Landa, B. B. ; Jimenez Gasco, Maria Del Mar ; Turgeon, B. G. ; Milgroom, M. G. / Comparison of genotyping by sequencing and microsatellite markers for unravelling population structure in the clonal fungus Verticillium dahliae. In: Plant Pathology. 2018 ; Vol. 67, No. 1. pp. 76-86.
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Rafiei, V, Banihashemi, Z, Jiménez-Díaz, RM, Navas-Cortés, JA, Landa, BB, Jimenez Gasco, MDM, Turgeon, BG & Milgroom, MG 2018, 'Comparison of genotyping by sequencing and microsatellite markers for unravelling population structure in the clonal fungus Verticillium dahliae', Plant Pathology, vol. 67, no. 1, pp. 76-86. https://doi.org/10.1111/ppa.12713

Comparison of genotyping by sequencing and microsatellite markers for unravelling population structure in the clonal fungus Verticillium dahliae. / Rafiei, V.; Banihashemi, Z.; Jiménez-Díaz, R. M.; Navas-Cortés, J. A.; Landa, B. B.; Jimenez Gasco, Maria Del Mar; Turgeon, B. G.; Milgroom, M. G.

In: Plant Pathology, Vol. 67, No. 1, 01.01.2018, p. 76-86.

Research output: Contribution to journalArticle

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AU - Rafiei, V.

AU - Banihashemi, Z.

AU - Jiménez-Díaz, R. M.

AU - Navas-Cortés, J. A.

AU - Landa, B. B.

AU - Jimenez Gasco, Maria Del Mar

AU - Turgeon, B. G.

AU - Milgroom, M. G.

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N2 - Microsatellite genotyping of a large sample of isolates of Verticillium dahliae from diverse locations recently identified seven distinct genotypic clusters. However, these clusters were not put in the context of phenotypes known to be correlated with clonal lineages in V. dahliae. The objective of this study was to compare clusters defined by microsatellite markers with clonal lineages defined by single-nucleotide polymorphisms (SNPs) and vegetative compatibility groups (VCGs). Genotyping isolates known to belong to specific clonal lineages (based on SNPs) with microsatellite markers determined the correspondence of clusters and lineages. All but one cluster corresponded to a known clonal lineage, allowing analysis of correlations of phenotypes with microsatellite genotypes from other studies. As shown previously, most race 1 isolates are in lineage 2A, and most isolates with the defoliating pathotype are in lineage 1A. Phylogenetic incompatibility was used to test for recombination or homoplasy caused by hypervariable microsatellite loci; incompatibility was highly correlated with the number of alleles per locus, suggesting that homoplasy caused by parallel evolution of microsatellite alleles is the cause of incompatibility. Microsatellite genotyping of lineage 1A isolates from cotton and olive in Spain over a 29-year period revealed remarkably little variation; these markers did not mutate enough to provide insight on the spatial and temporal expansion of this clone. Overall, this study showed that microsatellite genotyping can be used to identify clonal lineages in V. dahliae, which has predictive power for inferring phenotypes of phytopathological relevance such as race and pathotype.

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