Mycological Progress

, Volume 16, Issue 10, pp 955–963 | Cite as

Intra- and Intergenomic variation of Ploidy and Clonality characterize Phytophthora capsici on Capsicum sp. in Taiwan

  • Derek W. Barchenger
  • Kurt H. Lamour
  • Zong-Ming Sheu
  • Sandesh Shrestha
  • Sanjeet Kumar
  • Shih-Wen Lin
  • Rishi Burlakoti
  • Paul W. BoslandEmail author
Original Article


Phytophthora capsici is a devastating disease of pepper (Capsicum sp.) in Taiwan causing complete loss of commercial fields. The objective of this study was to characterize genetic diversity for 38 newly collected isolates and three historical isolates. Analysis of data includes whole genome sequence for two new isolates and for two isolates collected previously in 1987 and 1995. In addition, 63 single nucleotide polymorphism loci were genotyped using targeted-sequencing, revealing 27 unique genotypes. Genotypes fell into three genetic groups: two of the groups contain 90% (n = 33) of the 2016 isolates, are triploid (or higher), are exclusively the A2 mating type and appear to be two distinct clonal lineages. The isolates from 2016 that grouped with the historical isolates are diploid and the A1 mating type. Whole genome sequence revealed that ploidy varies by linkage group, and it appears the A2 clonal lineages may have switched mating type due to increased ploidy. Most of the isolates were recently race-typed on a set of differential C. annuum, and although there was no direct correlation between virulence and ploidy, many of the triploid isolates were less virulent as compared to the historical diploid isolates. The implications for breeding resistant pepper and conducting population analyses are discussed.


Capsicum annuum Oomycetes Single nucleotide polymorphism Multi-locus genotyping Bayesian clustering Loss of heterozygosity 



The authors thank Dr. Lowell Black for his advice and helpful comments throughout this project. This work was supported by the U.S. Borlaug Fellows in Global Food Security Program through Purdue University, funded by the United States Agency for International Development. Permission to harvest infected pepper was obtained from all landowners and pepper producers, and shipment and processing of isolates was conducted under USDA permit P526P-16-02522 to Kurt Lamour.

Supplementary material

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Copyright information

© German Mycological Society and Springer-Verlag GmbH Germany 2017

Authors and Affiliations

  • Derek W. Barchenger
    • 1
    • 2
  • Kurt H. Lamour
    • 3
  • Zong-Ming Sheu
    • 2
  • Sandesh Shrestha
    • 3
  • Sanjeet Kumar
    • 2
  • Shih-Wen Lin
    • 2
  • Rishi Burlakoti
    • 2
    • 4
  • Paul W. Bosland
    • 1
    Email author
  1. 1.Department of Plant and Environmental SciencesNew Mexico State UniversityLas CrucesUSA
  2. 2.World Vegetable CenterTainanTaiwan
  3. 3.Department of Entomology and Plant PathologyUniversity of TennesseeKnoxvilleUSA
  4. 4.Agassiz Research and Development Center, Agriculture and Agri-Food CanadaAgassizCanada

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