Evidence of genetically diverse virulent mating types of Phytophthora capsici from Capsicum annum L.

  • Kiran NawazEmail author
  • Ahmad Ali Shahid
  • Louis BengyellaEmail author
  • Muhammad Nasir Subhani
  • Muhammad Ali
  • Waheed Anwar
  • Sehrish Iftikhar
  • Shinawar Waseem Ali
Original Paper


Chili pepper (Capsicum annum L.) is an important economic crop that is severely destroyed by the filamentous oomycete Phytophthora capsici. Little is known about this pathogen in key chili pepper farms in Punjab province, Pakistan. We investigated the genetic diversity of P. capsici strains using standard taxonomic and molecular tools, and characterized their colony growth patterns as well as their disease severity on chili pepper plants under the greenhouse conditions. Phylogenetic analysis based on ribosomal DNA (rDNA), β-tubulin and translation elongation factor 1α loci revealed divergent evolution in the population structure of P. capsici isolates. The mean oospore diameter of mating type A1 isolates was greater than that of mating type A2 isolates. We provide first evidence of an uneven distribution of highly virulent mating type A1 and A2 of P. capsici that are insensitive to mefenoxam, pyrimorph, dimethomorph, and azoxystrobin fungicides, and represent a risk factor that could ease outpacing the current P. capsici management strategies.


Phylogeny β-Tubulin Pathogenicity test Oomycetes Root-rot Fungicide resistance 



This project was sponsored by the Higher Education Commission of Pakistan; via competitive Indigenous PhD fellowship program No: 112-34924-2AV1-197. We thank all the farm owners that allowed regular visits to their farms.

Compliance with ethical standards

Conflict of interest

The authors declare that they have no conflict of interest.

Research involving human and animal participants

This article does not contain any studies with human participants or animals performed by any of the authors.

Informed consent

Informed consent was obtained from all individual participants included in the study.

Supplementary material

11274_2018_2511_MOESM1_ESM.docx (22 kb)
Supplementary material 1 (DOCX 21 KB)


  1. Anonymous (2005) Agricultural Statistics of Pakistan, Government of Pakistan, Ministry of Food, Agriculture and Livestock. Economic Wing, Islamabad, p 76Google Scholar
  2. Appiah AA, Flood J, Archer SA (2003) Inter-and intraspecific morphometric variation and characterization of Phytophthora isolates from cocoa. Plant Pathol 52:168–180CrossRefGoogle Scholar
  3. Barchenger, DW, Lamour K, Sheu Z-M, Shrestha S, Kumar S, Lin S-W, Burlakoti RR, Bosland PW (2017) Intra- and intergenomic variation of ploidy and clonality characterize Phytophthora capsici on Capsicum sp. in Taiwan. Mycol Prog 16:893–904. CrossRefGoogle Scholar
  4. Bartnicki-Garcia S, Wang MC (1983) Biochemical aspects of morphogenesis in Phytophthora. In: Erwin DC, Bartnicki-Garcia S, Tsao PH (eds) Phytophthora: its biology, taxonomy, ecology, and pathology. The American Phytopathological Society, St. Paul, pp 121–137Google Scholar
  5. Castro-Rocha A, Hulvey JP, Wick R, Shrestha SK, Lamour K (2017) Genetic diversity of Phytophthora capsici recovered from Massachusetts between 1997 and 2014. Mycol Progress 16:999–1006CrossRefGoogle Scholar
  6. Cooke DEL, Duncan JM (1997) Phylogenetic analysis of Phytophthora spp. based on ITS1 and ITS2 sequences of rRNA. Mycol Research 101(6):667–677CrossRefGoogle Scholar
  7. Cooke DEL, Drenth A, Duncan JM, Wagels G, Brasier CM (2000) A molecular phylogeny of Phytophthora and related Oomycetes. Fungal Genet Biol 30(1):17–32CrossRefPubMedGoogle Scholar
  8. Edgar RC (2004) MUSCLE: multiple sequence alignment with high accuracy and high throughput. Nucleic Acids Res 32:1792–1797CrossRefPubMedPubMedCentralGoogle Scholar
  9. Elliott M, Shamoun SF, Sumampong G, James D, Masri S, Varga A (2009) Evaluation of several commercial biocontrol products on European and North American populations of Phytophthora ramorum. Biocontrol Sci Technol 19(10):1007–1021CrossRefGoogle Scholar
  10. Erwin DC, Ribeiro OK (1996) Phytophthora diseases worldwide. American Phytopathological Society, St Paul, p 562Google Scholar
  11. Fernández-Pavía SP, Biles CL, Waugh ME, OnsurezWaugh K, Rodríguez-Alvarado G, Liddell CM (2004) Characterization of southern New Mexico Phytophthora capsici Leonian isolates from pepper (Capsicum annuum L.). Rev Mex Fitopatol 22:82–89Google Scholar
  12. Förster H, Cummings MP, Coffey MD (2000) Phylogenetic relationships of Phytophthora species based on ribosomal ITS I DNA sequence analysis with emphasis on Waterhouse groups V and VI. Mycol Res 104(9):1055–1061CrossRefGoogle Scholar
  13. Gevens AJ, Donahoo RS, Lamour KH, Hausbeck MK (2008) Characterization of Phytophthora capsici causing foliar and pod blight of snap bean in Michigan. Plant Dis 92(2):201–209CrossRefGoogle Scholar
  14. Glosier BR, Qgundiwin EA, Sidhu GS, Sischo DR, Prince JP (2008) Adifferential series of pepper (Capsicum annuum) lines delineates fourteen physiologicalraces of Phytophthora capsici. Euphytica 162:23–30CrossRefGoogle Scholar
  15. Gobena D, Roig J, Galmarini C, Hulvey J, Lamour K (2012) Genetic diversityof Phytophthora capsici isolates from pepper and pumpkin in Argentina. Mycologia 104:102–107CrossRefPubMedGoogle Scholar
  16. Greenleaf WH (1986) Pepper breeding. In: Basset MJ (ed) Breeding vegetable crops. The AVI Publishing Company, Westport, pp 67–134Google Scholar
  17. GRIN (2010) Germplasm Resources Information Network. United States Department of Agriculture, 1997-01-22. Accessed Jan 2010
  18. Hasegawa M, Kishino H, Yano Y (1985) Dating the human-ape split by a molecular clock of mitochondrial DNA. J Mol Evol 22:160–174CrossRefPubMedGoogle Scholar
  19. Hassan F, Khan M, Jan M (1997) Isolation technique for chilies root rot pathogens. Sarhad J Agric 10:581–587Google Scholar
  20. Hausbeck MK, Lamour KH (2004) Phytophthora capsici on vegetable crops:research progress and management challenges. Plant Dis 88:1292–1303CrossRefGoogle Scholar
  21. Hurtado-Gonzales O, Aragon-Caballero L, Apaza-Tapia W, Donahoo R, Lamour K (2008) Survival and spread of Phytophthora capsici in coastal Peru. Phytopathology 98(6):688–694CrossRefPubMedGoogle Scholar
  22. Hwang BK, Ebrahim-Nesbat F, Ibenthal W-D, Heitefuss R (1990) An ultrastructural study of the effect of metalaxyl on Phytophthora capsici infected stems of Capsicum annuum. Pestic Sci 29(2):151–162CrossRefGoogle Scholar
  23. Kaosiri T, Zentmyer GA (1980) Protein, esterase, and peroxidase patterns in the Phytophthora palmivora complex from cacao. Mycologia 72:988–1000CrossRefGoogle Scholar
  24. Khan MTI, Ali Q, Ashfaq m, Waseem M (2017) Econonmic analysis of open field chilli (Capsicum annum L.) production in Punjab, Pakistan. J Exp Biol Agric Sci 5(1):120–125. CrossRefGoogle Scholar
  25. Ko WH (1988) Hormonal heterothallism and homothallism in Phytophthora. Annu Rev Phytopathol 26:57–73CrossRefGoogle Scholar
  26. Kroon LPNM, Bakker FT, Van Den Bosch GBM, Bonants PJM, Flier WG (2004) Phylogenetic analysis of Phytophthora species based on mitochondrial and nuclear DNA sequences. Fungal Genet Biol 41:766–782CrossRefPubMedGoogle Scholar
  27. Langella O, Valot B, Jacob D, Balliau T, Flores R, Hoogland C, Joets J, Zivy M (2013) Management and dissemination of MS proteomic data with PROTICdb: example of a quantitative comparison between methods of protein extraction. Proteomics 13(9):1457–1466CrossRefPubMedGoogle Scholar
  28. Latin RX, Rane K (1999) Identification and management of pumpkin diseases. Purdue University, LafayetteGoogle Scholar
  29. Leonian LH (1992) Stem and fruit blight of peppers caused by Phytophthora capsici sp. nov. Phytopathology 12(9):401–408Google Scholar
  30. Lewis IML, Miller SA (2014) Use of the vital stain FUN-1 indicates viability of Phytophthora capsici propagules and can be used to predict maximum zoospore production. Mycologia 106(2):362–367CrossRefGoogle Scholar
  31. Li P, Cao S, Dai YL, Li XL, Xu DF, Guo M, Pan YM, Gao ZM (2012) Genetic diversity of Phytophthora capsici (Pythiaceae) isolates in Anhui Province of China based on ISSR-PCR markers. Genet Mol Res 11(4):4285–4296CrossRefPubMedGoogle Scholar
  32. Louis B, Sayanika DW, Pranab R, Pardeep KB, Wakambam MS, Talukdar NC (2014) Host shifting dynamics of Cochliobolus lunatus: From a biocontrol agent to a severe environmental threat. BioMed Res Int. PubMedPubMedCentralCrossRefGoogle Scholar
  33. Majid MU, Awan MF, Fatima K, Tahir MS, Ali Q, Rasid B, Rao AQ, Nasit IA, Husnain T (2016) Phytophthora capsici on chili pepper (Capsicum annuum L.) and its management through genetic and bio-control: a review. Zemdirbyste 103(4):419–430CrossRefGoogle Scholar
  34. Matheron ME (1992) Effects of temperature on sporulation and growth of Phytophthora citropthora and P. parasitica and development of foot and root rot on citrus. Plant Dis 76:1103–1109CrossRefGoogle Scholar
  35. Matheron ME, Porchas M (2014) Effectiveness of 14 fungicides for suppressing lesions caused by Phytophthora capsici on inoculated stems of Chile pepper seedlings. Plant Health 15(4):166–171. CrossRefGoogle Scholar
  36. Matthew D, Alegbejo BL, Paul SC (2006) Outbreak of basal stem rot and wilt disease of pepper in Katsina, Nigeria. Arch Phytopathol Plant Protect 39(2):93–98CrossRefGoogle Scholar
  37. McDonald BA (1997) The population genetics of fungi: tools and techniques. Phytopathology 87:448–453CrossRefPubMedPubMedCentralGoogle Scholar
  38. McDonald BA, Linde C (2002) Pathogen population genetics, evolutionary potential, and durable resistance. Annu Rev Phytopathol 40:349–379CrossRefPubMedGoogle Scholar
  39. Miao J, Cai M, Dong X, Liu L, Lin D, Zhang C, Pang Z, Liu X (2016) Resistance assessment for oxathiapiprolin in Phytophthora capsici and the detection of a point mutation (G769W) in PcORP1 that confers resistance. Front Microbiol 7:615CrossRefPubMedPubMedCentralGoogle Scholar
  40. Palazon C, Gil R, Palazon I, Delgado D (1990) Efficacy of several fungicides against Phytophthora capsici on pepper. Rev Plant Pathol 69(10):6818Google Scholar
  41. Pang Z, Shao N, Chen L, Lu X, Hu J et al (2013) Resistance to the novel fungicide pyrimorph in Phytophthora capsici: risk assessment and detection ofpoint mutations in CesA3 that confer resistance. PLoS ONE 8(2):e56513. CrossRefPubMedPubMedCentralGoogle Scholar
  42. Patel VK (2014) An economic analysis of production and marketing of chilli (Capsicum annuum L.) in Raigarh district of Chhattisgarh. M.Sc. thesis submitted to the Department of Agricultural Economics, College of Agriculture, Raipur, IndiaGoogle Scholar
  43. Pei-Qing L, Min-Liang W, Ben-Jin L, Cheng-zhon L, Qi-Yong W, Qing-He C (2013) Development of expressed sequence TAG-drived simple sequence repeat markers and diversity analysis of Phytophthora capsici in China. Int J Plant Pathol 02(03):137–146Google Scholar
  44. Quesada-Ocampo LM, Hausbeck MK (2010) Resistance in tomato and wild relatives to crown and root rot caused by Phytophthora capsici. Phytopathology 100:619–627CrossRefPubMedGoogle Scholar
  45. Quesada-Ocampo LM, Granke LL, Mercier MR, Olsen J, Hausbeck MK (2011) Investigating the genetic structure of Phytophthora capsici populations. Phytopathology 101:1061–1073CrossRefPubMedGoogle Scholar
  46. Randall E, Young V, Sierotzki H, Scalliet G, Birch PRJ, Cooke DEL et al (2014) Sequence diversity in the large subunit of RNA polymerase I contributes to mefenoxam insensitivity in Phytophthora infestans. Mol Plant Pathol 15:664–676. CrossRefPubMedGoogle Scholar
  47. Sarma Y, Ramachandran R, Anandaraj M (1988) Black pepper diseases in India: In: Premkumar T, Sarma YR (eds) Proceedings of the international pepper community workshop on joint research for the control of black pepper diseases, Calicut, pp. 55–101Google Scholar
  48. Shrestha S, Miyasaka SC, Shintaku M, Kelly H, Lamour K (2017) Phytophthora colocasiae from Vietnam, China, Hawaii and Nepal: intra- and inter-genomic variations in ploidy and a long-lived, diploid Hawaiian lineage. Mycol Prog. CrossRefGoogle Scholar
  49. Tajima F (1989) Statistical methods to test for nucleotide mutation hypothesis by DNA polymorphism. Genetics 123:585–595PubMedPubMedCentralGoogle Scholar
  50. Tamura k, Nei M (1993) Estimation of the number of nucleotide substitutions in the control region of mitochondrial DNA in humans and chimpanzees. Mol Biol Evol 10:512–526PubMedGoogle Scholar
  51. Tamura K, Stecher G, Peterson D, Filipski A, Kumar S (2013) MEGA6: molecular evolutionary genetics analysis version 6.0. Mol Biol Evol 30:2725–2729CrossRefPubMedPubMedCentralGoogle Scholar
  52. Tomura T, Molli SD, Murata R, Ojika M (2017) Universality of Phytophthora mating hormones and diversity of their production profile. Sci Rep 7:5007. CrossRefPubMedPubMedCentralGoogle Scholar
  53. Tsao PH (1991) The identities, nomenclature and taxonomy of Phytophthora isolates from black pepper. Paper read at Diseases of black pepper. In: Proceedings of the International Pepper Communication Workshop on Pepper Diseases, GoaGoogle Scholar
  54. Tsao PH, Alizadeh A (1988) Recent advances in the taxonomy and nomenclature of the so-called “Phytophthora palmivora” MF4 occurring on cocoa and other tropical crops. In: Paper presented at 10th international cocoa research conference, Santo Domingo, pp 17–23Google Scholar
  55. Waterhouse GM (1970) Taxonomy in Phytophthora. Phytopathology 60:1141–1143CrossRefGoogle Scholar
  56. White TJ, Bruns T, Lee S, Taylor W (1990) Amplification and direct sequencing of fungal ribosomal RNA genes for phylogenetics. In: Innis MA, Gelfand DH, Sninsky JJ, White TJ (eds) PCR protocols: a guide to methods and applications. Academic Press, Inc., New York, pp 315–322Google Scholar
  57. Zhu C, Yang X, Lv R, Li Z, Ding X, Tyler BM, Zhang X (2015) Phytophthora capsici homologue of the cell cycle regulator SDA1 is required for sporangial morphology, mycelial growth and plant infection. Mol Plant Pathol 17(3):369–387CrossRefPubMedGoogle Scholar

Copyright information

© Springer Nature B.V. 2018

Authors and Affiliations

  • Kiran Nawaz
    • 1
    Email author
  • Ahmad Ali Shahid
    • 1
    • 2
  • Louis Bengyella
    • 3
    • 4
    Email author
  • Muhammad Nasir Subhani
    • 1
  • Muhammad Ali
    • 1
  • Waheed Anwar
    • 1
  • Sehrish Iftikhar
    • 1
  • Shinawar Waseem Ali
    • 1
  1. 1.Institute of Agricultural ScienceUniversity of the PunjabLahorePakistan
  2. 2.Centre of Excellence in Molecular BiologyUniversity of the PunjabLahorePakistan
  3. 3.Tree Fruit Research and Extension Center (TFREC), College of Agricultural, Human and Natural Resource Sciences (CAHNRS)Washington State UniversityWenatcheeUSA
  4. 4.Department of Biological ControlAdvanced Biotech CooperativeBali-NyongaCameroon

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