Elucidating genetic variability and population structure in Venturia inaequalis associated with apple scab diseaseusing SSR markers

Autoři: Sheikh Mansoor aff001;  Nazeer Ahmed aff002;  Vikas Sharma aff001;  Sumira Jan aff003;  Sajad Un Nabi aff003;  Javid I. Mir aff003;  Mudasir A. Mir aff002;  Khalid Z. Masoodi aff002
Působiště autorů: Division of Biochemistry, Sher-e-Kashmir University of Agricultural Sciences and Technology Jammu, Jammu and Kashmir, India aff001;  Transcriptomics Laboratory, Division of Plant Biotechnology, Sher-e-Kashmir University of Agricultural Sciences and Technology (SKUAST-K), Shalimar, Srinagar, Jammu and Kashmir, India aff002;  ICAR-Central Institute of Temperate Horticulture, Rangreth, Srinagar, Jammu and Kashmir, India aff003
Vyšlo v časopise: PLoS ONE 14(11)
Kategorie: Research Article
doi: 10.1371/journal.pone.0224300


Apple scab caused by Venturia inaequalis Cooke (Wint.) is one the important diseases of trade and industrial significance in apple. In present study variability studies in pathogen isolates were studied, which is one of the most important factors for devising management studies of scab disease in apple. Genetic diversity of 30 Venturia inaequalis isolates from 12 districts of two geographical distinct regions of Jammu and Kashmir was calculated based on the allele frequencies of 28 SSR markers and the internal transcribed spacer (ITS) region of the ribosomal DNA. The ITS based characterized sequences were submitted to NCBI GenBank and accession numbers were sanctioned. Dendrogram showed that all the accessions formed 2 main clusters with various degree of sub clustering within the clusters. Analysis based on SSR study reveals that the heterozygosity ranged from 0.0 and 0.5, with an average value of 0.39. The expected heterozygosis or gene diversity (He) ranged from 0.0 to 0.50 with an average of 0.40. The Fst value ranges from 0 to 0.6 with an average of 0.194. Diversity within each population (HS) values ranging from 0.26 to 0.33. Average differentiation among populations (GST) was 0.11 and populations were isolated by significant distance (r 2 = 0.50, P < 0.01). From the AMOVA analysis, 25% of variation was observed among population, 9% among individuals and 66% within individuals observed in the population. Structure analysis grouped isolates into two populations. Principle coordinate analysis explained variation of 36.6% in population 1, 14.30% in population 2 and 13.10% in population 3(Admixture) with 64.07% as overall cumulative percentage of variation. This indicates that extensive short-distance gene flow occurs in Kashmir region that dispersal over longer distances also appears to occur frequently enough to prevent differentiation due to genetic drift. Also it is evident that Jammu and Kashmir most likely has V. inaequalis subpopulations linked to diverse climatic conditions of the Jammu region compared to the mountainous inland Kashmir region. The results of present study would help to understand the genetic diversity of V. inaequalis from Jammu and Kashmir that would lead in the development of more effective management strategies and development of new resistant cultivars through marker-assisted selection.

Klíčová slova:

Apples – Fungal structure – Genetic polymorphism – Phylogenetics – Polymerase chain reaction – Population genetics – Sequence alignment – Sequence databases


1. Ferree DC, Warrington IJ. Apples: botany, production, and uses: CABI; 2003.

2. Nabi SU, Mir JI, Sharma OC, Singh DB, Zaffer S, Sheikh MA, et al. Optimization of tissue and time for rapid serological and molecular detection of Apple stem pitting virus and Apple stem grooving virus in apple’. Phytoparasitica. 2018;46(5):705–13.

3. Bowen JK, Mesarich CH, Bus VG, Beresford RM, Plummer KM, Templeton MD. Venturia inaequalis: the causal agent of apple scab. Molecular Plant Pathology. 2011;12(2):105–22. doi: 10.1111/j.1364-3703.2010.00656.x 21199562

4. Gladieux P, Zhang X-G, Afoufa-Bastien D, Sanhueza R-MV, Sbaghi M, Le Cam B. On the origin and spread of the scab disease of apple: out of central Asia. PLoS One. 2008;3(1):e1455. doi: 10.1371/journal.pone.0001455 18197265

5. MacHardy WE. Apple scab: biology, epidemiology, and management: APS press St. Paul; 1996.

6. Shafi SM. An Overview of Apple Scab, its Cause and Management Strategies. EC Microbiology. 2019;15:0.1–4.

7. Sivanesan A. The taxonomy and pathology of Venturia species1977.

8. Kodsueb R, Dhanasekaran V, Aptroot A, Lumyong S, McKenzie EH, Hyde KD, et al. The family Pleosporaceae: intergeneric relationships and phylogenetic perspectives based on sequence analyses of partial 28S rDNA. Mycologia. 2006;98(4):571–83. 17139850

9. Zhang L. Genetic diversity and temporal dynamics of Venturia inaequalis populations following two apple scab epidemics in Pennsylvania. 2010.

10. Bus VG, Rikkerink EH, Caffier V, Durel C-E, Plummer KM. Revision of the nomenclature of the differential host-pathogen interactions of Venturia inaequalis and Malus. Annual Review of Phytopathology. 2011;49:391–413. doi: 10.1146/annurev-phyto-072910-095339 21599495

11. Tenzer I, degli Ivanissevich S, Morgante M, Gessler C. Identification of microsatellite markers and their application to population genetics of Venturia inaequalis. Phytopathology. 1999;89(9):748–53. doi: 10.1094/PHYTO.1999.89.9.748 18944702

12. Guérin F, Gladieux P, Le Cam B. Origin and colonization history of newly virulent strains of the phytopathogenic fungus Venturia inaequalis. Fungal Genetics and Biology. 2007;44(4):284–92. doi: 10.1016/j.fgb.2006.10.005 17166752

13. Guérin F, Franck P, Loiseau A, Devaux M, Le Cam B. Isolation of 21 new polymorphic microsatellite loci in the phytopathogenic fungus Venturia inaequalis. Molecular Ecology Notes. 2004;4(2):268–70.

14. Sarkate A, Saini SS, Teotia D, Gaid M, Mir JI, Roy P, et al. Comparative metabolomics of scab-resistant and susceptible apple cell cultures in response to scab fungus elicitor treatment. Scientific reports. 2018;8(1):17844. doi: 10.1038/s41598-018-36237-y 30552373

15. McDonald BA. The population genetics of fungi: tools and techniques. Phytopathology. 1997;87(4):448–53. doi: 10.1094/PHYTO.1997.87.4.448 18945126

16. Stukenbrock EH, McDonald BA. The origins of plant pathogens in agro-ecosystems. Annu Rev Phytopathol. 2008;46:75–100. doi: 10.1146/annurev.phyto.010708.154114 18680424

17. Berbee ML, Taylor JW. Two ascomycete classes based on fruiting-body characters and ribosomal DNA sequence. Molecular Biology and Evolution. 1992;9(2):278–84. doi: 10.1093/oxfordjournals.molbev.a040719 1560763

18. Liyanage H, McMillan R, Kistler HC. Two genetically distinct populations of Colletotrichum gloeosporioides from citrus. Phytopathology. 1992;82(11):1371–6.

19. Alahakoon P, Brown A, Sreenivasaprasad S. Cross-infection potential of genetic groups of Colletotrichum gloeosporioides on tropical fruits. Physiological and Molecular Plant Pathology. 1994;44(2):93–103.

20. Birch JL, Walsh NG, Cantrill DJ, Holmes GD, Murphy DJ. Testing efficacy of distance and tree-based methods for DNA barcoding of grasses (Poaceae tribe Poeae) in Australia. PLoS One. 2017;12(10):e0186259. doi: 10.1371/journal.pone.0186259 29084279

21. Padder B, Shah M, Ahmad M, Sofi T, Ahanger F, Hamid A. Genetic Differentiation among Populations of Venturia inaequalis in. Asian Journal of Plant Pathology. 2011;5(2):75–83.

22. Winka K, Eriksson OE, Bång Å. Molecular evidence for recognizing the Chaetothyriales. Mycologia. 1998;90(5):822–30.

23. Ebrahimi L, Fotouhifar K-B, Nikkhah MJ, Naghavi M-R, Baisakh N. Correction: Population Genetic Structure of Apple Scab (Venturia inaequalis (Cooke) G. Winter) in Iran. PLoS One. 2016;11(11):e0167415. doi: 10.1371/journal.pone.0167415 27875584

24. Grimova L, Winkowska L, Konrady M, RYŠÁNEK P. Apple mosaic virus. Phytopathologia Mediterranea. 2016;55(1):1–19.

25. Kumar S, Stecher G, Tamura K. MEGA7: molecular evolutionary genetics analysis version 7.0 for bigger datasets. Molecular Biology and Evolution. 2016;33(7):1870–4. doi: 10.1093/molbev/msw054 27004904

26. Peakall R, Smouse PE. GENALEX 6: genetic analysis in Excel. Population genetic software for teaching and research. Molecular Ecology Notes. 2006;6(1):288–95.

27. Excoffier L, Lischer HE. Arlequin suite ver 3.5: a new series of programs to perform population genetics analyses under Linux and Windows. Molecular ecology resources. 2010;10(3):564–7. doi: 10.1111/j.1755-0998.2010.02847.x 21565059

28. Yeh F. POPGENE 32v. 1.31 Microsoft Window-based Freeware for Population Genetic Analysis. ftp://ftp.microsoft.com/Softlib/MSLFILES/HPGL.EXE.1999.

29. Smith JM, Smith NH, O’Rourke M, Spratt BG. How clonal are bacteria? Proceedings of the National Academy of Sciences. 1993;90(10):4384–8.

30. Brown A, Feldman M, Nevo E. Multilocus structure of natural populations of Hordeum spontaneum. Genetics. 1980;96(2):523–36. 17249067

31. Perrier X, Jacquemoud-Collet J. DARwin software http://DARwin.cirad.fr. DARwin; 2006.

32. Pritchard JK, Stephens M, Donnelly P. Inference of population structure using multilocus genotype data. Genetics. 2000;155(2):945–59. 10835412

33. Evanno G, Regnaut S, Goudet J. Detecting the number of clusters of individuals using the software STRUCTURE: a simulation study. Molecular ecology. 2005;14(8):2611–20. doi: 10.1111/j.1365-294X.2005.02553.x 15969739

34. Earl DA. STRUCTURE HARVESTER: a website and program for visualizing STRUCTURE output and implementing the Evanno method. Conservation genetics resources. 2012;4(2):359–61.

35. Frantz A, Plantegenest M, Mieuzet L, Simon JC. Ecological specialization correlates with genotypic differentiation in sympatric host‐populations of the pea aphid. Journal of evolutionary biology. 2006;19(2):392–401. doi: 10.1111/j.1420-9101.2005.01025.x 16599915

36. Sheikh MA, Bhat K, Mir J, Mir M, Nabi SU, Bhat HA, et al. Phenotypic and molecular screening for diseases resistance of apple cultivars and selections against apple scab (Venturia inaequalis). IJCS. 2017;5(4):1107–13.

37. Bhat TA, Lone TA. Potential and Prospects of J&K Economy: Educreation Publishing; 2017.

38. Cooke BM, Jones DG, Kaye B. The epidemiology of plant diseases: Springer; 2006.

39. Monje LD, Quiroga M, Manzoli D, Couri MS, Silvestri L, Venzal JM, et al. Sequence analysis of the internal transcribed spacer 2 (ITS2) from Philornis seguyi (García, 1952) and Philornis torquans (Nielsen, 1913)(Diptera: Muscidae). Systematic parasitology. 2013;86(1):43–51. doi: 10.1007/s11230-013-9428-5 23949648

40. Iwen PC, Hinrichs S, Rupp M. Utilization of the internal transcribed spacer regions as molecular targets to detect and identify human fungal pathogens. Medical mycology. 2002;40(1):87–109. doi: 10.1080/mmy. 11860017

41. Guérin F, Le Cam B. Breakdown of the scab resistance gene Vf in apple leads to a founder effect in populations of the fungal pathogen Venturia inaequalis. Phytopathology. 2004;94(4):364–9. doi: 10.1094/PHYTO.2004.94.4.364 18944112

42. Xu X, Harvey N, Roberts A, Barbara D. Population variation of apple scab (Venturia inaequalis) within mixed orchards in the UK. European journal of plant pathology. 2013;135(1):97–104.

43. Xu X, Yang J, Thakur V, Roberts A, Barbara DJ. Population variation of apple scab (Venturia inaequalis) isolates from Asia and Europe. Plant Disease. 2008;92(2):247–52. doi: 10.1094/PDIS-92-2-0247 30769384

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2019 Číslo 11