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Mining and characterization of microsatellites from a genome of Venturia carpophila

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Abstract

A total of 4021 microsatellites were mined from a genome of Venturia carpophila, and 192 were selected to screen 39 isolates of the fungus collected from peach and nectarine in the southeastern USA. Of the 192 selected, 32 primers consistently and reliably produced polymorphic amplicons. Subsequently, the genotyping data from these 32 primers were used for preliminary analysis of the genetic diversity among the 39 isolates. The number of alleles identified ranged from 2 to 9, and the polymorphic information content from 0.097 to 0.792. Over all isolates, Shannon’s information index was 0.914, indicating genetic diversity. Stoddart and Taylor’s index of diversity and Simpson’s index also indicated high diversity (32.4 and 0.969, respectively). Evenness within the sample was high (0.955), but there was strong evidence for haploid linkage disequilibrium (3.799, P = 0.001). Observations on diversity were supported by analysis of genetic distance, which showed little affinity for clustering based on isolate source population, location, or host. The microsatellites developed in this study should be useful in future research of the population genetic structure and dynamics of V. carpophila and evaluating the risks posed by the ability of the pathogen to adapt on peach and possibly other stone fruit hosts in the USA and elsewhere in the world.

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References

  • Bock CH, Hotchkiss MW, Okie WR, Wood BW (2011) The distribution of peach scab lesions on the surface of diseased peaches. Eur J Plant Pathol 130:393–402

    Article  Google Scholar 

  • Bock CH, Chen C, Yu F, Stevenson KL, Arias RS, Wood BW (2016) Characterization of microsatellites in Fusicladium effusum, cause of pecan scab. For Pathol 46:600–609

    Article  Google Scholar 

  • Bock CH, Hotchkiss MW, Young CA, Charlton ND, Chakradhar M, Stevenson KL, Wood BW (2017) Population genetic structure of Venturia effusa, cause of pecan scab, in the southeastern United States. Phytopathology 107:607–619

    Article  PubMed  Google Scholar 

  • Botstein D, White RL, Skolnick M, Davis RW (1980) Construction of a genetic-linkage map in man using restriction fragment length polymorphisms. Am J Hum Genet 32:314–331

    PubMed  PubMed Central  CAS  Google Scholar 

  • Chen C, Zhou P, Choi YA, Huang S, Gmitter FG (2006) Mining and characterizing microsatellites from citrus ESTs. Theor Appl Genet 112:1248–1257

    Article  PubMed  CAS  Google Scholar 

  • Chen C, Bock CH, Brannen PM, Adaskaveg JE, Hotchkiss MW, Brewer MT, Wood BW (2014) Genetic variability among populations of Fusicladium species from different host trees and geographic locations in the USA. Mycol Prog 13:1179–1190

    Google Scholar 

  • Chen C, Bock CH, Wood BW (2017) Draft genome sequence of Venturia carpophila, the causal agent of peach scab. Stand Genomic Sci 12:68

    Article  PubMed  PubMed Central  Google Scholar 

  • Cox K (2015) Fungicide resistance in Venturia inaequalis, the causal agent of apple scab, in the United States. In: Ishii H and Holloman DW (eds) Fungicide Resistance in Plant Pathogens: Principles and a Guide to Practical Management. Springer Japan, pp. 433–447

  • Ellsworth DL, Rittenhouse KD, Honeycutt RL (1993) Artifactual variation in randomly amplified polymorphic DNA banding-patterns. Biotechniques 14: 214-&

  • Fisher EE (1961) Venturia carpophila sp. nov., the ascigerous state of the apricot freckle fungus. Trans Br Mycol Soc 44:337–342

    Article  Google Scholar 

  • Gladieux P, Zhang XG, Afoufa-Bastien D, Sanhueza RMV, Sbaghi M, Le Cam B (2008) On the origin and spread of the scab disease of apple: out of Central Asia. PLoS One 3

  • Grunwald NJ, Goodwin SB, Milgroom MG, Fry WE (2003) Analysis of genotypic diversity data for populations of microorganisms. Phytopathology 93:738–746

    Article  PubMed  Google Scholar 

  • Guerin F, Le Cam B (2004) Breakdown of the scab resistance gene Vf in apple leads to a founder effect in populations of the fungal pathogen Venturia inaequalis. Phytopathology 94:364–369

    Article  PubMed  CAS  Google Scholar 

  • Kamvar ZN, Tabima JF, Grunwald NJ (2014) Poppr: an R package for genetic analysis of populations with clonal, partially clonal, and/or sexual reproduction. PeerJ 2:e281

    Article  PubMed  PubMed Central  Google Scholar 

  • Keitt GW (1917) Peach scab and its control. United States Department of Agriculture Bulletin No. 395, Washington, DC

  • Lan Z, Scherm H (2003) Moisture sources in relation to conidial dissemination and infection by Cladosporium carpophilum within peach canopies. Phytopathology 93:1581–1586

    Article  PubMed  CAS  Google Scholar 

  • Lewontin RC (1972) The apportionment of human diversity. Evol Biol 6:381–398

    Google Scholar 

  • Linde CC, Zhan J, McDonald BA (2002) Population structure of Mycosphaerella graminicola: from lesions to continents. Phytopathology 92:946–955

    Article  PubMed  CAS  Google Scholar 

  • Linde CC, Zala M, McDonald BA (2009) Molecular evidence for recent founder populations and human-mediated migration in the barley scald pathogen Rhynchosporium secalis. Mol Phylogenet Evol 51:454–464

    Article  PubMed  CAS  Google Scholar 

  • Linde CC, Liles JA, Thrall PH (2010) Expansion of genetic diversity in randomly mating founder populations of Alternaria brassicicola infecting Cakile maritima in Australia. Appl Environ Microbiol 76:1946–1954

    Article  PubMed  PubMed Central  CAS  Google Scholar 

  • Ludwig JA, Reynolds JF (1988) Statistical ecology: a primer in methods and computing. Wiley, New York

    Google Scholar 

  • McDonald BA, Zhan J, Yarden O, Hogan K, Garton J, Pettway RE (1999) The population genetics of Mycosphaerella graminicola and Phaeosphaeria nodorum. In: Lucas JA, Bowyer P, Anderson HM (eds) Septoria on cereals: a study of pathosystems. CAB International, Wallingford, pp 44–69

    Google Scholar 

  • McDonald BA, Linde C (2002a) Pathogen population genetics, evolutionary potential, and durable resistance. Annu Rev Phytopathol 40:349–379

    Article  PubMed  CAS  Google Scholar 

  • McDonald BA, Linde C (2002b) The population genetics of plant pathogens and breeding strategies for durable resistance. Euphytica 124:163–180

    Article  CAS  Google Scholar 

  • McDonald BA (2015) How can research on pathogen population biology suggest disease management strategies? The example of barley scald (Rhynchosporium commune). Plant Pathol 64:1005–1013

    Article  Google Scholar 

  • McDonald BA, Mundt CC (2016) How knowledge of pathogen population biology informs management of Septoria Tritici blotch. Phytopathology 106:948–955

    Article  PubMed  Google Scholar 

  • Novelo ND, Gomelsky B, Pomper KW (2010) Inheritance and reliability of random amplified polymorphic DNA-markers in two consecutive generations of common carp (Cyprinus carpio L.). Aquac Res 41:220–226

    Article  CAS  Google Scholar 

  • Ogawa JM, Zehr EI, Bird GW, Ritchie DF, Uriu K, Uyemoto JK (1995) Compendium of stone fruit diseases. The American Phytopathological Society. St. Paul, MN, p 98

    Google Scholar 

  • Peakall R, Smouse PE (2012) GenAlEx 6.5: genetic analysis in excel. Population genetic software for teaching and research—an update. Bioinformatics 28:2537–2539

    Article  PubMed  PubMed Central  CAS  Google Scholar 

  • Pielou EC (1975) Ecological diversity. Wiley, New York

    Google Scholar 

  • Richardson BA, Ekramoddoulah AKM, Liu JJ, Kim MS, Klopfenstein NB (2010) Current and future molecular approaches to investigate the white pine blister rust pathosystem. For Pathol 40:314–331

    Article  Google Scholar 

  • Rozen S, Skaletsky H (2000) Primer3 on the WWW for general users and for biologist programmers. Methods Mol Biol 132:365–386

    PubMed  CAS  Google Scholar 

  • Salamati S, Zhan J, Burdon JJ, McDonald BA (2000) The genetic structure of field populations of Rhynchosporium secalis from three continents suggests moderate gene flow and regular recombination. Phytopathology 90:901–908

    Article  PubMed  CAS  Google Scholar 

  • Scherm H, Brannen PM (2005) Peach scab. In: Horton D, Johnson D (eds) Southeastern peach growers’ handbook. University of Georgia, College of Agricultural and Environmental Sciences, Athens, GA, pp 134–136

    Google Scholar 

  • Scherm H, Savelle AT, Boozer RT, Foshee WG (2008) Seasonal dynamics of conidial production potential of Fusicladium carpophilum on twig lesions in southeastern peach orchards. Plant Dis 92:47–50

    Article  Google Scholar 

  • Schnabel G, Schnabel EL, Jones AL (1999) Characterization of ribosomal DNA from Venturia inaequalis and its phylogenetic relationship to rDNA from other tree-fruit Venturia species. Phytopathology 89:100–108

    Article  PubMed  CAS  Google Scholar 

  • Schnabel G, Layne DR (2004) Comparison of reduced-application and sulfur-based fungicide programs on scab intensity, fruit quality, and cost of disease control on peach. Plant Dis 88:162–166

    Article  CAS  Google Scholar 

  • Schubert K, Ritschel A, Braun U (2003) A monograph of Fusicladium s.Lat. (Hyphomycetes). Schlechtendalia 9:1–132

    Google Scholar 

  • Shannon CE, Weaver W (1949) The mathematical theory of communication. University of Illinois Press, Urbana, Illinois

    Google Scholar 

  • Simpson EH (1949) Measurement of diversity. Nature 163:688–688

    Article  Google Scholar 

  • Stevenson KL (1999) Fungicide resistance management in pecans. South East Pecan Growers Association 92:58–64

    Google Scholar 

  • Stoddart JA, Taylor JF (1988) Genotypic diversity—estimation and prediction in samples. Genetics 118:705–711

    PubMed  PubMed Central  CAS  Google Scholar 

  • Stukenbrock EH, McDonald BA (2008) The origins of plant pathogens in agro-ecosystems. Annu Rev Phytopathol 46:75–100

    Article  PubMed  CAS  Google Scholar 

  • Stukenbrock EH, Bataillon T, Dutheil JY, Hansen TT, Li RQ, Zala M, McDonald BA, Wang J, Schierup MH (2011) The making of a new pathogen: insights from comparative population genomics of the domesticated wheat pathogen Mycosphaerella graminicola and its wild sister species. Genome Res 21:2157–2166

    Article  PubMed  PubMed Central  CAS  Google Scholar 

  • Thiel T, Michalek W, Varshney RK, Graner A (2003) Exploiting EST databases for the development and characterization of gene-derived SSR-markers in barley (Hordeum vulgare L.). Theor Appl Genet 106:411–422

    Article  PubMed  CAS  Google Scholar 

  • Xu X, Roberts T, Barbara D, Harvey NG, Gao L, Sargent DJ (2009) A genetic linkage map of Venturia inaequalis, the causal agent of apple scab. BMC Res Notes 2:163

    Article  PubMed  PubMed Central  CAS  Google Scholar 

  • Xu XM, Yang JR, Thakur V, Roberts A, Barbara DJ (2008) Population variation of apple scab (Venturia inaequalis) isolates from Asia and Europe. Plant Dis 92:247–252

    Article  CAS  Google Scholar 

  • Xu XM, Harvey N, Roberts A, Barbara D (2013) Population variation of apple scab (Venturia inaequalis) within mixed orchards in the UK. Eur J Plant Pathol 135:97–104

    Article  Google Scholar 

Download references

Acknowledgements

We acknowledge the technical help of Minling Zhang, Wanda Evans, Kaylee Carson, Sue Burrell, and Jason Shipp. We thank Dr. Keith Yoder (Virginia Tech Agricultural Research and Extension Center, VA), Drs. Guido Schnabel and Karen Bryson (Clemson University, SC), Dr. Kari Peter (Penn State Fruit Research and Extension Center, PA), Dr. Nicole Gauttier (University of Kentucky, KY), Dr. Norman Lalancette (Rutgers, NJ), Dr. Mercy Olmstead (University of Florida, FL), Dr. David Ritchie (North Carolina State University, NC), and Dr. Tom Beckman (USDA-ARS-SEFTNRL, GA) for collecting diseased samples of peach from which the isolates were obtained. The research was supported by the USDA-ARS through CRIS project 6606-21220-011–00D and 6606-21000-004-00D.

This article reports the results of research only. Mention of a trademark or proprietary product is solely for the purpose of providing specific information and does not constitute a guarantee or warranty of the product by the U.S. Department of Agriculture and does not imply its approval to the exclusion of other products that may also be suitable.

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Authors and Affiliations

  1. USDA-ARS-SEFTNRL, 21 Dunbar Road, Byron, GA, 31008, USA

    Chunxian Chen & Clive H. Bock

  2. Department of Plant Pathology, University of Georgia, 2105 Miller Plant Science Building, Athens, GA, 30602, USA

    Phillip M. Brannen

  3. Department of Plant Pathology and Microbiology, University of California Riverside, Riverside, CA, 92521, USA

    James E. Adaskaveg

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  1. Chunxian Chen
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  2. Clive H. Bock
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  3. Phillip M. Brannen
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  4. James E. Adaskaveg
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Correspondence to Chunxian Chen.

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Section Editor: Dominik Begerow

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Chen, C., Bock, C.H., Brannen, P.M. et al. Mining and characterization of microsatellites from a genome of Venturia carpophila. Mycol Progress 17, 885–895 (2018). https://doi.org/10.1007/s11557-018-1401-x

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  • DOI: https://doi.org/10.1007/s11557-018-1401-x

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