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Population Genetics of Plant Pathogens
References
     
     
   

 

Introductory Concepts, Population Biology, and Coevolution

Anikster, Y., Wahl, I. 1979. Coevolution of the rust fungi on Gramineae and Liliaceae and their hosts. Annual Review of Phytopathology 17: 367-403.

Burdon J.J., Thrall P.H. 2000. Coevolution at multiple spatial scales: Linum marginale-Melampsora lini - from the individual to the species. Evolutionary Ecology 14:261-281.

Burdon J.J. 1987. Diseases and Plant Population Biology. Cambridge University Press, Cambridge.

Burdon J.J., Thrall P.H., Brown A.H.D. 1999. Resistance and virulence structure in two Linum marginale-Melampsora lini host-pathogen metapopulations with different mating systems. Evolution 53:704-716.

Futuyma, D.J. 1998. Evolutionary Biology. Third Edition. Sinauer Associates, Sunderland, MA.

Futuyuma, D.J. and Slatkin, M. eds. 1983. Coevolution. Sinauer Associates, Sunderland. MA.

Hartl, D. L. and A. G. Clark, 1997. Principles of Population Genetics. Third Edition. Sinauer Associates, Sunderland, Massachusetts.

Hartl, D.L. 2000. A Primer of Population Genetics. Third Edition. Sinauer Associates, Sunderland, Massachusetts.

Janzen, D.H. 1980. When is it coevolution? Evolution 34:611-612.

Tooley, P.W., Fry, W.E., Gonzalez, M.J.V. 1985. Isozyme characterization of sexual and asexual Phytophthora infestans populations. Journal of Heredity 76: 431-435.

Wolfe, M.S., and Caten C.E., eds. 1987. Populations of Plant Pathogens: Their Dynamics and Genetics. Blackwell Scientific Publications. Oxford, UK.

 

References and Extra Reading on Mutation

Flor H.H. 1958. Mutation to wider virulence in Melampsora lini. Phytopathology 48:297-301

Gassmann, W., Dahlbeck, D., Chesnokova, O., Minsavage, G.V., Jones, J.B., Staskawicz, B.J. 2000. Molecular evolution of virulence in natural field strains of Xanthomonas campestris pv. vesicatoria. Journal of Bacteriology 182:7053-7059.

Mundt, C.C. 1990. Probability of mutation to multiple virulence and durability of resistance gene pyramids. Phytopathology 80: 221-223.

Zimmer D.E., Schafer J.F., Patterson F.L. 1963. Mutations for virulence in Puccinia coronata. Phytopathology 53:171-176.

 

References on Genetic Drift

Chen, R.S., Boeger, J.M., McDonald, B.A. 1994. Genetic stability in a population of a plant pathogenic fungus over time. Molecular Ecology 3:209-218.

Goodwin, S.B., Cohen, B.A., Fry, W.E. 1994. Panglobal distribution of a single clonal lineage of the Irish potato famine fungus. Proc. Natl. Acad. Sci. USA 91: 11591-11595.

Milgroom, M.G., Wang, K.R., Zhou, Y., Lipari, S.E., Kaneko, S. 1996. Intercontinental population structure of the chestnut blight fungus, Cryphonectria parasitica. Mycologia 88:179-190.

Steele, K.A., Humphreys, E., Wellings, C.R., Dickinson, M.J. 2001. Support for a stepwise mutation model for pathogen evolution in Australasian Puccinia striiformis f.sp tritici by use of molecular markers. Plant Pathology 50: 174-180.

Zhan, J., Mundt, C.C., McDonald B.A. 2001. Using restriction fragment length polymorphisms to assess temporal variation and estimate the number of ascospores that initiate epidemics in field populations of Mycosphaerella graminicola.Phytopathology 91:1011-1017.

Zhan, J., Pettway, R.E., McDonald B.A. 2003. The global genetic structure of the wheat pathogen Mycosphaerella graminicola is characterized by high nuclear diversity, low mitochondrial diversity, regular recombination, and gene flow. Fungal Genetics and Biology 38:286-297.

 

References and Extra Reading on Gene and Genotype Flow

Bentley, S., Pegg, K.G., Moore, N.Y., Davis, R.D., Buddenhagen, I.W. 1998. Genetic variation among vegetative compatibility groups of Fusarium oxysporum f. sp. cubense analyzed by DNA fingerprinting. Phytopathology 88:1283-1293.

Boeger, J.M., Chen, R.S., McDonald, B.A. 1993. Gene flow between geographic populations of Mycosphaerella graminicola (anamorph Septoria tritici) detected with RFLP markers. Phytopathology 83:1148-1154.

Bousset, L., Hovmoller, M.S., Caffier, V., de Vallavieille-Pope, C., Ostergard, H. 2002. Observed and predicted changes over eight years in frequency of barley powdery mildew avirulent to spring barley in France and Denmark. Plant Pathology 51:33-44.

Caffier, V., Hoffstadt, T., Leconte, M., de Vallavieille-Pope, C. 1996. Seasonal changes in pathotype complexity in French populations of barley powdery mildew. Plant Pathology 45:454-468.

Goodwin, S.B. 1997. The population genetics of Phytophthora. Phytopathology 87:462-473.

Goodwin, S.B., Cohen, B.A., Fry, W.E. 1994. Panglobal distribution of a single clonal lineage of the Irish potato famine fungus. Proc. Nat. Acad. Sci. USA 91:11591-11595.

Goodwin, S.B., Spielman, L.J., Matuszak, J.M., Bergeron, S.N., Fry, W.E. 1992. Clonal diversity and genetic differentiation of Phytophthora infestans populations in northern and central Mexico. Phytopathology 82:955-961.

Goodwin, S.B., Sujkowski, L.S., Dyer, A.T., Fry, B.A., Fry, W.E. 1995. Direct detection of gene flow and probable sexual reproduction of Phytophthora infestans in Northern North America. Phytopathology 85:473-479.

Hovmoller M.S. 2001. Disease severity and pathotype dynamics of Puccinia striiformis f.sp tritici in Denmark. Plant Pathology 50:181-189.

Koenig, R.L., Ploetz, R.C., Kistler, H.C. 1997. Fusarium oxysporum f. sp. cubense consists of a small number of divergent and globally distributed clonal lineages. Phytopathology 87:915-923.

McDermott, J.M., McDonald, B.A. 1993. Gene flow in plant pathosystems. Annual Review of Phytopathology 31:353-373.

Zhan, J., Pettway, R.E., McDonald B.A. 2003. The global genetic structure of the wheat pathogen Mycosphaerella graminicola is characterized by high nuclear diversity, low mitochondrial diversity, regular recombination, and gene flow. Fungal Genetics and Biology 38:286-297.

 

References and Extra Reading on Reproductive/Mating System

Anderson, J.B., Kohn, L.M. 1995. Clonality in soilborne, plant pathogenic fungi. Annual Review of Phytopathology 33:369-391.

Anderson, J.B., Kohn, L.M., Leslie, J.F. Genetic mechanism in fungal adaptation. Chapter 5 pp. 73-98 in The Fungal Community: Its Organization and Role in the Ecosystem, 2nd Edition. G.C. Carroll and D.T. Wicklow eds. Marcel Dekker, New York.

Chen, R.S., McDonald, B.A. 1996. Sexual reproduction plays a major role in the genetic structure of populations of the fungus Mycosphaerella graminicola. Genetics 142:1119-1127.

Goodwin, S.B. 1997. The population genetics of Phytophthora. Phytopathology 87:462-473.

Keller, S.M., McDermott, J.M., Pettway, R.E., Wolfe, M.S. McDonald, B.A. 1997. Gene flow and sexual reproduction in the wheat glume blotch pathogen Phaeosphaeria nodorum (anamorph Stagonospora nodorum). Phytopathology 87:353-358.

Milgroom MG. 1996. Recombination and the multilocus structure of fungal populations. Annual Review of Phytopathology 34:457-477.

Nei, M. 1973. Analysis of gene diversity in subdivided populations. Proc. Natl. Acad. Sci.  USA 70:3321-3323.

Shattock, R.C., Tooley, P.W., Fry, W.E. 1986. Genetics of Phytophthora infestans-characterization of single-oospore cultures from A1 isolates induced to self by intraspecific stimulation. Phytopathology 76:407-410.


References and Extra Reading on Natural Selection

Brent K.J., Hollomon D.W. 1998. Fungicide resistance: the assessment of risk. FRAC Monograph No. 2, Global Protection Federation. Brussels, Belgium.

Bronson, C.R., Ellingboe, A.H. 1986. The influence of four unnecessary genes for virulence on the fitness of Erysiphe graminis f. sp. tritici. Phytopathology 76:154-158.

Browning, J.A., Frey, K.J. 1969. Multiline cultivars as a means of disease control. Annual Review of Phytopathology 7:355-382.

Chin, K.M., Wolfe, M.S. 1984. Selection on Erisyphe graminis in pure and mixed stands of barley. Plant Pathology 33:535-546.

Grant, M.W., Archer, S.A. 1983. Calculation of selection coefficients against unnecessary genes for virulence from field data. Phytopathology 73:547-551.

Huang, R., Kranz, J., Welz, H.G. 1994. Selection of pathotypes of Erisyphe graminis f. sp. hordei in pure and mixed stands of spring barley. Plant Pathology 43:458-470.

Kolmer, J.A. 1993. Selection in a heterogeneous population of Puccinia recondita f. sp. tritici. Phytopathology 83:909-914.

Leach, J.E., Cruz, C.M.V., Bai, J.F., Leung, H. 2001. Pathogen fitness penalty as a predictor of durability of disease resistance genes. Annual Review of Phytopathology 39:187-224.

Leonard, K.J. 1969. Selection in heterogeneous populations of Puccinia graminis f. sp. avenae. Phytopathology 59:1851-1857.

Leonard, K.J. 1994. Stability of equilibria in a gene-for-gene coevolution model of host-parasite interactions. Phytopathology 84: 70-77.

Leonard, K.J. and Czochor, R.J. 1980. Theory of genetic interactions among populations of plants and their pathogens. Annual Review of Phytopathology 18: 237-258.

Prud'homme, A., Sackston, W.E. 1990. Relative fitness of races 1 (0) and 3 (0, 1) of rust (Puccinia helianthi) in mixtures on susceptible sunflower (Helianthus annuus). Canadian Journal of Botany 68:1602-1608.

Welz, H.G., Leonard, K.J. 1993. Phenotypic variation and parasitic fitness of races of Cochliobolus carbonum on corn in North Carolina. Phytopathology 83:593-601.

Welz, H.G., Miedaner, T., Geiger H.H. 1995. 2 unnecessary powdery mildew resistance genes in a synthetic rye population are neutral on fitness. Euphytica 81:163-170.

Zhan, J., Mundt, C.C., Hoffer, M.E., McDonald, B.A. 2002. Local adaptation and effect of host genotype on the rate of pathogen evolution: an experimental test in a plant pathosystem. Journal of Evolutionary Biology 15:634-647.


References and Extra Reading on Interactions/Genetic Structure

Baayen, R.P., Forch, M.G., Waalwijk, C., Bonants, P.J.M., Loffler, H.J.M., Roebroeck, E.J.A. 1998. Pathogenic, genetic and molecular characterisation of Fusarium oxysporum f.sp. lilii. European Journal of Plant Pathology104:887-894.

Baayen, R.P., O'Donnell, K., Bonants, P.J.M., Cigelnik, E., Kroon, L.P.N.M., Roebroeck, E.J.A., Waalwijk, C. 2000. Gene genealogies and AFLP analyses in the Fusarium oxysporum complex identify monophyletic and nonmonophyletic formae speciales causing wilt and rot disease. Phytopathology 90:891-900.

Bao, J.R., Fravel, D.R., O'Neill, N.R., Lazarovits, G., van Berkum, P. 2002. Genetic analysis of pathogenic and nonpathogenic Fusarium oxysporum from tomato plants. Canadian Journal of Botany 80: 271-279.

Burdon, J.J. 1993. The structure of pathogen populations in natural plant communities. Annual Review of Phytopathology 31:305-323.

Burdon, J.J., Silk, J. 1997. Sources and patterns of diversity in plant-pathogenic fungi. Phytopathology 87:664-669Gordon, T.R., Martyn, R.D. 1997. The evolutionary biology of Fusarium oxysporum. Annual Review of Phytopathology 35:111-128.

Jimenez-Gasco, M.M., Milgroom, M.G., Jimenez-Diaz, R.M. 2002. Gene genealogies support Fusarium oxysporum f. sp ciceris as a monophyletic group. Plant Pathology 51:72-77.

Koenig, R.L., Ploetz, R.C., Kistler, H.C. 1997. Fusarium oxysporum f. sp. cubense consists of a small number of divergent and globally distributed clonal lineages. Phytopathology 87:915-923.

Leung, H., Nelson, R.J., Leach, J.E. 1993. Population structure of plant pathogenic fungi and bacteria. Advances in Plant Pathology 10:157-205.

Linde, C., Zhan, J., and B. A. McDonald. 2002. Population structure of Mycosphaerella graminicola: From lesions to continents. Phytopathology 92:946-955.

McDonald, B.A., McDermott, J.M. 1993. The population genetics of plant pathogenic fungi. BioScience 43:311-319.

Migheli, Q., Briatore, E., Garibaldi, A. 1998. Use of random amplified polymorphic DNA (RAPD) to identify races 1, 2, 4 and 8 of Fusarium oxysporum f. sp. dianthi in Italy. European Journal of Plant Pathology 104:49-57.

Milgroom, M.G. 1995. Analysis of population structure in fungal plant pathogens. pp. 213-230 in Disease Analysis through Genetics and Biotechnology: Interdisciplinary Bridges to Improved Sorghum and Millet Crops. J.F. Leslie, R.A. Frederiksen, eds. Iowa State University Press.

Mouyna, I., Renard, J.L., Brygoo, Y. 1996. DNA polymorphism among Fusarium oxysporum f sp elaeidis populations from oil palm, using a repeated and dispersed sequence ''palm''. Current Genetics 30:174-180.

Nelson, A.J., Elias, K.S., Arevalo, E., Darlington, L.C., Bailey, B.A. 1997. Genetic characterization by RAPD analysis of isolates of Fusarium oxysporum f. sp. erythroxyli associated with an emerging epidemic in Peru. Phytopathology 87:1220-1225.

O'Donnell, K., Kistler, H.C., Cigelnik, E., Ploetz, R.C. 1998. Multiple evolutionary origins of the fungus causing Panama disease of banana: Concordant evidence from nuclear and mitochondrial gene genealogies. Proc. Natl. Acad. Sci. U.S.A. 95:2044-2049.

Plyler, T.R., Simone, G.W., Fernandez, D., Kistler, H.C. 2000. Genetic diversity among isolates of Fusarium oxysporum f.sp canariensis. Plant Pathology 49:155-164.

Roelfs, A.P. 1982. Effects of barberry eradication on stem rust in the United States. Plant Disease 66:177-181.

Stakman, E.C. 1957. Problems in preventing plant disease epidemics. American Journal of Botany 44:259-267.

Woudt, L.P., Neuvel, A., Sikkema, A., Vangrinsven, M.Q.J.M., Demilliano, W.A.J., Campbell, C.L., Leslie, J.F. 1995. Genetic variation in Fusarium oxysporum from cyclamen. Phytopathology 85:1348-1355.

Zhan, J., Pettway, R.E., McDonald B.A. 2003. The global genetic structure of the wheat pathogen Mycosphaerella graminicola is characterized by high nuclear diversity, low mitochondrial diversity, regular recombination, and gene flow. Fungal Genetics and Biology 38:286-297.

Zhan, J., Mundt, C.C., McDonald, B.A. 1998. Measuring immigration and sexual reproduction in field populations of Mycosphaerella graminicola. Phytopathology 88:1330-1337.


References and Extra Reading on Applications

Garcia-Arenal, G., McDonald, B.A. 2003. an analysis of the durability of resistance to plant viruses. Phytopathology 93:941-952. Detailed information on the pathosystems analyzed, showing how risk categories were assigned and how breakdown or durability of resistance was determined. Click here for this supplement.

McDonald, B.A., Linde, C. 2002. Pathogen population genetics, evolutionary potential, and durable resistance. Annual Review of Phytopathology 40:349-379.

Milgroom, M.G., Fry, W.E. 1997. Contributions of population genetics to plant disease epidemiology and management. Advances in Botanical Research 24:1-30.