Chapter 14.18 References and further reading

Alexander, P., Brown, C., Arneth, A., Finnigan, J., Moran, D. & Rounsevell, M.D.A. (2017). Losses, inefficiencies and waste in the global food system. Agricultural Systems, 153: 190-200. DOI:

Anonymous. (2018). Aukland (NZ) Council’s Our Aukland website, posted 19th February 2018. URL:

Babiker, E.M., Gordon, T.C., Chao, S., Rouse, M.N., Wanyera, R., Newcomb, M., Brown-Guedira, G., Pretorius, Z.A. & Bonman, J.M. (2016). Genetic mapping of resistance to the Ug99 race group of Puccinia graminis f. sp. tritici in a spring wheat landrace CItr 4311. Theoretical and Applied Genetics, 129: 2161-2170. DOI:

Babiker, E.M., Gordon, T.C., Chao, S., Rouse, M.N., Wanyera, R., Acevedo, M., Brown-Guedira, G. & Bonman, J.M. (2017). Molecular mapping of stem rust resistance loci effective against the Ug99 race group of the stem rust pathogen and validation of a single nucleotide polymorphism marker linked to stem rust resistance gene Sr28. Phytopathology, 107: 208-215. DOI:

Bebber, D.P. (2015). Range-expanding pests and pathogens in a warming world. Annual Review of Phytopathology, 53: 335-356. DOI:

Bellincampi, D., Cervone, F. & Lionetti, V. (2014). Plant cell wall dynamics and wall-related susceptibility in plant-pathogen interactions. Frontiers in Plant Science, 5: 228. DOI:

Bendel, M., Kienast, F. & Rigling, D. (2006). Genetic population structure of three Armillaria species at the landscape scale: a case study from Swiss Pinus mugo forests. Mycological Research, 110: 705-712. DOI:

Bernier, L., Aoun, M., Bouvet, G.F., Comeau, A., Dufour, J., Naruzawa, E.S., Nigg, M. & Plourde, K.V. (2014). Genomics of the Dutch elm disease pathosystem: are we there yet? iForest - Biogeosciences and Forestry, 8: 149-157. DOI:

Beza, E., Silva, J.V., Kooistra, L. & Reidsma, P. (2017). Review of yield gap explaining factors and opportunities for alternative data collection approaches. European Journal of Agronomy, 82: 206-222. DOI:

Brasier, C., Franceschini, S., Forster, J. & Kirk, S. (2021). Enhanced outcrossing, directional selection and transgressive segregation drive evolution of novel phenotypes in hybrid swarms of the Dutch Elm Disease pathogen Ophiostoma novo-ulmi. Journal of Fungi, 7: article number 452. DOI:

Brown, J.S. & Holden, D.W. (1996). Insertional mutagenesis of pathogenic fungi. Current Opinion in Microbiology, 1: 390-394. DOI:

Cairney, J.W.G. (2005). Basidiomycete mycelia in forest soils: dimensions, dynamics and roles in nutrient distribution. Mycological Research, 109: 7-20. DOI:

Cerda, R., Avelino, J., Gary, C., Tixier, P., Lechevallier, E, & Allinne, C. (2017). Primary and secondary yield losses caused by pests and diseases: assessment and modeling in coffee. PLoS ONE, 12: article number e0169133. DOI:

Chambouvet, A., Monier, A., Maguire, F., Itoïz, S., del Campo, J., Elies, P., Edvardsen, B., Eikreim, W. & Richards, T.A. (2019). Intracellular infection of diverse diatoms by an evolutionary distinct relative of the fungi. Current Biology, 29: 4093-4101. Open access, DOI:

Comeau, A., Dufour, J., Bouvet, G., Jacobi, V., Nigg, M., Henrissat, B., Laroche, J., Levesque, R.C. & Bernier, L. (2015). Functional annotation of the Ophiostoma novo-ulmi genome: insights into the phytopathogenicity of the fungal agent of Dutch Elm Disease. Genome Biology and Evolution, 7: 410-430. DOI:

Couch, B.C. & Kohn, L.M. (2002). A multilocus gene genealogy concordant with host preference indicates segregation of a new species, Magnaporthe oryzae, from M. grisea. Mycologia, 94: 683-693. DOI:

Dean, R. A., Talbot, N. J., Ebbole, D. J., Farman, M. L., Mitchell, T. K., Orbach, M. J., Thon, M., Kulkarni, R., Xu, J.-R., Pan, H., Read, N. D., Lee, Y.-H., Carbone, I., Brown, D., Oh, Y. Y., Donofrio, N., Jeong, J. S., Soanes, D. M., Djonovic, S., Kolomiets, E., Rehmeyer, C., Li, W., Harding, M., Kim, S., Lebrun, M.-H., Bohnert, H., Coughlan, S., Butler, J., Calvo, S., Ma, L.-J., Nicol, R., Purcell, S., Nusbaum, C., Galagan, J. E. & Birren, B. W. (2005). The genome sequence of the rice blast fungus Magnaporthe grisea. Nature, 434: 980-986. DOI:

Deutch, A.Y. & Roth, R.H. (2014). Pharmacology and biochemistry of synaptic transmission: classical transmitters. In: From Molecules to Networks: an Introduction to Cellular and Molecular Neuroscience (Third Edition), (eds J. Byrne, R. Heidelberger & M.N. Waxham). Pp. 207-237. Boston: Academic Press, an imprint of Elsevier Inc. ISBN: 9780123971791. DOI: VIEW on Amazon.

Dixon, R.A. (2001). Natural products and plant disease resistance. Nature, 411: 843-847. DOI:

Donatelli, M., Magarey, R.D., Bregaglio, S., Willocquet, L., Whish, J.P.M. & Savary, S. (2017). Modelling the impacts of pests and diseases on agricultural systems. Agricultural Systems, 155: 213-224. DOI:

Dubin, H.J. & Brennan, J.P. (2009). Combating stem and leaf rust of wheat: historical perspective, impacts, and lessons learned. IFPRI Discussion Paper Number 910. Published in Washington, D.C.: International Food Policy Research Institute (IFPRI). 33 pages. URL:

Dyakov Y.T. & Ozeretskovskaya, O.L. (2007). Virulence genes and their products. In: Comprehensive and Molecular Phytopathology, a volume in Studies in Plant Science, (eds Y.T. Dyakov, V.G. Dzhavakhiya & T. Korpela). Pp. 327-349. Amsterdam: Elsevier Science. ISBN: 978-0-444-52132-3. DOI: VIEW on Amazon.

Ellis, J.G., Dodds, P.N. & Lawrence, G.J. (2007). The role of secreted proteins in diseases of plants caused by rust, powdery mildew and smut fungi. Current Opinion in Microbiology, 10: 326-331. DOI:

Erwin, D.C. & Ribeiro, O.K. (1996). Phytophthora Diseases Worldwide. St Paul, MN, USA: The American Phytopathological Society, APS Press, pp. 592. ISBN 0-89054-212-0. VIEW on Amazon.

Faulkner, C. & Robatzek, S. (2012). Plants and pathogens: putting infection strategies and defence mechanisms on the map. Current Opinion in Plant Biology, 15: 699-707. DOI:

Ferguson, B.A., Dreisbach, T.A., Parks, C.G., Filip G.M. & Schmitt, C.L. (2003). Coarse-scale population structure of pathogenic Armillaria species in a mixed-conifer forest in the Blue Mountains of northeast Oregon. Canadian Journal of Forest Research, 33: 612-623. DOI:

Fones, H., Fisher, M. & Gurr, S. (2017). Emerging fungal threats to plants and animals challenge agriculture and ecosystem resilience. In: The Fungal Kingdom, (eds J. Heitman, B. Howlett, P. Crous, E. Stukenbrock, T. James & N. Gow), pp. 787-809. Washington, DC: ASM Press. DOI: VIEW on Amazon.

Ford, S.A., Williams, D., Paterson, S. & King, K.C. (2017). Co-evolutionary dynamics between a defensive microbe and a pathogen driven by fluctuating selection. Molecular Ecology, 26: 1778-1789. DOI:

Freeman, B.C. & Beattie, G.A. (2008). An overview of plant defenses against pathogens and herbivores. In: The Plant Health Instructor. Published online by the American Phytopathological Society. DOI:

Garnica, D.P., Nemri, A., Upadhyaya, N.M., Rathjen, J.P. & Dodds, P.N. (2014). The ins and outs of rust haustoria. PLoS Pathogens, 10: article e1004329. DOI:

Gilbert, B.M. & Wolpert, T.J. (2013). Characterization of the LOV1-mediated, Victorin-induced, cell-death response with virus-induced gene silencing. Molecular Plant-Microbe Interactions, 26: 903-917. DOI:

Glazebrook, J. (2005). Contrasting mechanisms of defense against biotrophic and necrotrophic pathogens. Annual Review of Phytopathology, 43: 205-227. DOI:

Govrin, E.M. & Levine, A. (2000). The hypersensitive response facilitates plant infection by the necrotrophic pathogen Botrytis cinerea. Current Biology, 10: 751-757. DOI:

Hagle, S.K. (2010). Management Guide for Armillaria Root Disease. Published by the Forest Health Protection and State Forestry Organizations of the US Forest Service. URL:

Hane, J.K., Paxman, J., Jones, D.A.B., Oliver, R.P. & de Wit, P. (2020). ‘CATAStrophy,’ a genome-informed trophic classification of filamentous plant pathogens – how many different types of filamentous plant pathogens are there? Frontiers in Microbiology, 10: 3088. DOI:

Jeon, J., Park, S.-Y., Chi, M.-H., Choi, J., Park, J., Rho, H.-S., Kim, S., Goh, J., Yoo, S., Choi, J., Park, J.-Y., Yi, M., Yang, S., Kwon, M.-J., Han, S.-S., Kim, B. R., Khang, C. H., Park, B., Lim, S.-E., Jung, K., Kong, S., Karunakaran, M., Oh, H.-S., Kim, H., Kim, S., Park, J., Kang, S., Choi, W.-B., Kang, S. & Lee, Y.-H. (2007). Genome-wide functional analysis of pathogenicity genes in the rice blast fungus. Nature Genetics, 39: 561-565. DOI:

Jobic, C., Boisson, A.-M., Gout, E., Rascle, C., Fèvre, M., Pascale Cotton, P. & Bligny, R. (2007). Metabolic processes and carbon nutrient exchanges between host and pathogen sustain the disease development during sunflower infection by Sclerotinia sclerotiorum. Planta, 226: 251-265. DOI:

Juroszek, P. & von Tiedemann, A. (2015). Linking plant disease models to climate change scenarios to project future risks of crop diseases - a review. Journal of Plant Diseases and Protection, 122: 3-15. DOI:

Khan, J., del Rio, L.E., Nelson, R., Rivera-Varas, V., Secor, G.A. & Khan, M.F.R. (2008). Survival, dispersal, and primary infection site for Cercospora beticola in sugar beet. Plant Disease, 92: 741-745. DOI:

Knogge, W. (1998). Fungal pathogenicity. Current Opinion in Plant Biology, 1: 324-328. DOI:

Koh, S., André, A., Edwards, H., Ehrhardt, D. & Somerville, S. (2005). Arabidopsis thaliana subcellular responses to compatible Erysiphe cichoracearum infections. The Plant Journal, 44: 516-529.

Kuroki, M., Okauchi, K., Yoshida, S., Ohno, Y., Murata, S., Nakajima, Y., Nozaka, A., Tanaka, N., Nakajima, M., Taguchi, H., Saitoh, K.-i., Teraoka, T., Narukawa, M. & Kamakura, T. (2017). Chitin-deacetylase activity induces appressorium differentiation in the rice blast fungus Magnaporthe oryzae. Scientific Reports, 7: article number 9697. DOI:

Kwiatkowski, M., Engelstädter, J. & Vorburger, C. (2012). On genetic specificity in symbiont-mediated host-parasite coevolution. PLoS Computational Biology, 8: article e1002633. DOI:

Laluk, K. & Mengiste, T. (2010). Necrotroph attacks on plants: wanton destruction or covert extortion? The Arabidopsis Book (American Society of Plant Biologists), 8: e0136. DOI:

Łaźniewska, J., Macioszek, V.K. & Kononowicz, A.K. (2012). Plant-fungus interface: the role of surface structures in plant resistance and susceptibility to pathogenic fungi. Physiological and Molecular Plant Pathology, 78: 24-30. DOI:

Li, X., Gao, C., Li, L., Liu, M., Yin, Z., Zhang, H., Zheng, X., Wang, P. & Zhang, Z. (2017). MoEnd3 regulates appressorium formation and virulence through mediating endocytosis in rice blast fungus Magnaporthe oryzae. PLoS Pathogens, 13: article number e1006449. DOI:

Liu, H., Suresh, A., Willard, F.S., Siderovski, D.P., Lu, S. & Naqvi, N.I. (2007). Rgs1 regulates multiple G subunits in Magnaporthe pathogenesis, asexual growth and thigmotropism. The EMBO Journal, 26: 690-700. DOI:

Liu, W., Zhou, X., Li, G., Li, L., Kong, L., Wang, C., Zhang, H. & Xu, J.-R. (2011). Multiple plant surface signals are sensed by different mechanisms in the Rice Blast fungus for appressorium formation. PLoS Pathogens, 7: article e1001261. DOI:

Lorenz, M.C. (2002). Genomic approaches to fungal pathogenicity. Current Opinion in Microbiology, 5: 372-378. DOI:

Maloy, O.C. (2005). Plant Disease Management. In: The Plant Health Instructor. Published online by the American Phytopathological Society. DOI:

Mares, D., Romagnoli, C., Andreotti, E., Forlani, G., Guccione, S. & Vicentini, C.B. (2006). Emerging antifungal azoles and effects on Magnaporthe grisea. Mycological Research, 110: 686-696. DOI:

Martin-Urdiroz, M., Oses-Ruiz, M., Ryder, L.S. & Talbot, N.J. (2016). Investigating the biology of plant infection by the rice blast fungus Magnaporthe oryzae. Fungal Genetics and Biology, 90: 61-68. DOI:

Massart, S. & Jijakli, H.M. (2007). Use of molecular techniques to elucidate the mechanisms of action of fungal biocontrol agents: A review. Journal of Microbiological Methods, 69: 229-241. DOI:

McLeod, G., Gries, R., von Reuß, S.H., Rahe, J.E., McIntosh, R., König, W.A. & Gries, G. (2005). The pathogen causing Dutch elm disease makes host trees attract insect vectors. Proceedings of the Royal Society of London, series B, Biological Sciences, 272: 2499-2503. DOI:

Money, N.P. (1999). Biophysics: Fungus punches its way in. Nature, 401: 332-333. DOI:

Moore, D. (2000). Slayers, Saviors, Servants and Sex. An exposé of Kingdom Fungi. New York: Springer Verlag, Inc. 176 pp. ISBN-10: 0387951016, ISBN-13: 978-0387951010. VIEW on Amazon. VIEW on publisher's website. See Chapter 2, Blights, rusts, bunts and mycoses. Tales of fungal diseases. CLICK HERE to download the full text.

Moore, D. & Novak Frazer, L. (2002). Essential Fungal Genetics. New York: Springer-Verlag Inc. ISBN-10: 0387953671, ISBN-13: 978-0387953670. VIEW on Amazon. VIEW on Amazon.

Moscou, M.J. & van Esse, H.P. (2017). The quest for durable resistance. Science, 358: 1541-1542. DOI:

Moss, M.O. (2008). Fungi, quality and safety issues in fresh fruits and vegetables. Journal of Applied Microbiology, 104: 1239-1243. DOI:

Nikawa, H., Nishimura, H., Hamada, T. & Sadamori, S. (1997). Quantification of thigmotropism (contact sensing) of Candida albicans and Candida tropicalis. Mycopathologia, 138: 13-19. DOI:

Oerke, E.-C. (2006). Crop losses to pests. The Journal of Agricultural Science, 144: 31-43. DOI:

Oh, Y., Donofrio, N., Pan, H., Coughlan, S., Brown, D.E., Meng, S., Mitchell, T. & Dean, R.A. (2008). Transcriptome analysis reveals new insight into appressorium formation and function in the rice blast fungus Magnaporthe oryzae. Genome Biology, 9 (5): R85. DOI:

Oliver, R.P. & Ipcho, S.V.S. (2004). Arabidopsis pathology breathes new life into the necrotrophs-vs.-biotrophs classification of fungal pathogens. Molecular Plant Pathology, 5: 347-352. DOI:

Pandaranayaka, E.P.J., Frenkel, O., Elad, Y., Prusky, D. & Harel, A. (2019). Network analysis exposes core functions in major lifestyles of fungal and oomycete plant pathogens. BMC Genomics, 20: article number 1020 (2019). DOI:

Parker, B.J., Hrček, J., McLean, A.H.C. & Godfray, H.C.J. (2017). Genotype specificity among hosts, pathogens, and beneficial microbes influences the strength of symbiont-mediated protection. Evolution, 71: 1222-1231. DOI:

Patpour, M., Hovmøller, M.S., Shahin, A.A., Newcomb, M., Olivera, P., Jin, Y., Luster, D., Hodson, D., Nazari, K. & Azab, M. (2016). First report of the Ug99 race group of wheat stem rust, Puccinia graminis f. sp. tritici, in Egypt in 2014. Plant Disease, 100: 863-863. DOI:

Plassard, C. & Fransson, P. (2009). Regulation of low-molecular weight organic acid production in fungi. Fungal Biology Reviews, 23: 30-39. DOI:

Popa, V. I., Dumitru, M., Volf, I. & Anghel, N. (2008). Lignin and polyphenols as allelochemicals. Industrial Crops and Products, 27: 144-149. DOI:

Raffa, K.F., Grégoire, J.-C. & Lindgren, B.S. (2015). Natural history and ecology of Bark Beetles. In: Bark Beetles: Biology and Ecology of Native and Invasive Species, (eds F.E. Vega & R.W. Hofstetter), pp. 1-40. San Diego: Academic Press, an imprint of Elsevier Inc. ISBN: 9780124171565. DOI: VIEW on Amazon.

Reidsma, P. & Jeuffroy, M.-H. (2017). Farming systems analysis and design for sustainable intensification: new methods and assessments. European Journal of Agronomy, 82: 203-205. DOI:

Scheffer, R.J., Voeten, J.G.W.F. & Guries, R.P. (2008). Biological control of Dutch Elm disease. Plant Disease, 92: 192-200. DOI:

Serrano, M., Coluccia, F., Torres, M., L’Haridon, F. & Métraux, J.-P. (2014). The cuticle and plant defense to pathogens. Frontiers in Plant Science, 5: 274. DOI:

Skaracis, G.N., Pavli, O.I. & Biancardi, E. (2010). Cercospora leaf spot disease of sugar beet. Sugar Tech, 12: 220-228. DOI:

Slavica, M., Gullino, M.L. & Spadaro, D. (2017). The puzzle of bakanae disease through interactions between Fusarium fujikuroi and rice. Frontiers in Bioscience, Elite, 9: 333-344. DOI:

Smith, M.L., Bruhn  J.N. & Anderson, J.B. (1992). The fungus Armillaria bulbosa is among the largest and oldest living organisms. Nature, 356: 428-431. DOI:

Stephenson, K.S., Gow, N.A.R., Davidson, F.A. & Gadd, G.M. (2014). Regulation of vectorial supply of vesicles to the hyphal tip determines thigmotropism in Neurospora crassa. Fungal Biology, 118: 287-294. DOI:

Stergiopoulos, I. & Gordon, T.R (2014). Cryptic fungal infections: the hidden agenda of plant pathogens. Frontiers in Plant Science, 5: 506. DOI:

Tada, Y., Kusaka, K., Betsuyaku, S., Shinogi, T., Sakamoto, M., Ohura, Y., Hata, S., Mori, T., Tosa, Y. & Mayama, S. (2005). Victorin triggers programmed cell death and the defense response via interaction with a cell surface mediator. Plant and Cell Physiology, 46: 1787-1798. DOI:

Talbot, N.J. (2007). Fungal genomics goes industrial. Nature Biotechnology, 25: 542-543. DOI:

Urban, J. & Milon, D. (2014). Sap flow-based quantitative indication of progression of Dutch elm disease after inoculation with Ophiostoma novo-ulmi. Trees, 28: 1599-1605. DOI:

van Dijk, M., Morley, T., Jongeneel, R., van Ittersum, M., Reidsma, P. & Ruben, R. (2017). Disentangling agronomic and economic yield gaps: an integrated framework and application. Agricultural Systems, 154: 90-99. DOI:

van Kan, J.A.L. (2006). Licensed to kill: the lifestyle of a necrotrophic plant pathogen. Trends in Plant Science, 11: 247-253. DOI:

Voegele, R.T. (2006). Uromyces fabae: development, metabolism, and interactions with its host Vicia faba. FEMS Microbiology Letters, 259: 165-173. DOI:

Voegele, R.T. & Mendgen, K. (2003). Rust haustoria: nutrient uptake and beyond. New Phytologist, 159: 93-100. DOI:

Vogel, J., Kenter, C., Holst C. & Märländer, B. (2018). New generation of resistant sugar beet varieties for advanced integrated management of Cercospora leaf spot in central Europe. Frontiers in Plant Science, 9: 222. DOI:

Volk, T. (2002). The humongous fungus - ten years later. Inoculum, 53: 4-8. URLs:;

Yan, X. & Talbot, N.J. (2016). Investigating the cell biology of plant infection by the rice blast fungus Magnaporthe oryzae. Current Opinion in Microbiology, 34: 147-153. DOI:

Webber, J. (2016). The ups and downs of Dutch elm disease. Posted on the Observatree web blog at

Wight, W.D., Labuda, R. & Walton, J.D. (2013). Conservation of the genes for HC-toxin biosynthesis in Alternaria jesenskae. BMC Microbiology, 13: 165. DOI:

Zhang, L., Zhang, D., Chen, Y., Ye, W., Lin, Q., Lu, G., Ebbole, D.J., Olsson, S. & Wang, Z. (2019). Magnaporthe oryzae CK2 accumulates in nuclei, nucleoli, at septal pores and forms a large ring structure in appressoria, and is involved in Rice Blast pathogenesis. Frontiers in Cellular and Infection Microbiology, 9: article 113. DOI:

Zhang, W., Chen, S., Abate, Z., Nirmala, J., Rouse, M.N. & Dubcovsky, J. (2017). Identification and characterization of Sr13, a tetraploid wheat gene that confers resistance to the Ug99 stem rust race group. Proceedings of the National Academy of Sciences of the United States of America, 114: E9483-E9492. DOI:

Zipfel, C. (2014). Plant pattern-recognition receptors. Trends in Immunology, 35: 345-351. DOI:

Updated September, 2021