Method for modifying gene expression of a phytopathogenic fungus

[0001] This application is a continuation-in-part application of International Patent Application No. PCT/FR2004/003312, filed on Dec. 20, 2004, published as WO 2005/071091, which claims priority to FR 0315228, filed Dec. 23, 2003, and to FR 0407373, filed Jul. 2, 2004, each of which are incorporated by reference herein in their entireties.

[0002] The present invention relates to a system for controlling the development of fungi during a phytopathogenic attack. The system according to the invention consists in enabling the plant to express a construct for inhibiting the expression of a gene essential to the development or to the pathogenicity of the fungus. This system is commonly called RNA interference. The plants thus transformed constitute one of the aspects of the present invention.

[0003] Plant diseases cause considerable yield losses; this results in economical losses for farmers, but also a large amount of nutritional damage for the local population living off their agriculture. Economically and ecologically, it is very advantageous to have plants resistant to their pathogens, and more particularly to their fungi in the absence of plant-protection products. To date, it has been possible to use various strategies:

• • [0004] Methods of traditional selection have been used to develop plants specifically resistant to certain pathogens. However, these methods are limited to the species that can be crossed and the introgression of characteristics of resistance to pathogens constitutes long and laborious work.
  • [0005] The use of an antisense RNA makes it possible to decrease the expression of an endogenous target gene (EP 240 208).
  • [0006] The use of a sense gene makes it possible to decrease the expression of an endogenous target gene; this technology is called cosuppression (EP 465 572).

[0007] The technology used in the context of the present invention is RNA interference or RNAi. RNAi has in particular proved that it is effective when double-stranded RNA (dsRNA) is injected into the nematode Caenorhabditis elegans (Fire et al. 1998, Nature 391: 806-811 and Montgomery et al., 1998, PNAS 95: 15502-15507, WO99/32619).

[0008] The expression in an organism of a sequence homologous to the gene of interest capable of inducing the formation of small double-stranded RNA makes it possible, very specifically, to extinguish this gene and to observe the phenotype that results therefrom (Xiao et al., 2003, Plant Mol Biol., 52(5): 957-66). The most striking example that illustrates this ability is that of insects fed with bacteria expressing small double-stranded RNAs corresponding to a gene expressed in the insects, which is thus inhibited (WO 01/37654).

[0009] The dsRNA triggers the specific degradation of a homologous RNA only in the region of identity with the dsRNA (Zamore et al., 2000, Cell, 101: 25-33, Tang et al., 2003 Gene Dev., 17(1): 49-63). The dsRNA is an RNA molecule which contains a double-stranded sequence of at least 25 base pairs (bp) including a sense strand and an antisense strand. The dsRNA molecules are also characterized by the very large degree of complementarity between the two complementary RNA strands. The dsRNA is degraded into RNA fragments of 19 to 25 nucleotides (siRNA) and the cleavage sites on the target RNA are evenly spaced apart by 19 to 25 nucleotides. The small siRNAs resulting therefrom exhibit a very high degree of identity with respect to the target RNA; however, mismatches of 3 to 4 nucleotides between the siRNA and the corresponding portion of the target RNA nevertheless make it possible for the system to operate (Tang et al., 2003, Genes Dev., 17:49-63). It has thus been suggested that these fragments of 19 to 25 nucleotides constitute RNA guides for recognition of the target (Zamore et al., 2000, Cell, 101:25-33). These small RNAs have also been detected in extracts prepared from Schneider 2 cells of Drosophila melanogaster which had been transfected with dsRNAs before cell lysis (Hammond et al., 2000, Nature 404: 293-296). The guiding role of the fragments of 19 to 25 nucleotides in the cleavage of the mRNAs is supported by the observation that these fragments of 19 to 25 nucleotides isolated from dsRNA are capable of being involved in the degradation of mRNA (Zamore et al., 2000, Cell, 101:25-33). Sizable homologous RNA molecules also accumulate in plant tissues which undergo the PTGS phenomenon (Post Transcriptional Gene Silencing, Hamilton and Baulcome, 1999, Science 286: 950-952). These small RNAs can regulate gene expression at three different levels:

• • [0010] transcription (TGS for Transcriptional Gene Silencing),
  • [0011] messenger RNA degradation (PTGS for Post Transcriptional Gene Silencing),
  • [0012] translation.

[0013] Regulation involving messenger RNA degradation appears to exist in all eukaryotes, whereas regulation at the transcriptional level has only been described in plants, drosophile and C. elegans. As regards the regulation of translation, it has been characterized in C. elegans and drosophile and appears also to exist in mammals (Hannon, 2002, Nature, 418 (6894): 244-51). In the literature, reference is made to RNAi, to PTGS, to cosuppression or to quelling (reserved for fungi) when referring to this phenomenon, depending on the organisms in which it is studied.

[0014] The introduction of dsRNA was carried out in plants in order to induce silencing of an endogenous target gene (Hamilton et al., 1998, Plant J, 15: 737-746, WO99/15682), to induce resistance to RNA viruses by means of the use of a transgene expressing a dsRNA having substantial identity with respect to the viral genes (Waterhouse et al., 1998, PNAS 95: 13959-13964, Pandolfini et al., 2003, Biotechnol., 25; 3(1): 7, WO98/36083, WO99/15682, U.S. Pat. No. 5,175,102), but also to induce resistance to nematodes (Chuang and Meyerowitz, 2000, PNAS, 97: 4985-4990, WO01/96584) or alternatively to the bacterium Agrobacterium (WO00/26346, Escobar et al., 2001, Proc. Natl. Acad. Sci. USA., 98(23): 13437-13442).

[0015] In the case of the attack of a plant by a bacterium or by a virus, the mechanisms of interaction between the plant and the pathogen clearly involve nucleic acid transfers. In fact, in the case of Agrobacterium tumefaciens, the mechanisms of pathogenicity comprise two steps: the first corresponds to a horizontal gene transfer and to the integration of this or these gene(s) into the plant (this is transformation), the second corresponds to post-integration events that occur in the plant (this is tumorigenesis; Escobar et al., 2001, Proc. Natl. Acad. Sci. USA., 98(23): 13437-42) based on the use, by the plant, of the pathogen's genetic material. In the case of the infection of tobacco with the Plum Pox Virus (PPV), it is the transfer into the plant of the single-stranded RNA of the virus which allows the synthesis of the capsid proteins and of the polymerases required for the propagation of the infection (Pandolfini et al., 2003). There is therefore a link and very elaborate exchanges at the genetic level between the plant and its pathogen, and the siRNAs are transferred during its exchanges. The mechanisms of infection of a plant by a phytopathogenic fungus do not, for their part, involve any gene transfer.

[0016] A subject of the present invention is the creation of a construct and the use thereof in plants or cells genetically modified in order to make them resistant to pathogenic fungi. The technology used is based on the mechanism of RNA interference. These plants have the advantage of not producing proteins, and the risks of allergic problems are considerably reduced: the only elements overexpressed being RNAs. Furthermore, the mechanism of interference RNA is an exponential and self-replicating system, which means that it is sufficient to induce it in order for it to be maintained in the organism.

[0017] One of the subjects of the present invention concerns a method of producing a plant resistant to a phytopathogenic fungus, comprising the following steps:

• [0018] a) introducing into a plant cell a construct comprising:
  • [0019] a promoter regulatory sequence that is functional in plant cells,
  • [0020] a DNA sequence which, when it is transcribed, generates an RNA molecule comprising at least two sequences: sense and antisense at least partially complementary, said sense sequence comprising a sequence essentially homologous to a gene essential to the fungus or to its phytopathogenicity, said antisense sequence comprising a sequence essentially homologous to the sequence complementary to said essential gene,
  • [0021] a terminator regulatory sequence,
• [0022] b) placing the transformed cells in culture under conditions that allow the transcription of the construct,
• [0023] c) selecting the transformed cells,
• [0024] d) regenerating plants from the transformed cells.

[0025] Another subject of the present invention concerns a method of producing a plant resistant to a phytopathogenic fungus, comprising the following steps:

• [0026] a) introducing into a plant a construct comprising:
  • [0027] a promoter regulatory sequence that is functional in plant cells,
  • [0028] a DNA sequence which, when it is transcribed, generates an RNA molecule comprising at least two sequences: sense and antisense at least partially complementary, said sense sequence comprising a sequence essentially homologous to a gene essential to the fungus or to its phytopathogenicity, said antisense sequence comprising a sequence essentially homologous to the sequence complementary to said essential gene,
  • [0029] a terminator regulatory sequence,
• [0030] b) placing the transformed plants in culture under conditions that allow the transcription of the construct,
• [0031] c) selecting the transformed plants.

[0032] Another subject of the present invention concerns a method of producing a plant cell resistant to a phytopathogenic fungus, comprising the following steps:

• [0033] a) introducing into a plant cell a construct comprising:
  • [0034] a promoter regulatory sequence that is functional in plant cells,
  • [0035] a DNA sequence which, when it is transcribed, generates an RNA molecule comprising at least two sequences: sense and antisense at least partially complementary, said sense sequence comprising a sequence essentially homologous to a gene essential to the fungus or to its phytopathogenicity, said antisense sequence comprising a sequence essentially homologous to the sequence complementary to said essential gene,
  • [0036] a terminator regulatory sequence,
• [0037] b) selecting the transformed cells,
• [0038] c) placing the transformed cells in culture under conditions that allow the transcription of the construct.

[0039] The invention also concerns a plant resistant to a phytopathogenic fungus, comprising a construct characterized in that it comprises:

• • [0040] a promoter regulatory sequence that is functional in plant cells,
  • [0041] a DNA sequence which, when it is transcribed, generates an RNA molecule comprising at least two sequences: sense and antisense at least partially complementary, said sense sequence comprising a sequence essentially homologous to a gene essential to the fungus or to its phytopathogenicity, said antisense sequence comprising a sequence essentially homologous to the sequence complementary to said essential gene,
  • [0042] a terminator regulatory sequence.

[0043] The plant cells resistant to a phytopathogenic fungus comprising a construct characterized in that it comprises:

• • [0044] a promoter regulatory sequence that is functional in plant cells,
  • [0045] a DNA sequence which, when it is transcribed, generates an RNA molecule comprising at least two sequences: sense and antisense at least partially complementary, said sense sequence comprising a sequence essentially homologous to a gene essential to the fungus or to its phytopathogenicity, said antisense sequence comprising a sequence essentially homologous to the sequence complementary to said essential gene,
  • [0046] a terminator regulatory sequence,
    are another subject of the present invention.

[0047] Another aspect of the present invention concerns the use of a construct for creating a plant cell or a plant resistant to a fungus, said construct comprising a promoter regulatory sequence that is functional in plant cells, a DNA sequence which, when it is transcribed, generates an RNA molecule comprising at least two sequences: sense and antisense at least partially complementary, said sense sequence comprising a sequence essentially homologous to a gene essential to the fungus or to its phytopathogenicity, said antisense sequence comprising a sequence essentially homologous to the sequence complementary to said essential gene, and a terminator regulatory sequence.

[0048] A subject of the invention is also a method for identifying a gene essential to the development or to the pathogenicity of a phytopathogenic fungus, comprising the following steps:

• [0049] a) transforming a plant cell or a plant with a construct comprising:
  • [0050] a promoter regulatory sequence that is functional in plant cells,
  • [0051] a DNA sequence which, when it is transcribed, generates an RNA molecule comprising at least two sequences: sense and antisense at least partially complementary, said sense sequence comprising a sequence essentially homologous to a gene supposedly essential to the fungus or to its phytopathogenicity, said antisense sequence comprising a sequence essentially homologous to the sequence complementary to said supposed essential gene,
  • [0052] a terminator regulatory sequence,
• [0053] b) bringing the cells or the plants thus transformed into contact with the phytopathogenic fungus,
• [0054] c) studying the resulting phenotype,
• [0055] d) characterizing the gene corresponding to the sequence of nucleotides thus inserted.

[0056] A method for inhibiting the expression of a fungal gene, comprising the following steps:

• [0057] a) transforming a plant cell or a plant with a construct comprising:
  • [0058] a promoter regulatory sequence that is functional in plant cells,
  • [0059] a DNA sequence which, when it is transcribed, generates an RNA molecule comprising at least two sequences: sense and antisense at least partially complementary, said sense sequence comprising a sequence essentially homologous to a gene essential to the fungus or to its phytopathogenicity, said antisense sequence comprising a sequence essentially homologous to the sequence complementary to said essential gene,
  • [0060] a terminator regulatory sequence,
• [0061] b) selecting,
• [0062] c) placing the cells thus transformed in culture under conditions that allow the transcription of said construct,
• [0063] d) bringing the cells into contact with the fungus, constitutes yet another aspect of the invention.

[0064] The invention also concerns a method for reducing the expression of a fungal gene, comprising the following steps:

• [0065] a) transforming a plant cell or a plant with a construct comprising:
  • [0066] a promoter regulatory sequence that is functional in plant cells,
  • [0067] a DNA sequence which, when it is transcribed, generates an RNA molecule comprising at least two sequences: sense and antisense at least partially complementary, said sense sequence comprising a sequence essentially homologous to a gene essential to the fungus or to its phytopathogenicity, said antisense sequence comprising a sequence essentially homologous to the sequence complementary to said essential gene,
  • [0068] a terminator regulatory sequence,
• [0069] b) selecting,
• [0070] c) placing the cells thus transformed in culture under conditions that allow the transcription of said construct,
• [0071] d) bringing the cells into contact with the fungus.

[0079] According to the invention, the term “promoter regulatory sequence” is intended to mean any promoter regulatory sequence of a gene that is naturally expressed in plants, in particular a promoter that is expressed especially in the leaves of plants, for instance promoters referred to as constitutive of bacterial, viral or plant origin, or else promoters referred to as light-dependent, such as that of a plant ribulose-biscarboxylase/oxygenase (RuBisCO) small subunit gene, or any known suitable promoter that can be used. Among the promoters of plant origin, mention will be made of the histone promoters as described in application EP 0 507 698, or the rice actin promoter (U.S. Pat. No. 5,641,876). Among the promoters of a plant virus gene, mention will be made of that of the cauliflower mosaic virus (CaMV 19S or 35S) or of the cassava vein mosaic virus (CsVMV: WO97/48819) or the circovirus promoter (AU 689 311). Use may also be made of a promoter regulatory sequence specific for particular regions or tissues of plants, and more particularly seed-specific promoters (Datla, R. et al., 1997, Biotechnology Ann. Rev., 3, 269-296), especially the napin (EP 255 378), phaseolin, glutenin, helianthinin (WO 92/17580), albumin (WO 98/45460) and oleosin (WO 98/45461) promoters. An inducible promoter can also be used, it can be advantageously chosen from the promoters of phenylalanine ammonia lyase (PAL), of HMG-CoA reductase (HMG), of chitinases, of glucanases, of proteinase inhibitors (PI), of genes of the PR1 family, of nopaline synthase (nos) or of the vspB gene (U.S. Pat. No. 5,670,349), the HMG2 promoter (U.S. Pat. No. 5,670,349), the apple beta-galactosidase (ABG1) promoter or the apple amino cyclopropane carboxylate synthase (ACC synthase) promoter (WO 98/45445).

[0080] The term “terminator regulatory sequence” is intended to mean any sequence that is functional in plant cells or plants, also comprising polyadenylation sequences, whether they are of bacterial origin, for instance the nos or ocs terminator of Agrobacterium tumefaciens, of viral origin, for instance the CaMV 35S terminator, or else of plant origin, for instance a histone terminator as described in application EP 0 633 317.

[0081] The selection step for identifying the transformed cells and/or plants having integrated the construct according to the invention can be carried out by virtue of the presence of a selectable gene present in the construct according to the invention or in the plasmid used for the transformation of the cells or of the plants and comprising said construct. The selectable gene may be in the form of a chimeric gene comprising the following elements, functionally linked in the direction of transcription: a promoter regulatory sequence that is functional in plant cells, a sequence encoding a selectable marker, and a terminator regulatory sequence that is functional in plant cells.

[0082] Among the selectable markers that can be used, mention may be made of markers containing genes for resistance to antibiotics, such as, for example, that of the hygromycin phosphotransferase gene (Gritz et al., 1983, Gene 25: 179-188), of the neomycin phosphotransferase II gene inducing resistance to kanamycin (Wirtz et al., 1987, DNA, 6(3): 245-253), or of the aminoglycoside 3″-adenyltransferase gene, but also markers containing genes for tolerance to herbicides, such as the bar gene (White et al., NAR 18: 1062, 1990) for tolerance to bialaphos, the EPSPS gene (U.S. Pat. No. 5,188,642) for tolerance to glyphosate or else the HPPD gene (WO 96/38567) for tolerance to isoxazoles. Mention may also be made of genes encoding readily unidentifiable enzymes, such as the GUS enzyme, or genes encoding pigments or enzymes regulating pigment production in the transformed cells. Such selectable marker genes are in particular described in patent applications WO 91/02071, WO 95/06128, WO 96/38567, and WO 97/04103.

[0083] Preferably, the nucleotide sequence of the gene essential to the fungus or to its pathogenicity (target gene) corresponds to a region which is transcribed, and more particularly which is transcribed and translated.

[0084] The length of the sense nucleotide sequence has a minimum size of 19 nucleotides.

[0085] The sense sequence comprises a sequence essentially homologous to a gene essential to the fungus or to its pathogenicity. In fact, and preferably, the sense nucleotide sequence and the nucleotide sequence of the fungal target gene exhibit a degree of identity of at least 50% to 70%. Entirely preferably, the degree of identity is at least 75%, at least 80%, at least 85%, at least 90%, at least 95%, and entirely preferably, the degree of identity is 100%.

[0086] However, it is necessary for the sense nucleotide sequence to always comprise a sequence of approximately 19 nucleotides, particularly of 20 nucleotides, and more particularly of 25 nucleotides, exhibiting at least 80% identity with the corresponding portion of the target gene, at least 85% identity with the corresponding portion of the target gene, at least 90% identity with the corresponding portion of the target gene, at least 95% identity with the corresponding portion of the target gene, and entirely preferably 100% identity.

[0087] In one of the aspects of the invention, the sense and antisense sequences have identical sizes. According to another aspect of the invention, the size of the sense sequence is greater than that of the antisense sequence. By way of example, the size of the sense sequence can be about 200 nucleotides greater than the size of the antisense sequence. In another aspect of the invention, the size of the antisense sequence is greater than that of the sense sequence.

[0088] The antisense sequence comprises a sequence essentially homologous to the sequence complementary to the gene essential to the fungus or to its pathogenicity. In fact, and preferably, the antisense nucleotide sequence and the sequence complementary to the fungal target gene exhibit a degree of identity of at least 50% to 70%. Entirely preferably, the degree of identity is at least 75%, at least 80%, at least 85%, at least 90%, at least 95%, and entirely preferably, the degree of identity is 100%.

[0089] However, it is necessary for the antisense nucleotide sequence to always comprise a sequence of approximately 19 nucleotides, particularly of 20 nucleotides, and more particularly of 25 nucleotides, exhibiting at least 80% identity with the corresponding portion of the target gene, at least 85% identity with the corresponding portion of the target gene, at least 90% identity with the corresponding portion of the target gene, at least 95% identity with the corresponding portion of the target gene, and entirely preferably 100% identity.

[0090] Molecular hybridization is a pairing reaction which takes place between complementary strands of polynucleotides exhibiting a certain degree of identity between their nucleotide sequences. The greater the sequence identity between the polynucleotides, the more possible and easier the hybridization between said polynucleotides, and the greater the probability that these polynucleotides encode proteins with equivalent properties.

[0091] The degree of identity between two homologous polynucleotides is obtained by comparison of their sequences and is generally expressed by means of a percentage of nucleotides that are identical between these sequences. This degree of identity is measured over a given sequence length, the shortest of the sequences compared determining the length of sequence over which the degree of identity of the homologous sequences is measured. The invention therefore covers polynucleotides exhibiting one or more sequence modifications with respect to the other and being homologous to the gene essential to the fungus or to its pathogenicity.

[0092] The DNA sequence according to the invention can have two aspects; in the first, it comprises two nucleotide sequences, which are sense and antisense, separated by an intron that does not exhibit any homology with the fungal gene. FIG. 1 describes a promoter regulatory sequence that is functional in plant cells, which is in front of the nucleotide sequence in the sense orientation of the gene, followed by an intron and by the nucleotide sequence in the antisense orientation of this same gene. A terminator regulatory sequence is at the end of the sense/intron/antisense construct. The sequence cloned in the sense and antisense orientation is that whose expression in the pathogen it is intended to inhibit. The transcription of this DNA sequence (“DNA” in the figure) thus gives a large single-stranded RNA (“mRNA” in the figure) corresponding to the sense/intron/antisense construct. This long RNA transcript can be detected by RT-PCR. Since the sense and antisense sequences are homologous, they will pair, and the intron which separates them plays the role of a loop for folding. A dsRNA is then obtained (“dsRNA” in the figure) over all the homologous regions. The dsRNA is subsequently specifically degraded by an enzymatic complex called “DICER”. The degradation of the dsRNAs then forms siRNAs (“siRNA” in the figure), small double-stranded RNAs having a size of between 19 and 25 bases. These are then the siRNAs which, by pairing with the transcribed RNAs derived from the target gene will lead to their degradation via the plant's enzymatic machinery.

[0093] In the second aspect, the DNA sequence comprises two nucleotide sequences, which are sense and antisense, of different sizes, the loop structure corresponding to the part of the nucleotide sequence that does not exhibit any homology with the other nucleotide sequence. FIG. 2 represents a promoter regulatory sequence that is functional in plant cells, which is in front of the sense sequence of the gene, followed by the partial antisense sequence of this same gene. A terminator regulatory sequence is at the end of the sense/antisense construct. The nucleotide sequence cloned in the sense orientation is essentially homologous to the sequence of the target gene whose expression it is intended to inhibit. The antisense nucleotide sequence is essentially homologous to the complementary strand of the sequence of said target gene. The transcription of this DNA sequence (“DNA” in the figure) thus gives a large single-stranded RNA (“mRNA” in the figure) corresponding to the sense/antisense construct (this long RNA transcript can be detected by RT-PCR) The homologous sense/antisense sequences are paired. A dsRNA is then obtained (“dsRNA” in the figure) over all the homologous regions. The dsRNA is subsequently specifically degraded by an enzymatic complex called “DICER”. The degradation of the dsRNAs then forms siRNAs (“siRNA” in the figure), small doubled-stranded RNAs having a size of between 19 and 25 bases. These are then the siRNAs which, by pairing with the target RNAs, will lead to their degradation via the plant's enzymatic machinery.

[0094] The nucleotide sequences according to the present invention can be complementary to a gene essential to the fungus or to its pathogenicity.

[0095] According to the invention, the expression “gene essential to the fungus” is intended to mean a gene, the inhibition of which by a fungicidal molecule or the mutation thereof leads to the death of the fungus or an arrest of its development. By way of example, mention may be made of the following genes:

• • [0096] gene encoding beta-tubulin (Katiyar et al., 1994, Antimicrob. Agents Chemother., 38(9): 2086-90),
  • [0097] acetohydroxyacid isomerase (ilv5) involved in the branched-chain amino acid biosynthetic pathway (WO 03/022056),
  • [0098] C14-demethylase (erg11) or C24-methyltransferase (erg6) involved in the ergosterol synthetic pathway (Barrett and Dixon, 1995, Acta Biochem. Pol., 42(4): 465-479),
  • [0099] inositol phosphoceramide synthase (aur1) involved in the transfer of inositol phosphoceramide onto ceramide in the sphingolipid biosynthetic pathway (Nagiec et al., 1997, J. Biol. Chem., 272(15): 9809-9817) and inositol phosphoryltransferase (ipt1),
  • [0100] glucan synthase and chitin synthase (Kang et al., 2001, Pest. Mana. Sci., 57(6): 491-500, Binks et al., 1993, J. Gen. Microbiol., 139(6): 1371-1377),
  • [0101] ribosomal factors (ef2 and ef3, Belfiel and Tuite, 1993, Mol. Microbiol., 9(3): 411-418),
  • [0102] met4 and met30 (Aoki et al., 1996, Antimicrob. Agents Chemother, 40(1): 127-132).

[0103] Additional examples of genes encompassed by the expression “gene essential to the fungus” can be found in Table 1.

[0104] In one embodiment of the invention, the plants or plant cells comprise a complementary DNA sequence of a gene essential to the fungus, said essential gene being represented by the sequence identifier SEQ ID No. 4.

[0105] The invention also relates to a method of producing a tobacco cell resistant to the fungus Cercospora nicotianae, by introducing a construct comprising a DNA sequence represented by the sequence identifier SEQ ID No. 4.

[0106] According to the invention, the expression “gene essential to the pathogenicity of the fungus” is intended to mean a gene, the inhibition of which is not lethal for the fungus but inhibits its pathogenic capacity. By way of example, mention may be made of the following genes:

• • [0107] 763 of Magnaporthe grisea (WO 01/75115),
  • [0108] gene encoding polygalacturonase (Bonnin et al., 2001, Biochem. Biophys. Acta, 1526(3): 301-309),
  • [0109] tri5 of Fusarium graminearum, involved in the trichothecene biosynthetic pathway (Kimura et al., 2003, FEBS, 539(1-3): 105-110),
  • [0110] fum5 of Fusarium monoliforme, involved in the biosynthetic pathway for toxins of this fungus (Proctor et al., 1999, Fungal Genet. Biol., 27(1): 100-112, Proctor et al., 2003, Fungal Genet. Biol., 38(2): 237-249),
  • [0111] buf of Magnoporthe grisea, involved in the melanin biosynthetic pathway (Kawamura et al., 1997, Mol. Plant Microbe Interact, 10(4): 446-453).

[0112] In another embodiment of the invention, the plants or plant cells comprise a complementary DNA sequence of a gene essential to the pathogenicity of the fungus, said gene being represented by the sequence identifier SEQ ID No. 13.

[0113] The methods of the present invention may be utilized to target genes in a wide variety of fungi that infect plants. Plants which can be afflicted by fungal disease include, but are not limited to: African Daisy (Gerbera jamesonii H. Bolus ex J. D. Hook), African Violet (Saintpaulia ionantha Wendl.), Alfalfa (Medicago sativa L.), Almond (Prunus dulcis (Mill.) Webb), Anemone (Anemone coronaria L.), Apple (Malus×domestica Borkh.), Apricot (Prunus armeniaca L.), Asparagus (Asparagus officinalis), Avocado (Persea americana Miller), Azalea (Rhododendron spp.), Banana and Plantain (Musa spp.), Barley (Hordeum vulgare L.) Beet (Beta vulgaris L.), Beilfiower (Campanula carpatica Jacq.), Black Walnut (Juglans nigra L.), Bleeding Heart (Clerodendrum thomsoniae Balf.), Butterfly Flower, Poorman's Orchid (Schizanthus×wisetonensis hort.), Cacao (Theobroma cacao L.), Caneberries (Rubus spp.), Carnation (Dianthus caryophylium L.), Carrot (Daucus carota L. subsp. sativus (Hoffm.) (Arcang.), Cassava (Manihot esulenta Crantz), Cattleya Lindl. spp., Chickpea (Cicer arietinum L.), Cinerama (Pericallis×hybrida R. Nordenstam [Senecio×hybridus (Wilid.) Regel], Citrus (Citrus spp.), Coconut Palm (Cocos nucifera L.), Coffee (Coffea arabica L., Coffea canephora Pierre ex Froehner), Corn or Maize (Zea mays L.), Cotton (Gossypium spp.), Crucifers (Brassica and Raphanus spp.), Cucurbits (Citrullus spp., Cucumis spp., Cucurbita spp., and others), Cyclamen (Cyclamen persicum Mill.), Dahlia (Dahlia sp.), Date Palm (Phoenix dactylifera L.), Douglas-fir (Pseudotsuga menziezii [Mirb.] Franco), Elm (Ulmus spp.), English (Persian) Walnut (Juglans regia L.), Flax (Linum usitatissimum L. and other Linum spp.), Foliage Plants (House plants), Fuchsia (Fuchsia×hybrida Hort. ex Vilm), Geranium (Pelargonium), Grape (Vitis spp.), Hazelnut (Corylus avellana L. & Corylus spp.), Hemp (Cannabis sativa L.), Holiday Cacti (Schlumbergera truncata (Haw.) Moran), Hop (Humulus lupulus L.), Hydrangea (Hydrangea macrophylla) (Thunb.) Ser., Impatiens (Impatiens wallerana) and New Guinea impatiens (Impatiens hybrids), Jerusalem Cherry (Solanum pseudocapsicum L.), Kalanchoe (Kalanchoe blossfeldiana Poelln.), Lettuce (Lactuca sativa L.), Lentil (Lens culinaris Medik.), Lisianthus (Eustoma grandiflorum (Raf.) Shinn), Mango (Mangifera indica L.), Mimulus, Monkey-Flower (Mimulus×hybridus hort. ex Siebert & Voss), Mint (Mentha piperita L., M. cardiaca Baker, M. spicata L. and M. arvensis L.), Mustard (Brassica juncea (L.) Czernj. & J. M. Coulter var. crispifolia L. H. Bailey and B. nigra (L.) W. Koch), Oats (Avena sativa L.), Papaya (Carica papaya L.), Pea (Pisum sativum L.), Peach and Nectarine (Peach: Prunus persica (L.) Batsch; Nectarine: P. persica var. nucipersica (Suckow) C. K. Schneid.), Peanut (Arachis hypogaea L.), Pear (Pyrus communis L.), Pearl Millet (Pennisetum glaucum (L.) R. Br.), Pecan (Carya illinoinensis (Wang.) Koch.), Pepper (Capsicurii spp.), Persian Violet (Exacum affine), Pigeonpea (Cajanus cajan (L.) Millsp.), Pineapple (Ananas comosus (L.) Merr.), Pistachio (Pistacia vera L.), Pocketbook Plant (Calceolaria crenatiflora Cav.), Poinsettia (Euphorbia pulcherrima Willd. ex Klotzsch), Potato (Solanum tuberosum L.), Primulas: English primrose Primula vulgaris Huds. (P. acaulis), Polyanthus Primula Pruhonicensis hybrids, Fairy primrose P. malacoides Franch., German primrose P. obconica Hance, Chinese primrose P. sinensis Sabine ex Lindl., Rapeseed=Canola (B. napus L. and Brassica rapa L. (=B. campestris L.)), Red Clover (Trifolium pratense L.), Rhododendron (Rhododendron spp.), Rice (Oryza sativa L.), Rose (Rosa spp.), Rye (Secale cereale L.), Safflower (Carthamus tinctorius L.), Sapphire Flower (Browallia speciosa Hook.), Sorghum (Sorghum bicolor (L.) Moench), Soybeans (Glycine max (L.) Merrill), Spinach (Spinacia oleracea L.), Strawberry (Fragaria×ananassa Duch.), Sugarcane (Saccharum spp. hybrids), Sunflower (Helianthus annuus L.) and Jerusalem Artichoke (H. tuberosus L.), Sweetgum (Liquidambar spp.), Sweetpotato (Ipomoea batatas (L.) Lam.), Sycamore (Platanus spp.), Tea (Camellia sinesis (L.) 0. Kuntze), Tobacco (Nicotiana tabacum L.), Tomato (Lycopersicon esculentum Mill.), Verbena (Verbena×hybrida Groenl. & Ruempi.), Wheat (Triticum spp. L.), Wild Rice, Cultivated (Zizania palustris L.). Table 2 provides a list of common diseases which infect various types of plants, as well as identified sources of the disease. The prior list and Table 2 were compiled from data found at the International Society for Molecular Plant-Microbe Interactions Based upon the methods disclosed herein, a person of ordinary skill in the art will be capable of utilizing the methods described above to target specific genes essential to a fungus or its pathogenicity in the fungus responsible for a particular fungal diseases outlined in Table 2. For example, the beta-tubulin gene of a fungus described in Table 2 may be targeted. A person of ordinary skill in the art will also be capable of utilizing analogous methods to treat fungal diseases for the plants listed herein.

[0114] The invention also relates to a method of producing a rice cell resistant to the fungus Magnoporthe grisea, by introducing a construct comprising a DNA sequence represented by the sequence identifier SEQ ID No. 13.

[0115] The plants and the cells transformed according to the invention can be monocotyledons or dicotyledons. Preferably, these plants are plants of agronomic interest.

[0116] The plant cells and the plants of the present invention can be monocotyledons such as wheat, maize or rice.

[0117] A particular embodiment of the present invention corresponds to a rice plant resistant to Magnaporthe grisea, comprising a DNA sequence represented by the sequence identifier SEQ ID No. 13.

[0118] The plant cells and the plants of the present invention can be dicotyledons such as rapeseed, soybean, cotton or tobacco.

[0119] A particular embodiment of the present invention corresponds to a tobacco plant resistant to Cercospora nicotianae, comprising a DNA sequence represented by the sequence identifier SEQ ID No. 4.

[0120] Said plant can be obtained by regeneration of the transformed cells according to the invention.

[0121] To obtain the cells or plants according to the invention, those skilled in the art can use one of the numerous known methods of transformation.

[0122] One of these methods consists in bringing the cells or tissues of the host organisms to be transformed into contact with polyethylene glycol (PEG) and the vectors of the invention (Chang and Cohen, 1979, Mol. Gen. Genet. 168(1), 111-115; Mercenier and Chassy, 1988, Biochimie 70(4), 503-517). Electroporation is another method, which consists in subjecting the cells or tissues to be transformed and the vectors of the invention to an electric field (Andreason and Evans, 1988, Biotechniques 6(7), 650-660; Shigekawa and Dower, 1989, Aust. J. Biotechnol. 3(1), 56-62). Another method consists in directly injecting the vectors into the cells or the tissues by microinjection (Gordon and Ruddle, 1985, Gene 33(2), 121-136). Advantageously, the “biolistic” method may be used. It consists in bombarding cells or tissues with particles onto which the vectors of the invention are adsorbed (Bruce et al., 1989, Proc. Natl. Acad. Sci. USA 86(24), 9692-9696; Klein et al., 1992, Biotechnology 10(3), 286-291; U.S. Pat. No. 4,945,050). Preferably, the transformation of plant cells or tissues can be carried out using bacteria of the Agrobacterium genus, preferably by infection of the cells or tissues of said plants with A. tumefaciens (Knopf, 1979, Subcell. Biochem. 6, 143-173; Shaw et al., 1983, Gene 23(3): 315-330) or A. rhizogenes (Bevan and Chilton, 1982, Annu. Rev. Genet. 16: 357-384; Tepfer and Casse-Delbart, 1987, Microbiol. Sci. 4(1), 24-28). Preferably, the transformation of plant cells or tissues with Agrobacterium tumefaciens is carried out according to the protocol described by Hiei et al., (1994, Plant J. 6(2): 271-282). Those skilled in the art will choose the appropriate method according to the nature of the host organisms to be transformed.

[0123] The plants according to the invention contain transformed plant cells as defined above. In particular, the transformed plants can be obtained by regeneration of the transformed plant cells described above. The regeneration is obtained by any appropriate method, which depends on the nature of the species.

[0124] The invention also comprises parts of these plants, and the progeny of these plants. The term “part of these plants” is intended to mean any organ of these plants, whether above ground or below ground. The organs above ground are the stems, the leaves and the flowers comprising the male and female reproductive organs. The organs below ground are mainly the roots, but they may also be tubers. The term “progeny” is intended to mean mainly the seeds containing the embryos derived from the reproduction of these plants with one another. By extension, the term “progeny” applies to all the seeds formed at each new generation derived from crosses between the transformed plants according to the invention. Progeny and seeds can also be obtained by vegetative multiplication of said transformed plants. The seeds according to the invention can be coated with an agrochemical composition comprising at least one active product having an activity selected from fungicidal, herbicidal, insecticidal, nematicidal, bactericidal or virucidal activities.

[0125] The various aspects of the invention will be understood more fully by means of the experimental examples below.

[0126] All the methods or operations described below are given by way of example and correspond to a choice, made among the various methods available for achieving the same result. This choice has no effect on the quality of the result, and, consequently, any appropriate method can be used by those skilled in the art to achieve the same result. In particular, and unless otherwise specified in the examples, all the recombinant DNA techniques employed are carried out according to the standard protocols described in Sambrook and Russel (2001, Molecular cloning: A laboratory manual, Third edition, Cold Spring Harbor Laboratory Press, NY) in Ausubel et al. (1994, Current Protocols in Molecular Biology, Current protocols, USA, Volumes 1 and 2), and in Brown (1998, Molecular Biology LabFax, Second edition, Academic Press, UK). Standard materials and methods for plant molecular biology are described in Croy R. D. D. (1993, Plant Molecular Biology LabFax, BIOS Scientific Publications Ltd (UK) and Blackwell Scientific Publications (UK)). Standard materials and methods for PCR (Polymerase Chain Reaction) are also described in Dieffenbach and Dveksler (1995, PCR Primer: A laboratory manual, Cold Spring Harbor Laboratory Press, NY) and in McPherson et al. (2000, PCR—Basics: From background to bench, First edition, Springer Verlag, Germany).

[0127] Cercospora nicotianae is a pathogen of tobacco (Nicotiana tabacum). The target gene chosen in Cercospora nicotianae is the gene encoding beta-tubulin. Tubules are dynamic structures present in all cell types. In cells which have the ability to divide, the microtubules form the basis of the formation of the mitotic spindle; for the other cell types, they constitute a cytoplasmic network essential for the organization of the nucleus and of the organelles in the cytoplasmic space. Microtubules are heterodimers of alpha- and beta-tubulin. Beta-tubulin is a protein that is essential for the pathogen and is in particular the target for benzimidazoles (Katiyar et al., 1994, Antimicrob. Agents Chemother, 38(9): 2086-2090).

1.—Construct Used to Transform Tobacco Cells

[0128] The construct used to transform tobacco is the plasmid called pPAF 115; it comprises the following selectable markers: a gene for resistance to kanamycin under the control of the nos promoter, a gene for resistance to spectinomycin (aadA) under the control of a bacterial promoter. The CaMV 35S promoter allows transcription of the DNA sequence comprising part of the sense sequence of Cercospora nicotianae beta-tubulin, represented by the sequence identifier SEQ ID No. 1, itself followed by an intron represented by the sequence identifier SEQ ID No. 2 and by the antisense sequence of this same beta-tubulin, represented by the sequence identifier SEQ ID No. 3. An ocs terminator is downstream of the sense-intron-antisense assembly. This assembly is represented by the sequence identifier SEQ ID No. 4.

[0129] The Nicotiana tabacum variety Petit Havana is transformed with this vector pPAF 115.

2.—Transformation of Tobacco Foliar Tissues Using the Solution of Agrobacterium Transformed with the Plasmid pPAF115

[0130] The solution of Agrobacterium (OD=1) is washed in 10 mM MgSO₄. Disks are cut out of wild-type tobacco leaves and are disinfected for 10 min in 75% ethanol and then incubated for 5 min in the solution of Agrobacterium. They are then sponged, and placed with the lower face against a Petri dish containing MS 0.05-2 agar (Murashige & Skoog M5519, 30 g/l sucrose, 0.05 ppm ANA, 2 ppm BAP, 7 g/l phytagar, pH=5.7) for a culture of three days. The foliar disks are transferred onto MS 0.05-2 dishes in the presence of spectinomycin and kanamycin for two to four weeks. The foliar disks are then placed on MS 0-0 medium (Murashige & Skoog M5519, 30 g/l sucrose, 7 g/l phytagar, pH=5.7) also containing the antibiotics for seven to ten days. The tobacco shoots derived from the disks are isolated and rooted on MS ½-½ agar dishes (½ Murashige & Skoog, 15 g/l sucrose, 7 g/l phytagar, pH=5.7) containing the antibiotics. Once the first two leaves have appeared, the shoots are placed in earth in order for the plants to develop.

3.—Molecular Analyses Carried Out on the Transgenic Tobacco

[0131] Three different events were obtained.

3.1.—PCR

[0132] First PCR experiments are carried out on the genomic DNA of the various events in order to determine whether the latter contain the construct according to the invention. Primers for detecting the kanamycin gene and also the Cercospora-specific tubulin were used.

[0133]

	Event
	14	15	19	WT
	Kanamycin	+	+	+	−
	Tubulin	+	+	+	−
	WT: wild-type, nontransformed plant.

[0134] The sequences of the primers used are as follows:

[0135]

Kanamycin:
direct:	5′-CAA GAC CGA CCT GTC C-3′	(SEQ ID No. 5)
inverse:	5′-CCA TCC GAG TAC GTG C-3′	(SEQ ID No. 6)

[0136]

Cercospora nicotianae tubulin:
direct:	5′-ATC GAT AAC GAG GCC C-3′	(SEQ ID No. 7)
inverse:	5′-ACA TCG TAA GTC CTC GG-3′	(SEQ ID No. 8)

[0137] All the plants contain the plasmid pPAF115 according to the invention.

3.2.—Quantitative RT-PCR

[0138] The RNA of the events obtained is extracted and a reverse transcription is carried out before performing a quantitative PCR. The reverse transcription is carried out from 4 μg of RNA using random primers. The quantitative PCR is carried out according to this scheme:

[0139]

	cDNA 100 ng tobacco tubulin	cDNA 100 ng Cercospora
		tubulin
	cDNA 10 ng tobacco tubulin	cDNA 10 ng Cercospora
		tubulin
	RNA 100 ng tobacco tubulin	RNA 100 ng Cercospora
		tubulin
	RNA 10 ng tobacco tubulin	RNA 10 ng Cercospora
		tubulin

[0140] The RNA is used to carry out the PCR reaction in order to ensure that the detection of DNA obtained with the cDNA is indeed due to an amplification of complementary DNA and not of contaminating genomic DNA (the amplification from the RNA must be zero).

[0141] The detection of the tobacco tubulin complementary DNA by virtue of the use of the primers mentioned below (SEQ ID No. 9 and SEQ ID No. 10) serves as a reference expression level. The level of expression of the transgene was calculated relative to this expression of tobacco tubulin.

[0142]

	Tobacco tubulin
	direct
	5′-GAA AAC ACG TCC CTC G-3′	(SEQ ID No. 9)
	inverse
	5′-TCT TGC CGT AGT CCA C-3′	(SEQ ID No. 10)

[0143] For all the experiments:

• • [0144] The RNA controls are negative, there is therefore no contamination with genomic DNA.
  • [0145] The difference in expression between the concentrations of 100 and 10 ng is constant and in accordance with expectations for 10-fold dilutions.

[0146] FIG. 3 shows the position of the Cercospora nicotianae tubulin primers on the DNA and RNA sequences comprising the sense-intron-antisense assembly as defined by the sequence identifier SEQ ID No. 4. The dashed lines represent diagrammatically the primers with which the quantitative PCR (qPCR) is carried out after the reverse transcription (RT).

[0147] The qPCR can detect the transcripts derived from the construct according to the invention only if they are not degraded. The RT-qPCR detects only the long transcripts, mRNA or dsRNA.

[0148]

		Level of
		detection
		(quantitative
	Event	RT-PCR)	Results
	WT	−−−	No PCR detection of the
			construct
			No detection of RNA of
			the construct
	14, 15	+/−	Positive but weak PCR
			detection of the
			construct
			Weak detection of RNA
			of the construct
	19	+	Positive PCR detection
			of the construct
			Clear detection of RNA
			of the construct
	“+” signifies that the signal is clearly detected by RT-qPCR
	“+/−” signifies that the signal is weakly detected
	“−−−” corresponds to the absence of the transgene

3.3.—Quantitative RT-PCR in View of the In Vivo Tests

[0149] The in vivo tests are carried out on the T0 plants described above. This involves the events: 14, 15, 19 and WT. For these 4 events, clones derived from the initial T0 plant will therefore be used to carry out the tests. These clones are produced by cutting out from the leaves of each event, cultured again in vitro and regenerated (see above). In order to carry out a rapid control, a quantitative RT-PCR analysis is carried out on one clone of the events 14, 19 and WT (14A, 19A and WT, respectively).

[0150] All the controls (RNA, WT, and internal reference (tobacco tubulin)) are correct. Following validation of the controls, a level of expression can be given for each clone: the results are expressed qualitatively as a function of the values obtained by virtue of the quantitative PCR.

[0151]

		Level of
		expression
		(quantitative
	Event	RT-PCR)	Results
	WT	−−−	No PCR detection of the
			construct
			No detection of RNA of
			the construct
	14A	+/−	Positive but weak PCR
			detection of the
			construct
			Weak detection of RNA
			of the construct
	19A	+	Positive PCR detection
			of the construct
			Clear detection of RNA
			of the construct
	“+” signifies that the signal is clearly detected by RT-qPCR
	“+/−” signifies that the signal is weakly detected
	“−−−” corresponds to the absence of the transgene

4.—Pathological Tests In Vivo for Evaluating the Resistance of the Transgenic Tobacco Plants to Infection with Cercospora nicotianae
Plant Material:

[0152] Clones (at least nine) derived from the T0 events at a developmental stage of the plants comprising at least 5 developed leaves.

[0153] Production: S2 glass (25° C. daytime/20° C. night time; 60% RH; photoperiod 15 H of light).

Inoculum:

[0154] Suspension of Cercospora nicotianae (approximately 10⁴ spores/ml)

Evaluation of Symptoms:

[0155] The intensity of the symptoms is determined according to biological criteria as a function of the size and of the appearance of the lesions observed on the leaves. Thus, as can be seen in FIG. 4, the mark 1 corresponds to the visualization of very slight, barely perceptible, marks on the leaf. The mark 2 corresponds to clear, but very few, marks on the leaf. The mark 3 corresponds to clear and numerous marks on the leaf. The mark 4 corresponds to very clear and very numerous marks with the presence of large marks. The mark 5 corresponds either to complete rotting of the leaf, or to numerous very large marks. The differences between 1, 2, 3, 4 and 5 therefore correspond to real and clear differences in symptoms. Thus, plants having symptom marks of 4 or 5 are considered to be very severely affected. Plants with a mark of 3 are affected but remain acceptable. Plants with a mark of 2 are weakly affected and those with a mark of 1 are only very weakly affected.

[0156] There are, moreover, three different readings:

[0157] 1st reading: 10 days after inoculation

[0158] 2nd reading: 21 days after inoculation

[0159] 3rd reading: 1 month after inoculation

[0160] Furthermore, the determination of the percentage contamination of the foliar surface ranges from 0% to 100%. 0% corresponds to an observation where no symptom is visible on the leaf, there appears to be a complete absence of the pathogen. 100% corresponds to a leaf completely covered by the pathogen, i.e. a brown and rotten leaf. Since the result of the reading was obtained with the average of the leaves of the same plant, values that are so extreme cannot be obtained. It can thus be considered that, above 30% of foliar surface which is contaminated, the plant is very severely affected by the disease. Below 20%, the contamination can be judged to be weak and below 10-15% as very weak.

[0161] The results are presented in the form of histograms corresponding to the means of the plants per event (results at 28 days after infection). The confidence interval is represented for each histogram.

[0162] For each event, the number of plants analyzed is indicated below along with the corresponding number of leaves:

[0163] WT: 19 plants (87 leaves)

[0164] event 14: 14 plants (67 leaves)

[0165] event 15: 21 plants (102 leaves)

[0166] event 19: 12 plants (60 leaves).

[0167] FIG. 5 represents the intensity of the symptoms noted for each event.

[0168] FIG. 6 represents the percentage of contaminated foliar surface for each event.

[0169] The results of the in vivo test are clearly correlated with the molecular analyses: the detection of the long transcripts derived from the construct according to the invention is completely correlated with a weaker intensity of the symptoms and therefore resistance of the transgenic plant.

[0170]

	Pathological tests on T0
	tobacco plants
	Results at 28 days after
	infection
			% of
			contaminated
		RT-qPCR	foliar	Intensity
	Presence	Detection	surface	of symptoms
	of the	of long	(confidence	(confidence
Event	transgene	RNAs	interval)	interval)
WT	No	−−−	37% (6.6)	4 (0.26)
14	Yes	−/+	11% (3.8)	2 (0.37)
15	Yes	−/+	17% (3.85)	3 (0.22)
19	Yes	+	19% (4.8)	3.2 (0.34)
−/+: weak detection
+: clear detection
−−−: no detection

[0171] The results presented below are established using statistically validated tests for biological assays. The population of each event makes it possible to establish statistically robust confidence intervals.

[0172] Magnaporthe grisea is a pathogen of rice (Oryza sativa). The chosen target in Magnaporthe grisea is the buf gene.

[0173] The buf gene is a gene essential to the pathogenicity of Magnaporthe grisea. In the case of deletion, Magnaporthe grisea is non-virulent and cannot contaminate rice (Kawamura et al., 1997, Mol. Plant Microb. Interact., 10(4): 446-53).

1.—Construct Used to Transform Rice Cells

[0174] The construct used to transform rice is the plasmid called pPAF 74; it comprises the following selectable marker: a gene for resistance to gentamycin under the control of a bacterial promoter. The CaMV 35S promoter allows transcription of the DNA sequence comprising part of the sense sequence of the buf gene, represented by the sequence identifier SEQ ID No. 11, itself followed by the antisense sequence of this same buf gene which is partially deleted compared with the sense sequence, represented by the sequence identifier SEQ ID No. 12. A Nos terminator is downstream of the sense-antisense assembly which is represented by the sequence identifier SEQ ID No. 13. The Oryza sativa variety Nippon Bare is transformed with this vector pPAF 74.

2.—Transformation of Rice Tissues with the Solution of Agrobacterium Transformed with the Plasmid pPAF 74

[0175] The embryos are removed from the pericarp and are immersed in a solution of 70% ethanol for 1 min. They are then placed in one third-diluted commercial bleach for 30 min and stirred from time to time. Finally, they are rinsed 3 times with sterile water.

[0176] The embryos thus decontaminated are placed on the side (12 per dish), on NB medium (macroelements N6, FeEDTA, microelements B5, vitamins B5, myoinositol, proline glutamine, casein hydrolysate, sucrose, 2,4-D, phytagel). The dish is left half-open under the hood so as to dry the seed well (incubator at 28° C.—in the dark—17 to 20 days). After a period of 17 to 20 days (28° C.—in the dark), the small embryogenic units (nodules of diameter from 0.5 to 1 mm) which form from the primary callus, in contact with the medium, are excised and subcultured on NB medium in a 100×15 dish (incubator at 280° C.—in the dark—10 days).

[0177] A culture of Agrobacteria (3-5×10⁹ bacteria/ml (OD₆₀₀=1)) is used for the transformation.

[0178] An inoculation and a coculture must then be performed: Calluses of 3 to 5 mm, that are nicely round, rough, whitish and opaque, are immersed in the solution of agrobacteria containing the plasmid pPAF 74 (3-5×10⁹ bacteria/ml) (20 ml per dish) for 15 min with slight stirring.

[0179] The calluses are transferred onto sterile Whatman paper and are dried. The calluses are then placed in culture on R2-CS medium (macroelements R2-I, macroelements R2-II, FeEDTA, microelements R2, vitamins R2, glucose, 2,4-D, type I agarose) in the dark, at a temperature of 25° C., for 3 days (10 calluses per dish).

[0180] The calluses are transferred onto R2S selection medium (macroelements R2-I, macroelements R2-II, FeEDTA, microelements R2, vitamins R2, sucrose, 2,4-D, type I agarose, vancomycin, cefotaxime, hygromycin) (28° C.—in the dark—2 weeks). The calluses are subcultured on NBS medium (macroelements N6, FeEDTA, microelements B5, vitamins B5, myoinositol, proline, glutamine, casein hydrolysate, sucrose, 2,4-D, type I agarose, cefotaxime, vancomycin, hygromycin) (280° C.—in the dark—1 week). The proliferations (globules) are spread out around their callus of origin, so as to bring them into contact with the selection medium (280° C.—in the dark—1 to 2 weeks).

The Transformants Must then Enter into Maturation:

[0181] The resistant proliferations are subcultured (well-developed globules, yellow-white in color) on PR-AG medium (macroelements N6, FeEDTA, microelements B5, vitamins B5, myoinositol, proline, glutamine, casein hydrolysate, sucrose, ABA, BAP, ANA, type I agarose, cefotaxime, hygromycin, vancomycin), identifying the callus of origin (10 calluses per dish) (280° C.—in the dark—8 days).

Regeneration of the Transformants:

[0182] The calluses are subcultured on RN regeneration medium (macroelements N6, FeEDTA, microelements B5, vitamins B5, myoinositol, proline, glutamine, casein hydrolysate, sucrose, BAP, ANA, phytagel) (28° C.—continuous light—3 weeks).

[0183] The regenerated plants are subcultured in a tube (MS medium, sucrose, phytagel).

[0184] They are subsequently subcultured in compost, acclimatized, and cultivated under glass.

Acclimatation of the Transformed Plants:

[0185] The plantlets are acclimatized when they have become well developed in the tube (after approximately 3-4 weeks). The plantlet is removed from the tube. The roots are passed under a trickle of water in order to remove the agar. The end of the leaves and of the roots is cut. The dead leaves are removed. The plantlet is placed in a pot, in a small glasshouse (“small greenhouse”) containing 1-2 cm of water or none at all in order to avoid rotting, with the door closed. The top of the small glasshouse is protected with absorbent paper. The assembly is placed in an in vitro culture chamber. The door is gradually half opened and the paper is removed. When the roots emerge from the pot (after approximately 15 days), the plants are planted out in compost, in a pot. Eight different events were obtained.

3.—Molecular Analyses Carried Out on the Transgenic Rice

3.1.—PCR

[0186] First PCR experiments are carried out on the genomic DNA of the various events in order to determine whether the latter contain the construct according to the invention. Primers for detecting the Magnaporthe buf gene were used.

[0187]

	Event
	M	L	F	WT
	buf	+	+	+	−
	WT: wild-type, nontransformed plant.

[0188] The sequences of primers used are as follows:

[0189]

	Magnaporthe buf:
	Direct:
	5′-TGA CCG TGT CTT TAC CA-3′	(SEQ ID No. 16)
	Indirect:
	5′-AGC AAC CAC ATT AAC AGT-3′	(SEQ ID No. 17)

[0190] All the plants contain the plasmid according to the invention.

3.2. Quantitative RT-PCR:

[0191] The RNA of these 4 events is extracted and a reverse transcription is carried out before performing a quantitative PCR. The reverse transcription is carried out from 4 μg of RNA using random primers. The quantitative PCR is carried out according to this scheme:

[0192]

	cDNA 100 ng rice tubulin	cDNA 100 ng Magnaporthe buf
	cDNA 10 ng rice tubulin	cDNA 10 ng Magnaporthe buf
	RNA 100 ng rice tubulin	RNA 100 ng Magnaporthe buf
	RNA 10 ng rice tubulin	RNA 10 ng Magnaporthe buf

[0193] The RNA is used to carry out the PCR reaction in order to ensure that the detection of DNA obtained with the DNA is indeed due to an amplification of complementary DNA and not of contaminating genomic DNA (the amplification from the RNA must be zero).

[0194] The detection of tobacco tubulin complementary DNA serves as a reference expression level. The level of expression of the transgene was calculated relative to this expression of tobacco tubulin.

[0195] The sequences of primers are as follows:

[0196]

	Rice tubulin:
	Direct:
	5′-CAT TGA CTT CAC GCG G-3′	(SEQ ID No. 14)
	Indirect:
	5′-GAC ACT GGA TTT GAC GTT-3′	(SEQ ID No. 15)
	Magnaporthe buf:
	Direct:
	5′-TGA CCG TGT CTT TAC CA-3′	(SEQ ID No. 16)
	Indirect:
	5′-AGC AAC CAC ATT AAC AGT-3′.	(SEQ ID No. 17)

For all the Experiments:

• • [0197] The RNA controls are negative, there is therefore no contamination with genomic DNA.
  • [0198] The difference in expression between the concentrations of 100 and 10 ng is constant and in accordance with expectations for 10-fold dilutions.

[0199]

		Expression
		level
		(quantitative
	Event	RT-PCR)	Results
	WT	−−−	No PCR detection of the
			construct
			No detection of RNA
			corresponding to the
			buf gene
	M	+/−	PCR detection of the
			construct
			Weak detection of RNA
			corresponding to the
			buf construct
	L	+	PCR detection of the
			construct
			Clear detection of RNA
			corresponding to the
			buf construct
	F	++	PCR detection of the
			construct
			Very clear detection of
			RNA corresponding to
			the buf construct
	“+” signifies that the signal is detected by RT-qPCR
	“−−−” corresponds to the absence of the transgene
	“++” signifies that the signal is strongly detected by RT-qPCR.

4.—Pathological Tests In Vivo for Evaluating the Resistance of the Transgenic Rice Plants to Infection with Magnaporthe grisea
Plant Material:

[0200] T0 events at a developmental stage of the plants comprising at least 5 developed leaves.

[0201] Production: S2 glass

Inoculum:

[0202] Suspension of Magnaporthe grisea (10⁴ spores/ml).

Evaluation of Symptoms:

[0203] The intensity of the symptoms is determined according to biological criteria as a function of the size and the appearance of the lesions observed on the leaves. Thus, the mark 1 corresponds to the visualization of very slight, barely perceptible, marks on the leaf. The mark 2 corresponds to clear, but very few, marks on the leaf. The mark 3 corresponds to clear and numerous marks on the leaf. The mark 4 corresponds to very clear and very numerous marks with the presence of large marks. The mark 5 corresponds either to complete rotting of the leaf, or to numerous very large marks. The mark 6 corresponds to a plant 100% affected by the disease.

[0204] The differences between 1, 2, 3, 4, 5 and 6 therefore correspond to real and clear differences in symptoms. Thus, plants having symptom marks of 6 are dead, the plants 4 or 5 are considered to be very severely affected. Plants with a mark of 3 are affected but remain acceptable. Plants with a mark of 2 are weakly affected and those with a mark of 1 are only very weakly affected.

[0205] The results are presented in the form of histograms corresponding to the means of the plants per event. The confidence interval is represented for each histogram. FIG. 7 presents the intensity of the symptoms noted for each event.

[0206] The results of the in vivo test are clearly correlated with the molecular analyses: the detection of the long transcripts derived from our construct is completely correlated with a weaker intensity of the symptoms and therefore resistance of the transgenic plant.

[0207]

				Intensity of
			RT-qPCR:	the symptoms
		Presence of	detection of	15 days
		the	the long	after
	Event	transgene	RNAs	infection
	WT	No	−−−	5-6
	M	Yes	−/+	1
	L	Yes	+	2-3
	F	Yes	++	2-3
	−/+: weak detection
	+: detection
	++: strong detection
	−−−: no detection

[0208]

TABLE 1
DQ026402	Mycosphaerella arachidis strain 255 beta-tubulin gene, partial cds
DQ026347	Mycosphaerella coffeicola strain 172 beta-tubulin gene, exon 8 and
	partial cds
DQ026336	Cercospora beticola strain 21 beta-tubulin gene, exon 8 and partial cds
AY856374	Cercospora beticola isolate AD-762 beta-tubulin (TUB1) gene, complete
	cds
AY856373	Cercospora beticola isolate C-3 beta-tubulin (TUB1) gene, complete cds
AY373578	Cercospora kikuchii isolate DLS5012-1A beta-tubulin gene, partial cds
AY373577	Cercospora kikuchii isolate DLL6013-1B beta-tubulin gene, partial cds
AF146117	Cercospora piaropi strain 2619 beta-tubulin (tub) gene, partial cds
AF146116	Cercospora beticola strain Cb beta-tubulin (tub) gene, partial cds
AF146115	Cercospora piaropi strain TX20 beta-tubulin (tub) gene, partial cds
AF146114	Cercospora piaropi strain TX15 beta-tubulin (tub) gene, partial cds
AF146113	Cercospora piaropi strain TX18 beta-tubulin (tub) gene, partial cds
AF146112	Cercospora piaropi strain 62-4 beta-tubulin (tub) gene, partial cds
AF146111	Cercospora piaropi strain WHK beta-tubulin (tub) gene, partial cds
AF146110	Cercospora piaropi strain I75-102 beta-tubulin-like (tub) gene, partial
	sequence
AF146109	Cercospora piaropi strain 62-2 beta-tubulin (tub) gene, partial cds
AF146108	Cercospora piaropi strain 400 beta-tubulin (tub) gene, partial cds
AF146107	Cercospora piaropi strain 34 beta-tubulin (tub) gene, partial cds
AF146106	Cercospora piaropi strain 18 beta-tubulin (tub) gene, partial cds
AF146105	Cercospora piaropi strain 114 beta-tubulin (tub) gene, partial cds
AF146104	Cercospora piaropi strain RR29 beta-tubulin (tub) gene, partial cds
AF146103	Cercospora piaropi strain BA57 beta-tubulin (tub) gene, partial cds
AF146102	Cercospora piaropi strain WHV beta-tubulin (tub) gene, partial cds
AF146101	Cercospora piaropi strain WH9BR beta-tubulin (tub) gene, partial cds
AF146100	Cercospora piaropi strain WH83 beta-tubulin (tub) gene, partial cds
AF146099	Cercospora piaropi strain 2867 beta-tubulin (tub) gene, partial cds
AF146098	Cercospora piaropi strain 28-1 beta-tubulin (tub) gene, partial cds
AF146097	Cercospora piaropi strain 10 beta-tubulin (tub) gene, partial cds
AF146096	Cercospora piaropi strain MX3 beta-tubulin (tub) gene, partial cds
XM_370153	Magnaporthe grisea 70-15 chromosome II hypothetical protein
	(MG06650.4) partial mRNA
XM_368640	Magnaporthe grisea 70-15 chromosome VI hypothetical protein
	(MG00604.4) partial mRNA
XM_368283	Magnaporthe grisea 70-15 chromosome VI hypothetical protein
	(MG00961.4) partial mRNA
AY944078	Magnaporthe oryzae isolate CH072 beta-tubulin 1 gene, partial cds
AY944077	Magnaporthe oryzae isolate SJ10-2-1 beta-tubulin 1 gene, partial cds
AY944076	Magnaporthe oryzae isolate SAG00T15 beta-tubulin 1 gene, partial cds
AY063737	Magnaporthe grisea isolate 8470 beta-tubulin gene, partial cds
AY063736	Magnaporthe grisea isolate 8465 beta-tubulin gene, partial cds
AF396004	Magnaporthe salvinii beta-tubulin gene, partial cds
AF396000	Magnaporthe grisea strain A119 beta-tubulin gene, partial cds
AF395999	Magnaporthe grisea strain Py-D beta-tubulin gene, partial cds
AF395998	Magnaporthe grisea strain 91T16 beta-tubulin gene, partial cds
AF395997	Magnaporthe grisea strain 81T4 beta-tubulin gene, partial cds
AF395996	Magnaporthe grisea strain JP34 beta-tubulin gene, partial cds
AF395995	Magnaporthe grisea strain RW12 beta-tubulin gene, partial cds
AF395994	Magnaporthe grisea strain NI909 beta-tubulin gene, partial cds
AF395993	Magnaporthe grisea strain 1122 beta-tubulin gene, partial cds
AF395992	Magnaporthe grisea strain 330 beta-tubulin gene, partial cds
AF395991	Magnaporthe grisea strain 365 beta-tubulin gene, partial cds
AF395990	Magnaporthe grisea strain T28 beta-tubulin gene, partial cds
AF395989	Magnaporthe grisea strain BK-19 beta-tubulin gene, partial cds
AF395988	Magnaporthe grisea strain BK-6 beta-tubulin gene, partial cds
AF395987	Magnaporthe grisea strain ML-56 beta-tubulin gene, partial cds
AF395986	Magnaporthe grisea strain R707-1E beta-tubulin gene, partial cds
AF395985	Magnaporthe grisea strain R694-2b beta-tubulin gene, partial cds
AF395984	Magnaporthe grisea strain Guy11 beta-tubulin gene, partial cds
AF395983	Magnaporthe grisea strain A598 beta-tubulin gene, partial cds
AF395982	Magnaporthe grisea strain C10 beta-tubulin gene, partial cds
AF395981	Magnaporthe grisea strain A264 beta-tubulin gene, partial cds
AF395980	Magnaporthe grisea strain ML-91 beta-tubulin gene, partial cds
AF395979	Magnaporthe grisea strain G48 beta-tubulin gene, partial cds
AF395978	Magnaporthe grisea strain A347 beta-tubulin gene, partial cds
AF395977	Magnaporthe grisea strain K76-79 beta-tubulin gene, partial cds
AF395976	Magnaporthe grisea strain 1152 beta-tubulin gene, partial cds
AY944090	Magnaporthe oryzae isolate SJ-5-1-2 chitin synthase 1 gene, partial cds
AY944089	Magnaporthe oryzae isolate G48 chitin synthase 1 gene, partial cds
AY944088	Magnaporthe oryzae isolate ML91 chitin synthase 1 gene, partial eds
AY944087	Magnaporthe oryzae isolate GUY11 chitin synthase 1 gene, partial cds
AY944086	Magnaporthe oryzae isolate G8 chitin synthase 1 gene, partial cds
AY944085	Magnaporthe oryzae isolate G17 chitin synthase 1 gene, partial cds
AY944084	Magnaporthe oryzae isolate G119 chitin synthase 1 gene, partial cds
AY944083	Magnaporthe oryzae isolate BK6 chitin synthase 1 gene, partial cds
AY944082	Magnaporthe oryzae isolate A119 chitin synthase 1 gene, partial cds
AY944081	Magnaporthe oryzae isolate 1122 chitin synthase 1 gene, partial cds
AY944080	Magnaporthe oryzae isolate 365 chitin synthase 1 gene, partial cds
AB018251	Magnaporthe grisea gene for Csm1, complete cds
X96416	M. grisea CHS4 gene
X96415	M. grisea CHS3 gene
X96414	M. grisea CHS2 gene
X96413	M. grisea CHS1 gene
AF020528	Magnaporthe grisea Class IV chitin synthase (chs4) gene, complete cds

[0209]

TABLE 2
Plant	Diseases
Barley	Anthracnose
(Hordeum	Colletotrichum graminicola (Ces.) G. W. Wils.
vulgare L.)	Glomerella graminicola Politis [teleomorph]
	Barley stripe
	Drechslera graminea (Rabenh.) Shoemaker
	Cephalosporium stripe
	Hymenula cerealis Ellis & Everh. = Cephalosporium
	gramineum Nisikado & Ikata in
	Nisikado el al.
	Common root rot, crown rot and seedling blight
	Bipolaris sorokiniana (Sacc.) Shoemaker
	Fusarium culmorum (Wm. G. Smith) Sacc.
	F. graminearum Schwabe
	Gibberella zeae (Schwein.) Petch [teleomorph]
	Downy mildew
	Sclerophthora rayssiae Kenneth et al.
	Dwarf bunt
	Tilletia controversa Kuhn in Rebenh.
	Ergot
	Claviceps purpurea (Fr.:Fr.) Tul.
	Sphacelia segetum Lev. [anamorph]
	Eyespot
	Pseudocercosoporella herpotrichoides (Fron) Deighton
	Tapesia yallundae Wallwork & Spooner [teleomorph]
	Halo spot
	Pseudoseptoria donacis (Pass.) Sutton = Selenophoma
	donacis (Pass.) R. Sprague & A. G. Johnson = Septoria donacis
	Kernel blight = black point
	Alternaria spp.
	Arthrinium arundinis Dyko. & Sutton
	Apiospora montagnei Sacc. [teleomorph]
	Cochliobolus sativus (Ito & Kuribayashi) Drechs. Ex Dastur
	Fusarium spp.
	Leaf spot
	Ascochyta hordei K. Hara (United States, Japan)
	A. graminea (Sacc.) R. Sprague & A. G. Johnson
	A. sorghi Sacc.
	A. tritici S. Hori & Enjoji
	Net blotch
	Drechslera teres (Sacc.) Shoemaker
	Pyrenophora teres Drechs. [teleomorph]
	Net blotch (spot form)
	Drechslera teres f. maculata Smedeg.
	Powdery mildew
	Erysiphe graminis DC. f. sp. hordei Em. Marchal = Blumeria
	graminis (DC.) E. O. Speer
	Oidium monilioides (Nees) Link [anamorph]
	Pythium root rot
	Pythium spp.
	P. arrhenomanes Drechs.
	P. graminicola Subramanian
	P. tardicrescens Vanderpool
	Rhizoctonia root rot
	Rhizoctonia solani Kuhn
	Thanatephorus cucumeris (A. B. Frank) Donk
	[teleomorph]
	Rusts
	Crown rust
	Puccinia coronata Corda
	Leaf rust
	Puccinia hordei Otth
	Stem rust
	Puccinia graminis Pers.:Pers.
	Stripe rust = yellow rust
	Puccinia striiformis Westend.
	Scab = head blight
	Fusarium spp.
	F. graminearum Schwabe
	Scald
	Rhynchosporium secalis (Oudem.) J. J. Davis
	Septoria speckled leaf blotch
	Septoria passerinni Sacc.
	Stagonospora avenae f. sp. triticea T. Johnson
	Sharp eyespot
	Rhizoctonia cerealis Van der Hoeven
	Ceratobasidium cereale D. Murray & L. L. Burpee
	[teleomorph]
	Smuts
	Covered smut
	Ustilago hordei (Pers.) Lagerh.
	False loose smut
	Ustilago avenae (Pers.) Rostr. = U. nigra
	Tapke
	Loose smut
	Ustilago tritici (Pers.) Rostr. = U. nuda
	(C. N. Jensen) Rostr., nom. nud.
	Snow molds
	Gray snow mold = Typhula blight
	Typhula incarnata Fr.
	T. ishikariensis Imai
	Pink snow mold = Fusarium patch
	Microdochium nivale (Fr.) Samuel & I. C. Hallett = Fusarium
	nivale (Fr.) Sorauer
	Monographella nivalis (Schaffnit) E. Müller [teleomorph]
	Speckled snow mold
	Typhula idahoensis Remsberg
	Snow rot
	Pythium iwayamai Ito
	P. okanoganense Lipps
	P. paddicum Harane
	Snow scald = Sclerotinia snow mold
	Myriosclerotinia borealis (Bubak & Vleugel) L. M. Kohn = Sclerotinia
	borealis Bubak & Vleugel
	Southern blight
	Sclerotium rolfsii Sacc. (India, California, Puerto
	Rico)
	Athelia rolfsii (Curzi) Tu & Kimbrough [teleomorph]
	Spot blotch
	Cochliobolus sativus (Ito & Kuribayashi) Drechs. ex
	Dastur
	Drechslera teres (Sacc.) Shoemaker [anamorph]
	Stagonospora blotch
	Stagonospora avenae f. sp. triticea T. Johnson
	Phaeosphaeria avenaria f. sp. triticea T. Johnson
	[teleomorph]
	Stagonospora nodrum (Berk.) Castellani & E. G. Germano = Septoria
	nodorum (Berk.) Berk. in Berk. & Broome
	Phaeosphaeria nodorum (E. Muller) Hedjaroude
	[teleomorph]
	Take-all
	Gaeumannomyces graminis var. tritici J. Walker
	Tan spot
	Pyrenophora tritici-repentis (Died.) Drechs. = P. trichostoma
	(Fr.) Fuckel
	Drechslera tritici-repentis (Died.) Shoemaker [anamorph] = Helminthosporium
	tritici-repentis Died.
	Verticillium wilt
	Verticillium dahliae Kleb. (Idaho)
	Wirrega blotch
	Drechslera wirreganensis Wallwork et al. (Australia)
Beet	Alternaria leaf spot
(Beta vulgaris L.)	Alternaria alternata (Fr.:Fr.) Keissl.
	A. brassicae (Berk.) Sacc.
	Anthracnose*
	Colletotrichum dematium (Pers.) Grove f. spinaciae
	(Ellis & Halst.) Arx
	Aphanomyces root rot (black root)
	Aphanomyces cochlioides Drechs.
	Black wood vessel*
	Pythium irregulare Buisman
	Cercospora leaf spot
	Cercospora beticola Sacc.
	Charcoal rot
	Macrophomina phaseolina (Tassi) Goidanich
	Choanephora rot*
	Choanephora cucurbitatum (Berk. & Ravenel) Thaxt.
	Damping-off, black leg, black root and seedling blight
	Aphanomyces cochlioides Drechs.
	Cylindrocladium sp.*
	Fusarium spp.
	Phoma betae A. B. Frank
	Pleospora betae (Berl.) Nevodovsky [teleomorph]
	Pythium spp.
	Rhizoctonia solani Kühn
	Thanatephorus cucumeris (A. B. Frank) Donk
	[teleomorph]
	Downy mildew
	Peronospora farinosa (Fr.:Fr.) Fr. = P. farinosa
	(Fr.:Fr) Fr. f. sp. betae Byford = P. schachtii
	Fuckel
	Fusarium yellows
	Fusarium oxysporum Schlechtend.:Fr. f. sp. spinaciae
	(Sherb.) W. C. Snyder & H. N. Hans.
	Fusarium yellows and root rot
	Fusarium oxysporum Schlechtend.:Fr. f. sp. betae (D. Stewart)
	W. C. Snyder & H. N. Hans. (Texas isolates)
	Leaf gall (beet tumor, or crown wart)
	Physoderma leproides (Trab.) Karling = Urophlyctis
	leproides (Trab.) Magnus
	Phoma leaf spot and root rot
	Phoma betae A. B. Frank
	Phymatotrichum root rot (cotton root rot)
	Phymatotrichopsis omnivora (Duggar) Hennebert = Phymatotrichum
	omnivorum Duggar
	Phytophthora wet rot
	Phytophthora drechsleri Tucker
	Powdery mildew
	Erysiphe polygoni DC. = E. betae
	Weltzien
	Pythium root rot
	Pythium aphanidermatum (Edson) Fitzp.
	P. deliense Meurs
	Ramularia leaf spot
	Ramulariabeticola Fautrey & Lambotte
	Rhizoctonia foliar blight, crown and root rot
	Rhizoctonia solani Kühn
	Rhizopus root rot
	Rhizopus arrhizus A. Fischer
	R. stolonifer (Ehrenb.:Fr.) Vuill.
	Rust
	Uromycesbetae J. Kickx fil.
	Sclerotinia crown & root rot
	Sclerotinia sclerotiorum (Lib.) de Bary
	Seedling rust
	Puccinia subnitens Dietel
	Slime molds*
	Physarum cinereum (Batsch) Pers.
	Southern blight (Sclerotium root rot and stem rot)
	Sclerotium rolfsii Sacc.
	Athelia rolfsii (Curzi) Tu & Kimbrough [teleomorph]
	Stemphylium leaf spot*
	Stemphylium botryosum Wallr.
	Pleospora tarda E. Simmons [teleomorph]
	Storage rots
	Botrytis cinerea Pers.: Fr.
	Botryotinia fuckeliana (de Bary) Whetzel
	[teleomorph]
	Penicillium spp.
	Phoma betae A. B. Frank
	Verticillium wilt
	Verticillium albo-atrum Reinke & Berthier
	Violet root rot
	Helicobasidium brebissonii (Desmaz.) Donk
	Rhizoctonia crocorum (Pers.:Fr.) DC. [anamorph]
Coffee	Anthracnose
(Coffea arabica L. -	Colletotrichum gloeosporioides Penz
arabica	(teleomorph = Glomerella cingulata (Stonem.) Spauld, &
coffee)	Shrenk.)
(Coffea	Colleotrichum kahawae Waller & Bridge
canephora Pierre	Armillaria root rot
ex Froehner -	Armillaria mellea (Vahl ex Fries) Kummer
robusta coffee)	Bark disease
	Fusarium stilboides Wollenw.
	(teleomorph = Gibberella stilboides)
	Berry blotch
	Cercospora coffeicola Berk. & Cke
	Black (Rosellinia) root rot
	Rosellinia spp.
	Black (seedling) root rot
	Rhizoctonia solani Kuhn.
	Blister spot
	Virus (uncharacterised)
	Brown blight
	Colleotrichum gloeosporioides Penz.
	(teleomorph = Glomerella cingulata (Stonem.) Spauld. &
	Schrenk
	Colletotrichum kahawae Waller & Bridge
	Brown eye spot
	Cercospora coffeicola Berk. & Cke
	Brown leaf spot
	Phoma costarricensis Ech.
	Canker
	Ceratocystis fimbriata (Ell. & Halst.) Hunt
	Phomopsis coffeae Bondarzeva-Monteverde
	Collar rot
	Fusarium stilboides Wollenz
	(telemorph = Gibberella stilboides)
	Coffee berry disease
	Colletotrichum kahawae Waller & Bridge
	Die-back
	Ascochta tarda Stewart
	Dry root rot
	Fusarium solani (Mart.) Sacc.
	Leaf blight
	Ascochyta tarda Stewart
	Leaf spot
	Phyllosticta coffeicola Speg.
	Pink disease
	Corticium salmonicola Berk. & Br.
	Red blister disease (robusta coffee)
	Cercospora coffeicola Berk. & Br.
	Red root rot
	Ganoderma philippi (Bres & P. Henn.) Bres.
	Root knot
	Meloidogyne spp.
	Rust (orange or leaf rust)
	Hemileia vastatrix Berk. & Br.
	Rust (powdery or grey rust)
	Hemileia coffeicola Mauble. & Rog.
	South America leaf spot
	Mycena citricola (Berk. & Curt.) (=Omphalia flavida
	Maubl, & Rang. Anamorph = Stilbum flavidum Cke)
	Thread blight
	Corticium koleroga (Cke) Hoehnel
	Tip blast
	Phoma costarricensis Ech.
	Tracheomycosis (Wilt)
	Gibberella xylarioides Heim & Saccas
	(anamorph = Fusarium eylarioides Steyaert)
	Wilt
	Ceratocystis fimbriata (Ell. & Halst.) Hunt
	Fusarium oxysporum Schl. f. sp. Coffea (Garcia) Wellman
	Warty berry
	Botrytis cinerea Pers. Ex Fries var. coffeae Hendr.
Corn or Maize	Anthracnose leaf blight and anthracnose stalk rot
(Zea mays L.)	Colletotrichum graminicola (Ces.) G. W. Wils.
	(teleomorph: Glomerella graminicola Politis)
	Glomerella tucumanensis (Speg.) Arx & E. Muller
	(anamorph: Glomerella falcatum Went)
	Aspergillus ear and kernel rot
	Aspergillus flavus Link:Fr.
	Banded leaf and sheath spot*
	Rhizoctonia solani Kühn = Rhizoctonia
	microsclerotia J. Matz
	(teleomorph: Thanatephorus cucumeris (A. B. Frank) Donk)
	Black bundle disease
	Acremonium strictum W. Gams = Cephalosporium
	acremonium Auct. non Corda
	Black kernel rot*
	Lasiodiplodia theobromae (Pat.) Griffon & Maubl. = Botryodiplodia
	theobromae Pat.
	Borde blanco*
	Marasmiellus sp.
	Brown spot (black spot, stalk rot)
	Physoderma maydis (Miyabe) Miyabe
	Cephalosporium kernel rot
	Acremonium strictum W. Gams = Cephalosporium
	acremonium Auct. non Corda
	Charcoal rot
	Macrophomina phaseolina (Tassi) Goidanich
	Corticium ear rot*
	Thanatephorus cucumeris (A. B. Frank) Donk = Corticium
	sasakii (Shirai) Matsumoto
	Curvularia leaf spot
	Curvularia clavata P. C. Jain
	C. eragrostidis (Henn.) J. A. Meyer = C. maculans
	(Bancroft) Boedijn
	(teleomorph: Cochliobolus eragrostidis (Tsuda & Ueyama)
	Sivanesan
	Curvularia inaequalis (Shear) Boedijn
	C. intermedia Boedijn
	(teleomorph: Cochliobolus intermedius R. R. Nelson)
	Curvularia lunata (Wakk.) Boedijn
	(teleomorph: Cochliobolus lunatus R. R. Nelson & Haasis)
	Curvularia pallescens Boedijn
	(teleomorph: Cochliobolus pallescens (Tsuda & Ueyama)
	Sivanesan)
	Curvularia senegalensis (Speg.) Subramanian
	C. tuberculata P. C. Jain
	(teleomorph: Cochliobolus tuberculatus Sivanesan)
	Didymella leaf spot*
	Didymella exitalis (Morini) E. Muller
	Diplodia ear rot and stalk rot
	Diplodia frumenti Ellis & Everh.
	(teleomorph: Botryosphaeria festucae (Lib.) Arx & E. Müller
	Diplodia ear rot, stalk rot, seed rot and seedling blight
	Diplodia maydis (Berk.) Sacc.
	Diplodia leaf spot or leaf streak
	Stenocarpella macrospora (Earle) Sutton = Diplodia
	macrospora Earle
	Downy mildews:
	Brown stripe downy mildew*
	Sclerophthora rayssiae Kenneth et al. var. zeae Payak &
	Renfro
	Crazy top downy mildew
	Sclerophthora macrospora (Sacc.) Thirumalachar et al. = Sclerospora
	macrospora Sacc.
	Green ear downy mildew (graminicola downy mildew)
	Sclerospora graminicola (Sacc.) J. Schröt.
	Java downy mildew*
	Peronosclerospora maydis (Racib.) C. G. Shaw = Sclerospora
	maydis (Racib.) Butler
	Philippine downy mildew*
	Peronosclerospora philippinensis (W. Weston) C. G. Shaw = Sclerospora
	philippinensis W. Weston
	Sorghum downy mildew
	Peronosclerospora sorghi (W. Weston & Uppal) C. G. Shaw = Sclerospora
	sorghi W. Weston & Uppal
	Spontaneum downy mildew*
	Peronosclerospora spontanea (W. Weston) C. G. Shaw = Sclerospora
	spontanea W. Weston
	Sugarcane downy mildew*
	Peronosclerospora sacchari (T. Miyake) Shirai & Hara = Sclerospora
	sacchari T. Miyake
	Dry ear rot (cob, kernel and stalk rot)
	Nigrospora oryzae (Berk. & Broome) Petch
	(teleomorph: Khuskia oryzae H. J. Hudson)
	Ear rots, minor
	Alternaria alternata (Fr.:Fr.) Keissl. = A. tenuis
	Nees
	Aspergillus glaucus Link:Fr.
	A. niger Tiegh.
	Aspergillus spp.
	Botrytis cinerea Pers.:Fr.
	(teleomorph: Botryotinia fuckeliana (de Bary) Whetzel)
	Cunninghamella sp.
	Curvularia pallescens Boedijn
	Doratomyces stemonitis (Pers.:Fr.) F.J. = Cephalotrichum
	stemonitis (Pers.:Fr.) Link
	Fusarium culmorum (Wm. G. Sm.) Sacc.
	Gonatobotrys simplex Corda
	Pithomyces maydicus (Sacc.) M. B. Ellis
	Rhizopus microsporus Tiegh.
	R. stolonifer (Ehrenb.:Fr.) Vuill. = R. nigricans
	Ehrenb.
	Scopulariopsis brumptii Salvanet-Duval
	Ergot* (horse's tooth, diente de caballo)
	Claviceps gigantea Fuentes et al.
	(anamorph: Sphacelia sp.)
	Eyespot
	Aureobasidium zeae (Narita & Hiratsuka) J. M. Dingley = Kabatiella
	zeae Narita & Hiratsuka
	Fusarium ear and stalk rot
	Fusarium subglutinans (Wollenweb. & Reinking)
	P. E. Nelson et al. = F. moniliforme
	J. Sheld. var. subglutinans Wollenweb.
	& Reinking
	Fusarium kernel, root and stalk rot, seed rot and seedling blight
	Fusarium moniliforme J. Sheld.
	(teleomorph: Gibberella fujikuroi (Sawada) Ito in Ito &
	K. Kimura)
	Fusarium stalk rot, seedling root rot
	Fusarium avenaceum (Fr.:Fr.) Sacc.
	(teleomorph: Gibberella avenacea R. J. Cooke)
	Gibberella ear and stalk rot
	Gibberella zeae (Schwein.) Petch
	(anamorph: Fusarium graminearum Schwabe)
	Gray ear rot
	Botryosphaeria zeae (G. L. Stout) Arx & E. Müller = Physalospora
	zeae G. L. Stout
	(anamorph: Macrophoma zeae Tehon & E. Y. Daniels)
	Gray leaf spot (Cercospora leaf spot)
	Cercospora sorghi Ellis & Everh. = C. sorghi
	Ellis & Everh. var. maydis Ellis & Everh.
	C. zeae-maydis Tehon & E. Y. Daniels
	Helminthosporium root rot
	Exserohilum pedicellatum (A. W. Henry) K. J. Leonard
	& E. G. Suggs = Helminthosporium
	pedicellatum A. W. Henry
	(teleomorph: Setosphaeria pedicellata (R. R. Nelson)
	K. J. Leonard
	& E. G. Suggs)
	Hormodendrum ear rot (Cladosporium rot)
	Cladosporium cladosporioides (Fresen.) G. A. De Vries = Hormodendrum
	cladosporioides (Fresen.) Sacc.
	C. herbarum (Pers.:Fr.) Link
	(teleomorph: Mycosphaerella tassiana (De Not.) Johans.)
	Hyalothyridium leaf spot*
	Hyalothyridium maydis Latterell & Rossi
	Late wilt*
	Cephalosporium maydis Samra et al.
	Leaf spots, minor
	Alternaria alternata (Fr.:Fr.) Keissl.
	Ascochyta maydis G. L. Stout
	A. tritici S. Hori & Enjoji
	A. zeicola Ellis & Everh.
	Bipolaris victoriae (F. Meehan & Murphy) Shoemaker = Helminthosporium
	victoriae F. Meehan & Murphy
	(teleomorph: Cochliobolus victoriae R. R. Nelson)
	C. sativus (Ito & Kuribayashi) Drechs. ex Dastur
	(anamorph: Bipolaris sorokiniana (Sacc.) Shoemaker = H. sorokinianum
	Sacc. in Sorokin = H. sativum
	Pammel et al.)
	Epicoccum nigrum Link
	Exserohilum prolatum K. J. Leonard & E. G. Suggs = Drechslera
	prolata (K. J. Leonard & E. G. Suggs)
	Sivanesan
	(teleomorph: Setosphaeria prolata K. J. Leonard & E. G. Suggs)
	Graphium penicillioides Corda
	Leptosphaeria maydis G. L. Stout
	Leptothyrium zeae G. L. Stout
	Ophiosphaerella herpotricha (Fr.:Fr.) J. C. Walker
	(anamorph: Scolecosporiella sp.)
	Paraphaeosphaeria michotii (Westend.) O. Eriksson
	Phoma sp.
	Septoria zeae G. L. Stout
	S. zeicola G. L. Stout
	S. zeina G. L. Stout
	Northern corn leaf blight (white blast, crown stalk rot, stripe)
	Setosphaeria turcica (Luttrell) K. J. Leonard & E. G. Suggs
	(anamorph: Exserohilum turcicum (Pass.) K. J. Leonard &
	E. G. Suggs = Helminthosporium
	turcicum Pass.)
	Northern corn leaf spot, Helminthosporium ear rot (race 1)
	Cochlioboluscarbonum R. R. Nelson (anamorph: Bipolaris
	zeicola (G. L. Stout) Shoemaker = Helminthosporium
	carbonum Ullstrup)
	Penicillium ear rot (blue eye, blue mold)
	Penicillium spp.
	P. chrysogenum Thom
	P. expansum Link
	P. oxalicum Currie & Thom
	Phaeocytostroma stalk rot and root rot
	Phaeocytostroma ambiguum (Mont.) Petr. & Syd. = Phaeocytosporella
	zeae G. L. Stout
	Phaeosphaeria leaf spot*
	Phaeosphaeria maydis (P. Henn.) Rane, Payak & Renfro = Sphaerulina
	maydis P. Henn.
	Physalospora ear rot (Botryosphaeria ear rot)
	Botryosphaeria festucae (Lib.) Arx & E. Müller = Physalospora
	zeicola Ellis & Everh.
	(anamorph: Diplodia frumenti Ellis & Everh.)
	Purple leaf sheath
	Hemiparasitic bacteria and fungi
	Pyrenochaeta stalk rot and root rot
	Phoma terrestris E. M. Hans. = Pyrenochaeta
	terrestris (E. M. Hans.) Gorenz et al.
	Pythium root rot
	Pythiumn spp.
	P. arrhenomanes Drechs.
	P. graminicola Subramanian
	Pythium stalk rot
	Pythium aphanidermatum (Edson) Fitzp. = P. butleri
	L. Subramanian
	Red kernel disease (ear mold, leaf and seed rot)
	Epicoccum nigrum Link
	Rhizoctonia ear rot (sclerotial rot)
	Rhizoctonia zeaeVoorhees
	(teleomorph: Waitea circinata Warcup & Talbot)
	Rhizoctonia root rot and stalk rot
	Rhizoctonia solani Kühn
	R. zeae Voorhees
	Root rots, minor
	Alternaria alternata (Fr.:Fr.) Keissl.
	Cercospora sorghi Ellis & Everh.
	Dictochaeta fertilis (S. J. Hughes & Kendrick)
	Holubova-Jechova
	Fusarium acuminatum Ellis & Everh.
	(teleomorph: Gibberella acuminata Wollenweb.)
	F. equiseti (Corda) Sacc.
	(teleomorph: G. intricans Wollenweb.)
	F. oxysporum Schlechtend.:Fr.
	F. pallidoroseum (Cooke) Sacc.
	F. poae (Peck) Wollenweb.
	F. roseum Link:Fr.
	G. cyanogena (Desmaz.) Sacc.
	(anamorph: F. sulphureum Schlechtend.)
	Microdochium bolleyi (R. Sprague) DeHoog &
	Hermanides-Nijhof
	Mucor sp.
	Periconia circinata (L. Mangin) Sacc.
	Phytophthora cactorum (Lebert & Cohn) J. Schrot.
	P. drechsleri Tucker
	P. nicotianae Breda de Haan var. parasitica (Dastur)
	G. M. Waterhouse
	Rhizopus arrhizus A. Fischer
	Rostratum leaf spot (Helminthosporium leaf disease, ear and
	stalk rot)
	Setosphaeria rostrata K. J. Leonard (anamorph:
	Exserohilum rostratum (Drechs.) K. J. Leonard & E. G. Suggs = Helminthosporium
	rostratum Drechs.)
	Rust, common corn
	Puccinia sorghi Schwein.
	Rust, southern corn
	Puccinia polysora Underw.
	Rust, tropical corn
	Physopella pallescens (Arth.) Cummins & Ramachar
	P. zeae (Mains) Cummins & Ramachar = Angiopsora
	zeae Mains
	Sclerotium ear rot* (southern blight)
	Sclerotium rolfsii Sacc.
	(teleomorph: Athelia rolfsii (Curzi) Tu & Kimbrough)
	Seed rot-seedling blight
	Bipolaris sorokiniana (Sacc.) Shoemaker
	B. zeicola (G. L. Stout) Shoemaker = Helminthosporium
	carbonum Ullstrup
	Diplodia maydis (Berk.) Sacc.
	Exserohilum pedicillatum (A. W. Henry) K. J. Leonard &
	E. G. Suggs
	Exserohilum turcicum (Pass.) K. J. Leonard & E. G. Suggs = Helminthosporium
	turcicum Pass.
	Fusarium avenaceum (Fr.:Fr.) Sacc.
	F. culmorum (Wm. G. Sm.) Sacc.
	F. moniliforme J. Sheld.
	Gibberella zeae (Schwein.) Petch
	(anamorph: F. graminearum Schwabe)
	Macrophomina phaseolina (Tassi) Goidanich
	Penicillium spp.
	Phomopsis sp.
	Pythium spp.
	Rhizoctonia solani Kühn
	R. zeae Voorhees
	Sclerotium rolfsii Sacc.
	Spicaria sp.
	Selenophoma leaf spot*
	Selenophoma sp.
	Sheath rot
	Gaeumannomyces graminis (Sacc.) Arx & D. Olivier
	Shuck rot
	Myrothecium gramineum Lib.
	Silage mold
	Monascus purpureus Went
	M. ruber Tiegh.
	Smut, common
	Ustilago zeae (Beckm.) Unger = U. maydis
	(DC.) Corda)
	Smut, false
	Ustilaginoidea virens (Cooke) Takah.
	Smut, head
	Sphacelotheca reiliana (Kuhn) G. P. Clinton) = Sporisorium
	holci-sorghi (Rivolta) K. Vanky
	Southern corn leaf blight and stalk rot
	Cochliobolus heterostrophus (Drechs.) Drechs.
	(anamorph: Bipolaris maydis (Nisikado & Miyake)
	Shoemaker = Helminthosporium
	maydis (Nisikado & Miyake)
	Southern leaf spot
	Stenocarpella macrospora (Earle) Sutton = Diplodia
	macrospora Earle)
	Stalk rots, minor
	Cercospora sorghi Ellis & Everh.
	Fusarium episphaeria (Tode) W. C. Snyder & H. N. Hans.
	F. merismoides Corda
	F. oxysporum Schlechtend.:Fr.
	F. poae (Peck) Wollenweb.
	F. roseum Link:Fr.
	F. solani (Mart.) Sacc.
	(teleomorph: Nectria haematococca Berk. & Broome)
	F. tricinctum (Corda) Sacc.
	Mariannaea elegans (Corda) R. A. Samson
	Mucor sp.
	Rhopographus zeae Pat.
	Spicaria sp.
	Storage rots
	Aspergillus spp.
	Penicillium spp. and other fungi
	Tar spot*
	Phyllachora maydis Maubl.
	Trichoderma ear rot and root rot
	Trichoderma viride Pers.:Fr. = T. lignorum
	(Tode)
	(teleomorph: Hypocrea sp.)
	White ear rot, root and stalk rot
	Stenocarpella maydis (Berk.) Sutton = Diplodia
	zeae (Schwein.) Lév.
	Yellow leaf blight
	Ascochyta ischaemi Sacc.
	Phyllosticta maydis D. C. Arny & R. R. Nelson
	(teleomorph: Mycosphaerella zeae-maydis Mukunya &
	Boothroyd)
	Zonate leaf spot
	Gloeocercospora sorghi Bain & Edgerton ex Deighton
Cotton	Anthracnose
(Gossypium spp.)	Glomerella gossypii Edgerton
	Colletotrichum gossypii Southworth [anamorph]
	Areolate mildew
	Ramularia gossypii (Speg.) Cif. = Cercosporella
	gossypii Speg.
	Mycosphaerella areola J. Ehrlich & F. A. Wolf
	[teleomorph]
	Ascochyta blight
	Ascochyta gossypii Woronichin
	Black root rot
	Thielaviopsis basicola (Berk. & Broome) Ferraris
	Chalara elegans Nag Raj & Kendrick [synanamorph]
	Boll rot
	Ascochyta gossypii Woronichin
	Colletotrichum gossypii Southworth
	Glomerella gossypii Edgerton [teleomorph]
	Fusarium spp.
	Lasiodiplodia theobromae (Pat.) Griffon & Maubl. = Diplodia
	gossypina (Cooke)
	Botryosphaeria rhodina (Cooke) Arx [teleomorph] = Physalospora
	rhodina Cooke
	Phytophthora spp.
	Rhizoctonia solani Kühn
	Charcoal rot
	Macrophomina phaseolina (Tassi) Goidanich
	Escobilla*
	Colletotrichum gossypii Southworth
	Glomerella gossypii Edgerton [teleomorph]
	Fusarium wilt
	Fusarium oxysporum Schlechtend.:Fr. f. sp. vasinfectum
	(Atk.) W. C. Snyder & H. N. Hans.
	Leaf spot
	Alternaria macrospora A. Zimmerm.
	A. alternata (FR.:FR.) Keissl.
	Cercospora gossypina Cooke
	Mycosphaerella gossypina (Atk.) Earle [teleomorph]
	Cochliobolus spicifer R. R. Nelson
	Bipolaris spicifera (Bainier) Subramanian
	[anamorph] = Curvularia
	spicifera (Bainier) Boedijn
	Myrothecium roridum Tode:Fr
	Rhizoctonia solani Kühn
	Stemphylium solani G. F. Weber
	Lint contamination
	Aspergillus flavus Link:Fr.
	Nematospora spp.
	Nigrospora oryzae (Berk. & Broome) Petch
	Phymatotrichum root rot = cotton root rot
	Phymatotrichopsis omnivora (Duggar) Hennebert = Phymatotrichum
	omnivorum Duggar
	Powdery mildew*
	Leveillula taurica (Lev) G. Arnaud
	Oidiopsis sicula Scalia [anamorph] = Oidiopsis
	gossypii (Wakef.) Raychaudhuri
	Salmonia malachrae (Seaver) Blumer & E. Muller
	Rust
	Cotton rust
	Puccinia schedonnardi Kellerm. & Swingle
	Southwestern cotton rust
	Puccinia cacabata Arth. & Holw. in Arth.
	Tropical cotton rust*
	Phakopsora gossypii (Lagerh.) Hiratsuka
	Sclerotium stem and root rot = southern blight
	Sclerotium rolfsii Sacc.
	Athelia rolfsii (Curzi) Tu & Kimbrough [teleomorph]
	Seedling disease complex
	Colletotrichum gossypii Southworth
	Fusarium spp.
	Pythium spp.
	Rhizoctonia solani Kühn
	Thanatephorus cucumeris (A. B. Frank) Donk
	[teleomorph]
	Thielaviopsis basicola (Berk. & Broome) Ferraris
	Chalara elegans Nag Raj & Kendrick [synanamorph]
	Stem canker
	Phoma exigua Desmaz.
	Verticillium wilt
	Verticillium dahliae Kleb.
Hop	Alternaria cone disorder
(Humulus lupulus L.)	Alternaria alternata (Fr.:Fr.) Keissl. = Alternaria
	tenuis Nees
	Armillaria root rot (shoestring root rot)
	Armillaria mellea (Vahl: Fr.) P. Kumm.
	(anamorph: Rhizomorpha subcorticalis Pers.)
	Black root rot
	Phytophthora citricola Sawada = P. cactorum
	(Lebert & Cohn) J. Schröt. var. applanat
	F. Chester
	Canker
	Fusarium sambucinum Fuckel
	(teleomorph: Gibberella pulicaris (Fr.:Fr.) Sacc.)
	Downy mildew
	Pseudoperonospora humuli (Miyabe & Takah.) G. W. Wils.
	Gray mold
	Botrytis cinerea Pers.:Fr.
	(teleomorph: Botryotinia fuckeliana (de Bary) Whetzel)
	Leaf spots
	Septoria humuli Westend. = Ascochyta
	humuli Lasch
	Mycocentrospora cantuariensis (Salmon & Wormald)
	Deighton = Cercospora
	cantuariensis Salmon & Wormald
	Phoma wilt
	Phoma herbarum Westend.
	Powdery mildew
	Sphaerotheca macularis (Wallr.:Fr.) Lind = Sphaerotheca
	humuli (DC.) Burrill
	Rosellinia root rot (Dematophora root rot)
	Rosellinia necatrix Prill.
	(anamorph: Dematophora necatrix R. Hartig)
	Sclerotinia wilt
	Sclerotinia sclerotiorum (Lib.) de Bary
	Verticillium wilt
	Verticillium albo-atrum Reinke & Berthier
	V. dahliae Kleb.
Oats	Anthracnose
(Avena sativa L.)	Colletotrichum graminicola (Ces.) G. W. Wils.
	(teleomorph: Glomerella graminicola Politis)
	Blast
	Unfavorable environmental conditions and/or any of
	several pathogens
	Downy mildew
	Sclerophthora macrospora (Sacc.) Thirumalachar et al.
	Ergot
	Claviceps purpurea (Fr.:Fr.) Tul.
	(anamorph: Sphacelia segetum Lév.)
	Fusarium foot rot
	Fusarium culmorum (Wm. G. Sm.) Sacc.
	Head blight
	Bipolaris sorokiniana (Sacc.) Shoemaker
	(teleomorph: Cochliobolus sativus (Ito & Kuribayashi)
	Drechs. ex Dastur)
	Drechslera avenacea (M. A. Curtis ex Cooke) Shoemaker
	Fusarium graminearum Schwabe
	(teleomorph: Gibberella zeae (Schwein.) Petch)
	Fusarium spp.
	Leaf blotch and crown rot (Helminthosporium leaf blotch)
	Drechslera avenacea (M. A. Curtis ex Cooke) Shoemaker = Helminthosporium
	avenaceum M. A. Curtis ex Cooke
	D. avenae (Eidam) Scharif = H. avenae
	Eidam
	(teleomorph: Pyrenophora avenae Ito & Kuribayashi)
	Powdery mildew
	Erysiphe graminis DC. f. sp. avenae Em. Marchal
	E. graminis DC.
	(anamorph: Oidium monilioides (Nees) Link)
	Rhizoctonia root rot
	Rhizoctonia solani Kühn
	(teleomorph: Thanatephorus cucumeris (A. B. Frank) Donk)
	Root rot
	Bipolaris sorokiniana (Sacc.) Shoemaker
	Fusarium spp.
	Pythium spp.
	P. debaryanum Auct. non R. Hesse
	P. irregulare Buisman
	P. ultimum Trow
	Rust, crown
	Pucciniacoronata Corda
	Rust, stem
	Puccinia graminis Pers.
	Seedling blight
	Bipolaris sorokiniana (Sacc.) Shoemaker
	Drechslera avenae (Eidam) Scharif
	Fusarium culmorum (Wm. G. Sm.) Sacc.
	Pythium spp.
	Rhizoctonia solani Kühn
	Sharp eyespot
	Rhizoctonia cerealis Van der Hoeven
	(teleomorph: Ceratobasidium cereale D. Murray &
	L. L. Burpee)
	Smut, covered
	Ustilago segetum (Bull.:Pers.) Roussel = U. kolleri
	Wille
	Smut, loose
	Ustilago avenae (Pers.) Rostr.
	Snow mold, pink (Fusarium patch)
	Microdochium nivale (Fr.) Samuel & I. C. Hallett = Fusarium
	nivale Ces. ex Berl. & Voglino
	(teleomorph: Monographella nivalis (Schaffnit) E. Müller)
	Snow mold, speckled or gray (Typhula blight)
	Typhula idahoensis Remsberg
	T. incarnata Lasch:Fr.
	T. ishikariensis Imai
	Speckled blotch (Septoria blight)
	Stagonospora avenae (A. B. Frank) Bissett = Septoria
	avenae A. B. Frank
	(teleomorph: Phaeosphaeria avenaria G. F. Weber)
	O. Eriksson)
	Take-all (white head)
	Gaeumannomyces graminis (Sacc.) Arx & D. Olivier var.
	avenae (E. M. Turner) Dennis
	G. graminis (Sacc.) Arx & D. Olivier
	Victoria blight
	Bipolaris victoriae (F. Meehan & Murphy) Shoemaker
	(teleomorph: Cochliobolus victoriae R. R. Nelson)
Peanut (Arachis	Alternaria leaf blight
hypogaea L.)	Alternaria tenuissima (Kunze:Fr.) Wiltshire
	Alternaria leaf spot
	Alternaria arachidis Kulk.
	Alternaria spot and veinal necrosis
	Alternaria alternata (Fr.:Fr.) Keissl.
	Anthracnose
	Colletotrichum arachidis Sawada (not validly published)
	C. dematium (Pers.) Grove
	C. mangenoti Chevaugeon
	Aspergillus crown rot
	Aspergillus niger Tiegh.
	Blackhull
	Thielaviopsis basicola (Berk. & Broome) Ferraris
	(synanamorph: Chalara elegans Nag Raj & Kendrick)
	Botrytis blight
	Botrytis cinerea Pers.:Fr.
	(teleomorph: Botryotinia fuckeliana (de Bary) Whetzel)
	Charcoal rot and Macrophomina leaf spot
	Macrophomina phaseolina (Tassi) Goidanich = Rhizoctonia
	bataticola (Tassi) E. J. Butler
	Choanephora leaf spot
	Choanephora spp.
	Collar rot
	Lasiodiplodia theobromae (Pat.) Griffon & Maubl. = Diplodia
	gossypina Cooke
	Colletotrichum leaf spot
	Colletotrichum gloeosporioides (Penz.) Penz. & Sacc. in
	Penz.
	(teleomorph: Glomerella cingulata (Stoneman) Spauld. &
	H. Schrenk)
	Cylindrocladium black rot
	Cylindrocladium crotalariae (C. A. Loos) D. K. Bell &
	Sobers
	(teleomorph: Calonectria crotalariae (C. A. Loos) D. K. Bell
	& Sobers)
	Cylindrocladium leaf spot
	Cylindrocladium scoparium Morg.
	(teleomorph: Calonectria keyotensis Terishita)
	Damping-off, Aspergillus
	Aspergillus flavus Link:Fr.
	A. niger Tiegh.
	Damping-off, Fusarium
	Fusarium spp.
	Damping-off, Pythium
	Pythium spp.
	Damping-off, Rhizoctonia
	Rhizoctonia spp.
	Damping-off, Rhizopus
	Rhizopus spp.
	Drechslera leaf spot
	Bipolaris spicifera (Bainier) Subramanian = Drechslera
	spicifera (Bainier) Arx
	(teleomorph: Cochliobolus spicifer R. R. Nelson)
	Fusarium peg and root rot
	Fusarium spp.
	Fusarium wilt
	Fusarium oxysporum Schlechtend.:Fr.
	Leaf spot, early
	Cercospora arachidicola S. Hori
	(teleomorph: Mycosphaerella arachidis Deighton)
	Leaf spot, late
	Phaeoisariopsis personata (Berk. & M. A. Curtis) Arx = Cercosporidium
	personatum (Berk. & M. A. Curtis)
	Deighton
	(teleomorph: Mycosphaerella berkeleyi Jenk.)
	Melanosis
	Stemphylium botryosum Wallr.
	(teleomorph: Pleospora tarda E. Simmons)
	Myrothecium leaf blight
	Myrothecium roridum Tode:Fr.
	Olpidium root rot
	Olpidium brassicae (Woronin) P. A. Dang.
	Pepper spot and scorch
	Leptosphaerulina crassiasca (Sechet) C. R. Jackson &
	D. K. Bell
	Pestalotiopsis leaf spot
	Pestalotiopsis arachidis Satya
	Phoma leaf blight
	Phoma microspora Berk. & M. A. Curtis nom. nud. non
	Sacc. non Pat. hom. illeg.
	Phomopsis foliar blight
	Phomopsis phaseoli (Desmaz.) Sacc. = P. sojae
	Lehman
	(teleomorph: Diaporthe phaseolorum (Cooke & Ellis)
	Sacc.)
	Phomopsis leaf spot
	Phomopsis spp.
	Phyllosticta leaf spot
	Phyllosticta arachidis-hypogaea V. G. Rao
	P. sojicola C. Massal.
	(teleomorph: Pleosphaerulina sojicola Miura)
	Phymatotrichum root rot
	Phymatotrichopsis omnivora (Duggar) Hennebert = Phymatotrichum
	omnivorum Duggar
	Pod rot (pod breakdown)
	Fusarium equiseti (Corda) Sacc. = F. scirpi
	Lambotte & Fautrey
	(teleomorph: Gibberella intricans Wollenweb.)
	F. solani (Mart.) Sacc.
	(teleomorph: Nectria haematococca Berk. & Broome)
	Pythium myriotylum Drechs.
	Rhizoctonia solani Kühn
	(teleomorph: Thanatephorus cucumeris (A. Frank) Donk)
	Powdery mildew
	Oidium arachidis Chorin
	Pythium peg and root rot
	Pythium myriotylum Drechs.
	P. aphanidermatum (Edson) Fitzp.
	P. debaryanum Auct. non R. Hesse
	P. irregulare Buisman
	P. ultimum Trow
	Pythium wilt
	Pythium myriotylum Drechs.
	Rhizoctonia foliar blight, peg and root rot
	Rhizoctonia solani Kühn
	Rust
	Puccinia arachidis Speg.
	Scab
	Sphaceloma arachidis Bitancourt & Jenk.
	Sclerotinia blight
	Sclerotinia minor Jagger
	S. sclerotiorum (Lib.) de Bary
	Stem rot (southern blight)
	Sclerotium rolfsii Sacc.
	(teleomorph: Athelia rolfsii (Curzi) Tu & Kimbrough)
	Verticillium wilt
	Verticillium albo-atrum Reinke & Berthier
	V. dahliae Kleb.
	Web blotch (net blotch)
	Phoma arachidicola Marasas et al. = Ascochyta
	adzamethica Schoschiaschvili
	(teleomorph: Didymosphaeria arachidicola (Chochrjakov)
	Alcorn et al. = Mycosphaerella
	arachidicola Chochrjakov)
	Yellow mold
	Aspergillus flavus Link:Fr.
	A. parasiticus Speare
	Zonate leaf spot
	Cristulariella moricola (Hino) Redhead
	(synanamorph: Sclerotium cinnomomi Sawada)
	(teleomorph: Grovesinia pyramidalis M. Cline et al.)
Potato	Black dot
(Solanum	Colletotrichum coccodes (Wallr.) S. J. Hughes = C. atramentarium
tuberosum L.)	(Berk. & Broome) Taubenhaus
	Brown spot and Black pit
	Alternaria alternata (Fries.) Keissler = A. tenuis
	Ness.
	Cercospora leaf blotch
	Mycovellosiella concors (Casp.) Deighton = Cercospora
	concors (Casp.) Sacc.
	Cercospora solani Thiim
	C. solani-tuberosi Thirumalachur*
	Charcoal rot
	Macrophomina phaseolina (Tassi) Goidanich = M. phaseoli
	(Maubl.)
	Sclerotium bataticola Taubenhaus
	Choanephora blight
	Choanephora cucurbitarum (Berk. & Rav.) Thaxter
	Common rust
	Puccinia pittieriana P. Henn.
	Deforming rust
	Aecidium cantensis Arthur
	Early blight
	Alternaria solani (E&M) Jones & Grout
	Fusarium dry rot
	Fusarium spp.
	F. sambucinum
	Giberella pulicaris (Fr.:Fr.) Sacc. [teleomorph] = Fusarium
	sulphureum Schlechtendahl
	F. solani (Mart.) Sacc. var. coeruleum (Lib. ex Sacc.)
	C. Booth
	Other Fusarium spp. include: F. avenaceum (Fr.) Sacc.
	F. oxysporum Schlechtend.:Fr.
	F. culmorum (Wm. G. Sm.) Sacc.
	Less common Fusarium spp. include: F. acuminatum
	Ellis & Everh.
	F. equiseti (Corda) Sacc.
	F. crookwellense
	Fusarium wilt
	Fusarium spp.
	F. avenaceum (Fr.) Sacc.
	F. oxysporum Schlechtend.:Fr.
	F. solani f. sp. eumartii (Carp.) Snyd and Hans.
	Gangrene
	Phoma solanicola f. foveata (Foister) Malcolmson
	P. foveata Foister = P. exigua
	var. foveata (Foister) Boerema = P. exigua
	Desm. f. sp. foveata (Foister) Malcolmson &
	Gray
	P. exigua Desm. var. exigua (more ubiquitous but weaker
	pathogen)
	Gray mold
	Botrytis cinerea Pers.:Fr.
	Botryotinia fuckeliana (de Bary) Whetzel
	[teleomorph]
	Late blight
	Phytophthora infestans (Mont.) de Bary
	Leak
	Pythium spp.
	Pythium ultimum var. ultimum Trow. = P. debaryanum
	R. Hesse
	Pythium aphanidermatum (Edson) Fitz.
	P. deliense Meurs
	Phoma leaf spot*
	Phoma andigena var. andina Turkensteen
	Pink rot
	Phytophthora spp.
	P. cryptogea Pethybr. & Lafferty
	P. drechsleri Tucker
	P. erythroseptica Pethybr.
	P. megasperma Drechsler
	P. nicotianae van Breda de Haan var. parasitica
	(Dastur)
	Waterhouse
	Pleospora herbarum
	Pleospora herbarum (Pers. ex Fr.) Rabenh.
	Stemphylium herbarum E. Simmons [anamorph]
	Powdery mildew
	Erysiphe cichoracearum DC. ex Merat
	Powdery scab
	Spongospora subterranea (Wallr.) Lagerh. f. sp.
	subterranea Tomlinson
	Rhizoctonia canker and black scurf
	Rhizoctonia solani Kühn
	Thanatephorus cucumeris (A. B. Frank) Donk
	[teleomorph]
	Rosellinia black rot*
	Rosellinia sp.
	Dematophora sp. [anamorph]
	Septoria leaf spot
	Septoria lycopersici Speg. var. malagutii Ciccarone &
	Boerema
	Silver scurf
	Helminthosporium solani Dur. & Mont.
	Skin spot
	Polyscytalum pustulans (Owen & Wakef.) Ellis
	Stem rot (southern blight)
	Sclerotium rolfsii Sacc.
	Athelia rolfsii (Curzi) Tu & Kimbrough [teleomorph]
	Thecaphora smut
	Angiosorus solani (Barrus) Thirum. & O'Brien = Thecaphora
	solani Barrus
	Ulocladium blight
	Ulocladium atrum Preuss
	Verticillium wilt
	Verticillium albo-atrum Reinke & Berthier
	V. dahliae Kleb.
	Wart
	Synchytrium endobioticum (Schilb.) Perc.
	White mold
	Sclerotinia sclerotiorum (Lib.) de Bary
Rice	Aggregate sheath spot
(Oryza sativa L.)	Ceratobasidium oryzae-sativae Gunnell & Webster
	(anamorph: Rhizoctonia oryzae-sativae (Sawada) Mordue)
	Black kernel
	Curvularia lunata (Wakk.) Boedijn
	(teleomorph: Cochiobolus lunatus R. R. Nelson & Haasis)
	Blast (leaf, neck [rotten neck], nodal and collar)
	Pyricularia grisea Sacc. = P. oryzae Cavara
	(teleomorph: Magnaporthe grisea (Hebert) Barr)
	Brown spot
	Cochliobolus miyabeanus (Ito & Kuribayashi) Drechs. ex
	Dastur (anamorph: Bipolaris oryzae (Breda de Haan)
	Shoemaker)
	Crown sheath rot
	Gaeumannomyces graminis (Sacc.) Arx & D. Olivier
	Downy mildew
	Sclerophthora macrospora (Sacc.) Thirumalachar et al.
	Eyespot
	Drechslera gigantea (Heald & F. A. Wolf) Ito
	False smut
	Ustilaginoidea virens (Cooke) Takah.
	Kernel smut
	Tilletia barclayana (Bref.) Sacc. & Syd. in Sacc. = Neovossia
	horrida (Takah.) Padwick & A. Khan
	Leaf smut
	Entyloma oryzae Syd. & P. Syd.
	Leaf scald
	Microdochium oryzae (Hashioka & Yokogi) Samuels & I. C. Hallett = Rhynchosporium
	oryzae Hashioka & Yokogi
	Narrow brown leaf spot
	Cercospora janseana (Racib.) O. Const. = C. oryzae
	Miyake
	(teleomorph: Sphaerulina oryzina K. Hara)
	Pecky rice (kernel spotting)
	Damage by many fungi including Cochliobolus miyabeanus
	(Ito & Kuribayashi) Drechs. ex Dastur, Curvularia spp.,
	Fusarium spp., Microdochium oryzae (Hashioka & Yokogi)
	Samuels & I. C. Halett, Sarocladium oryzae (Sawada) W. Gams
	& D. Hawksworth and other fungi.
	Root rots
	Fusarium spp.
	Pythium spp.
	P. dissotocum Drechs.
	P. spinosum Sawada
	Seedling blight
	Cochliobolus miyabeanus (Ito & Kuribayashi) Drechs. ex
	Dastur, Curvularia spp., Fusarium spp., Rhizoctonia
	solani Kühn, Sclerotium rolfsii Sacc.
	(teleomorph: Athelia rolfsii (Curzi) Tu & Kimbrough),
	and
	other pathogenic fungi.
	Sheath blight
	Thanatephorus cucumeris (A. B. Frank) Donk
	(anamorph: Rhizoctonia solani Kühn)
	Sheath rot
	Sarocladium oryzae (Sawada) W. Gams & D. Hawksworth = Acrocylindrium
	oryzae Sawada
	Sheath spot
	Rhizoctonia oryzae Ryker & Gooch
	Stackburn (Alternaria leaf spot)
	Alternaria padwickii (Ganguly) M. B. Ellis
	Stem rot
	Magnaporthe salvinii (Cattaneo) R. Krause & Webster
	(synanamorphs: Sclerotium oryzae Cattaneo, Nakataea
	sigmoidae (Cavara) K. Hara)
	Water-mold (seed-rot and seedling disease)
	Achlya conspicua Coker
	A. klebsiana Pieters
	Fusarium spp.
	Pythium spp.
	P. dissotocum Drechs.
	P. spinosum Sawada
Rye	Anthracnose
(Secale cereale L.)	Colletotrichum graminicola (Ces.) G. W. Wilson
	(teleomorph: Glomerella graminicola Politis)
	Black head molds
	Alternaria spp.
	Cladosporium herbarum (Pers.:Fr.) Link
	(teleomorph: Mycosphaerella tassiana (De Not.) Johans.)
	Epicoccum spp.
	Sporobolomyces spp.
	Stemphylium spp.
	Black point
	Bipolaris sorokiniana (Sacc.) Shoemaker
	(teleomorph: Cochliobolus sativus (Ito & Kuribayashi)
	Drechs. ex Dastur)
	Fusarium spp.
	Bunt (stinking smut)
	Tilletiacaries (DC.) Tul. & C. Tul. = T. tritici
	(Bjerk.) G. Wint. in Rabenh.
	T. laevis Kühn in Rabenh. = T. foetida
	(Wallr.) Liro
	Cephalosporium stripe
	Hymenula cerealis Ellis & Everh. = Cephalosporium
	gramineum Nisikado & Ikata in Nisikado
	et al.
	Common root rot and seedling blight
	Bipolaris sorokiniana (Sacc.) Shoemaker = Helminthosporium
	sativum Pammel et al.
	Cottony snow mold (winter crown rot)
	Coprinus psychromorbidus Redhead & J. A. Traquair
	Dilophospora leaf spot (twist)
	Dilophospora alopecuri (Fr.:Fr.) Fr.
	Dwarf bunt
	Tilletia controversa Kühn in Rabenh.
	Ergot
	Claviceps purpurea (Fr.:Fr.) Tul.
	(anamorph: Sphacelia segetum Lév.)
	Fusarium root rot
	Fusarium culmorum (W. G. Sm.) Sacc.
	Halo spot
	Pseudoseptoria donacis (Pass.) Sutton = Selenophoma
	donacis (Pass.) Sprague & A. G. Johnson
	Karnal bunt (partial bunt)
	Neovossia indica (Mitra) Mundkur = Tilletia
	indica Mitra
	Leaf rust (brown rust)
	Puccinia recondita Roberge ex Desmaz.
	(anamorph: Aecidium clematidis DC.)
	Leaf streak
	Cercosporidium graminis (Fuckel) Deighton = Scolicotrichum
	graminis Fuckel
	Leptosphaeria leaf spot
	Phaeosphaeria herpotrichoides (De Not.) L. Holm = Leptosphaeria
	herpotrichoides De Not.
	Loose smut
	Ustilago tritici (Pers.) Rostr.
	Pink snow mold (Fusarium patch)
	Microdochium nivale (Fr.) Samuels & I. C. Hallet = Fusarium
	nivale Ces. ex Berl. & Voglino
	(teleomorph: Monographella nivalis (Schaffnit) E. Muller)
	Powdery mildew
	Erysiphe graminis DC. f. sp. Em. Marchal
	Pythium root rot
	Pythium aphanidermatum (Edson) Fitzp.
	P. arrhenomanes Drechs.
	P. debaryanum Auct. non Hesse
	P. graminicola Subramanian
	P. ultimum Trow
	Scab
	Gibberella zeae (Schwein.) Petch
	(anamorph: Fusarium graminearum Schwabe)
	Scald
	Rhynchosporium secalis (Oudem.) J. J. Davis
	Septoria leaf blotch
	Septoria secalis Prill. & Delacr.
	Septoria tritici blotch (speckled leaf blotch)
	Septoriatritici Roberge in Desmaz.
	(teleomorph: Mycosphaerella graminicola (Fuckel) J. Schröt.
	in Cohn)
	Sharp eyespot and Rhizoctonia root rot
	Rhizoctonia cerealis Van der Hoeven
	(teleomorph: Ceratobasidium cereale D. Murray & L. L. Burpee)
	Snow scald (Sclerotinia snow mold)
	Myriosclerotinia borealis (Bubák. & Vleugel) L. M. Kohn = Sclerotinia
	borealis Bubák. & Vleugel
	Speckled (or gray) snow mold (Typhula blight)
	Typhula idahoensis Remsberg
	T. incarnata Fr.
	T. ishikariensis Imai
	T. ishikariensis Imai var. canadensis J. D. Smith &
	Arsvoll in
	Arsvoll & J. D. Smith
	Spot blotch
	Bipolaris sorokiniana (Sacc.) Shoemaker
	Stagonospora blotch (glume blotch)
	Stagonospora nodorum (Berk.) Castellani & E. G. Germano = Septoria
	nodorum Berk. in Berk. & Broome
	(teleomorph: Phaeosphaeria nodorum (E. Müller)
	Hedjaroude = Leptosphaeria
	nodorum E. Müller)
	Stalk smut (stripe smut)
	Urocystis occulta (Wallr.) Rabenh. ex Fuckel
	Stem rust
	Puccinia graminis Pers.:Pers. = P. graminis
	Pers. f. sp. secalis Eriks. & E. Henn.
	Storage molds
	Alternaria spp.
	Aspergillus spp.
	Epicoccum spp.
	Nigrospora spp.
	Penicillium spp.
	Rhizopus spp.
	Strawbreaker (eyespot or foot rot)
	Pseudocercosporella herpotrichoides (Fron) Deighton
	Stripe rust (yellow rust)
	Puccinia striiformis Westend.
	(anamorph: Uredo glumarum J. C. Schmidt)
	Take-all
	Gaeumannomyces graminis (Sacc.) Arx & Olivier var.
	tritici J. Walker
	Tan spot (yellow leaf spot)
	Pyrenophora tritici-repentis (Died.) Drechs.
	(anamorph: Drechslera tritici-repentis (Died.)
	Shoemaker = Helminthosporium
	tritici-repentis Died.)
Soybeans	Alternaria leaf spot
(Glycine max (L.)	Alternaria spp.
Merrill)	Anthracnose
	Colletotrichum truncatum (Schwein.) Andrus &
	W. D. Moore
	C. dematium (Pers.) Grove f. truncatum (Schwein.)
	Andrus
	& W. D. Moore
	Glomerella glycines F. Lehm. & F. A. Wolf
	Colletotrichum destructivum O'Gara [anamorph]
	Black leaf blight*
	Arkoola nigra J. Walker & G. Stovold
	Black root rot
	Thielaviopsis basicola (Berk. & Broome) Ferraris
	Chalara elegans Naj Raj & Kendrick [synanamorph]
	Brown spot
	Septoria glycines Hemmi
	Mycosphaerella usoenskajae Mashk & Tomil
	[teleomorph]
	Brown stem rot
	Phialophora gregata (Allington & D. W. Chamberlain)
	W. Gams = Cephalosporium
	gregatum Allington & D. W. Chamberlain
	Charcoal rot
	Macrophomina phaseolina (Tassi) Goidanich
	Choanephora leaf blight
	Choanephora infundibulifera (Currey) Sacc.
	C. trispora (Thaxter)
	Damping-off
	Rhizoctonia solani Kühn
	Thanatephorus cucumeris (A. B. Frank) Donk
	[teleomorph]
	Pythium aphanidermatum (Edison) Fitzp.
	P. debaryanum Auct. non R. Hesse
	P. irregulare Buisman
	P. myriotylum Drechs.
	P. ultimum Trow
	Downy mildew
	Peronospora manshurica (Naumov) Syd. In Gaum.
	Drechslera blight
	Drechslera glycines Narayanasamy & Durairj
	Frogeye leaf spot
	Cercospora sojina K. Hara
	Fusarium root rot
	Fusarium spp.
	Leptosphaerulina leaf spot
	Leptosphaerulina trifolii (Rostr.) Petr.
	Mycoleptodiscus root rot
	Mycoleptodiscus terrestris (Gerdemann) Ostazeski
	Neocosmospora stem rot
	Neocosmospora vasinifecta E. F. Sm.
	Acremonium sp. [anamorph]
	Phomopsis seed decay
	Phomopsis spp.
	Phytophthora root and stem rot
	Phytophthora sojae Kaufmann & Gerdemann
	Phyllosticta leaf spot
	Phyllosticta sojicola C. Massal
	Phymatotrichum root rot = cotton root rot
	Phymatotrichopsis omnivora (Duggar) Hennebert = Phymatotrichum
	omnivorum Duggar
	Pod and stem blight
	Diaporthe phaseolorum (Cke. & Ell.) Sacc. var. sojae
	(Lehman) Wehm.
	Phomopsis sojae Lehman [anamorph]
	Powdery mildew
	Microsphaera diffusa Cooke & Peck
	Purple seed stain
	Cercospora kikuchii (Mastsumoto & Tomoyasu) M. W. Gardner
	Pyrenochaeta leaf spot*
	Pyrenochaeta glycines Stewart
	Pythium rot
	Pythium aphanidermatum (Edison) Fitzp.
	P. debaryanum Auct. non R. Hesse
	P. irregulare Buisman
	P. myriotylum Drechs.
	P. ultimum Trow
	Red crown rot
	Cylindrocladium crotalariae (C. A. Loos) D. K. Bell &
	Sobers
	Calonectria crotalariae (C. A. Loos) D. K. Bell &
	Sobers
	[teleomorph]
	Red leaf blotch = Dactuliophora leaf spot*
	Dactuliochaeta glycines (R. B. Stewart) Hartman &
	Sinclair = Pyrenochaeta
	glycines (R. B. Stewart)
	Dactuliophora glycines Leaky [synanamorph]
	Rhizoctonia aerial blight
	Rhizoctonia solani Kühn
	Thanatephorus cucumeris (A. B. Frank) Donk
	[teleomorph]
	Rhizoctonia root and stem rot
	Rhizoctonia solani Kühn
	Rust*
	Phakopsora pachyrhizi Syd.
	Scab*
	Spaceloma glycines Kurata & Kuribayashi
	Sclerotinia stem rot
	Sclerotinia sclerotiorum (Lib.) deBary
	Southern blight (damping-off and stem rot) = Sclerotium blight
	Sclerotium rolfsii Sacc.
	Athelia rolfsii (Curzi) Tu & Kimbrough [teleomorph]
	Stem canker
	Diaporthe phaseolorum (Cooke & Ellis) Sacc.
	D. phaseolorum (Cooke & Ellis) Sacc. var. caulivora
	Athow & Caldwell
	Phomopsis phaseoli (Desmaz) Sacc [anamorph]
	Stemphylium leaf blight*
	Stemphylium botryosum Wallr.
	Pleospora tarda (E. Simmons) [teleomorph]
	Sudden death syndrome
	Fusarium solani (Mart.) Sacc. f. sp. glycines
	Target spot
	Corynespora cassiicola (Berk. & M. A. Curtis) C. T. Wei
Tobacco	Anthracnose
(Nicotiana	Colletotrichum destructivum O'Gara
tabacum L.)	(teleomorph: Glomerella glycines F. Lehm. and F. A. Wolf)
	Barn spot
	Cercospora nicotianae Ellis & Everh.
	Barn rot
	Several fungi and bacteria
	Black root rot
	Thielaviopsis basicola (Berk. & Broome) Ferraris
	Black shank
	Phytophthora parasitica Dastur var. nicotianae (Breda
	de
	Haan) Tucker
	P. nicotianae Breda de Haan var. nicotianae G. M. Waterhouse
	Blue mold (downy mildew)
	Peronospora tabacina D. B. Adam = P. hyoscyami
	de Bary f. sp. tabacina
	Brown spot
	Alternaria alternata (Fr.:Fr.) Keissl.
	Charcoal rot
	Macrophomina phaseolina (Tassi) Goidanich
	Collar rot
	Sclerotinia sclerotiorum (Lib.) de Bary
	Damping-off, Pythium
	Pythium spp.
	P. aphanidermatum (Edson) Fitzp.
	P. ultimum Trow
	Frogeye leaf spot
	Cercospora nicotianae Ellis & Everh.
	Fusarium wilt
	Fusarium oxysporum Schlechtend.:Fr. (several f. sp.)
	Gray mold
	Botrytis cinerea Pers.:Fr.
	(teleomorph: Botryotinia fuckeliana (de Bary) Whetzel)
	Olpidium seedling blight
	Olpidium brassicae (Woronin) P. A. Dang.
	Phyllosticta leaf spot
	Phyllosticta nicotiana Ellis & Everh.
	Powdery mildew
	Erysiphe cichoracearum DC.
	Ragged leaf spot
	Phoma exigua Desmaz. var. exigua = Ascochyta
	phaseolorum Sacc.
	Scab
	Hymenula affinis (Fautrey & Lambotte) Wollenweb. = Fusarium
	affine Fautrey & Lambotte
	Sore shin and damping-off
	Rhizoctonia solani Kühn
	(teleomorph: Thanatephorus cucumeris (A. B. Frank) Donk)
	Southern stem rot (southern blight)
	Sclerotium rolfsii Sacc.
	(teleomorph: Athelia rolfsii (Cursi) Tu & Kimbrough)
	Stem rot of tranplants
	Pythium spp.
	Target spot
	Rhizoctonia solani Kühn
	Verticillium wilt
	Verticllium albo-atrum Reinke & Berthier
	V. dahliae Kleb.
Wheat	Alternaria leaf blight
(Triticum spp. L.)	Alternaria triticina Prasada & Prabhu
	Anthracnose
	Colletotrichum graminicola (Ces.) G. W. Wils.
	Glomerella graminicola Politis [teleomorph]
	Ascochyta leaf spot
	Ascochyta tritici S. Hori & Enjoji
	Aureobasidium decay
	Microdochium bolleyi (R. Sprague) DeHoog &
	Hermanides-Nijhof = Aureobasidium
	bolleyi (R. Sprague) Arx
	Black head molds = sooty molds
	Alternaria spp.
	Cladosporium spp.
	Epicoccum spp.
	Sporobolomyces spp.
	Stemphylium spp.
	and other genera
	Black point = kernel smudge
	associated with various fungi and physiological
	circumstances
	Cephalosporium stripe
	Hymenula cerealis Ellis & Everh. = Cephalosporium
	gramineum Nisikado & Ikata in Nisikado
	et al
	Common bunt = stinking smut
	T. tritici (Bjerk.) G. Wint. in Rabenh. = Tilletia
	caries (DC.) Tul. & C. Tul.
	T. laevis Kühn in Rabenh. = T. foetida
	(Wallr.) Liro
	Common root rot
	Bipolaris sorokiniana (Sacc.) Shoemaker
	Cochliobolus sativus (Ito & Kuribayashi) Drechs. Ex
	Dast.
	[teleomorph]
	Cottony snow mold
	Coprinus psychromorbidus Redhead & Traquair
	Crown rot = foot rot, seedling blight, dryland root rot
	Fusarium spp.
	F. pseudograminearum O'Donnell et. T. Aoki sp. nov.
	Gibberella zeae (Schwein.) Petch
	F. graminearum Schwabe, Group II [anamorph]
	G. avenacea R. J. Cook
	F. avenaceum (Fr.:Fr.) Sacc. [anamorph]
	F. culmorum (W. G. Smith) Sacc.
	Dilophospora leaf spot = twist
	Dilophospora alopecuri (Fr.)Fr.
	Downy mildew = crazy top
	Sclerophthora macrospora (Sacc.)Thirumalachar et al.
	Dwarf bunt
	Tilletia controversa Kühn in Rabenh
	Ergot
	Claviceps purpurea (Fr.:Fr.) Tul.
	Sphacelia segetum Lév. [anamorph]
	Eyespot = foot rot, strawbreaker
	Tapesia yallundae Wallwork & Spooner
	Ramulispora herpotrichoides (From) Arx [anamorph] = Pseudocercosporella
	herpotrichoides (Fron) Deighton
	T. acuformis (Boerema, Pieters & Hamers) Crous
	Ramulispora acuformis (Nirenberg) Crous [anamorph] = Pseudocercosporella
	herpotrichoides var. acuformis
	Nirenberg
	False eyespot
	Gibellina cerealis Pass.
	Flag smut
	Urocystis agropyri (G. Preuss) Schrot.
	Foot rot = dryland foot rot
	Fusarium spp.
	Halo spot
	Pseudoseptoria donacis (Pass.) Sutton = Selenophoma
	donacis (Pass.) R. Sprague & A. G. Johnson
	Karnal bunt = partial bunt
	Tilletia indica Mitra = Neovossia
	indica (M. Mitra) Mundk.
	Leaf rust = brown rust
	Puccinia triticina Eriks. = P. recondita
	Roberge ex Desmaz. f. sp. tritici
	(Eriks. &
	E. Henn.) D. M. Henderson
	P. tritici-duri Viennot-Bourgin
	Leptosphaeria leaf spot
	Phaeosphaeria herpotrichoides (De Not.) L. Holm = Leptosphaeria
	herpotrichoides De Not.
	Stagonospora sp. [anamorph]
	Loose smut
	Ustilago tritici (Pers.) Rostr. = U. segetum
	tritici, U. segetum nuda, U. segetum avena
	Microscopica leaf spot
	Phaeosphaeria microscopica (P. Karst.) O. Eriksson = Leptosphaeria
	microscopica P. Karst
	Phoma spot
	Phoma spp.
	P. glomerata (Corda) Wollenweb. & Hochapfel
	P. sorghina (Sacc.) Boerema et al. = P. insidiosa
	Tassi
	Pink snow mold = Fusarium patch
	Microdochium nivale (Fr.) Samuels & I. C. Hallett = Fusarium
	nivale Ces. ex Berl. & Voglino
	Monographella nivalis (Schaffnit) E. Müller
	[teleomorph]
	Platyspora leaf spot
	Clathrospora pentamera (P. Karst.) Berl. = Platyspora
	pentamera (P. Karst.) Wehmeyer
	Powdery mildew
	Erysiphe graminis DC. f. sp. tritici Em. Marchal
	Blumeria graminis (DC.) E. O. Speer = E. graminis
	DC.
	Oidium monilioides (Nees) Link [anamorph]
	Pythium root rot
	Pythium aphanidermatum (Edison) Fitzp.
	P. arrhenomanes Drechs.
	P. graminicola Subramanian
	P. myriotylum Drechs
	P. volutum Vanterpool & Truscot
	Rhizoctonia root rot
	Rhizoctonia solani Kühn
	Thanatephorus cucumeris (A. B. Frank) Donk
	[teleomorph]
	Ring spot = Wirrega blotch
	Pyrenophora semeniperda (Brittlebank & Adam)
	Schoemaker = Drechslera
	campanulata (Lev.) Sutton
	D. wirreganesis Wallbork, Lichon & Sivanesan
	Scab = head blight
	Fusarium spp.
	Gibberella zeae (Schwein.) Petch
	Fusarium graminearum Schwabe, Group II [anamorph]
	G. avenacea R. J. Cook
	F. avenaceum (Fr.:Fr.) Sacc. [anamorph]
	F. culmorum (Wm. G. Sm.) Sacc.
	Microdochium nivale (Fr.) Samuels & I. C. Hallett = F. nivale
	Ces ex Berl. & Voglino
	Monographella nivale (Schaffnit) E. Müller
	[teleomorph]
	Sclerotinia snow mold = snow scald
	Myriosclerotinia borealis (Bubák & Vleugel) L. M. Kohn = Sclerotinia
	borealis Bubák & Vleugel
	Sclerotium wilt (see Southern blight)
	Sclerotium rolfsii Sacc.
	Athelia rolfsii (Curzi) Tu & Kimbrough [teleomorph]
	Septoria blotch
	Septoria tritici Roberge in Desmaz.
	Mycosphaerella graminicola (Fuckel) J. Schröt. In
	Cohn [teleomorph]
	Sharp eyespot
	Rhizoctonia cerealis Van der Hoeven
	Ceratobasidium cereale D. Murray & L. L. Burpee
	[teleomorph]
	Snow rot
	Pythium spp.
	P. aristosporum Vanterpool
	P. iwayamai Ito
	P. okanoganense Lipps
	Southern blight = Sclerotium base rot
	Sclerotium rolfsii Sacc.
	Athelia rolfsii (Curzi) Tu & Kimbrough [teleomorph]
	Speckled snow mold = gray snow mold or Typhula blight
	Typhula idahoensis Remsberg
	T. incarnata Fr.
	T. ishikariensis Imai
	T. ishikariensis Imai var. canadensis Smith & Arsvoll
	Spot blotch
	Bipolaris sorokiniana (Sacc.)Shoemaker
	Stagonospora blotch
	Phaeosphaeria avenaria (G. F. Weber) O. Eriksson f. sp.
	triticea T. Johnson
	Stagonospora avenae (A. B. Frank) Bissett f. sp.
	tritica
	T. Johnson [anamorph] = Septoria
	avenae A. B. Frank f. sp. triticea T. Johnson
	Phaeosphaeria nodorum (E. Müller) Hedjaroude
	Stagonospora nodorum (Berk.) Castellani & E. G. Germano
	[anamorph] = Septoria
	nodorum (Berk.) Berk. in Berk. & Broome
	Stem rust = black rust
	Puccinia graminis Pers.:Pers. = P. graminis
	Pers.:Pers. f. sp. tritici Eriks. & E. Henn.
	Storage molds
	Aspergillus spp.
	Penicillium spp.
	and others
	Stripe rust = yellow rust
	Puccinia striiformis Westend.
	Uredo glumarum J. C. Schmidt [anamorph]
	Take-all
	Gaeumannomyces graminis (Sacc.) Arx & D. Olivier var.
	tritici J. Walker
	G. graminis (Sacc.) Arx & D. Olivier var. avenae (E. M. Turner)
	Dennis
	Tan spot = yellow leaf spot, red smudge
	Pyrenophora tritici-repentis (Died.) Drechs.
	Drechslera tritici-repentis (Died.) Shoemaker
	[anamorph]
	Tar spot
	Phyllachora graminis (Pers.:Fr.) Nitschke
	Linochora graminis (Grove) D. G. Parbery [anamorph]
	Zoosporic root rot
	Lagena radicicola Vant & Ledingham
	Ligniera pilorum Fron & Gaillat
	Olpidium brassicae (Woronin) Dang.
	Rhizophydium graminis Ledingham
Cultivated Wild	Anthracnose
Rice	Colletotrichum sublineolum
(Zizania palustris L.)	Ergot
	Claviceps zizaniae
	Fungal brown spot
	Bipolaris oryzae
	Phytophthora crown and root rot
	Phytophthora erythroseptica
	Scab
	Fusarium spp.
	Spot blotch
	Bipolaris sorokiniana
	Stem rot
	Sclerotium hydrophilum
	Sclerotium oryzae
	Stem smut
	Entyloma lineatum
	Zonate eye spot
	Drechslera gigantea