GENERATION OF PLANTS WITH IMPROVED PATHOGEN RESISTANCE

CROSS REFERENCE TO RELATED APPLICATION(S) This application claims the benefit of U.S. Provisional Application No. 60/813,637, filed June 13, 2006, the entirety of which is incorporated herein by reference.

BACKGROUND

The control of infection of plants by pathogens, which can inhibit production of fruits, seeds, foliage and flowers and cause reductions in the quality and quantity of the harvested crops, is of significant economic importance. Pathogens annually cause billions of dollars in damage to crops worldwide (Baker et al 1997, Science 276:726-733). Consequently, an increasing amount of research has been dedicated to developing novel methods for controlling plant diseases. Such studies have centered on the plant's innate ability to resist pathogen invasion in an effort to buttress the plant's own defenses to counter pathogen attacks (Staskawicz et al. 1995, Science 268:661 -667 ; Baker et al. supra).

Although most crops are treated with agricultural anti-fungal, anti-bacterial agents and/or other pesticidal agents, damage from pathogenic infection still results in revenue losses to the agricultural industry on a regular basis. Furthermore, many of the agents used to control such infection or infestation cause adverse side effects to the plant and/or to the environment. Plants with enhanced resistance to infection by pathogens would decrease or eliminate the need for application of chemical anti-fungal, anti-bacterial and/or pesticidal agents.

There has been significant interest in developing transgenic plants that show increased resistance to a broad range of pathogens (Atkinson et al, 2003, Annu. Rev.

Phytopathol. 41 -.615-639; Williamson and Gleason, 2003, Curr. Opin. Plant Biol. 6:327- 333; Stuiver and Custers, 2001, Nature 411:865-8; Melchers and Stuiver, 2000, Curr. Opin. Plant Biol. 3:147-152; Rommens and Kishόre, 2000, Curr. Opin, Biotechnol. 11 :120-125; Williamson, 1999, Curr. Opin. Plant Biol. 2:327-331 ; Mourgues et al. 1998, Trends , Biotechnol. 16:203-210; Simons et al, 1998, Plant Cell, 10: 1055-1068; Epple et al, 1997, Plant Cell, 9:509-520; Jongedijk et al, 1995, Euphytica, 85: 173-180). The fungal pathogen Fusarium oxysporum causes severe vascular wilt diseases and major loses in a wide variety of economically important crops (Beckman, 1987, The Nature of Wilt Diseases of Plants). The F. oxysporum pathogen infects plants through the root system, often though wounds. The vascular system of the plant is adversely affected by the organism as it grows due to

reduced nutrient and water flower through the plant. Individual pathogenic strains within the species have a limited host range, and strains with similar or identical host ranges are assigned to groups called formae speciales (f. sp.; Armstrong and Armstrong, 1981, In Fusarium: Disease, Biology and Taxonomy, Nelson et al, eds, pp.391-399). A number of genes from plants and from F. oxysporum that have been associated with altered resistance to F. oxysporum have been identified by mis-expression of these genes. For example, plant thionin proteins such as Arabidopsis Thi2.1 (Epple et al. , supra; Epple et al, 1995, Plant Physiol, 109:813-820), the / locus in tomato (Ori et al, 1997, Plant Cell, 9:521-532; Segal et al, \992, Mol Gen. Genet., 231:179-185; Bournival ef al, 1990, Theor. λppl. Genet, 79:641-645; Sarfatti et al, 1991, Theor. Appl. Genet., 82:22-26), the Fowl protein of F. oxysporum (Inoue et al, 2002, Plant Cell, 14:1869-1883), and a class V chitin synthase of F. oxysporum (Madrid et al, 2003, MoI. Microbiol, 47:257-266) have all been associated with altered F. oxysporum resistance.

Due to the importance of pathogen resistance in plants, methods for producing plants with increased pathogen resistance are desirable.

SUMMARY OF THE DISCLOSURE

The disclosure provides a transgenic plant having increased resistance to a pathogen, such as a fungus (for example,- Fusarium oxysporum) relative to control plants. The transgenic plant has incorporated (e.g., stably incorporated) into its genome a DNA construct comprising a nucleotide sequence that encodes a protein having pathogen resistance activity. The nucleotide sequence may be a nucleotide sequence identified in column 3 of Tables 3 and 4, or a complement thereof; a nucleotide sequence having at least 90% sequence identity to a nucleotide sequence identified in column 3 of Tables 3 and 4, or a complement thereof; a nucleotide sequence encoding a polypeptide comprising an amino acid sequence identified in column 4 of Tables 3 and 4; or a nucleotide sequence encoding a polypeptide having at least 90% sequence identity to an amino acid sequence identified in column 4 of Tables 3 and 4. The nucleotide sequence is, for instance, operably linked to a promoter that drives expression of a coding sequence in a plant cell. In some embodiments, the transgenic plant is selected from the group consisting of rapeseed, soy, corn, sunflower, cotton, cocoa, safflower, oil palm, coconut palm, flax, castor and peanut, tomato, carrot, lettuce, bean, asparagus, cauliflower, pepper, beetroot, cabbage, eggplant, endive, leek, long cucumber, melon, pea, radish, rootstock, short cucumber (Beϊt alpha), squash, watermelon,

white onion, witloof, yellow onion, broccoli, brussel sprout, bunching onion, celery, mache, cucumber, fennel, gourd, pumpkin, sweet corn, and zucchini.

The transgenic plants may be produced by introducing into the plant or a cell thereof at least one plant transformation vector comprising a nucleotide sequence that encodes or is complementary to a sequence that encodes an FUR polypeptide identified in column 4 of Tables 3 and 4, or a variant thereof, and growing the transformed plant or cell to produce a transgenic plant, wherein said transgenic plant exhibits increased resistance to at least one pathogen. In one embodiment, the FUR polypeptide has at least about 70% sequence identity to an amino acid sequence referred to in column 4 of Tables 3 and 4. In other embodiments, the FUR polypeptide has at least about 80% or 90% sequence identity to or has the amino acid sequence referred to in column 4 of Tables 3 and 4.

Methods are provided for producing a plant with increased pathogen resistance, including increased fungal resistance, comprising identifying a plant having an altered FUR gene, and generating progeny of the plant, wherein the progeny have increased pathogen resistance, and wherein the FUR gene is one that is identified in column 4 of Tables 3 and 4. Methods are also provided for identifying a plant having increased pathogen resistance, comprising analyzing at least one FUR gene from the plant, and identifying a plant with an altered FUR gene, wherein the plant has increased pathogen resistance. The disclosure further provides plants and plant paits obtained by the methods described herein.

SEQUENCE LISTING

The nucleic and/or amino acid sequences listed in the accompanying sequence listing are shown using standard letter abbreviations for nucleotide bases, and three letter code for amino acids, as defined in 37 C.F.R. 1.822. Only one strand of each nucleic acid sequence is shown, but the complementary strand is understood as included by any reference to the displayed strand. In the accompanying sequence listing:

SEQ ID NOs: 1 and 2 show the nucleic acid (GI|42567450|ref|NM_l 19792.3) and protein (GI|15234336|ref|NP_195347.1) sequences of Arabidopsis thaliana transcription factor (AT4G36240)). SEQ ID NOs: 3 and 4 show the nucleic acid (GI|42567451 |ref|NMJ 19793.3) and protein (GI|42567452|ref|NP_195348.2| ALDH3F1) sequences of Arabidopsis thaliana ALDH3F1; aldehyde dehydrogenase/ oxidoreductase (ALDH3F1)).

SEQ ID NOs: 5 and 6 show the nucleic acid (GI|30690618|reflNMJ 19794,2) and protein (GI|15234365|ref|NP_l 95349.1) sequences of Arabidopsis thaliana STY2 (STYLISH 2) (STY2)).

SEQ ID NOs: 7 and 8 show the nucleic acid (GI|42562349|reflNM_l 02507.2) and protein (GI|18396334|reflNP_564283.1) sequences Arabidopsis thaliana unknown protein (AT1G27435)).

SEQ ID NOs: 9 and 10 show the nucleic acid (GI|42562350|ref|NM_102508.2) and protein (GI| 15223522|ref|NP_l 74064.1 Sequences Arabidopsis thaliana catalytic (AT1 G27440)). SEQ ID NOs: 1 1 and 12 show the nucleic acid (GI|30689933|rcf)NMJ 79383.1) and protein sequences (GI|306899341ref|NP_849714.1 ) of Arabidopsis thaliana APT] (ADENINE PHOSPHORIBOSYLTRANSFERASE 1) (APTl)).

■ SEQ ID NOs: 13 and 14 show the nucleic acid (GI|30689927|reflNM_102509.2) and protein (GI|18396344|refjNP_564284.1) sequences of Arabidopsis thaliana APTl (ADENINE PHOSPHORIBOSYLTRANSFERASE 1); adenine phosphoribosyltransferase (APTl)).

SEQ ID NOs: 15 and 16 show the nucleic acid (GI)18396346|ref)NM_102510.1) and protein (GI|18396347|τef]NP_564285.1 | NPGRl ) sequences of Arabidopsis thaliana NPGRl (NO POLLEN GERMINATION RELATED 1); calmodulin binding (NPGRl)). SEQ ID NOs: 17 and 18 show the nucleic acid (GI|30689942|ref|NMJ 02511.3) and protein ()GI|22329818|ref)NP_l 74067.2sequences of Arabidopsis thaliana nucleotide binding (AT1G27470)).

SEQ ID NOs: 19 and 20 show the nucleic acid (GI|30689946|ref|NM_l 02512.2) and protein (GI|18396359|refjNP_564286.1) sequences of Arabidopsis thaliana catalytic/ phosphatidylcholine-sterol O-acyltransferase (ATI G27480)).

SEQ ID NOs: 21 and 22 show the nucleic acid (GI|42573346|refpsrM_203041.1) and protein (GI|42573347|ref|NP_974770.1 ) sequences of Arabidopsis _, thaliana catalytic (AT5G12210)).

SEQ ID NOs: 23 and 24 show the nucleic acid (GI|30683990|rcf|NMJ21259.2) and protein (GI|184168061ref]NP_568259.1) sequences of Arabidopsis thaliana catalytic (AT5G12210)).

SEQ ID NOs: 25 and 26 show the nucleic acid (GI|22326748|reflNM_l 21260.2) and protein (GI|22326749|ref|NP_l 96783.2) sequences of Arabidopsis thaliana unknown protein (AT5G12220)).

SEQ ID NOs: 27 and 28 show the nucleic acid (GI|30683998|refjNM_121261.2) and protein (GI|l5239910|ref|NP_196784.1) sequences of Arabidopsis thaliana unknown protein (AT5G12230)).

SEQ ID NOs: 29 and 30 show the nucleic acid (GI|22326750|reflNM_l 47857.1) and protein (GIJ22326751 |ref]NP_680162.1 ) sequences of Arabidopsis thaliana CLE22 (CLAVATA3/ESR-RELATED 22); receptor binding (CLE22)).

SEQ ID NOs: 31 and 32 show the nucleic acid (GI|18416813|ref]NM_121262.1) and protein (GI|15239912jref|NP_196785.1) sequences of Arabidopsis thaliana unknown protein (AT5G12240)). SEQ ID NOs: 33 and 34 show the nucleic acid (GI|30684010|ref|NM_121263.2) and protein (GI|15239914|ref|NP_196786.1) sequences of Arabidopsis thaliana TUB6 (BETA-6 TUBULIN) (TUB6)).

SEQ ID NOs: 35 and 36 show the nucleic acid (GI|30679917|ref|NM_120394.2) and protein (GI|l5242650|ref|NP_195936.1) sequences of Arabidopsis thaliana heat shock protein binding / unfolded protein binding (AT5G03160)).

SEQ ID NOs: 37 and 38 show the nucleic acid (GI|18414145]ref]NM_120395.1) and protein (GI|15242651|refjNP_195937.1) sequences of Arabidopsis thaliana FLAIl (FLAI l)).

SEQ ID NOs: 39 and 40 show the nucleic acid (GI|30679924|ref|NM_120396.2) and protein (GI|18414148|ref|NP_568111.1) sequences of Arabidopsis thaliana protein binding / ubiquitin-protein ligase/ zinc ion binding (AT5G03180)).

SEQ ID NOs: 41 and 42 show the nucleic acid (GI|30679928(rcf|NM_120397.2) and protein (GI| 15242672|ref|NP_l 95939.1 ) sequences of Arabidopsis thaliana expressed protein (At5gO3190)). SEQ ID NOs: 43 and 44 show the nucleic acid (GI|18414154|reflNM_120398.1) and protein (GI|15242675|ref|NP_195940.1) sequences of Arabidopsis thaliana protein binding / ubiquitin-protein ligase/ zinc ion binding (AT5G03200)).

SEQ ID NOs: 45 and 46 show the nucleic acid (GI|42567607|ref|NM_120399.2) and protein (GI|42567608|ref|NP_l 95941.2) sequences of Arabidopsis thaliana unknown protein (AT5G03210)).

SEQ ID NOs: 47 and 48 show the nucleic acid (GI) 18403251 |ref|NM_l 13104.1 ) and protein (GI[15233264|refjNP_l 88846.1 ) sequences of Arabidopsis thaliana unknown protein (AT3G22080)).

SEQ ID NOs: 49 and 50 show the nucleic acid (GI|42565103|ref|NM_l 13105.2) and protein (GI|42565104|ref]NP_l 88847.2) sequences of Arabidopsis thaliana unknown protein (AT3G22090)).

SEQ ID NOs: 51 and 52 show the nucleic acid (Gl|18403258|ref|NM_l 13106.1) and protein (GI|15233267|reflNPJ 88848.1 ) sequences of Arabidopsis thaliana DNA binding / transcription factor (AT3G22100)).

SEQ ID NOs: 53 and 54 show the nucleic acid (GI|42565105|ref(NM_l 13107.4) and protein (GI|42565106|ref|NIM 88849,3) sequences of Arabidopsis thaliana protein binding / signal transducer (AT3G22104)). SEQ ID NOs: 55 and 56 show the nucleic acid (GI|42565107|ref|NM_l 13108.3) and protein (GI|15233268|reflNP_188850.1| PACl) sequences of Arabidopsis thaliana PACl ; endopeptidase/ peptidase/ threonine endopeptidase (PACl)).

SEQ ID NOs: 57 and 58 show the nucleic acid (GI|42565108|ref]NM_l 13109.3) and protein GI|42565109|ref|NP_l 88851.2 () sequences of Arabidopsis thaliana CWLP (CELL WALL-PLASMA MEMBRANE LINKER PROTEIN); lipid binding / structural constituent of cell wall (CWLP)).

SEQ ID NOs: 59 and 60 show the nucleic acid (GI|42569667|ref|NM_129189.3) and protein (GI|18404102|ref]NP_565844.1) sequences of Arabidopsis thaliana zinc finger (ANl-like) family protein (At2g36320)). SEQ ID NOs: 61 and 62 show the nucleic acid (GI|30684399lreflNM_101419.2) and protein (GI|15218214|ref|NP_173003.1) sequences of Arabidopsis thaliana ATP:ADP antiporter (AT1G15500)).

SEQ ID NOs: 63 and 64 show the nucleic acid (QIjI 840645 l |ref|NM_l 29973.1) and protein (GI|15224814|ref|NP_181938.1) sequences of Arabidopsis thaliana ATGDIl (ATGDIl)).

SEQ ID NOs: 65 and 66 show the nucleic acid (GI|30683725|ref|NM_101298.2) and protein (GI|30683726|ref|NP_563945.2) sequences of Arabidopsis thaliana structural constituent of ribosome (AT1G14320)).

SEQ ID NOs: 67 and 68 show the nucleic acid (GI|30698233|reflNM_126051.2) and protein (GI|15240009|ref|NP_201454.1 |) sequences of Arabidopsis thaliana aldose 1 - epimerase (AT5G66530)).

SEQ ID NOs: 69 and 70 show the nucleic acid (GI|30685376|ref]NM_121553.2) and protein (GI|15242316|ref|NP_l 97053.1) sequences of Arabidopsis thaliana UDP- glucose 6-dchydrogcnasc (AT5G15490)).

SEQ ID NOs: 71 and 72 show the nucleic acid (GI|30690203|refjNM_l 19675.2) and protein (GI|15236264|ref|NP_l 95235.1) sequences of Arabidopsis thaliana CAT2 (CATALASE 2); catalase (CAT2)).

SEQ ID NOs: 73 and 74 show the nucleic acid (GI|30686208|reflNM_l 18476.3) and protein (GI|22328885|ref|NP J 94078.2) sequences of Arabidopsis thaliana rhodopsin- like receptor (AT4G23470)).

SEQ ID NOs: 75 and 76 show the nucleic acid (GI|42573000|ref]NM_202868.1) and protein (GI|42573001|ref|NP_974597.1) sequences of Arabidopsis thaliana rhodopsin- like receptor (AT4G23470)). SEQ ID NOs: 77 and 78 show the nucleic acid (GI)42565568|reflNM_l 14399.3) and protein (GI|15230664|ref|NP_l 90116.1) sequences of Arabidopsis thaliana IVD (ISOVALERYL-COA-DEHYDROGENASE) (IVD)).

SEQ ID NOs: 79 and 80 show the nucleic acid (GI|30679196|refpS[M_120205.2) and protein (GI115240932|ref|NP_195747.1) sequences of Arabidopsis thaliana double- stranded RNA-binding domain (DsRBD)-containing protein (At5g01270)).

SEQ ID NOs; 81 and 82 show the nucleic acid (GI|42572532|refjNM_202633.1) and protein (GI|42572533|reflNP_974362.1) sequences of Arabidopsis thaliana Ran GTPase binding (AT3G2610O)).

SEQ ID NOs: 83 and 84 show the nucleic acid (GI|30688164|refpSM_l 13515.2) and protein (GI|184048041ref|NP_566789.1) sequences of Arabidopsis thaliana Ran GTPase binding (AT3G26100)).

SEQ ID NOs: 85 and 86 show the nucleic acid (GI|30688736|refpSM_l 19206.3) and protein (GI|15234792|refjNP_l 94789.1) sequences of Arabidopsis thaliana GTP binding / GTPase/ RNA binding / nucleoside-triphosphatase/ nucleotide binding / signal recognition particle binding (AT4G30600)).

SEQ ID NOs: 87 and 88 show the nucleic acid (GI|42567267|refINM_l 19190.3) and protein (GI|15234745|ref|NP_194773.1) sequences of Arabidopsis thaliana GAEl (UDP-D-GLUCURONATE 4-EPIMERASE 1); NAD binding / catalytic (GAEl)).

SEQ ID NOs: 89 and 90 show the nucleic acid (GI|30683948|ref(NM_l 17821.2) and protein (GI|15235981|ref|NP_193450.1) sequences of Arabidopsis thaliana AT-RAB2; GTP binding (AT-RAB2)).

SEQ ID NOs: 91 and 92 show the nucleic acid (GI|42566248|refjNM_l 16472.3) and protein (GI|30679124|ref|NP_l 92148.2) sequences of

Arabidopsis thaliana APP (ARABIDOPSIS POLY(ADP-RIBOSE) POLYMERASE); DNA binding / NAD+ ADP-ribosyltransferase (APP)).

DETAILED DESCRIPTION Definitions

Unless otherwise indicated, all technical and scientific terms used herein have the same meaning as they would to one skilled in the art of the present invention. Practitioners are particularly directed to Sambrook et al., 1989, Molecular Cloning: A Laboratory Manual (Second Edition), Cold Spring Harbor Press, Plainview, N. Y,, and Ausubel FM et al, 1993, Current Protocols in Molecular Biology, John Wiley & Sons, New York, N. Y., for definitions and terms of the art. It is to be understood that this invention is not limited to the particular methodology, protocols, and reagents described, as these may vary.

As used herein, the term "vector" or "transformation vector" refers to a nucleic acid construct designed for transfer between different host cells. An "expression vector" refers to a vector that has the ability to incorporate and express heterologous DNA fragments in a foreign cell. Many prokaryotic and cukaryotic vectors, including example expression vectors, are commercially available. Selection of appropriate vectors is within the knowledge of those having skill in the art.

A "heterologous" nucleic acid construct or sequence has at least a portion of the sequence that is not native to the plant cell in which it is expressed. Heterologous, with respect to a control sequence, refers to a control sequence (e.g., promoter or enhancer) that docs not function in nature to regulate the same gene the expression of which it is currently regulating. Generally, heterologous nucleic acid sequences are not endogenous to the cell or part of the native genome in which they are present, and have been added to the cell by infection, transfection, microinjection, electroporation, or the like. A "heterologous" nucleic acid construct may contain a control sequence/DNA coding sequence combination that is the same as, or different from a control sequence/DNA coding sequence combination found in the native plant.

As used herein, the term "gene" means the segment of DNA involved in producing a polypeptide chain, which may or may not include regions preceding and following the coding region, e.g. 5' untranslated (5' UTR) or "leader" sequences and 3' UTR or "trailer" sequences, as well as intervening sequences (introns) between individual coding segments (exons) and non-transcribed regulatory sequence.

As used herein, the term "nucleic acid molecule" is intended to include DNA molecules (e.g., cDNA or genomic DNA) and RNA molecules {e.g., mRNA) and analogs of the DNA or RNA generated using nucleotide analogs. The nucleic acid molecule can be single-stranded or double-stranded, but preferably is double-stranded DNA. By "complement" is intended a nucleotide sequence that is sufficiently complementary to a given nucleotide sequence such that it can hybridize to the given nucleotide sequence to thereby form a stable duplex.

As used herein, "recombinant" includes reference to a cell oτ vector that has been modified by the introduction of a heterologous nucleic acid sequence or that the cell is derived from a cell so modified. Thus, for example, recombinant cells express genes that are not found in identical form within the native (non-recombinant) form of the cell or express native genes that are otherwise abnormally expressed, under expressed, or not expressed at all as a result of deliberate human intervention.

As used herein, the term "gene expression" refers to the process by which a polypeptide is produced based on the nucleic acid sequence of a gene. The process includes both transcription and translation; accordingly, "expression" may refer to either a polynucleotide or polypeptide sequence, or both. Sometimes, expression of a polynucleotide sequence will not lead to protein translation. "Over-expression" refers to increased expression of a polynucleotide and/or polypeptide sequence relative to its expression in a wild-type (or other reference [e.g., non-transgenic]) plant and may relate to a naturally-occurring or non-naturally occurring sequence. "Ectopic expression" refers to expression at a time, place, and/or increased level that docs not naturally occur in the non- altered or wild-type plant. "Under-expression" refers to decreased expression of a polynucleotide and/or polypeptide sequence, generally of an endogenous gene, relative to its expression in a wild-type plant. The terms "mis-expression" and "altered expression" encompass over-expression, under-expression, and ectopic expression.

The term "introduced" in the context of inserting a nucleic acid sequence into a cell, includes, for example, "transfection", or "transformation" or "transduction" and includes reference to the incorporation of a nucleic acid sequence into a cukaryotic or prokaryotic cell where the nucleic acid sequence may be incorporated into the genome of the cell (for example, chromosome, plasmid, plastid, or mitochondrial DNA), converted into an autonomous replicon, or transiently expressed (for example, transfected mRNA).

As used herein, a "plant cell" refers to any cell derived from a plant, including cells from undifferentiated tissue (e.g., callus) as well as plant seeds, pollen, propagules, and embryos.

As used herein, the terms "native" and "wild-type" relative to a given plant trait or phenotype refers to the form in which that trait or phenotype is found in the same variety of plant in nature.

As used herein, the term "modified" regarding a plant trait, refers to a change in the phenotype of a transgenic plant relative to the similar non-transgenic plant. An "interesting phenotype (trait)" with reference to a transgenic plant refers to an observable or measurable phenotype demonstrated by a Tl and/or subsequent generation plant, which is not displayed by the corresponding non-transgenic (e.g., a genotypically similar plant that has been raised or assayed under similar conditions). An interesting phenotype may represent an improvement in the plant or may provide a means to produce improvements in other plants. An "improvement" is a feature that may enhance the utility of a plant species or variety by providing the plant with a unique and/or novel quality.

An "altered pathogen resistance phenotype" or "altered pathogen resistance" refers to a detectable change in the response of a genetically modified plant to pathogenic infection, compared to the similar, but non-modified plant. The phenotype may be apparent in the plant itself (e.g., in growth, viability or particular tissue morphology of the plant) or may be apparent in the ability of the pathogen to proliferate on and/or infect the plant. As used herein, "improved pathogen resistance" refers to increased resistance to a pathogen. Methods for measuring pathogen resistance arc well known in the art. Sec, for example, Epple et al, Plant Cell, 1997, 9:509-520, Jach et al, Plant J., 1995, 8:97-109, Lorito et al, Proc Natl Acad Sci USA, 1998, 95:7860-7865, McDowell et al, Plant J., 2000, 22:523- 529, McDowell et al, MoI Plant Microbe Interact., 2005, 18:1226-1234, Schweizer et al, Plant Physiol, 1993, 102:503-511, Simons et al, Plant Cell, 1998, 10:1055-1068, Stein et al, Plant Cell, 2006, 18:731-746, Epub 2006 Feb; Thomma et al, Ciirr Opin Immunol, 2001 , 13:63-68. By "pathogen resistance activity" or "pathogen resistance" is therefore intended the ability to grow or survive during a pathogenic infection. An "altered fungal resistance phenotype" or "altered fungal resistance" refers to detectable change in the response of a genetically modified plant to fungal infection, compared to the similar, but non-modified plant. The phenotype may be apparent in the plant itself (e.g., in growth, viability or particular tissue morphology of the plant) or may be apparent in the ability of the pathogen to proliferate on and/or infect the plant, or both. As

7 07H46

used herein, "improved fungal resistance" refers to increased resistance to a fungal pathogen. Methods for measuring fungal resistance are well known in the art. See, for example: Adam & Somerville, PZa^ /., 1996, 9:341-356, Alan & Earle, MoI. Plant Microbe Interact, 2002, 15:701-708, Castillo-Lluva ef al, J. Cell ScL, 2004, 117:4143-4156, Dufresne et al, MoI. Plant Microbe Interact., 1998, 11 :99-108, Epple et al, Plant Cell,

1997, 9:509-520, Geffrey et al, MoI. Plant Microbe Interact., 2000, 13:287-296, Geraats et al, Mol. Plant Microbe Interact., 2002, 15:1078-1085, Gold et al, Plant Cell, 1997, 9:1585-1594, Holtorf et al, Plant MoI. Biol, 1998, 36:673-680, Jach et al, Plant J., 1995, 8:97-109, Lopez-Garcia ef α/., Mo/. Plant Microbe Interact., 2000, 13:837-846, Lorito el al, Proc. Natl Acad. ScL U.S.A., 1998, 95:7860-7865, Lu et al., J. Biochem. MoI Biol, 2005, 38:420-431, Oldach et al, MoI Plant Microbe Interact., 2001, 14:832-838; Rollins, MoI. Plant Microbe Interact., 2003, 16:785-795, Schweizer et al, Plant Physiol, 1993, 102:503- 511, Simons et al, Plant Cell, 1998, 10:1055-1068, Thomma et al, Proc. Natl. Acad. ScL U.S.A., 1998, 95:15107-15111; and Thomma et al, Plant J., 1999, 19:163-171. By "fungal resistance activity" or "fungal resistance" is therefore intended the ability to grow or survive during a fungal infection.

As used herein, a "mutant" polynucleotide sequence or gene differs from the corresponding wild type polynucleotide sequence or gene either in terms of sequence or expression, where the difference contributes to a modified plant phenotype or trait. Relative to a plant or plant line, the term "mutant" refers to a plant or plant line which has a modified plant phenotype or trait, where the modified phenotype or trait is associated with the modified expression of a wild type polynucleotide sequence or gene.

As used herein, the term "Tl" refers to the generation of plants from the seed of TO plants. The Tl generation is the first set of transformed plants that can be selected by application of a selection agent, e.g., an antibiotic or herbicide, for which the transgenic plant contains the corresponding resistance gene. The term "T2" refers to the generation of plants by self-fertilization of the flowers of Tl plants, previously selected as being transgenic.

As used herein, the term "plant part" includes any plant organ or tissue, including, without limitation, seeds, embryos, meristematic regions, callus tissue, leaves, roots, shoots, gametophytes, sporophytes, pollen, and microspores. Plant cells can be obtained from any plant organ or tissue and cultures prepared therefrom. The category of plants which can be used in the methods of the present disclosure is generally as broad as the category of higher

2007/071146

plants amenable to transformation techniques, including both monocotyledenous and dicotyledenous plants.

As used herein, "transgenic plant" includes reference to a plant that comprises within its genome a heterologous polynucleotide. The heterologous polynucleotide can be either stably integrated into the genome, or can be extra-chromosomal. Preferably, the polynucleotide of the present disclosure is stably integrated into the genome such that the polynucleotide is passed on to successive generations. A plant cell, tissue, organ, or plant into which the heterologous polynucleotides have been introduced is considered "transformed," "transfected," or "transgenic." Direct and indirect progeny of transformed plants or plant cells that also contain the heterologous polynucleotide are also considered transgenic.

An "isolated" or "purified" nucleic acid molecule or protein, or biologically active portion thereof, is substantially free of other cellular material, or culture medium when produced by recombinant techniques, or substantially free of chemical precursors or other chemicals when chemically synthesized. Preferably, an "isolated" nucleic acid is free of sequences (preferably protein encoding sequences) that naturally flank the nucleic acid {e.g. , sequences located at the 5' and 3' ends of the nucleic acid) in the genomic DNA of the organism from which the nucleic acid is derived. For purposes of the disclosure, "isolated" when used to refer to nucleic acid molecules excludes isolated chromosomes. For example, in various embodiments, the isolated FUR nucleic acid molecule can contain less than about 5 kb, 4 kb, 3 kb, 2 kb, 1 kb, 0.5 kb, or 0.1 kb of nucleotide sequences that naturally flank the nucleic acid molecule in genomic DNA of the cell from which the nucleic acid is derived. A FUR protein that is substantially free of cellular material includes preparations of protein having less than about 30%, 20%, 10%, or 5% (by dry weight) of non-FUR protein (also referred to herein as a "contaminating protein").

Identification of Plants with an Improved Pathogen Resistance Phenotype

Activation tagging in plants refers to a method of generating random mutations by insertion of a heterologous nucleic acid construct comprising regulatory sequences (e.g., an enhancer) into a plant genome. The regulatory sequences can act to enhance transcription of one or more native plant genes; accordingly, activation tagging is a fruitful method for generating gain-of-function mutations that are generally dominant (see, e.g., Hayashi et al., Science, 1992, 258: 1350-1353; Weigel et al, Plant Physiology, 2000, 122:1003-1013). The inserted construct also provides a molecular tag for rapid identification of the native

plant gene or sequence the mis-expression of which causes the mutant phenotype. Activation tagging may also cause loss-of-function phenotypes. For instance, the insertion may result in disruption of a native plant gene, in which case the phenotype is generally recessive. Activation tagging has been used in various species, including tobacco and

Arabidopsis, to identify many different kinds of mutant phenotypes and the genes associated with these phenotypes (Wilson et al, Plant Cell, 1996, 8:659-671 ; Schaffer et al, Cell, 1998, 93: 1219-1229; Fridborg et al, Plant Cell, 1999, 11: 1019-1032; Kardailsky et al, Science, 1999, 286: 1962-1965; Christensen et al, 2000, Cell 100:469-478). Activation tagging has also been used to identify mutants with altered disease resistance (Weigcl et al, Plant Physiology, 2000, 122: 1003-1013).

A screen of Arabidopsis activation tagged (ACTTAG) mutants was used to identify the genes [designated FUR# listed in column 1 of TablevS 3 and 4 (below)] which are responsible for an altered pathogen resistance phenotype (specifically, a fungal resistance phenotype).

Briefly and as further described in the Examples, a large number of Arabidopsis plants were mutated with the pSKI015 vector, which comprises a T-DNA from the Ti plasmid of Agrobacterium tumefaciens, a viral enhancer element, and a selectable marker gene (Weigel et al, Plant Physiology, 2000, 122:1003- 1013). When the T-DNA inserts into the genome of transformed plants, the enhancer element can cause up-regulation of genes in the vicinity, generally within about 10 kilobase (kb) of the insertion. Tl plants were exposed to the selective agent in order to specifically recover transformed plants that expressed the selectable marker and therefore harbored T-DNA insertions. Tl plants were allowed to grow to maturity, self-fertilize and produce seed. T2 seed was harvested, labeled and stored. ACTTAG lines showing increased resistance to the fungus Fusarium oxysporum sp. conglutinans were identified either in a "forward genetics" or a "reverse genetics" screen.

ACTTAG lines that showed increase resistance to F. oxysporum sp. conglulinans were identified by comparing the phenotype of ACTTAG seedlings and of wild-type seedlings after F. oxysporum sp. conglutinans infection. The association of the FUR gene with the pathogen resistance phenotype was discovered by analysis of the genomic DNA sequence flanking the T-DNA insertion in the identified line. Accordingly, FUR genes and/or polypeptides may be employed in the development of genetically modified plants having a modified pathogen {e.g., fungal) resistance phenotype ("a FUR phenotype"). FUR

genes may be used in the generation of crops and/or other plant species that haλ'e improved resistance to infection by F, oxyspomm sp. conglutinans, other subspecies, isolates or races of F. oxyspomm, other pathogens causing vascular wilt disease and may also be useful in the generation of a plant with improved resistance to fungal, bacterial, and/or other pathogens. Mis-expression of FUR genes may thus reduce the need for fungicides and/or pesticides. The modified pathogen resistance phenotype may further enhance the overall health of the plant.

FUR Nucleic Acids and Polypeptides The FUR genes discovered in the "forward genetics" activation tagging screen and

"reverse genetics" activation tagging screen are listed in column 1 of Tables 3 and 4, respectively. The Arabidopsis Information Resource (TAIR) identification numbers are provided in column 2. Columns 3-4 provide GenBank identifier numbers (GI#s) for the nucleotide and polypeptide sequences, respectively; each of the referenced published sequences is incorporated herein by reference as of the date on which this application is filed. Column 5 lists biochemical function and/or protein name. Column 6 lists the conserved protein domains. Column 7 provides the GI#s for nucleic acid and polypeptide sequences of orthologous genes from other plant species; each of the referenced published sequences is incorporated herein by reference as of the date on which this application is filed.

As used herein, the term "FUR polypeptide" refers to a full-length FUR protein as listed in column 1 of Tables 3 and 4. Fragments, derivatives (variants), or orthologs thereof that are "functionally active", meaning that the protein fragment, derivative, or ortholog exhibits one or more or the functional activities associated with the full-length FUR polypeptide, may also be used in the methods or compositions disclosed herein. By

"fragment" is intended a portion of the nucleotide sequence encoding a FUR protein or a portion of the amino acid sequence of the FUR protein. A fragment of a nucleotide sequence may encode a biologically active portion of a FUR protein, a biologically active nucleic acid (e.g., an antisense or small inhibitory nucleic acid), or it may be a fragment that can be used as a hybridization probe or PCR primer using methods known in the art.

Nucleic acid molecules that are fragments of a FUR nucleotide sequence comprise at least about 15, 20, 50, 75, 100, 200, 300, 350, 400, 450, 500, 550, 600, 650, 700, 750, 800, 850, 900, 950, 1000, 1050, 1 100, 1150, 1200, 1250, 1300, 1400, 1500, 2000, 2500, 3000 contiguous nucleotides, or up to the number of nucleotides present in a full-length FUR-

encoding nucleotide sequence disclosed herein, depending upon the intended use. By "contiguous" nucleotides or amino acids are intended nucleotide or amino acid residues that arc immediately adjacent to one another.

In one embodiment,- a functionally active FUR polypeptide causes an altered pathogen resistance phenotype when mis-expressed in a plant. In a further embodiment, mis-expression of the functionally active FUR polypeptide causes increased resistance to F. oxysporum sp conglutinans, and/or other pathogens causing vascular wilt disease. In another embodiment, a functionally active FUR polypeptide is capable of rescuing defective (including deficient) endogenous FUR activity when expressed in a plant or in plant cells; the rescuing polypeptide may be from the same or from a different species as that with defective activity.

In another embodiment, a functionally active fragment of a full length FUR polypeptide (e.g., a native polypeptide having the sequence of a FUR polypeptide or a naturally occurring ortholog thereof) retains one of more of the biological properties associated with the full-length FUR polypeptide, such as signaling activity, binding activity, catalytic activity, or cellular or extra-cellular localizing activity.

The term binding activity refers to the ability of a protein to bind to another protein, a DNA fragment or some other molecule (Bogdanove, Plant MoI Biol, 2002, 50:981-989, Inohara et al, Annu Rev Biochem., 2005, 74:355-383, Testerink & Munnik, Trends Plant ScL, 2005, 10:368-375).

The term catalytic activity refers to the ability of a protein to catalyze a chemical reaction; sec, e.g., Bhatia et al., CHt Rev Biotechnol., 2002, 22:375-407, Pcdlcy & Martin, Curr Opin Plant Biol., 2005, 8:541-547, Rosahl, Z Naturforsch [C]. 1996, 51 : 123-138, Stone & Walker, Plant Physiol, 1995, 108:451-457. The term cellular or extra-cellular localizing activity refers to portions of the protein that interact with other components of the cell to localize the protein to a specific subcellular or extra-cellular location. See, for instance, Crofts et al, Plant Physiol, 2004, 136:3414-3419, Matsuoka & Bednarek, Curr Opin Plant Biol, 1998, 1 :463-469, Rusch & Kendall, MoI Memhr- Biol, 1995, 12:295-307, and Schnell & Hebert, Cell, 2003, 112:491- 505.

A FUR fragment preferably comprises a FUR domain, such as a C- or N-terminal or catalytic domain, among others, and may comprise at least about 15, 25, 30, 50, 75, 100, 125, 150, 175, 200, 250, 300, 350, 400, or 450 contiguous amino acids of a FUR protein, or up to the total number of amino acids present in a full-length FUR protein disclosed herein.

Representative functional domains of FUR genes are listed in column 6 of Table 3 and Table 4 and can be identified using the INTERPRO program (Mulder et al. , 2003 Nucleic Acids Res. 31, 315-318; Mulder el al., 2005 Nucleic Acids Res. 33-.D201-D205). ^" Functionally active variants of full-length FUR polypeptides or fragments thereof include polypeptides with amino acid insertions, deletions, or substitutions that retain one of more of the biological activities associated with the full-length FUR polypeptide. By "retains biological activity" is intended that the variant will have at least about 30%, preferably at least about 50%, more preferably at least about 70%, even more preferably at least about 80% of the biological activity of the native protein, such as for instance an anti-fungal activity. In some cases, variants are generated that change the post-translational processing of a FUR polypeptide. For instance, variants may have altered protein transport or protein localization characteristics or altered protein half-life compared to the native polypeptide. As used herein, the term "FUR nucleic acid" encompasses nucleic acids with the sequence provided in the GenBank entry referenced in column 3 of Table 3 and Table 4. Nucleic acid sequences complementary to the GenBank entry referenced in column 3 of Table 3 and Table 4, as well as functionally active fragments, derivatives, or orthologs thereof may also be used in the methods and compositions disclosed herein. A FUR nucleic acid of this disclosure may be DNA, derived from genomic DNA or cDNA, or RNA. In one embodiment, a functionally active FUR nucleic acid encodes or is complementary to a nucleic acid that encodes a functionally active FUR polypeptide.

Included within this definition is genomic DNA that serves as a template for a primary RNA transcript (e.g., an mRNA precursor) that requires processing, such as splicing, before encoding the functionally active FUR polypeptide. A FUR nucleic acid can include other non-coding sequences, which may or may not be transcribed; such sequences include 5' and 3' UTRs, polyadenylation signals and regulatory sequences that control gene expression, among others, as are known in the art. Some polypeptides require processing events, such as proteolytic cleavage, covalent modification, etc., in order to become fully active. Accordingly, functionally active nucleic acids may encode the mature or the pre-processed FUR polypeptide, or an intermediate form. A FUR polynucleotide can also include heterologous coding sequences, for example, sequences that encode a marker included to facilitate the purification of the fused polypeptide, or a transformation marker.

In another embodiment, a functionally active FUR nucleic acid is capable of being used in the generation of loss-of- function pathogen resistance phenotypes, for instance, via antisensc suppression, co-suppression, etc.

A FUR nucleic acid used in the methods of this disclosure may comprise a nucleic acid sequence that encodes or is complementary to a sequence that encodes a FUR polypeptide having at least about 60%, about 70%, about 75%, about 80%, about 85%, about 90%, about 91%, about 92%, about 93%, about 94%, about 95%, about 96%, about 97%, about 98%, or about 99% sequence identity to the polypeptide sequence of the

GenBank entry referenced in column 4 of Tables 3 and 4. In another embodiment a FUR polypeptide of the disclosure may include a conserved protein domain of the FUR polypeptide, such as one or more protein domain(s) listed in column 6 of Tables 3 and 4. In another embodiment, a FUR polypeptide comprises a polypeptide sequence with at least about 50%, about 60%, about 70%, about 80%, about 85%, about 90% or about 95% or more sequence identity to a functionally active fragment of the polypeptide of the GenBank entry referenced in column 4 of Tables 3 and 4. In yet another embodiment, a FUR polypeptide comprises a polypeptide sequence with at least about 50%, about 60 %, about 70%, about 80%, or about 90% identity to the polypeptide sequence of the GenBank entry referenced in column 4 of Tables 3 and 4 over its entire length and comprises a conserved protein domain(s) listed in column 6 of Tables 3 and 4.

In another embodiment, a FUR nucleic acid sequence used in the methods of the present disclosure comprises a nucleic acid sequence that has at least about 60%, about 70%, about 75%, about 80%, about 85%, about 90%, about 91%, about 92%, about 93%, about 94%, about 95%, about 96%, about 97%, about 98%, or about 99% sequence identity to the nucleic acid sequence of the GenBank entry referenced in column 3 of Tables 3 and 4, or nucleic acid sequences that are complementary to such a FUR sequence or a functionally active fragment thereof.

As used herein, "percent (%) sequence identity" with respect to a specified subject sequence, or a specified portion thereof, is defined as the percentage of nucleotides or amino acids in the candidate derivative sequence identical with the nucleotides or amino acids in the subject sequence (or specified portion thereof), after aligning the sequences and introducing gaps, if necessary to achieve the maximum percent sequence identity, as generated by the program WU-BLAST-2.0al9 (Altschul et al., J. MoI. Biol., 215:403-410 1990) with search parameters set to default values. The HSP S and HSP S2 parameters are dynamic values and are established by the program itself depending upon the composition of the particular sequence and composition of the particular database against which the sequence of interest is being searched. A "% identity value" is determined by the number of matching identical nucleotides or amino acids, divided by the sequence length for which the

percent identity is being reported. "Percent (%) amino acid sequence similarity" is determined by doing the same calculation as for determining % amino acid sequence identity, but including conservative amino acid substitutions in addition to identical amino acids in the computation. A "conservative amino acid substitution" is one in which the amino acid residue is replaced with an amino acid residue having a similar side chain. Families of amino acid residues having similar side chains have been defined in the art. These families include amino acids with basic side chains (e.g., lysine, arginine, histidine), acidic side chains (e.g., aspartic acid, glutamic acid), uncharged polar side chains (e.g., glycine, asparagine, glutamine, serine, threonine, tyrosine, cysteine), nonpolar side chains (e.g., alanine, valine, leucine, isoleucine, proline, phenylalanine, methionine, tryptophan), beta-branched side chains (e.g., threonine, valine, isoleucine) and aromatic side chains (e.g., tyrosine, phenylalanine, tryptophan, histidine).

"Variants" of FUR-encoding nucleotide sequences include those sequences that encode the FUR proteins disclosed herein but that differ conservatively because of the degeneracy of the genetic code as well as those that have a specific sequence identity as discussed above. For example, preferably, conservative amino acid substitutions may be made at one or more predicted, preferably nonessential amino acid residues. A "nonessential" amino acid residue is a residue that can be altered from the wild-type sequence of a FUR protein without altering the biological activity, whereas an "essential" amino acid residue is required for biological activity. Amino acid substitutions may be made in non-conserved regions that retain function. In general, such substitutions would not be made for conserved amino acid residues, or for amino acid residues residing within a conserved motif, where such residues are essential for protein activity. Derivative nucleic acid molecules of the subject nucleic acid molecules include sequences that selectively hybridize to the nucleic acid sequence of the GenBank entry referenced in column 3 of Tables 3 and 4. The stringency of hybridization can be controlled by temperature, ionic strength, pH, and the presence of denaturing agents such as formamide during hybridization and washing. Conditions routinely used are well known (see, e.g., Current Protocol in Molecular Biology, Vol. 1 , Chap. 2,10, John Wiley & Sons, Publishers (1994); Sambrook et α/., supra). In some embodiments, a nucleic acid molecule of the disclosure is capable of hybridizing to a nucleic acid molecule containing the nucleotide sequence of the GenBank entry referenced in column 3 of Tables 3 and 4 under stringent hybridization conditions that comprise; prehybridization of filters containing nucleic acid

for 8 hours to overnight at 65 ⁰ C in a solution comprising 6X single strength citrate (SSC) (IX SSC is 0.15 M NaCl, 0.015 M Na citrate; pH 7.0), 5X Denhardt's solution, 0.05% sodium pyrophosphate and 100 μg/ml herring sperm DNA; hybridization for 18-20 hours at 65 ⁰ C in a solution containing 6X SSC, IX Denhardt's solution, 100 μg/ml yeast tRNA and 0.05% sodium pyrophosphate; and washing of filters at 65 ⁰ C for 1 hour in a solution containing 0.2X SSC and 0.1% SDS (sodium dodecyl sulfate). In other embodiments, moderately stringent hybridization conditions are used that comprise: pretreatment of filters containing nucleic acid for 6 hours at 40° C in a solution containing 35% formamide, 5X SSC, 50 mM Tris-HCl (pH 7.5), 5 niM EDTA, 0.1% PVP, 0.1% Ficoll, 1% BSA, and 500 μg/ml denatured salmon sperm DNA; hybridization for 18-20 h at 40° C in a solution containing 35% formamide, 5X SSC, 50 mM Tris-HCl (pH 7.5), 5 mM EDTA, 0.02% PVP, 0.02% Ficoll, 0.2% BSA, 100 μg/ml salmon sperm DNA, and 10% (wt/vol) dextran sulfate; followed by washing twice for 1 hour at 55 ⁰ C in a solution containing 2X SSC and 0.1% SDS. Alternatively, low stringency conditions can be used that comprise: incubation for 8 hours to overnight at 37°C in a solution comprising 20% formamide, 5 x SSC, 50 mM sodium phosphate (pH 7.6), 5X Denhardt's solution, 10% dextran sulfate, and 20 μg/ml denatured sheared salmon sperm DNA; hybridization in the same buffer for 18 to 20 hours; and washing of filters in I x SSC at about 37°C for 1 hour.

As a result of the degeneracy of the genetic code, a number of polynucleotide sequences encoding a FUR polypeptide can be produced. For example, codons may be selected to increase the rate at which expression of the polypeptide occurs in a particular host species, in accordance with the optimum codon usage dictated by the particular host organism (see, e.g., Nakamura et al, Nucleic Acids Res., 27:292, 1999). Such sequence variants may be used in the methods of this disclosure. The methods of the disclosure may use orthologs of the Arabidopsis FUR gene.

Examples of orthologs of each of the Arabidopsis FUR genes are identified in column 7 of Tables 3 and 4. Methods of identifying the orthologs in other plant species are known in the art. Normally, orthologs in different species retain the same function, due to the presence of one or more protein motifs and/or 3-dimensional structures. In evolution, when a gene duplication event follows speciation, a single gene in one .species, such as Arabidopsis, may correspond to multiple genes (paralogs) in another. As used herein, the term "orthologs" encompasses paralogs. When sequence data is available for a particular plant species, orthologs are generally identified by sequence homology analysis, such as BLAST analysis, usually using protein bait sequences. Sequences arc assigned as a potential ortholog if the

best hit sequence from the forward BLAST result retrieves the original query sequence in the reverse BLAST (Huynen & Bork, Proc. Natl. Acad. ScL U.S.A., 95:5849-5856, 1998; Huynen el al, Genome Research, 10:1204-1210, 2000). Programs for multiple sequence alignment, such as CLUSTAL (Thompson JD et al., Nucleic Acids Res. 22:4673-4680, 1994) may be used to highlight conserved regions and/or residues of orthologous proteins and to generate phylogenetic trees. In a phylogenetic tree representing multiple homologous sequences from diverse species {e.g., retrieved through BLAST analysis), orthologous sequences from two species generally appear closest on the tree with respect to all other sequences from these two species. Structural threading or other analysis of protein folding (e.g. , using software by ProCeryon, Biosciences, Salzburg, Austria) may also identify potential orthologs. Nucleic acid hybridization methods may also be used to find orthologous genes and are preferred when sequence data are not available. Degenerate PCR and screening of cDNA or genomic DNA libraries are common methods for finding related gene sequences and are well known in the art (see, e.g., Sambrook, supra; Dieffenbach and Dveksler (Eds.) PCR Primer: A Laboratory Manual, Cold Spring Harbor Laboratory Press, NY, 1989). For instance, methods for generating a cDNA library from the plant species of interest and probing the library with partially homologous gene probes are described in Sambrook et al, supra. A highly conserved portion of the Arabidopsis FUR coding sequence may be used as a probe. FUR ortholog nucleic acids may hybridize to the nucleic acid of the GenBank entry referenced in column 3 of Tables 3 and 4 under high, moderate, or low stringency conditions. After amplification or isolation of a segment of a putative ortholog, that segment may be cloned and scqucnccd by standard techniques and utilized as a probe to isolate a complete cDNA or genomic clone. Alternatively, it is possible to initiate an EST project to generate a database of sequence information for the plant species of interest. In another approach, antibodies that specifically bind known FUR polypeptides are used for ortholog isolation. Western blot analysis can determine that a FUR ortholog (e.g., an orthologous protein) is present in a crude extract of a particular plant species. When reactivity is observed, the sequence encoding the candidate ortholog may be isolated by screening expression libraries representing the particular plant species. Expression libraries can be constructed in a variety of commercially available vectors, including lambda gtl 1 , as described in Sambrook, el al., supra. Once the candidate ortholog(s) are identified by any of these means, candidate orthologous sequence are used as bait (the "query") for the reverse BLAST against sequences from Arabidopsis or other species in which FUR nucleic acid and/or polypeptide sequences have been identified.

FUR nucleic acids and polypeptides may be obtained using any available method. For instance, techniques for isolating cDNA or genomic DNA sequences of interest by screening DNA libraries or by using polymerase chain reaction (PCR), as previously described, are well known in the art. Alternatively, nucleic acid sequence may be synthesized. Any known method, such as site directed mutagenesis (Kunkel TA el a L, 1991, Methods Enzymol., 204:125-39) or PCR-mediated mutagenesis, may be used to introduce desired changes into a cloned nucleic acid.

In general, the methods of the disclosure involve incorporating the desired form of the FUR nucleic acid into a plant expression vector for transformation of plant cells, and the FUR polypeptide is expressed in the host plant.

Generation of Genetically Modified Plants with a Pathogen Resistance Phenotype

FUR nucleic acids and polypeptides may be used in the generation of genetically modified plants having a modified pathogen resistance phenotype; in general, improved resistance phenotypes are of interest. Pathogenic infection may affect seeds, fruits, blossoms, foliage, stems, tubers, roots, etc. Accordingly, resistance may be observed in any part of the plant. In one embodiment, altered expression of the FUR gene in a plant is used to generate plants with increased resistance to F. oxysporum sp conglutinans. In further embodiments, plants that mis-express FUR may also display altered resistance to other pathogens. Other fungal pathogens of interest include, but are not limited to, Alternaria brassicicola, Botrγtis cinerea, Erysiphe cichoracearum, Fusarium oxysporum, Fusarium spp., Plasmodiophora brassica, Rhizoctonla solani, Colletotrichum coccode, Sclerotinia spp., Aspergillus spp,, Penicillium spp., Ustilaga spp., and Tilletia spp., Phytophthora megaspernia f.sp. glyάnea, Macrophomina phaseoliria, Sclerotinia sclerotiorum, Diaporthe phaseolorum var. sojae (Phomopsis sojae), Diaporthe phaseolorum var. caulivora,

Sclerotium rolftsi, Cercospora ldkuchii, Cercospora sojina, Peronospora manshurica, Colletotrichum dematium {Colletotichwn truncatuni), Corynespora cassiicola, Septoria glycines, Phylhsticta sojicola, Alternaria alternata, Pseudomonas syringae p.v. glycinea, Xanthomonas campestris p.v. phaseoli, Microsphaera diffusa, Fusarium semitectum, Phialophora gregata, Phakopsora pachyrhizi, Pythium aphanidermaturn, Pythium ultimum, Pythium debaryanum, He ^' terodera glycines Fusarium solani, Albugo Candida, Alternaria brassicae, Leptosphaeria maculaπs, Rhizoctonia solani, Sclerotinia sclerotiorum, Mycosphaerella brassiccola, Pythium ultimum, Peronospora parasitica, Fusarium roseum, Alternaria alternate, Clavibacter michiganensis subsp. insidiosum, Pythium ultimum,

Pythium iiregulare, Pythium splendens, Pyihium debaryanum, Pythium aphanidermatum, Phytophthora megaspenna, Peronospora trifoliorum, Phoma medicaginis var. medicaginis, Cercospora medicaginis, Pseudopeziza medicaginis, Leplotrochila medicaginis, Fusarium, Xanthomonas campestris p.v. alfalfae, Aphanomyces euteiches, Stemphylium herbarum, Stemphylium alfalfae, Pseudomonas syringae p.v. atrofaciens, Urocystis agropyri,

Xanthomonas campestris p.v. translucens, Pseudomonas syringae p.v. syringae, Alternaria alternata, Cladosporium herbarum, Fusarium graminearum, Fusarium avenaceum, Fusarium culmorum, Ustilago tritici, Ascochyta tritici, Cephalosporium gramineum, Collotetrichum graminicola, Erysiphe graminis f.sp. tritici, Puccinia graminis f.sp. tritici, Puccinia recondila f.sp. Irilici, Puccinia slriiformis, Pyrenophora trilici-repenlis, Seploria nodorum, Septoria tritici, Septoria avenae, Pseudocercosporella herpotrichoides, Rhizoctonia solani, Rhizoctonia cerealis, Gaeumannomyces graminis var. tritici, Pythium aphanidermatum, Pythium arrhenomanes, Pythium ultimum, Bipolaris sorokiniana, Claviceps purpurea, Tilletia tritici, Tilletia laevis, Ustilago tritici, Tilletia indica, Rhizoctonia solani, Pythium arrhenomanes, Pythium gramicola, Pythium aphanidermatum, Plasmophora halsledii, Sclerolinia scleroliorum, Seploria helianthi, Phomopsis helianlhi, Alternaria helianthi, Alternaria zinniae, Phoma inacdonaldii, Macrophomina phaseolina, Rhizopus otyzae, Rhizopus arrhizus, Rhizopus stolonifer, Puccinia helianthi, Verticillium ^' dahliae, Envinia carotovomm p.v. carotovora, Cephalosporium acremonium, Phytophthora cryptogea, Albugo tragopogonis, Fusarium monilifoπne var. subglutinans, Envinia stewartii, Fusarium verticilloides, Fusarium monilifonne, Gibberella zeae (Fusarium graminearum), Stenocarpella maydis (Diplodia maydis), Pythium irregulare, Pythium debaryanum, Pythium graminicola, Pythium splendens, Pythium ultimum, Pythium aphanideimatum, Aspergillus flavus, Bipolaris maydis O, T (Cochliobolus heterostwphus), Helminthosporium carbonum I, II & III (Cochliobolus carbonum), Exserohilum turcicum I, II & III, Helminthosporium pedicellatum, Physoderma maydis, Phyllosticta maydis, Kabatiella maydis, Cercospora sorghi, Ustilago maydis, Puccinia sorghi, Puccinia polysora, Macrophomina phaseolina, Penicillium oxalicum, Nigrospora oiγzae, Cladosporium herbamm, Curvularia lunata, Curvularia inaequalis, Cumularia pallescens, Clavibacter michiganense subsp. nebraskense, Trichoderma viride, Claviceps sorghi, Pseudomonas avenae, Erwinia chrysanthemi p.v. zea, Erwinia carotovora, Corn stunt spiroplasma, Diplodia macrospora, Sclerophthora macrospora, Peronosclerospora sorghi, Peronosclerospora philippinensis, Peronosclerospora maydis, Peronosclerospora sacchari, Sphacelolheca reiliana, Physopella zeae, Cephalosporium maydis, Cephalosporium

acremonium, Exserohilum turcicum, Colletotrichum graminicola {Glomerella graminicola), Cercospora sorghi, Gloeocercospora sorghi, Ascochyta sorghina, Pseudomonas syringae p.v. syringae, Xanthomonas campeslris p.v. holcicola, Pseudomonas andwpogonis, Puccinia purpurea, Macrophomina phaseolina, Peήconia circinata, Fusarium moniliforme, Alternaria altemata, Bipolaris sorghicola, Helminthosporium sorghicola, Cnn'ularia lunata, Phoma insidiosa, Pseudomonas avenae (Pseudomonas alhoprecipitans), Ramulispora sorghi, Ramulispora sorghicola, Phyllachara sacchari, Sporisorium reilianum (Sphacelotheca reiliana), Sphacelotheca cruenta, Sporisorium sorghi, Claviceps sorghi, Rhizoctonia solani, Acremonium strictum, Sclerophthora macrospora, Peronosclerospora sorghi, Peronosclerospora philippinensis, Sclerospora graminicola, Fusarium graminearum, Fusarium oxysporum, Pythium arrhenomanes, Pythium graminicola, Magnaporthe grisea, Rhizoctonia solani.

Increased resistance to bacterial pathogens is also of interest. The bacterial pathogens of interest include, but are not limited to, Agrobacterium tumefaciens, Erwinia tracheiphila, Erwinia stewartii, Xanthomonas phaseoli, Erwinia amylovora, Erwinia carolovora, Pseudomonas syringae, Pelargonium spp, Pseudomonas cichorii, Xanlhomonas fragariae, Pseudomonas morsprunorum, and Xanthomonas campestris. Pathogenic ^' infection may affect seeds, fruits, blossoms, foliage, stems, tubers, roots, etc. Accordingly, resistance may be observed in any part of the plant. The methods described herein are generally applicable to all plants, as the FUR gene (or an ortholog, variant or fragment thereof) may be expressed in any type of plant. In some embodiments, the disclosure is directed to crops such as maize, soybean, cotton, rice, wheat, barley, tomato, canola, turfgrass, and flax. Other crops include alfalfa, tobacco, and other forage crops. The disclosure may also be directed to fruit- and vegetable-bearing plants including tomato, carrot, lettuce, bean, asparagus, cauliflower, pepper, beetroot, cabbage, eggplant, endive, leek, long cucumber, melon, pea, radish, rootstock, short cucumber (Beϊt alpha), squash, watermelon, white onion, witloof, yellow onion, bunching onion, broccoli, brussel sprout, celery, mache, cucumber, fennel, pumpkin, sweet corn, and zucchini, plants used in the cut flower industry, grain-producing plants, oil-producing plants, and nut-producing plants, among others.

The skilled artisan will recognize that a wide variety of transformation techniques exist in the art, and new techniques are continually becoming available. Any technique that is suitable for the target host plant can be employed within the scope of the present disclosure. For example, the constructs can be introduced in a variety of forms including,

but not limited to, as a strand of DNA, in a plasmid, or in an artificial chromosome. The introduction of the constructs into the target plant cells can be accomplished by a variety of techniques, including, but not limited to Agrobaclerium-medi&ted transformation, electroporation, microinjection, microprojectile bombardment calcium-phosphate-DNA co- precipitation or liposome-mediated transformation of a heterologous nucleic acid. The transformation of the plant is preferably permanent, i.e. by integration of the introduced expression constructs into the host plant genome, so that the introduced constructs are passed onto successive plant generations. Depending upon the intended use, a heterologous nucleic acid construct comprising a FUR polynucleotide may encode the entire protein or a biologically active portion thereof,

In one embodiment, binary Ti-based vector systems may be used to transfer polynucleotides. Standard Agro bacterium binary vectors are known to those of skill in the art, and many are commercially available (e.g., pBI121 Clontech Laboratories, Palo Alto, CA). The optimal procedure for transformation of plants with Agrobacterium vectors will vary with the type of plant being transformed. Exemplary methods for Agrobacterium- mediated transformation include transformation of explants of hypocotyl, shoot tip, stem or leaf tissue, derived from sterile seedlings and/or plantlets. Such transformed plants may be reproduced sexually, or by cell or tissue culture. Agrobacterium transformation has been previously described for a large number of different types of plants and methods for such transformation may be found in the scientific literature. Of particular relevance are methods to transform commercially important crops, such as maize (Fromm et al, Biotechnology, 1990, 8:833-839; Ishida et al, Nature Biotechnology 14:745 - 750, 1996), rapeseed (De Block et al, Plant Physiol, 91 :694-701, 1989), sunflower (Everett et al, Bio/Technology, 5:1201, 1987) and soybean (Christou et al, 1989, Proc, Natl. Acad. Sci U.S.A., 86:7500- 7504, 1989; Kline et al, Nature, 327:70, 1987).

Expression (including transcription and translation) of a FUR gene may be regulated with respect to the level of expression, the tissue type(s) where expression takes place and/or the developmental stage of expression. A number of heterologous regulatory sequences (e.g., promoters and enhancers) are available for controlling the expression of a FUR nucleic acid. These include constitutive, inducible and regulatable promoters, as well as promoters and enhancers that control expression in a tissue- or temporal-specific manner. Exemplary constitutive promoters include the raspberry E4 promoter (U.S. Patent Nos. 5,783,393 and 5,783,394), the 35S CaMV (Jones JD el al, Transgenic Res., 1:285-297,

1992), the CsVMV promoter (Verdaguer el al, Plant MoI. Biol., 37: 1055-1067, 1998) and the melon actin promoter (published PCT application WO00/56863). Exemplary tissue- specific promoters include the tomato E4 and E8 promoters (U.S. Patent No. 5,859,330) and the tomato 2AII gene promoter (Van Haaren et al., Plant MoI. Biol., 21 :625-640, 1993). In one embodiment, the FUR gene expression is under the control of a pathogen-inducible promoter (Rushton et al., The Plant Cell, 14:749-762, 2002). In one embodiment, expression of the FUR gene is under control of regulatory sequences from genes whose expression is associated with the CsVMV promoter.

In yet another aspect, it may be desirable to inhibit the expression of the endogenous FUR gene in a host cell. Exemplary methods for practicing this aspect of the disclosure include, but are not limited to, antisense suppression (Smith et al., Nature, 334:724-726, 1988; van der Krol et al, Biotechniques, 6:958-976, 1988); co-suppression (Napoli, et al, Plant Cell, 2:279-289, 1990); ribozymes (PCT Publication WO 97/10328); and combinations of sense and antisense (Waterhouse et al, Proc. Natl. Acad. Sci. U.S.A., 95:13959-13964, 1998). Methods for the suppression of endogenous sequences in ahost cell typically employ the transcription or transcription and translation of at least a portion of the sequence to be suppressed. Such sequences may be homologous to coding as well as non-coding regions of the endogenous sequence. Antisense inhibition may use the entire cDNA sequence (Sheehy et al., Proc. Natl. Acad. ScL U.S.A., 85:8805-8809, 1988), a partial cDNA sequence including fragments of 5' coding sequence (Cannon et al, Plant MoI. Biol, 15:39-47, 1990), or 3' non-coding sequences (Ch'ng et al, Proc. Natl Acad. Sci. U.S.A., 86:10006-10010, 1989). Cosuppression techniques may use the entire cDNA sequence (Napoli et al, supra; van der Krol et al, The Plant Cell, 2:291-299, 1990), or a partial cDNA sequence (Smith ed/., MoI Gen. Genetics, 224:477-481, 1990). Standard molecular and genetic tests may be performed to further analyze the association between a gene and an observed phenotype. Exemplary techniques are described below.

1. DNA/RNA analysis The stage- and tissue-specific gene expression patterns in mutant versus wild-type lines may be determined, for instance, by in situ hybridization. Analysis of the methylation status of the gene, especially flanking regulatory regions, may be performed. Other suitable techniques include over-expression, ectopic expression, expression in other plant species

and gene knock-out (reverse genetics, targeted knock-out, viral induced gene silencing (VIGS) (see Baulcombe, Arch. Virol Suppl. 15:189-201, 1999).

In a representative application, expression profiling, generally by microarray analysis, is used to simultaneously measure differences or induced changes in the expression of many different genes. Techniques for microarray analysis are well known in the art (see, for example, Schena et al, Science, 270:467-470, 1995; Baldwin et al, Cur. Opin. Plant Biol, 2(2):96-103, 1999; Dangond, Physiol. Genomics, 2:53-58, 2000; van Hal et al, J. Biotechnol, 78:271-280, 2000; Richmond & Somerville, Cur. Opin. Plant Biol, 3:108-116, 2000). Expression profiling of individual tagged lines may be performed. Such analysis can identify other genes that are coordinately regulated as a consequence of the over- expression of the gene of interest, which may help to place an unknown gene in a particular pathway.

2. Gene Product Analysis Analysis of gene products may include recombinant protein expression, antisera production, immuno localization, biochemical assays for catalytic or other activity, analysis of phosphorylation status, and analysis of interaction with other proteins via yeast two- hybrid assays.

3. Pathway Analysis

Pathway analysis may include placing a gene or gene product within a particular biochemical, metabolic or signaling pathway based on its mis-cxprcssion phcnotypc or by sequence homology with related genes. Alternatively, analysis may comprise genetic crosses with wild-type lines and other mutant lines (creating double mutants) to order the gene in a pathway, or determining the effect of a mutation on expression of downstream "reporter" genes in a pathway.

Generation of Mutated Plants with a Pathogen Resistance Phenotype

The disclosure further provides a method of identifying plants having increased pathogen resistance, in particular, plants that have a mutation in an endogenous FUR gene that confers such resistance. This method comprises analyzing at least one- FUR gene from a population of plants, and identifying a plant with an altered (e.g., mutated) FUR gene. The FUR gene may have a mutation that confers the pathogen resistance, or it may have an altered expression as compared to a wild-type plant. Pathogen-resistant progeny of these

plants that are not genetically modified may be generated. Methods for producing and identifying plants with mutations that confer pathogen resistance are known in the art. In one method, called "TILLING" (for targeting induced local lesions in genomes), mutations are induced in the seed of a plant of interest, for example, using EMS treatment. The resulting plants are grown and self-fertilized, and the progeny are used to prepare DNA samples. PCR amplification and sequencing of the FUR gene is used to identify whether a mutated plant has a mutation in the FUR gene. Plants having FUR mutations may then be tested for pathogen resistance, or alternatively, plants may be tested for pathogen resistance, and then PCR amplification and sequencing of the FUR gene is used to determine whether a , plant having increased pathogen resistance has a mutated FUR gene. TILLING can identify mutations that may alter the expression of specific genes or the activity of proteins encoded by these genes (see Colbert et al, 2001, Plant Physiolλ 26:480-484; McCallum et al, 2000, Nature Biotechnology 18:455-457).

In another method, a candidate gene/Quantitative Trait Loci (QTLs) approach can be used in a marker-assisted breeding program to identify mutations in the FUR gene or ■ orthologs of FUR gene that may confer resistance to pathogens (sec Foolad el al, , Theor. Appl Genet, 2002, 104(6-7):945-958; Roman i a/., 2002, Theor. Appl. Genet., 105(l):145- 159; Dekkers and Hospital, 2002, Nat. Rev. Genet., Jan;3(l):22-32). Thus, in a further aspect of the disclosure, a FUR nucleic acid is used to identify whether a pathogen-resistant plant has a mutation in the endogenous FUR gene or has a particular allele that causes a pathogen resistance phenotype.

While the invention has been described with reference to specific methods and embodiments, it will be appreciated that various modifications and changes may be made without departing from the invention. All publications cited herein are expressly incorporated herein by reference for the purpose of describing and disclosing compositions and methodologies that might be used in connection with the invention. All cited patents, patent applications, and sequence information in referenced public databases (as of the date of filing of this application) are also incorporated by reference.

T US2007/071146

EXAMPLES

EXAMPLE 1

Generation of Plants with a Pathogen Resistance Phenotvpe by Transformation with an Activation Tagging Construct Mutants were generated using the activation tagging (ACTTAG) vector, pSKIOl 5

(GI 6537289; Weigel et al. , supra). Standard methods were used for the generation of Arabidopsis transgenic plants, and were essentially as described in published application PCT WOO 1/83697, Briefly, TO Arabidopsis (CoI-O) plants were transformed with Agrobacterium carrying the pSKIOl 5 vector, which comprises T-DNA derived from the Agrobacterium Ti plasmid, an herbicide resistance selectable marker gene, and the 4X

CaMV 35S enhancer element. Transgenic plants were selected at the Tl generation based on herbicide resistance. T2 seed was collected from Tl plants and stored in an indexed collection, and a portion of the T2 seed was accessed for the forward genetic screen. T3 seed was used in the reverse genetic screen. T2 seed was sown in soil and plants were exposed to the herbicide to kill plants lacking the ACTTAG vector. T2 plants were grown to maturity, allowed to self- fertilize and set seed. T3 seed (from the T2 plants) was harvested in bulk for each line, and a portion of the T3 seed was accessed for the reverse genetic screen (see below).

The position of the ACTTAG element in the genome in each line was determined using T3 seed by inverse PCR. The PCR product was subjected to sequence analysis and placed on the genome using a basic BLASTN search and/or a search of the' Arabidopsis Information Resource (TAIR) database (available at the arabidopsis.org website). 38,090 lines with recovered flanking sequences were considered in the reverse genetic screen.

EXAMPLE 2

Forward Genetic Screen for Lines Resistant to the fungus Fusarium oxysporum sp conglυtinans

The forward genetics screen was conducted as a primary and secondary screen. In the primary screen, T2 seed from lines from the Arabidopsis ACTTAG collection and seed from wild-type CoI-O were planted in soil. The seeds were stratified for 2 days at 4°C and then grown in a growth chamber at 23 ⁰ C with 75% relative humidity on a long-day light cycle of 16 hours light and 8 hours dark for 1 week. The plants were sprayed with a solution containing 3xlO ⁵ spores of F. oxysporum sp. conglutinans. The plants were covered with domes and allowed to grow in growth chambers at 25 ⁰ C with 95% relative

humidity for 4 weeks. Each plant was then evaluated for stress caused by the fungus. Any lines with a plant showing no stress were submitted for further analysis. •

In the secondary screen, T2 seed from Arabidopsis ACTTAG lines identified in the primary screen and seed from wild-type CoI-O were planted in the same flat. Planting was performed in triplicate for each ACTTAG line identified in the primary screen. These plants were grown, inoculated with F. oxysporum sp. conglutinans spores, and evaluated for stress as described in the primary screen.

As a result of these analyses, 25 ACTTAG lines were identified as resistant to the fungus Fusarium oxyspomm sp conglutinans,

EXAMPLE 3

Characterization of the T-DNA Insertion in Plants Exhibiting the Altered Pathogen

Resistance Phenotype: ACTTAG locus number determination and ACTTAG copy number determination Because ACTTAG lines may have inserts at more than one genetic locus, the number of genetic loci containing the ACTTAG inserts was estimated in each line identified in Example 2. In Tl plants, ACTTAG inserts are present in the hemizygous state (that is, they are present inserted in one of the two copies of the genome of the diploid plant). Because of genetic segregation, in T2 plants each genetic locus containing an ACTTAG insert is present in a 3: 1 ratio; 75% of the T2 plants will have the ACTTAG insert at that locus and 25% will not. If a Tl plant contains two ACTTAG elements at independently segregating loci, the number of T2 plants containing any ACTTAG element will be 87.5% and 12.5% of the plants will not contain an insert. Because each ACTTAG element contains a gene conferring resistance to the herbicide BASTA, the number of genetic loci containing an ACTTAG element can be estimated by determining the percentage of T2 plants that are resistant to BASTA.

To determine the number of genetic loci carrying ACTTAG inserts in each line, the proportion T2 plants resistant to the selective agent 50-100 T2 seeds were sown in soil, allowed to germinate, and the number of germinated T2 seedlings was recorded. The T2 seedlings were sprayed with 60 mg/L of the herbicide BASTA 6 times over a period of 2 weeks to kill plants lacking the ACTTAG inserts. The number of BASTA resistant T2 seedlings was determined and the percentage of BASTA resistant plants calculated. Lines that had 60-80% BASTA-resistant T2 seedlings were estimated to carry an ACTTAG insert

at a single genetic locus. Lines that had greater than 80% BASTA-resistant T2 seedlings were estimated to carry an ACTTAG insert at more than one genetic locus.

Because each genetic locus can contain more than one insert, the number of ACTTAG elements was estimated in each line identified in Example 2. To determine the number of ACTTAG inserts present in each line, a TaqMan® polymerase chain reaction (PCR) based method was used using TaqMan® Universal PCR master Mix (Applied Biosystems) and ABI PRISM 7700 Sequence Detection System (Applied Biosystems). Briefly, genomic DNA was isolated from a pool of at least 18 T2 seedlings. Two PCR reactions were carried out simultaneously in a reaction mixture using the DNA of an ACTTAG line as the template. One PCR reaction detects the presence of the BAR gene, which confers resistance to the herbicide glufosinate-ammonium, using the PCR primers specific to the BAR gene. The other PCR reaction detects the presence of the ELF3 gene in Arabidopsis using PCR primers specific to the ELFl gene. The relative amounts of the two PCR products accumulated during the course of the reaction were used to determine the ACTTAG copy number.

Based on these analyses, five ACTTAG lines were chosen for further molecular analysis (see Example 4). The ACTTAG locus number estimate and ACTTAG copy number estimate for these lines are show in Table 1 below.

Table 1. ACTTAG locus number estimate and ACTTAG copy number estimate for five fungal resistant lines.

EXAMPLE 4

Characterization of the T-DNA Insertion in Plants Exhibiting the Altered Fungal Resistance

Phenotype: Determination of ACTTAG insertion site in the Arabidopsis genome

Plasmid rescue (Weigel et al, supra) and/or inverse PCR (iPCR; Triglia et al., 1988, Nucleic Acid Res., 16:8186) were used to recover Arabidopsis genomic DNA flanking the T-DNA insertion. The products of these analyses were analyzed by DNA sequencing and the sequence was subjected to a basic BLASTN search of the Arabidopsis genome housed in the Exelixis database and/or in the Arabidopsis Information Resource (TAIR) database (available at the arabidopsis.org website). The location of the ACTTAGs for FUR 1 , FUR2, FUR3 , FUR4 and FUR5 are described below.

FURl : The right border of the ACTTAG insert is just upstream of nucleotide -54372 of Arabidopsis thaliana DNA chromosome 4, BAC clone F23E13 (>gi|2961370).

FUR2: The left border of the ACTTAG insert is just downstream of nucleotide ~ 79693 Arabidopsis thaliana genomic DNA, chromosome 1 , BAC clone:F17L21 (>gi|9755398).

FUR3: The right border of the ACTTAG insert is just upstream of nucleotide ~ 64641 Arabidopsis thaliana genomic DNA, chromosome 5, Pl clone:MXC9 (gi|2696018).

FUR4: The right border of the ACTTAG insert is just upstream of nucleotide ~61146 Arabidopsis thaliana genomic DNA, chromosome 5, BAC clone:F15A17 (>gi|7413574).

FUR5: The right border of the ACTTAG insert is just upstream of nucleotide ~ 78585 Arabidopsis thaliana genomic DNA, chromosome 3, Pl clone: MZN24 (>gi|5041975).

EXAMPLE 5

Identification and expression analysis of candidate genes in ACTTAG plants exhibiting the altered pathogen resistance phenotype

Genes with the translation initiation codons within about 10 kbp of the ACTTAG inserts in the fungal resistant lines are considered to be within "activation space". The expressions of these candidate genes are likely to be up-regulated in the fungal resistant lines due to the 4X CaMV 35S enhancer elements in the ACTTAG inserts. The candidate genes for the ACTTAG lines FURl, FUR2, FUR3, FUR4 and FUR5 are listed in column 2 of Table 2.

These candidate genes were analyzed for altered expression in leaves of 28 day-old BASTA resistant T2 plants grown under 23 ⁰ C on a long-day light cycle of 16 hours light and 8 hours dark in a growth room. Wild-type plants grown in the same flat and therefore the same environmental conditions were used as controls for the SYBR green dye real-time quantitative RT-PCR assay. Specifically, RNA was extracted from tissues derived from plants exhibiting the pathogen resistance phenotype and from wild-type COL-O plants. SYBR green dye real-time quantitative RT-PCR was performed using primers specific to the genes with sequence IDs presented in column 3 of Table 2 and to a constitutively expressed actin gene (ACT2, positive control). The results of the expression analyses of the candidate genes for the ACTTAG lines FURl , FUR2, FUR3, FUR4 and FUR5 arc shown in column 5 of Table 2.

Table 2. Expression analysis of the candidate genes for the ACTTAG lines FURl, FUR2, FUR3, FUR4 and FUR5

EXAMPLE 6

Analysis of Arabidopsis FUR Sequence

Analyses of the FUR sequences were performed with BLAST (Altschul et al., 1990, J. MoI. Biol. 215:403-410), PFAM (Bateman et al., 1999, Nucleic Acids Res. 27:260-262), and/or TNTERPRO (Mulder et al., 2003 Nucleic Acids Res. 31 , 315-318; Mulder et al. , 2005 Nucleic Acids Res. 33:D201-D205). The results of these analyses are listed in Table 3.

Table 3 ^■ _' . Analysis of Arabidopsis FUR Sequences identified in a forward genetic screen

EXAMPLE 7

Identification of Arabidopsis fungal resistance genes using a "reverse genetics" screen

A "reverse genetics" screen was used as an alternative approach to identify Arabidopsis fungal resistance (FUR) genes. In this approach, a number of Arabidopsis genes were considered candidate fungal resistance genes. To determine if mis-expression of these genes caused a fungal resistance phenotype, ACTTAG lines with the predicted CaMV 35S enhancer elements within 9 kbp ("activation space") of the translational initiation codons Of these genes were identified from the 38,090 ACTTAG lines with an FST placement described in Example 1. ACTTAG lines with inserts near the candidate genes were evaluated for a fungus (Fusarium oxysponim sp. conglutinans) resistance phenotype as described in Example 2. ACTTAG lines containing ACTTAG inserts within the "activation space" of fifteen candidate genes were determined to be resistant to fungus. These genes are listed in Table 4.

The results of PFAM (Bateman et al, 1999, Nucleic Acids Res. 27:260-262), and/or INTERPRO (Mulder et al, 2003 Nucleic Acids Res. 31, 315-318; Mulder el al, 2005 Nucleic Acids Res. 33:D201-D205) analyses are shown in Table 4.

EXAMPLE 8

Recapitulation of the Fusarium resistant phenotype

Genes identiiϊed in the forward and reverse genetic screens were tested to identify whether direct over-expression can confer resistance to fusarium. To do this the genes listed in column 2 of Tables 3 and 4 were cloned into a plant transformation vector behind the constitutive CsVMV promoter and transformed into Arabidopsis plants using the floral dip method. The plant transformation vector contains a gene encoding a selectable marker driven by the RE4 promoter, to provide resistance to a cytotoxic agent, and serve as a selectable marker. Seed from the transformed plants were plated on agar medium containing the cytotoxic agent. After 10 days, transgenic plants were identified as healthy green plants and transplanted to soil. T2 seed was collected from 20 primary transformants containing each construct, T2 plants were tested for resistance to Fusarium in replicated experiments. In each experiment, approximately 16 T2 seeds from a transgenic event were planted in soil in a 10 row tray. Each tray contained 8 rows seeded with 16 transgenic lines (1 event per row) and 2 rows seeded with wild-type CoI-O seeds; 1 of the rows containing CoI-O was inoculated and served as the negative control, the other was not inoculated and served as the positive control. The seeds were stratified for 2 days at 4 ⁰ C and then grown in

a growth chamber at 23 ⁰ C with 75% relative humidity on a long-day light cycle of 16 hours light and 8 hours dark for 1 week. The plants were sprayed with a solution containing 3xlO ⁵ spores of F. oxysporum sp. conglulinans. The plants were covered with domes and allowed to grow in growth chambers at 25°C with 95% relative humidity for 4 weeks. Each plant was then evaluated for stress caused by the fungus. Resistant plants were identified as plants showing no stress symptoms. The genes in Table 5 showed positiye recapitulation results.

TABLE 5

EXANϊPLE 9

Fusarium resistance is conferred by over-expression of At4g36240

The effect of over-expression of At4g36240 (FURl-A) on Fusarium resistance was tested by growing T2 plants containing the CsVMV promoter driving expression of At4g36240 from 20 independent transformation events as described above. Each plant was evaluated for symptoms of Fusarium infection and scored as either resistant or susceptible. Six of the transformation events produced more plants than the control that were score resistant to Fusarium. Table 6 shows the events that produced plants resistant to Fusarium and how many plants were scored resistant. The number of control plants that were scored is also listed in the table.

TABLE 6

EXAMPLE lO

Fusarium resistance is conferred by over-expression of At4g362S0

The effect of over-expression of At4g36250 (FURl-B) on Fusarium resistance was tested by growing T2 plants containing the CsVMV promoter driving expression of At4g36250 from 20 independent transformation events as described above. Each plant was evaluated for symptoms of Fusarium infection and scored as either resistant or susceptible. Five of the transformation events produced more plants than the control that were score resistant to Fusarium. Table 7 shows the events that produced plants resistant to Fusarium and how many plants were scored resistant. The number of control plants that were scored is also listed in the table.

TABLE 7

EXAMPLE 11

Pusarium resistance is conferred by over-expression of Atlg27460

The effect of over-expression of Atlg27460 (FUR2-D) on Fusarium resistance was tested by growing T2 plants containing the CsVMV promoter driving expression of Atlg27460 from 20 independent transformation events as described above. Each plant was evaluated for symptoms of Fusarium infection and scored as either resistant or susceptible.

Six of the transformation events produced more plants than the control that were score resistant to Fusarium. Table 8 shows the events that produced plants resistant to Fusarium and how many plants were scored resistant. The number of control plants that were scored is also listed in the table.

TABLE 8

EXAMPLE 12

Fusarium resistance is conferred by over-expression of At5gl 2210 The effect of over-expression of At5gl2210 (FUR3-A) on Fusarium resistance was tested by growing T2 plants containing the CsVMV promoter driving expression of At5gl2210 from 20 independent transformation events in two separate experiments as described above. Each plant was evaluated for symptoms of Fusarium infection and scored as either resistant or susceptible. Five of the transformation events produced more plants than the control that were score resistant to Fusarium in both experiments. Table 9 shows the events that produced plants resistant to Fusarium and how many plants were scored resistant. The number of control plants that were scored is also listed in the table.

TABLE 9

EXAMPLE 13

Fusarium resistance is conferred by over-expression of At5gl2230 ,

The effect of over-expression of At5gl2230 (FUR3-C) on Fusarium resistance was tested by growing T2 plants containing the CsVMV promoter driving expression of At5gl2230 from 20 independent transformation events as described above. Each plant was evaluated for symptoms of Fusarium infection and scored as either resistant or susceptible. Three of the transformation events produced more plants than the control that were score resistant to Fusarium. Table 10 shows the events that produced plants resistant to Fusarium and how many plants were scored resistant. The number of control plants that were scored is also listed in the table.

TABLE l O

EXAMPLE 14

Fusarium resistance is conferred by over-expression of At5gl 2235

The effect of over-expression of At5gl2235 (FUR3-D) on Fusarium resistance was tested by growing T2 plants containing the CsVMV promoter driving expression of At5gl2235 from 20 independent transformation events as described above. Each plant was evaluated for symptoms of Fusarium infection and scored as either resistant or susceptible. Ten of the transformation events produced more plants than the control that were score resistant to Fusarium. Table 1 1 shows the events that produced plants resistant to Fusarium and how many plants were scored resistant. The number of control plants that were scored is also listed in the table.

EXAMPLE 15

Fusarium resistance is conferred by over-expression of At5gO3180

The effect of over-expression of At5g03180 (FUR4-C) on Fusarium resistance was tested by growing T2 plants containing the CsVMV promoter driving expression of At5gO3180 from 20 independent transformation events as described above. Each plant was evaluated for symptoms of Fusarium infection and scored as either resistant or susceptible. Eleven of the transformation events produced more plants than the control that were score resistant to Fusarium. Table 12 shows the events that produced plants resistant to Fusarium and how many plants were scored resistant. The number of control plants that were scored is also listed in the table. '

TABLE 12

EXAMPLE 16

Fusarium resistance is conferred by over-expression of At5gO3190

The effect of over-expression of At5g03190 (FUR4-D) on Fusarium resistance was tested by growing T2 plants containing the CsVMV promoter driving expression of At5g03190 from 20 independent transformation events as described above. Each plant was evaluated for symptoms of Fusarium infection and scored as either resistant or susceptible. Fourteen of the transformation events produced more plants than the control that were score resistant to Fusarium. Table 13 shows the events that produced plants resistant to Fusarium and how many plants were scored resistant. The number of control plants that were scored is also listed in the table.

TABLE 13

EXAMPLE 17

Fusarium resistance is conferred by over-expression of At3g22080

The effect of over-expression of At3g22080 (FUR5-A) on Fusarium resistance was tested by growing T2 plants containing the CsVMV promoter driving expression of

At3g22080 from 20 independent transformation events as described above. Each plant was evaluated for symptoms of Fusarium infection and scored as either resistant or susceptible. Four of the transformation events produced more plants than the control that were score resistant to Fusarium. Table 14 shows the events that produced plants resistant to Fusarium and how many plants were scored resistant. The number of control plants that were scored is also listed in the table.

TABLE 14

EXAMPLE 18

Fusarium resistance is conferred by over-expression of At3g22090

The effect of over-expression of At3g22090 (FUR5-B) on Fusarium resistance was tested by growing T2 plants containing the CsVMV promoter driving expression of At3g22090 from 20 independent transformation events as described above. Each plant was evaluated for symptoms of Fusarium infection and scored as either resistant or susceptible. Eleven of the transformation events produced more plants than the control that were score resistant to Fusarium. Table 15 shows the events that produced plants resistant to Fusarium and how many plants were scored resistant. The number of control plants that were scored is also listed in the table.

TABLE 15

EXAMPLE 19 ' Fusarium resistance is conferred by over-expression of At3g22120

The effect of over-expression of At3g22120 (FUR5-D) on Fusarium resistance was tested by growing T2 plants containing the CsVMV promoter driving expression of At3g22120 from 20 independent transformation events as described above. Each plant was evaluated for symptoms of Fusarium infection and scored as either resistant or susceptible. Six of the transformation events produced more plants than the control that were score resistant to Fusarium. Table 16 shows the events that produced plants resistant to Fusarium and how many plants were scored resistant. The number of control plants that were scored is also listed in the table.

TABLE 16

EXAMPLE 20

Fusarium resistance is conferred by over-expression of At2g44100

The effect of over-expression of At2g44100 (FURl 003) on Fusarium resistance was tested by growing T2 plants containing the CsVMV promoter driving expression of At2g44100 from 20 independent transformation events in two separate experiments as described above. Each plant was evaluated for symptoms of Fusarium infection and scored as either resistant or susceptible. Five of the transformation events produced more plants

than the control that were score resistant to Fusarium in both experiments. Table 17 shows the events that produced plants resistant to Fusarium and how many plants were scored resistant. The number of control plants that were scored is also listed in the table.

TABLE 17

EXAMPLE 21 ^• i

Fusarium resistance is conferred by over-expression of At4g35090

The effect of over-expression of At4g35090 (FURl 007) on Fusarium resistance was tested by growing T2 plants containing the CsVMV promoter driving expression of

At4g35090 from 20 independent transformation events as described above. Each plant was evaluated for symptoms of Fusarium infection and scored as either resistant or susceptible.

Seven of the transformation events produced more plants than the control that were score resistant to Fusarium. Table 18 shows the events that produced plants resistant to Fusarium and how many plants were scored resistant. The number of control plants that were scored is also listed in the table.

TABLE 18

EXAMPLE 22

Fusarium resistance is conferred by over-expression of At3g45300

The effect of over-expression of At3g45300 (FURl 009) on Fusarium resistance was tested by growing T2 plants containing the CsVMY promoter driving expression of At3g45300 from 20 independent transformation events in two separate experiments as described above. Each plant was evaluated for symptoms of Fusarium infection and scored as either resistant or susceptible. Six of the transformation events produced more plants than the control that were score resistant to Fusarium in both experiments. Table 19 shows the events that produced plants resistant to Fusarium and how many plants were scored resistant. The number of control plants that were scored is also listed in the table.

TABLE 19

EXAMPLE 23

Fusarium resistance is conferred by over-expression of At3g26100

The effect of over-expression of At3g26100 (FURlOl 1) on Fusarium resistance was tested by growing T2 plants containing the CsVMV promoter driving expression of At3g26100 from 20 independent transformation events in two separate experiments as described above. Each plant was evaluated for symptoms of Fusarium infection and scored as either resistant or susceptible. Four of the transformation events produced more plants

than the control that were score resistant to Fusarium in both experiments. Table 20 shows the events that produced plants resistant to Fusarium and how many plants were scored resistant. The number of control plants that were scored is also listed in the table.

TABLE 20

EXAMPLE 24

Fusarium resistance is conferred by over-expression of At2g36320

The effect of over-expression of At2g36320 (FURlOOl) on Fusarium resistance was tested by growing T2 plants containing the CsVMV promoter driving expression of

At2g36320 from 20 independent transformation events as described above. Each plant was evaluated for symptoms of Fusarium infection and scored as either resistant or susceptible.

Seven of the transformation events produced more plants than the control that were score resistant to Fusarium. Table 21 shows the events that produced plants resistant to Fusarium and how many plants were scored resistant. The number of control plants that were scored is also listed in the table.

TABLE 21