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1. (WO2018187796) METHODS FOR INCREASING RESISTANCE TO COTTON BACTERIAL BLIGHT AND PLANTS PRODUCED THEREBY
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What Is Claimed Is:

1. A transgenic cotton plant resistant to infection by, or damage from, a cotton pathogen selected from the group consisting of a bacterial pathogen, a fungal pathogen, a viral pathogen, and a oomycete pathogen,

wherein the genome of cells of the transgenic cotton plant comprises one or more pathogen susceptibility genes.

2. The transgenic cotton plant of claim 1, wherein the infection by, or damage from, the cotton pathogen is reduced within a range of from about 50%, from about 60%>, from about 70%, from about 80%, from about 90%, or from about 95%, to about 100%, compared to the extent of infection by, or damage from, the cotton pathogen within an otherwise identical control cotton plant grown under the same conditions as the transgenic cotton plant.

3. The transgenic cotton plant of claim 1 or 2, wherein the reduced infection by, or damage from, the cotton pathogen comprises one or more plant characteristics selected from yield, growth, development, boll formation, boll rot, seed set, seedling pre-emergent damping-off, seedling post-emergent damping-off, black arm on petioles, black arm on stems, water-soaked spots on leaves, water-soaked spots on bracts, angular-shaped lesions on leaves, coalesced angular-shaped lesions on leaves, systemic vein infection, wilting, root rot, decreased photosynthetic activity and/or stunted growth.

4. The transgenic cotton plant of any one of claims 1 to 3, wherein the genome of cells thereof comprises one or more nucleotide sequences having at least about 80%>, about 85%, about 90%, about 91%, about 92%, about 93%, about 94%, about 95%, about 96%, about 97%), about 98%>, about 99%>, or 100%> sequence identity to one or more nucleotide sequences selected from SEQ ID NO: l, SEQ ID NO:3, SEQ ID NO:5, and SEQ ID NO:28,

wherein each of the nucleotide sequences comprises a transcription activator-like effector binding element to which a cognate transcriptional activator-like effector binds, and

wherein the nucleotide sequence of the transcription activator-like effector binding element is modified.

5. The transgenic cotton plant of claim 4, wherein the modification comprises insertion of nucleotides and/or deletion of nucleotides and/or substitution of nucleotides and/or modification of nucleotides within the nucleotide sequence of the transcription activatorlike effector binding element.

6. The transgenic cotton plant of claim 4 or 5, wherein the transcription activator-like

effector binding element modification results in reduced binding of the cognate transcription activator-like effector to the transcription activator-like effector binding element.

7. The transgenic cotton plant of any one of claims 4 to 6, wherein the binding of the

cognate transcription activator-like effector is reduced by about 10%, about 20%, about 30%, about 40%, about 50%, about 60%, about 70%, about 80%, about 90%, about 95%, or about 100% compared to binding thereof in the unmodified transcription activator-like effector binding element.

8. The transgenic cotton plant of any one of claims 1 to 7, wherein the expression of one or more pathogen susceptibility genes, comprising a nucleotide sequence having at least about 80%, about 85%, about 90%, about 91%, about 92%, about 93%, about 94%, about 95%, about 96%, about 97%, about 98%, about 99%, or 100% sequence identity to one or more nucleotide sequences selected from SEQ ID NO:2, SEQ ID NO: 4, SEQ ID NO:6, SEQ ID NO:7, SEQ ID NO:8, and SEQ ID NO:29, is reduced compared to the expression of the one or more corresponding pathogen susceptibility genes in an otherwise identical control cotton plant grown under the same conditions as the transgenic cotton plant.

9. The transgenic cotton plant of claim 8, wherein the expression of the one or more

pathogen susceptibility genes is reduced by about 10%, about 20%, about 30%, about 40%, about 50%, about 60%, about 70%, about 80%, about 90%, about 95%, or about 100%) compared to the expression of the corresponding pathogen susceptibility gene in an otherwise identical control cotton plant grown under the same conditions as the transgenic cotton plant.

10. The transgenic cotton plant of any one of claims 1 to 9, which further exhibits insect resistance, and/or fungal resistance, and/or herbicide resistance.

11. The transgenic cotton plant of any one of claims 1 to 10, wherein plant growth,

development, reproduction, and boll formation are normal or near normal compared to

plant growth, development, reproduction, and boll formation in an otherwise identical control cotton plant grown under the same conditions as the transgenic cotton plant.

12. A method of making a transgenic cotton plant resistant to infection by, or damage from, a cotton pathogen selected from the group consisting of a bacterial pathogen, a fungal pathogen, a viral pathogen, and a oomycete pathogen, the method comprising reducing the expression of one or more pathogen susceptibility genes present within the genome of cells of the cotton plant.

13. The method of claim 12, wherein reducing the expression of one of more pathogen

susceptibility genes comprises modifying a nucleotide sequence comprising a

transcription activator-like effector binding element of a nucleotide sequence of one or more pathogen susceptibility genes present within the genome of cells of the cotton plant, wherein the binding of a cognate transcription activator-like effector is reduced compared to binding thereof in the nucleotide sequence of the unmodified transcription activator-like effector binding element present in the nucleotide sequence of a pathogen susceptibility gene present within the genome of cells of the cotton plant.

14. The method of claim 13, wherein the modification comprises insertion of nucleotides, and/or deletion of nucleotides and/or substitution of nucleotides and/or modification of nucleotides within the nucleotide sequence of the transcription activator-like effector binding element.

15. The method of claim 13 or 14, wherein the binding of the transcription activator-like effector is reduced by about 10%, about 20%, about 30%, about 40%, about 50%, about 60%, about 70%, about 80%, about 90%, about 95%, or about 100% compared to the binding thereof in the unmodified transcription activator-like effector binding element nucleotide sequence.

16. The method of any one of claims 13 to 15, wherein the nucleotide sequence comprising the transcription activator-like effector binding element is at least about 80%, about 85%, about 90%, about 91%, about 92%, about 93%, about 94%, about 95%, about 96%, about 97%), about 98%), about 99%, or 100% identical to one or more nucleotide sequences selected from SEQ ID NO: l, SEQ ID NO:3, SEQ ID NO:5, and SEQ ID NO:28.

17. The method of any one of claims 12 to 16, wherein the expression of one or more

pathogen susceptibility genes, comprising a nucleotide sequence having at least about 80%, about 85%, about 90%, about 91%, about 92%, about 93%, about 94%, about 95%, about 96%), about 97%, about 98%>, about 99%, or 100%> sequence identity to one or more sequences selected from SEQ ID NO:2, SEQ ID NO: 4, SEQ ID NO:6, SEQ ID NO:7, SEQ ID NO:8 and SEQ ID NO:29, is reduced compared to the expression of the corresponding one or more pathogen susceptibility genes in an otherwise identical control cotton plant grown under the same conditions as the transgenic cotton plant.

18. The method of any one of claims 12 to 17, wherein the extent of infection by, or damage from, the cotton pathogen is reduced within a range of from about 50%, from about 60%>, from about 70%, from about 80%, from about 90%, or from about 95%, to about 100%), compared to the extent of infection by, or damage from, the cotton pathogen within an otherwise identical control cotton plant grown under the same conditions as the transgenic cotton plant.

19. The method of claim 18, wherein the parameters of reduced infection by, or damage from, comprise one or more plant characteristics selected from yield, growth,

development, boll formation, boll rot, seed set, seedling pre-emergent damping-off, seedling post-emergent damping-off, black arm on petioles, black arm on stems, water- soaked spots on leaves, water-soaked spots on bracts, angular-shaped lesions on leaves, coalesced angular-shaped lesions on leaves, systemic vein infection, wilting, root rot, decreased photosynthetic activity and/or stunted growth.

20. A transgenic cotton plant resistant to infection by, or damage from, a cotton pathogen selected from the group consisting of a bacterial pathogen, a fungal pathogen, a viral pathogen, and a oomycete pathogen made by the method of any one of claims 12 to 19.

21. The transgenic cotton plant of claim 20, wherein plant growth, development,

reproduction, and boll formation are normal or near normal compared to plant growth, development, reproduction, and boll formation in an otherwise identical control cotton plant grown under the same conditions as the transgenic cotton plant.

22. A nucleotide sequence, comprising a first nucleotide sequence having at least about 80%, about 85%, about 90%, about 91%, about 92%, about 93%, about 94%, about 95%, about 96%, about 97%, about 98%, about 99%, or 100% sequence identity to SEQ ID NO:2, SEQ ID NO:4, SEQ ID NO:6, SEQ ID NO:7, SEQ ID NO:8, or SEQ ID NO:29.

23. The nucleotide sequence of claim 22, further comprising a second nucleotide sequence operably linked upstream of the first nucleotide sequence, wherein the second nucleotide sequence is at least about 80%, about 85%, about 90%, about 91%, about 92%, about 93%, about 94%, about 95%, about 96%, about 97%, about 98%, about 99%, or 100% sequence identical to SEQ ID NO: l, SEQ ID NO:3, SEQ ID NO:5, or SEQ ID NO:28.

24. The nucleotide sequence of claim 22, further comprising a second nucleotide sequence operably linked upstream of the first nucleotide sequence, wherein the second nucleotide sequence is at least about 80%, about 85%, about 90%, about 91%, about 92%, about 93%, about 94%, about 95%, about 96%, about 97%, about 98%, about 99%, or 100% sequence identical to SEQ ID NO: 11, SEQ ID NO: 14, SEQ ID NO: 15, SEQ ID NO: 18, SEQ ID NO:21, SEQ ID NO:24 or SEQ ID NO:27.

25. The nucleotide sequence of claim 23 or 24, wherein the second nucleotide sequence

comprises a modified transcription activator-like effector binding element nucleotide sequence to which a cognate transcription activator-like effector binds in a reduced amount compared to the binding of the cognate transcription activator-like effector to the unmodified transcription activator-like effector binding element nucleotide sequence.

26. The nucleotide sequence of claim 25, wherein the binding of the cognate transcription activator-like effector is reduced by about 10%, about 20%, about 30%, about 40%, about 50%, about 60%, about 70%, about 80%, about 90%, about 95%, or about 100% compared to the binding thereof in the unmodified transcription activator-like effector binding element nucleotide sequence.

27. The nucleotide sequence of any one of claims 23 to 26, wherein the second nucleotide sequence comprises an intact TATAAA box and/or wherein the second nucleotide sequence is operably linked to an intact TATAAA box.

28. The nucleotide sequence of any one of claims 25 to 27, wherein the modified

transcription activator-like effector binding element nucleotide sequence imparts resistance to a cotton pathogen selected from the group consisting of a bacterial pathogen, a fungal pathogen, a viral pathogen, and a oomycete pathogen when it is present in cells of a transgenic cotton plant, while still permitting normal, or near normal, plant growth, development, reproduction, and boll formation.

29. A transgenic cotton plant, cells of which comprise within their genome one or more nucleotide sequences of any one of claims 25 to 28.

30. The transgenic cotton plant of claim 29, wherein plant growth, development,

reproduction, and boll formation are normal or near normal compared to plant growth, development, reproduction, and boll formation in an otherwise identical control cotton plant grown under the same conditions as the transgenic cotton plant.

31. A recombinant vector or recombinant construct, comprising one or more nucleotide sequences of any one of claims 22 to 28.

32. A part, product obtained from, material from, progeny, or derivative of the transgenic cotton plant of any one of claims 1-11, 20, 21, 29, or 30, or part, product obtained from, material from, progeny, or derivative of a transgenic cotton plant made by the method of any one of claims 12 to 19.

33. The plant part of claim 32, which is selected from among a protoplast, a cell, a tissue, an organ, a cutting, an explant, a reproductive tissue, a vegetative tissue, a biomass, fiber, an inflorescence, a flower, a sepal, a petal, a pistil, a stigma, a style, an ovary, an ovule, an embryo, a receptacle, a seed, a fruit, a stamen, a filament, an anther, a male or female gametophyte, a pollen grain, a meristem, a terminal bud, an axillary bud, a leaf, a stem, a root, an offset, a cell of said plant in culture, a tissue of said plant in culture, an organ of said plant in culture, a homogenate, and a callus.

34. The progeny or derivative of claim 32, which is selected from among clones, hybrids, samples, seeds, and harvested material thereof.

35. The progeny or derivative of claim 32 or 34, which is produced sexually or asexually.

36. A consumer or industrial product obtained from, or produced from, a transgenic cotton plant or progeny of any one of claims 1-11, 20, 21, 29, 30, 34 or 35, or a transgenic cotton plant made by the method of any one of claims 12 to 19.

37. The transgenic cotton plant or progeny of any one of claims 1-11, 20, 21, 29, 30, 34 or 35, or a transgenic cotton plant made by the method of any one of claims 12 to 19, wherein the infection by, or damage from, a cotton pathogen is cotton bacterial blight caused by a species of Xanthomonas.

38. The transgenic cotton plant or progeny of claim 37, wherein the species of Xanthomonas is Xanthomonas citripv. malvacearum.

The transgenic cotton plant or progeny of claim 37 or 38, wherein the species of Xanthomonas is Xanthomonas citri pv. malvacearum Race 18.