Genes for modifying plant traits xi

• US 20030188330A1
• Filed: 03/18/2002
• Published: 10/02/2003
• Est. Priority Date: 03/18/2002
• Status: Abandoned Application

• Current Assignee: Mendel Biotechnology, Inc. (KOCH Industries Incorporated)
• Original Assignee: Mendel Biotechnology, Inc. (KOCH Industries Incorporated)
• Inventors: Heard, Jacqueline
• Application Number:
  US10/112,887
• Publication Number:
  US 20030188330A1
• Time in Patent Office: Days
• US Class Current: 800/278
• CPC Class Codes: C07K 14/415 from plants
• CPC Class Codes: C12N 15/8214 Plastid transformation
• CPC Class Codes: C12N 15/8216 Methods for controlling, regulating or enhancing expression of transgenes in plant cells
• CPC Class Codes: C12N 15/8247 involving modified lipid metabolism, e.g. seed oil composition
• CPC Class Codes: C12N 15/8251 Amino acid content, e.g. synthetic storage proteins, altering amino acid biosynthesis
• CPC Class Codes: C12N 15/8261 with agronomic (input) traits, e.g. crop yield
• CPC Class Codes: C12N 15/8267 Seed dormancy, germination or sprouting
• CPC Class Codes: C12N 15/8271 for stress resistance, e.g. heavy metal resistance
• CPC Class Codes: C12N 15/8273 for drought, cold, salt resistance
• CPC Class Codes: C12N 15/8282 for fungal resistance
• CPC Class Codes: Y02A 40/146 Genetically Modified [GMO] plants, e.g. transgenic plants

Abstract

The invention relates to plant transcription factor polypeptides, polynucleotides that encode them, homologs and orthologs from a variety of plant species, and methods of using the polynucleotides and polypeptides to produce transgenic plants having advantageous properties compared to a reference plant. Sequence information related to these polynucleotides and polypeptides can also be used in bioinformatic search methods and is also disclosed.

Claims

1. A transgenic plant comprising a recombinant polynucleotide having a nucleotide sequence selected from the group consisting of:

(a) a nucleotide sequence encoding a polypeptide comprising a sequence selected from those of SEQ ID NOs;

2, 4, or a complementary nucleotide sequence thereof;

(b) a nucleotide sequence encoding a polypeptide comprising a conservatively substituted variant of a polypeptide of (a);

(c) one of SEQ ID NOs;

1, 3, or a complementary nucleotide sequence thereof;

(d) a nucleotide sequence comprising silent substitutions in a nucleotide sequence of (c);

(e) a nucleotide sequence which hybridizes under stringent conditions to a nucleotide sequence of one or more of;

(a), (b), (c), or (d);

(f) a nucleotide sequence comprising at least 15 consecutive nucleotides outside of a conserved domain of any of (a)-(e);

(g) a nucleotide sequence comprising a subsequence or fragment of any of (a)-(f), which subsequence or fragment encodes a polypeptide that modifies a plant'"'"'s trait;

(h) a nucleotide sequence having at least 31% sequence identity to a nucleotide sequence of any of (a)-(g);

(i) a nucleotide sequence having at least 60% sequence identity to a nucleotide sequence of any of (a)-(g);

(j) a nucleotide sequence having at least 95% sequence identity to a nucleotide sequence of any of (a)-(g);

(k) a nucleotide sequence which encodes a polypeptide having at least 31% sequence identity outside of a conserved domain of a polypeptide of SEQ ID NOs;

2 or 4;

(l) a nucleotide sequence which encodes a polypeptide having at least 60% sequence identity outside of a conserved domain of a polypeptide of SEQ ID NOs;

2 or 4;

(m) a nucleotide sequence which encodes a polypeptide having at least 75% sequence identity outside of a conserved domain of a polypeptide of SEQ ID NOs;

2 or 4;

(n) a nucleotide sequence which encodes a polypeptide having at least 95% sequence identity outside of a conserved domain of a polypeptide of SEQ ID NOs;

2 or 4;

(o) a nucleotide sequence encoding a polypeptide having an amino acid domain with at least 86% sequence identity to a conserved domain of a polypeptide of SEQ ID NOs;

2 or 4;

(p) a nucleotide sequence encoding a polypeptide having an amino acid domain with at least about 90% sequence identity to a conserved domain of a polypeptide of SEQ ID NOs;

2 or 4;

(q) a nucleotide sequence encoding a polypeptide having an amino acid domain with at least about 95% sequence identity to a conserved domain of a polypeptide of SEQ ID NOs;

2 or 4;

(r) a nucleotide sequence encoding a polypeptide having an amino acid domain with at least about 98% sequence identity to a conserved domain of a polypeptide of SEQ ID NOs;

2 or 4;

(s) a nucleotide sequence which encodes a polypeptide having at least 31% sequence identity over the entire length of a polypeptide of SEQ ID NOs;

2 or 4;

(t) a nucleotide sequence which encodes a polypeptide having at least 60% sequence identity over the entire length of a polypeptide of SEQ ID NOs;

2 or 4;

(u) a nucleotide sequence which encodes a polypeptide having at least 75% sequence identity over the entire length of a polypeptide of SEQ ID NOs;

2 or 4; and

(v) a nucleotide sequence which encodes a polypeptide having at least 95% sequence identity over the entire length of a polypeptide of SEQ ID NOs;

2 or 4;

wherein the plant possesses an altered trait as compared to a wild type plant, or the plant exhibits an altered phenotype as compared to a wild type plant, or the plant expresses an altered level of one or more genes associated with a plant trait as compared to a wild type plant.

2. The transgenic plant of claim 1, further comprising a constitutive, inducible, or tissue-specific promoter operably linked to said nucleotide sequence.

3. The transgenic plant of claim 1, wherein the plant is selected from the group consisting of:

soybean, wheat, corn, potato, cotton, rice, oilseed rape, sunflower, alfalfa, sugarcane, turf, banana, blackberry, blueberry, strawberry, raspberry, cantaloupe, carrot, cauliflower, coffee, cucumber, eggplant, grapes, honeydew, lettuce, mango, melon, onion, papaya, peas, peppers, pineapple, pumpkin, spinach, squash, sweet corn, tobacco, tomato, watermelon, mint and other labiates, rosaceous fruits, and vegetable brassicas.

8. The transgenic plant of claim 1, wherein the trait is selected from the group consisting of:

enhanced tolerance to freezing, chilling, heat, drought, water saturation, radiation and ozone;

improved tolerance to microbial, fungal or viral diseases;

improved tolerance to pest infestations, decreased herbicide sensitivity;

improved tolerance of heavy metals or enhanced ability to take up heavy metals;

improved growth under poor photoconditions.

9. The transgenic plant of claim 1, wherein the trait is an alteration in the level of one or more of the compounds selected from the group consisting of:

taxol, tocopherol, tocotrienol, sterols, phytosterols, vitamins, wax monomers, anti-oxidants, amino acids, lignins, cellulose, tannins, prenyllipids, glucosinolates, and terpenoids.

10. The transgenic plant of claim 1, wherein the trait is an alteration in one or more physical characteristics selected from the group consisting of:

the number of trichomes, fruit and seed size and number, yield of stems, leaves, or roots, stability of seeds during storage, susceptibility of the seed to shattering, root hair length and quantity, internode distances, or the quality of seed coat.

11. The transgenic plant of claim 1, wherein the trait is an alteration in a plant growth characteristic selected from the group consisting of:

growth rate, germination rate of seeds, vigor of plants and seedlings, leaf and flower senescence, male sterility, apomixis, flowering time, flower abscission, rate of nitrogen uptake, biomass or transpiration characteristics, apical dominance, branching patterns, number of organs, organ identity, and organ shape or size.

12. The transgenic plant of claim 1, wherein the trait is an alteration in one or more characteristics selected from the group consisting of protein or oil production, seed protein or oil production, insoluble sugar level, soluble sugar level, and starch composition.

4. An isolated or recombinant polynucleotide comprising a nucleotide sequence selected from the group consisting of:

(a) a nucleotide sequence encoding a polypeptide comprising a sequence selected from those of SEQ ID NOs;

2, 4, or a complementary nucleotide sequence thereof;

(b) a nucleotide sequence encoding a polypeptide comprising a conservatively substituted variant of a polypeptide of (a);

(c) one of SEQ ID NOs;

1, 3, or a complementary nucleotide sequence thereof;

(d) a nucleotide sequence comprising silent substitutions in a nucleotide sequence of (c);

(e) a nucleotide sequence which hybridizes under stringent conditions to a nucleotide sequence of one or more of;

(a), (b), (c), or (d);

(f) a nucleotide sequence comprising at least 15 consecutive nucleotides outside of a conserved domain of any of (a)-(e);

(g) a nucleotide sequence comprising a subsequence or fragment of any of (a)-(f), which subsequence or fragment encodes a polypeptide that modifies a plant'"'"'s trait;

(h) a nucleotide sequence having at least 31% sequence identity to a nucleotide sequence of any of (a)-(g);

(i) a nucleotide sequence having at least 60% sequence identity to a nucleotide sequence of any of (a)-(g);

(j) a nucleotide sequence having at least 95% sequence identity to a nucleotide sequence of any of (a)-(g);

(k) a nucleotide sequence which encodes a polypeptide having at least 31% sequence identity outside of a conserved domain of a polypeptide of SEQ ID NOs;

2 or 4;

(l) a nucleotide sequence which encodes a polypeptide having at least 60% sequence identity outside of a conserved domain of a polypeptide of SEQ ID NOs;

2 or 4;

(m) a nucleotide sequence which encodes a polypeptide having at least 75% sequence identity outside of a conserved domain of a polypeptide of SEQ ID NOs;

2 or 4;

(n) a nucleotide sequence which encodes a polypeptide having at least 95% sequence identity outside of a conserved domain of a polypeptide of SEQ ID NOs;

2 or 4;

(o) a nucleotide sequence encoding a polypeptide having an amino acid domain with at least 86% sequence identity to a conserved domain of a polypeptide of SEQ ID NOs;

2 or 4;

(p) a nucleotide sequence encoding a polypeptide having an amino acid domain with at least about 90% sequence identity to a conserved domain of a polypeptide of SEQ ID NOs;

2 or 4;

(q) a nucleotide sequence encoding a polypeptide having an amino acid domain with at least about 95% sequence identity to a conserved domain of a polypeptide of SEQ ID NOs;

2 or 4;

(r) a nucleotide sequence encoding a polypeptide having an amino acid domain with at least about 98% sequence identity to a conserved domain of a polypeptide of SEQ ID NOs;

2 or 4;

(s) a nucleotide sequence which encodes a polypeptide having at least 31% sequence identity over the entire length of a polypeptide of SEQ ID NOs;

2 or 4;

(t) a nucleotide sequence which encodes a polypeptide having at least 60% sequence identity over the entire length of a polypeptide of SEQ ID NOs;

2 or 4;

(u) a nucleotide sequence which encodes a polypeptide having at least 75% sequence identity over the entire length of a polypeptide of SEQ ID NOs;

2 or 4; and

(v) a nucleotide sequence which encodes a polypeptide having at least 95% sequence identity over the entire length of a polypeptide of SEQ ID NOs;

2 or 4.

5. The isolated or recombinant polynucleotide of claim 4, further comprising a constitutive, inducible, or tissue-specific promoter operably linked to the nucleotide sequence.

6. An isolated or recombinant polypeptide comprising a subsequence of at least about 15 contiguous amino acids encoded by the recombinant or isolated polynucleotide of claim 4.

7. A method of using the isolated or recombinant polynucleotide of claim 4 for producing a plant having a modified trait, the method comprising selecting a polynucleotide that encodes a polypeptide, inserting the polynucleotide into an expression vector, introducing the vector into a plant or a cell of a plant to overexpress the polypeptide, thereby producing a modified plant, and selecting for a modified trait.

13. The method of claim 7, wherein the trait is selected from the group consisting of:

enhanced tolerance to freezing, chilling, heat, drought, water saturation, radiation and ozone;

improved tolerance to microbial, fungal or viral diseases;

improved tolerance to pest infestations, decreased herbicide sensitivity;

improved tolerance of heavy metals or enhanced ability to take up heavy metals, improved growth under poor photoconditions.

14. The method of claim 7, wherein the trait is an alteration in the level of one or more of the compounds selected from the group consisting of:

taxol, tocopherol, tocotrienol, sterols, phytosterols, vitamins, wax monomers, anti-oxidants, amino acids, lignins, cellulose, tannins, prenyllipids, glucosinolates, and terpenoids.

15. The method of claim 7, wherein the trait is an alteration in one or more physical characteristics selected from the group consisting of:

the number of trichomes, fruit and seed size and number, yield of stems, leaves, or roots, stability of seeds during storage, susceptibility of the seed to shattering, root hair length and quantity, internode distances, or the quality of seed coat.

16. The method of claim 7, wherein the trait is an alteration in a plant growth characteristic selected from the group consisting of:

growth rate, germination rate of seeds, vigor of plants and seedlings, leaf and flower senescence, male sterility, apomixis, flowering time, flower abscission, rate of nitrogen uptake, biomass or transpiration characteristics, apical dominance, branching patterns, number of organs, organ identity, and organ shape or size.

17. The method of claim 7, wherein the trait is an alteration in one or more characteristics selected from the group consisting of protein or oil production, seed protein or oil production, insoluble sugar level, soluble sugar level, and starch composition.

18. A plant produced by the method of claim 13.

19. A plant produced by the method of claim 14.

20. A plant produced by the method of claim 15.

21. A plant produced by the method of claim 16.

22. A plant produced by the method of claim 17.

23. A method of using the isolated or recombinant polynucleotide of claim 4 for producing a plant having a modified trait, the method comprising selecting a polynucleotide that when expressed produces an antisense nucleic acid sequence, inserting the polynucleotide into an expression vector, introducing the vector into a plant or a cell of a plant to express the antisense nucleic acid, thereby producing a modified plant, and selecting for a modified trait.

24. The method of claim 23, wherein the trait is selected from the group consisting of:

enhanced tolerance to freezing, chilling, heat, drought, water saturation, radiation and ozone;

improved tolerance to microbial, fungal or viral diseases;

improved tolerance to pest infestations, decreased herbicide sensitivity;

improved tolerance of heavy metals or enhanced ability to take up heavy metals, improved growth under poor photoconditions.

25. The method of claim 23, wherein the trait is an alteration in the level of one or more of the compounds selected from the group consisting of:

taxol, tocopherol, tocotrienol, sterols, phytosterols, vitamins, wax monomers, anti-oxidants, amino acids, lignins, cellulose, tannins, prenyllipids, glucosinolates, and terpenoids.

26. The method of claim 23, wherein the trait is an alteration in one or more physical characteristics selected from the group consisting of:

the number of trichomes, fruit and seed size and number, yield of stems, leaves, or roots, stability of seeds during storage, susceptibility of the seed to shattering, root hair length and quantity, internode distances, or the quality of seed coat.

27. The method of claim 23, wherein the trait is an alteration in a plant growth characteristic selected from the group consisting of:

growth rate, germination rate of seeds, vigor of plants and seedlings, leaf and flower senescence, male sterility, apomixis, flowering time, flower abscission, rate of nitrogen uptake, biomass or transpiration characteristics, apical dominance, branching patterns, number of organs, organ identity, and organ shape or size.

28. The method of claim 23, wherein the trait is an alteration in one or more characteristics selected from the group consisting of protein or oil production, seed protein or oil production, insoluble sugar level, soluble sugar level, and starch composition.

29. A plant produced by the method of claim 24.

30. A plant produced by the method of claim 25.

31. A plant produced by the method of claim 26.

32. A plant produced by the method of claim 27.

33. A plant produced by the method of claim 28.

34. An isolated or recombinant polypeptide comprising a subsequence of at least about 10 contiguous amino acids encoded by the recombinant or isolated polynucleotide of claim 4, wherein the contiguous amino acids are outside of a conserved domain.

35. An isolated or recombinant polypeptide comprising a subsequence of at least about 20 contiguous amino acids encoded by the recombinant or isolated polynucleotide of claim 4, wherein the contiguous amino acids are outside of a conserved domain.

36. An isolated or recombinant polypeptide comprising a subsequence of at least about 30 contiguous amino acids encoded by the recombinant or isolated polynucleotide of claim 4, wherein the contiguous amino acids are outside of a conserved domain.

37. An isolated or recombinant polypeptide comprising a subsequence of at least about 10 contiguous amino acids encoded by the recombinant or isolated polynucleotide of claim 4, wherein the contiguous amino acids are within a conserved domain.

38. An isolated or recombinant polypeptide comprising a subsequence of at least about 20 contiguous amino acids encoded by the recombinant or isolated polynucleotide of claim 4, wherein the contiguous amino acids are within a conserved domain.

39. An isolated or recombinant polypeptide comprising a subsequence of at least about 30 contiguous amino acids encoded by the recombinant or isolated polynucleotide of claim 4, wherein the contiguous amino acids are within a conserved domain.

40. A polypeptide having at least 31% sequence identity over the entire length of a polypeptide of SEQ ID NOs:

2 or 4, or the length of the polypeptide itself.

41. A polypeptide having at least 60% sequence identity over the entire length of a polypeptide of SEQ ID NOs:

2 or 4, or the length of the polypeptide itself.

42. A polypeptide having at least 75% sequence identity over the entire length of a polypeptide of SEQ ID NOs:

2 or 4, or the length of the polypeptide itself.

43. A polypeptide having at least 95% sequence identity over the entire length of a polypeptide of SEQ ID NOs:

2 or 4, or the length of the polypeptide itself.