CA2625371A1 - Compositions providing tolerance to multiple herbicides and methods of use thereof - Google Patents

Compositions providing tolerance to multiple herbicides and methods of use thereof Download PDF

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Publication number
CA2625371A1
CA2625371A1 CA002625371A CA2625371A CA2625371A1 CA 2625371 A1 CA2625371 A1 CA 2625371A1 CA 002625371 A CA002625371 A CA 002625371A CA 2625371 A CA2625371 A CA 2625371A CA 2625371 A1 CA2625371 A1 CA 2625371A1
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crop
glyphosate
als inhibitor
herbicide
effective amount
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CA002625371A
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CA2625371C (en
Inventor
Billy Fred Mccutchen
Linda A. Castle
Timothy K. Chicoine
Hyeon-Je Cho
Jon S. Claus
Jerry M. Green
Anthony D. Guida, Jr.
Christine B. Hazel
Matthew J. Heckert
Jeffrey M. Hegstad
James M. Hutchison
Donglong Liu
Albert L. Lu
Wayne J. Mehre
York Moy
Paul D. Olson
Kenneth A. Peeples
David W. Saunders
Mark D. Vogt
Jack Q. Wilkinson
James F. H. Wong
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Pioneer Hi Bred International Inc
EIDP Inc
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Individual
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Abstract

Methods and compositions are provided related to improved plants that are tolerant to more than one herbicide. Particularly, the invention provides plants that are tolerant of glyphosate and are tolerant to at least one ALS
inhibitor, and methods of use thereof. The glyphosate/ALS inhibitor-tolerant plants comprise a polynucleotide that encodes a polypeptide that confers tolerance to glyphosate and a polynucleotide that encodes an ALS inhibitor-tolerant polypeptide. In specific embodiments, a plant of the invention expresses a GAT polypeptide and an HRA polypeptide. Methods to control weeds, improve plant yield, and increase transformation efficiencies are provided.

Claims (84)

1. A method for controlling weeds in an area of cultivation comprising a) planting the area with crop seeds or plants which comprise i) a first polynucleotide encoding a polypeptide that can confer tolerance to glyphosate operably linked to a promoter active in said plant;
and, ii) a second polynucleotide encoding an ALS inhibitor-tolerant polypeptide operably linked to a promoter active in said plant;
b) applying to any crop, crop part, weed or area of cultivation thereof a combination of herbicides comprising at least an effective amount of a first herbicide and an effective amount of a second herbicide, wherein said combination of herbicides does not include glyphosate and wherein said effective amount of said first and said second herbicide is tolerated by the crop and controls weeds.
2. The method of claim 1, wherein said first herbicide comprises an ALS
inhibitor.
3. The method of claim 2, wherein said second herbicide comprises a second ALS inhibitor.
4. The method of claim 2 or 3, wherein said effective amount of the first ALS
inhibitor comprises about 0.1 to about 5000 g ai/hectare.
5. The method of claim 4, wherein said effective amount of the first ALS
inhibitor comprises about 0.5 to about 350 g ai/hectare or about 1 to about 150 g ai/hectare.
6. The method of claim 3, wherein said effective amount of the second ALS
inhibitor comprises about 0.1 to about 5000 g ai/hectare, about 0.5 to about 350 g ai/hectare or about 1 to about 150 g ai/hectare.
7. The method of any one of claims 1-6, wherein said first polynucleotide encodes a glyphosate-N-acetyltransferase.
8. The method of any one of claims 1-6, wherein said first polynucleotide encodes a glyphosate-tolerant 5-enolpyruvylshikimate-3-phosphate synthase or a glyphosate-tolerant glyphosate oxido-reductase.
9. The method of any one of claims 1-6, wherein said ALS inhibitor-tolerant polypeptide comprises a mutated acetolactate synthase polypeptide.
10. The method of claim 9, wherein said mutated acetolactate synthase polypeptide comprises HRA.
11. The method of any one of claims 1-10, wherein said combination of herbicides comprises an ALS inhibitor selected from the group consisting of a sulfonylurea, a triazolopyrimidine, a pyrimidinyloxy(thio)benzoate, an imidazolinone, and a sulfonylaminocarbonyltriazolinone.
12. The method of claim 11, wherein said ALS inhibitor is selected from the group consisting of:
a) Azimsulfuron;
b) Chlorimuron-ethyl;
c) Metsulfuron-methyl;
d) Nicosulfuron;
e) Rimsulfuron;
f) Sulfometuron-methyl;
g) Thifensulfuron-methyl;
h) Tribenuron-methyl;
i) Amidosulfuron;
j) Bensulfuron-methyl;
k) Chlorsulfuron;
l) Cinosulfuron;
m) Cyclosulfamuron;
n) Ethametsulfuron-methyl;
o) Ethoxysulfuron;
p) Flazasulfuron;
q) Flupyrsulfuron-methyl;

r) Foramsulfuron;
s) Imazosulfuron;
t) Iodosulfuron-methyl;
u) Mesosulfuron-methyl;
v) Oxasulfuron;
w) Primisulfuron-methyl;
x) Prosulfuron;
y) Pyrazosulfuron-ethyl;
z) Sulfosulfuron;
aa) Triasulfuron;
bb) Trifloxysulfuron;
cc) Triflusulfuron-methyl;
dd) Tritosulfuron;
ee) Halosulfuron-methyl;
ff) Flucarbazone;
gg) Procarbazone;
hh) Cloransulam-methyl;
ii) Flumetsulam;
jj) Diclosulam;
kk) Florasulam;
ll) Imazamox;
mm) Bispyribac;
nn) Pyriftalid;
oo) Pyribenzoxim;
pp) Pyrithiobac;
qq) Pyriminobac-methyl;
rr) Imazapyr;
ss) Imazethapyr;
tt) Imazaquin;
uu) Imazapic;
vv) Imazamethabenz-methyl;
ww) Imazamox;
xx) Flucetosulfuron;
yy) Metosulam;

zz) Penoxsulam; and, aaa) Pyroxsulam.
13. The method of any one of claims 1-12, wherein said combination of herbicides comprises at least a triazine or a phosphinic acid.
14. The method of any one of claims 1, 2, 4 or 7-12, wherein said second herbicide and said first herbicide have different mechanisms of action.
15. The method of any one of claims 1-13, wherein said second herbicide and said first herbicide have the same mechanism of action.
16. The method of any one of claims 1-15, wherein said combination of herbicides comprises at least an effective amount of a third herbicide.
17. The method of any one of claims 1-16, wherein said first herbicide is applied pre-emergence, post-emergence or pre- and post-emergence to the weeds or the crop; and, said second herbicide is applied pre-emergence, post-emergence or pre- or post-emergence to the weed or the crop.
18. The method of any one of claims 1-17, wherein said first and said second herbicides are applied together or are applied separately.
19. The method of any one of claims 1-17, wherein at least said first and said second herbicides comprise a homogeneous granule blend.
20. The method of any one of claims 1-19, wherein said method further comprises applying an agricultural chemical selected from the group consisting of a fungicide, a nematicide, a growth regulator, a safener, an adjuvant, an insecticide, and any combination thereof.
21. The method of claim 20, wherein said agricultural chemical is applied pre-emergence, post-emergence or pre- and post-emergence to the weed or the crop.
22. The method of any one of claims 1-21, wherein said agricultural chemical is applied together or separately with said first herbicide, said second herbicide, or said first and said second herbicide.
23. The method of any one of claims 1-22, wherein the first herbicide comprises a sulfonylurea and the second herbicide comprises an ALS inhibitor.
24. The method of any one of claims 1-22, wherein the first herbicide comprises a sulfonylurea and the second herbicide comprises an imidazolinone.
25. The method of claim 23 or 24, wherein the effective amount of said first or said second herbicide provides a safening effect.
26. The method of any one of claims 1-25, wherein at least one of said first or said second polynucleotides is operably linked to at least one copy of the enhancer sequence set forth in SEQ ID NO: 72.
27. The method of any one of claims 1-26, wherein said crop is a dicot.
28. The method of claim 27, wherein said dicot is soybean, canola, sunflower, cotton, alfalfa, an ornamental, a fruit, a vegetable, a sugar beet, or an Arabidopsis.
29. The method of any one of claims 1-26, wherein said plant is a monocot.
30. The method of claim 29, wherein said monocot is maize, wheat, rice, barley, sorghum, sugar cane, Switchgrass, or rye.
31. The method of claim 1, wherein said crop is maize and said first herbicide is applied at the V7 stage or later.
32. The method of claim 1, wherein step (b) is performed at least once prior to step (a).
33. A method for controlling weeds in an area of cultivation comprising:
a) evaluating environmental conditions in an area of cultivation;
b) selecting an effective amount of a combination of herbicides comprising at least an effective amount of a first herbicide and an effective amount of a second herbicide, wherein said combination of herbicides does not include glyphosate and wherein said effective amount of said first and said second herbicide is tolerated by a crop and controls weeds; and, c) applying the combination of herbicides to a crop, crop part, seed or an area of cultivation of said crop, wherein the crop comprises a plant having i) a first polynucleotide encoding a polypeptide that can confer tolerance to glyphosate operably linked to a promoter active in said plant;
and, ii) a second polynucleotide encoding an ALS inhibitor-tolerant polypeptide operably linked to a promoter active in said plant.
34. The method of claim 33, wherein said first herbicide comprises an ALS
inhibitor.
35. The method of claim 34, wherein said second herbicide comprises a second ALS inhibitor.
36. The method of claim 34 or 35, wherein said effective amount of the first or said second ALS inhibitor comprises about 0.1 to about 5000 g ai /hectare.
37. The method of claim 34 or 35, wherein said effective amount of the first or the second ALS inhibitor comprises about 1 to about 150 g ai/hectare.
38. The method of claim 34 or 35, wherein said effective amount of the first or the second ALS inhibitor comprises about 0.5 to about 350 g ai/hectare.
39. The method of any one of claims 33-38, wherein said first polynucleotide encodes a glyphosate-N-acetyltransferase.
40. The method of any one of claims 33-38, wherein said ALS inhibitor-tolerant polypeptide comprises a mutated acetolactate synthase polypeptide.
41. The method of claim 40, wherein said mutated acetolactate synthase polypeptide comprises HRA.
42. The method of any one of claim 33-41, wherein said herbicide combination comprises an ALS inhibitor selected from the group consisting of a sulfonylurea, a triazolopyrimidine, a pyrimidinyloxy(thio)benzoate, an imidazolinone, and a sulfonylaminocarbonyltriazolinone.
43. The method of claim 42, wherein said ALS inhibitor is selected from the group consisting of:
a) Azimsulfuron;
b) Chlorimuron-ethyl;
c) Metsulfuron-methyl;
d) Nicosulfuron;
e) Rimsulfuron;
f) Sulfometuron-methyl;
g) Thifensulfuron-methyl;
h) Tribenuron-methyl;
i) Amidosulfuron;
j) Bensulfuron-methyl;
k) Chlorsulfuron;
l) Cinosulfuron;
m) Cyclosulfamuron;
n) Ethametsulfuron-methyl;
o) Ethoxysulfuron;
p) Flazasulfuron;
q) Flupyrsulfuron-methyl;
r) Foramsulfuron;
s) Imazosulfuron;
t) Iodosulfuron-methyl;
u) Mesosulfuron-methyl;
v) Oxasulfuron;
w) Primisulfuron-methyl;

x) Prosulfuron;
y) Pyrazosulfuron-ethyl;
z) Sulfosulfuron;
aa) Triasulfuron;
bb) Trifloxysulfuron;
cc) Triflusulfuron-methyl;
dd) Tritosulfuron;
ee) Halosulfuron-methyl;
ff) Flucarbazone;
gg) Procarbazone;
hh) Cloransulam-methyl;
ii) Flumetsulam;
jj) Diclosulam;
kk) Florasulam;
ll) Imazamox;
mm) Bispyribac;
nn) Pyriftalid;
oo) Pyribenzoxim;
pp) Pyrithiobac;
qq) Pyriminobac-methyl;
rr) Imazapyr;
ss) Imazethapyr;
tt) Imazaquin;
uu) Imazapic;
vv) Imazamethabenz-methyl;
ww) Imazamox.
xx) Flucetosulfuron;
yy) Metosulam;
zz) Penoxsulam; and, aaa) Pyroxsulam.
44. The method of any one of claims 33-43, wherein said second herbicide and said first herbicide have the same or a different mechanism of action.
45. The method of any one of claims 33-44, wherein said first herbicide is applied pre-emergence, post-emergence or pre- and post-emergence to the weeds or the crop; and, said second herbicide is applied pre-emergence, post-emergence or pre- and post-emergence to the weed or the crop.
46. The method of any one of claims 33-44, wherein said first and said second herbicides are applied together or are applied separately.
47. The method of any one of claims 33-44, wherein at least said first and said second herbicides comprise a homogeneous granule blend.
48. The method of any one of claims 33-47, wherein said method further comprises applying an agricultural chemical selected from the group consisting of a fungicide, a nematicide, a growth regulator, a safener, an adjuvant, an insecticide, or any combination thereof.
49. The method of any one of claims 33-48, wherein at least one of said first or said second polynucleotides is operably linked to at least one copy of the enhancer sequence set forth in SEQ ID NO: 72.
50. The method of any one of claims 33-49, wherein said crop is a dicot.
51. The method of claim 50, wherein said dicot is soybean, canola, sunflower, cotton, alfalfa, an ornamental, a fruit, a vegetable, a sugar beet, or an Arabidopsis.
52. The method of any one of claims 33-39, wherein said plant is a monocot.
53. The method of claim 52, wherein said monocot is maize, wheat, rice, barley, sorghum, sugar cane, Switchgrass, or rye.
54. A method for controlling weeds in an area of cultivation comprising a) planting the area with crop seeds or plants which comprise i) a first polynucleotide encoding a polypeptide that can confer tolerance to glyphosate operably linked to a promoter active in a plant; and, ii) a second polynucleotide encoding an ALS inhibitor-tolerant polypeptide operably linked to a promoter active in a plant;
b) applying to the crop, crop part, weed or area of cultivation thereof a combination of herbicides comprising at least an effective amount of a first and a second ALS inhibitor, wherein i) the effective amount of the combination of herbicides controls weeds;
ii) the effective amount of the first ALS inhibitor is not tolerated by the crop when applied alone when compared to a control crop that has not been exposed to the first ALS inhibitor; and, iii) the effective amount of the second ALS inhibitor is sufficient to produce a safening effect, wherein said safening effect provides an increase in crop tolerance upon the application of the first and the second ALS inhibitor when compared to the crop tolerance when the first ALS inhibitor is applied alone.
55. The method of claim 54, wherein at least said first or said second ALS
inhibitor comprises a sulfonylurea.
56. The method of claim 54, wherein said second ALS inhibitor comprises a sulfonylurea and the first ALS inhibitor comprises an imidazolinone.
57. The method of claim 54, wherein said combination of herbicides further comprises glyphosate.
58. A method for controlling weeds in an area of cultivation comprising:
a) evaluating environmental conditions in an area of cultivation;
b) selecting a combination of herbicides comprising at least an effective amount of a first and a second ALS inhibitor, wherein said effective amount of the combination controls weeds, and the effective amount of the first ALS
inhibitor is not tolerated by the crop when applied alone when compared to a control crop that has been applied with the first ALS inhibitor, and the effective amount of the second ALS inhibitor is sufficient to produce a safening effect, wherein said safening effect provides an increase in crop tolerance upon the application of the first and the second ALS inhibitor when compared to the crop tolerance when the first ALS inhibitor is applied alone; and, c) applying the combination of herbicides to a crop, crop part, seed or an area of cultivation of said crop, wherein the crop comprises a plant having i) a first polynucleotide encoding a polypeptide that can confer tolerance to glyphosate operably linked to a promoter active in said plant;
and, ii) a second polynucleotide encoding an ALS inhibitor-tolerant polypeptide operably linked to a promoter active in said plant.
59. The method of claim 58, wherein at least said first or said second ALS
inhibitor comprises a sulfonylurea.
60. The method of claim 58, wherein said second ALS inhibitor comprises a sulfonylurea and the first ALS inhibitor comprises an imidazolinone.
61. A method for controlling weeds in an area of cultivation comprising a) planting the area with crop seeds or plants which comprise i) a first polynucleotide encoding a polypeptide that can confer tolerance to glyphosate operably linked to a promoter active in a plant; and, ii) a second polynucleotide encoding an ALS inhibitor-tolerant polypeptide operably linked to a promoter active in a plant;
b) applying to any crop, crop part, weed or area of cultivation thereof an effective amount of a combination of herbicides selected from the group consisting of:
i) the combination of herbicides comprising glyphosate, imazapyr, chlorimuron-ethyl, quizalofop, and fomesafen, wherein said effective amount is tolerated by the crop and controls weeds;
ii) the combination of herbicides comprising glyphosate, imazapyr, chlorimuron-ethyl, quizalofop, and fomesafen, wherein said effective amount is tolerated by the crop and controls weeds; or, iii) the combination of herbicides comprising glyphosate, chlorimuron-ethyl, and thifensulfuron-methyl, wherein said effective amount is tolerated by the crop and controls weeds.
62. The method of claim 61, wherein said crop is soybean, corn or cotton.
63. The method of claim 59, wherein the effective amount of the combination of herbicides of part (b)(i) comprises glyphosate comprising about 1110 to about 1130 g ai/hectare; the effective amount of imazapyr comprises about 7.5 to about 27.5 g ai/hectare;
the effective amount of chlorimuron-ethyl comprises about 7.5 to about 27.5 g ai/hectare; the effective amount of quizalofop comprises about 50 to about 70 g ai/hectare;
and, the effective amount of fomesafen comprises about 240 to about 260 g ai/hectare.
64. A plant comprising a polynucleotide encoding a polypeptide which confers tolerance to glyphosate or a polynucleotide that encodes and ALS inhibitor that encodes an ALS inhibitor-tolerant polypeptide, wherein said polynucleotide is operably linked to (a) a promoter that drives expression in the plant; and, (b) at least one copy of the enhancer sequence set forth in SEQ ID NO: 1, 72, 85, 88, or 89 or an enhancer sequence having at least 90% sequence identity to SEQ ID
NO: 1, 72, 85, 88, or 89, wherein said enhancer sequence modulates the level of transcription wherein said plant is tolerant to glyphosate or an ALS inhibitor applied at a level effective to inhibit the growth of a control plant which does not comprise said polynucleotide operably linked to said enhancer sequence.
65. The plant of claim 64, wherein said polynucleotide which confers tolerance to glyphosate encodes a glyphosate-N-acetyltransferase.
66. The plant of claim 64, wherein said polynucleotide which confers tolerance to glyphosate encodes a glyphosate-tolerant 5-enolpyruvylshikimate-3-phosphate synthase or a glyphosate-tolerant glyphosate oxido-reductase.
67. The transgenic plant of claim 64, wherein said ALS inhibitor-tolerant polypeptide comprises HRA.
68. The transgenic plant of any one of claim 64-67, wherein said polynucleotide is operably linked to at least three copies of the enhancer sequence set forth in SEQ ID NO: 72.
69. The transgenic plant of any one of claims 64-67, wherein said promoter is a ubiquitin promoter.
70. The transgenic plant of any one of claims 64-68, wherein said enhancer is heterologous to said promoter.
71. The transgenic plant of any one of claims 64-70, wherein said promoter is a maize ubiquitin promoter or an Arabidopsis ubiquitin promoter.
72. The plant of any one of claims 64-71, wherein said crop is a dicot.
73. The plant of claim 72, wherein said dicot is is soybean, canola, sunflower, cotton, alfalfa, an ornamental, a fruit, a vegetable, a sugar beet, or an Arabidopsis.
74. The plant of any one of claims 64-70, wherein said plant is a monocot.
75. The plant of claim 74, wherein said monocot is maize, wheat, rice, barley, sorghum, sugar cane, Switchgrass, or rye.
76. An expression cassette comprising a first polynucleotide that encodes a polypeptide which confers tolerance to glyphosate or a polynucleotide that encodes an ALS
inhibitor-tolerant polypeptide, wherein said polynucleotide is operably linked to:
(a) a promoter that drives expression in the plant; and (b) at least one copy of the enhancer sequence set forth in SEQ ID NO: 1, 72, 85, 88, or 89, or an enhancer sequence having at least 90% sequence identity to SEQ ID
NO: 1, 72, 85, 88, or 89, wherein said enhancer sequence modulates transcription and said enhancer sequence is heterologous to said promoter;
wherein said expression cassette confers glyphosate tolerance or ALS inhibitor tolerance on a plant containing it, wherein said plant is tolerant to glyphosate or the ALS
inhibitor applied at a level effective to inhibit the growth of a control plant which does not comprise said expression cassette.
77. The expression cassette of claim 76, wherein said polynucleotide which confers tolerance to glyphosate encodes a glyphosate-N-acetyltransferase.
78. The expression cassette of claim 76, wherein said polynucleotide which confers tolerance to glyphosate encodes a glyphosate-tolerant 5-enolpyruvylshikimate-3-phosphate synthase or a glyphosate-tolerant glyphosate oxido-reductase.
79. The expression cassette of any one of claims 76-78, wherein said polynucleotide is operably linked to at least three copies of the enhancer sequence set forth in SEQ ID NO: 72.
80. The expression cassette of any one of claims 76-79, wherein said promoter is a ubiquitin promoter.
81. The expression cassette of any one of claims 76-79, wherein said enhancer is heterologous to said promoter.
82. The expression cassette of claim 81, wherein said promoter is an Arabidopsis ubiquitin promoter or a maize ubiquitin promoter.
83. The expression cassette of any one of claims 76-83, wherein said polypeptide comprises the sequence set forth in SEQ ID NO:45.
84. The expression cassette of any one of claims 76-83, wherein said expression cassette comprises the polynucleotide which confers tolerance to glyphosate and the polynucleotide that encodes the ALS inhibitor-tolerant polypeptide.

86. The expression cassette of claim 76 or 84, wherein said ALS inhibitor-tolerant polypeptide comprises HRA.

87. A method of selecting cotton which has been transformed with a first polynucleotide encoding a first polypeptide which confers glyphosate tolerance and a second polynucleotide encoding an ALS inhibitor-tolerant polypeptide, said method comprising the step of growing transformed cotton callus while exposing it to glyphosate and/or an ALS
inhibitor herbicide.

88. The method of claim 87, wherein said polypeptide which confers glyphosate tolerance comprise GAT and said ALS inhibitor-tolerant polypeptide comprises HRA.

89. The method of claim 88, wherein the callus is grown while exposing it to a medium containing chlorsulfuron at a concentration of 50-200 micrograms per liter.

90. The method of claim 88, wherein the callus is grown while exposing it to a medium containing glyphosate at a concentration of up to 450 µM.

91. A method for controlling weeds in an area of cultivation comprising a) planting the field with crop seeds or plants which comprise i) a first polynucleotide encoding a polypeptide that can confer tolerance to glyphosate operably linked to a promoter active in a plant; and, ii) a second polynucleotide encoding an ALS inhibitor resistance polypeptide operably linked to a promoter active in a plant;
b) applying to said crop, crop part, seed of said crop or the area of cultivation thereof an effective amount of an herbicide, wherein said effective amount is tolerated by the crop and controls weeds, wherein said herbicide is not glyphosate, chlorimuron-ethyl, rimsulfuron, tribenuron-methyl or thifensufuron-methyl.

92. The method of claim 91, wherein said herbicide is selected from the group consisting of (i) a sulfonylaminocarbonyltriazolinone;
(ii) a triazolopyrimidine;
(iii) a pyrimidinyl(thio)benzoate;
(iv) an imidazolinone;
(v) a triazine; and (vi) a phosphinic acid.

93. A method for controlling weeds in a field containing a crop comprising a) planting the field with crop seeds or plants which comprise i) a first polynucleotide encoding a polypeptide that can confer tolerance to glyphosate; and, ii) a second polynucleotide encoding an ALS inhibitor-tolerant polypeptide;

b) applying to any crop and weeds in the field an effective amount of a first herbicide comprising an ALS inhibitor and an effective amount of at least one additional agricultural agent selected from the group consisting of a fungicide, a nematicide, an insecticide, a safener, or an adjuvant, wherein said effective amount of said ALS inhibitor herbicide is tolerated by the crop, and, wherein said effective amount of said combination is not tolerated by a control plant which does not express both of said first and said second polypeptide.

94. The method of claim 93, wherein step (b) is performed at least once prior to step (a).

95. A method for improving transformation efficiency, increasing a single copy integration event, or increasing transformation efficacy of a plant comprising:
a) introducing in the plant a cassette comprising a polynucleotide encoding a polypeptide that confers tolerance to glyphosate or a polynucleotide encoding an ALS inhibitor-tolerant polypeptide, wherein said polynucleotide is operably linked to a promoter active in said plant and is operably linked to at least one copy of the enhancer sequence set forth in SEQ ID NO:1, 72, 85, 88, or 89 or an enhancer sequence having at least 90% sequence identity to SEQ ID NO: 1, 72, 85, 88, or 89, wherein said sequence modulates transcription;
b) contacting said plant with an effective concentration of an appropriate herbicide; and, c) selecting the plant expressing said polynucleotide.

96. The method of claim 95, wherein said cassette further comprises a polynucleotide of interest.

97. The method of claim 95 or 96, wherein said polypeptide conferring tolerance to glyphosate comprises a GAT polypeptide or said ALS inhibitor-tolerant polypeptide comprises HRA.

98. A method for controlling weeds comprising a) planting the area with crop seeds or plants which express i) a first nucleotide sequence encoding a polypeptide that can confer tolerance to glyphosate; and, ii) a second nucleotide sequence encoding an ALS inhibitor-tolerant polypeptide;
b) applying to said crop, crop part, seed of said crop or the area under cultivation, an effective amount of a herbicides, wherein said effective amount comprises i) an amount that is not tolerated by a first control crop when applied to the first control crop, crop part, seed or the area of cultivation, wherein said first control crop expresses the first polynucleotide that confers tolerance to glyphosate and does not express the second polynucleotide that encodes an ALS inhibitor-tolerant polypeptide;
ii) an amount that is not tolerated by a second control crop when applied to the second crop, crop part, seed or the area of cultivation, wherein said second control crop expresses the second polynucleotide and does not express the first polynucleotide; and, iii) an amount that is tolerated when applied to the crop, crop part, seed, or the area of cultivation thereof of step (b).

99. A method for controlling weeds in an area of cultivation comprising:
a) evaluating environmental conditions in an area of cultivation;
b) selecting an effective amount of a herbicide wherein the effective amount of the herbicide comprises i) an amount that is not tolerated by a first control crop when applied to the first control crop, crop part, seed or the area of cultivation, wherein said first control crop expresses a first polynucleotide that confers tolerance to glyphosate and does not express a second polynucleotide that encodes an ALS inhibitor-tolerant polypeptide;
ii) an amount that is not tolerated by a second control crop when applied to the second crop, crop part, seed or the area of cultivation, wherein said second control crop expresses the second polynucleotide and does not express the first polynucleotide; and, iii) an amount that is tolerated when applied to a crop of interest, a crop part or interest, a seed of the crop of interest, or the area of cultivation thereof, wherein said crop of interest expresses the first nucleotide sequence encoding the polypeptide that can confer tolerance to glyphosate; and, the second nucleotide sequence encoding the ALS
inhibitor-tolerant polypeptide.
c) applying to the crop of interest, crop part of interest, weed or area of cultivation thereof, the effective amount of said herbicide.

100. A method for controlling weeds in an area of cultivation, the method comprising:
a) planting the area with crop seeds or crop plants, wherein the crop seeds or crop plants comprise:
i) a first polynucleotide encoding a polypeptide that can confer tolerance to glyphosate operably linked to a promoter active in the crop seeds or crop plants;
and ii) a second polynucleotide encoding an ALS inhibitor-tolerant polypeptide operable linked to a promoter active in the crop seeds or crop plants; and b) applying to any crop, crop part, weed, area of cultivation, or a combination thereof, an effective amount of a herbicide composition comprising at least one of a synergistically effective amount of glyphosate and a synergistically effective amount of a sulfonylurea herbicide, or agriculturally suitable salts thereof, wherein at least one of:
i) the synergistically effective amount of the glyphosate is lower than an amount of glyphosate required to control the weeds in the absence of the sulfonylurea herbicide;
ii) the synergistically effective amount of the sulfonylurea herbicide is lower than an amount of the sulfonylurea required to control the weeds in the absence of glyphosate; and iii) combinations thereof; and wherein the effective amount of the herbicide composition is tolerated by the crop seeds or crop plants and controls the weeds in the area of cultivation.

101. The method of claim 100, wherein the first polynucleotide encodes a glyphosate-N-acetyltransferase.

102. The method of claim 100 or 101, wherein the ALS inhibitor-tolerant polypeptide comprises a mutated acetolactate synthase polypeptide comprising HRA.

103. The method of claim 100, 101, or 102, wherein the sulfonylurea herbicide is selected from the group consisting of metsulfuron-methyl, chlorsulfuron, and triasulfuron.
104. The method of claim 100, 101, 102, or 103, wherein the glyphosate is applied pre-emergence, post-emergence or pre- and post-emergence to the weeds or the crop plants; and the sulfonylurea herbicide is applied pre-emergence, post-emergence or pre-and post-emergence to the weeds or the crop plants.

105. The method of any one of claims 100-104, wherein the glyphosate and the sulfonylurea herbicide are applied together or are applied separately.

106. The method of claim 100, wherein step (b) is performed at least once prior to step (a).

107. The method of any one of claim 100-106, wherein the herbicide composition comprises an ammonium sulfate-based adjuvant.

108. The method of claim 107, wherein the herbicide composition comprises an effective amount of a pyrimidinyloxy(thio)benzoate herbicide.

109. The method of claim 108, wherein the pyrimidinyloxy(thio)benzoate herbicide comprises bispyribac, or an agriculturally suitable salt thereof.

110. The method of claim 54, 58, 61, 91, 93, 98, or 100, wherein the crop plant is a dicot.

111. The method of claim 110, wherein the dicot is soybean, canola, sunflower, cotton, alfalfa, an ornamental, a fruit, a vegetable, a sugar beet, or an Arabidopsis.

112. The method of claim 54, 58, 61, 91, 93, 98, or 100, wherein the crop plant is a monocot.

113. The method of claim 112, wherein the monocot is maize, wheat, rice, barley, sorghum, sugar cane, Switchgrass, or rye.
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