阅读说明：本技术 烟草植物中腋芽生长的遗传控制 (Genetic control of axillary bud growth in tobacco plants ) 是由 C·库迪蒂普迪 沈燕新 许冬梅 J·弗雷德里克 梁在模 于 2015-10-06 设计创作，主要内容包括：本公开提供了许多参与烟草中的腋芽生长的序列、使用此类序列的方法、携带对此类序列的修饰或此类序列的转基因的烟草植物、和从自此类植物收获的烟草叶制备的烟草产品。(The present disclosure provides a number of sequences involved in axillary bud growth in tobacco, methods of using such sequences, tobacco plants carrying modifications to such sequences or transgenes of such sequences, and tobacco products prepared from tobacco leaves harvested from such plants.)

1. A method of making a transgenic tobacco plant, comprising introducing an expression vector comprising a promoter operably linked to a heterologous nucleic acid molecule, wherein expression of the nucleic acid molecule results in a plant that exhibits reduced axillary bud growth relative to a tobacco plant that does not express the nucleic acid molecule, and wherein the heterologous nucleic acid molecule encodes a polypeptide having at least 98% identity to SEQ ID NO: 80.

2. The method of claim 1, wherein the promoter is selected from the group consisting of: 113, 114, 115, 116, 117 and 118.

3. The method of claim 1, wherein the polypeptide has at least 99% identity to SEQ ID NO 80.

4. The method of claim 1, wherein the polypeptide has 100% identity to SEQ ID NO 80.

5. An expression vector comprising a promoter selected from the group consisting of: 113, 114, 115, 116, 117 and 118, operably linked to a heterologous second nucleic acid molecule, and wherein the heterologous nucleic acid molecule encodes a polypeptide having at least 98% identity to SEQ ID No. 80.

6. The expression vector of claim 5, wherein the polypeptide has at least 99% identity to SEQ ID NO 80.

7. The expression vector of claim 5, wherein the polypeptide has 100% identity to SEQ ID NO 80.

8. A method of making a transgenic tobacco plant comprising introducing the expression vector of claim 5 into a tobacco plant.

9. Dried tobacco leaf comprising the expression vector of claim 5.

10. A tobacco product comprising the dried tobacco leaf of claim 9.

11. The tobacco product of claim 10, wherein the tobacco product is selected from the group consisting of: cigarillo, non-ventilated recess filter cigarette, cigar, snuff, pipe tobacco, cigar tobacco, cigarette tobacco, chewing tobacco, leaf tobacco, shredded tobacco, and cut tobacco.

Technical Field

Generally, the present disclosure relates to tobacco plants.

Background

Tobacco is a plant species that exhibits exceptionally strong apical dominance. Molecular signaling from shoot apical meristems (shoot apical meristems) mediates a hormonal environment effective in inhibiting the growth of axillary buds. After removal of the apical meristem (also known as "topping"), signaling is lost, which enables new branches (or "suckers") to form from the axillary buds. Root-sucking growth results in loss of yield and leaf quality. Root suction has been controlled by manual removal and by the application of chemicals. Maleic Hydrazide (MH) and flumetralin (flumetralin) are routinely used on truncated plants to inhibit axillary bud growth (becoming root-sucking). However, labor and chemicals for controlling root suction are very expensive. The control of axillary bud growth in tobacco via conventional breeding, mutant breeding and transgenic approaches has been a major goal for decades, but to date, successful inhibition has not been achieved by genetic approaches. Thus, the development of tobacco traits with limited or no axillary bud growth will result in reduced use of chemical agents and will reduce the costs and labor associated with tobacco production.

Summary of The Invention

A number of nucleotide and polypeptide sequences involved in the formation of axillary bud growth are described herein. Methods of using such sequences are also described. The methods described herein allow for the generation of tobacco plants that exhibit reduced axillary bud growth after truncation.

In one aspect, there is provided a tobacco hybrid, variety, line or cultivar comprising a plant having a mutation in one or more nucleic acids shown in: SEQ ID NO: 1. 3, 5,7, 9, 11, 13, 15, 17, 19, 21, 23, 25, 27, 29, 31, 33, 35, 37, 39, 41, 43, 45, 47, 49, 51, 53, 57, 59, 61, 63, 65, 69, 71, 73, 75, or 77. In some embodiments, the plant exhibits reduced axillary bud growth relative to a plant lacking the mutation, and may be selected.

In one aspect, there is provided a seed produced from any one of a tobacco hybrid, variety, line or cultivar, the seed comprising a mutation in one or more nucleic acids.

In another aspect, a method of making a tobacco plant is provided. Such methods generally include the steps of: inducing mutagenesis in tobacco cells to generate mutagenized cells; obtaining one or more plants from the mutagenized cells; and identifying at least one plant comprising a mutation in one or more nucleic acids having a sequence shown in seq id no: SEQ ID NO: 1. 3, 5,7, 9, 11, 13, 15, 17, 19, 21, 23, 25, 27, 29, 31, 33, 35, 37, 39, 41, 43, 45, 47, 49, 51, 53, 57, 59, 61, 63, 65, 69, 71, 73, 75, or 77. Such methods may further comprise identifying at least one plant that exhibits reduced axillary bud growth relative to a plant lacking the mutation.

In some embodiments, the mutagenesis is induced using a chemical mutagen or ionizing radiation. Representative chemical mutagens include, but are not limited to, nitrous acid, sodium azide, acridine orange, ethidium bromide, and Ethyl Methanesulfonate (EMS). Representative ionizing radiation includes, but is not limited to, x-rays, gamma rays, fast neutron irradiation, and UV irradiation. In some embodiments, TALEN is used to induce mutagenesis. In some embodiments, zinc finger technology is used to induce mutagenesis.

In another aspect, a method for producing a tobacco plant is provided. Such methods generally include the following steps: crossing at least one plant of a first tobacco line with at least one plant of a second tobacco line, and selecting progeny tobacco plants having the mutation. Typically, the plants of the first tobacco line have a mutation in one or more nucleic acids having a sequence shown in seq id no: SEQ ID NO: 1. 3, 5,7, 9, 11, 13, 15, 17, 19, 21, 23, 25, 27, 29, 31, 33, 35, 37, 39, 41, 43, 45, 47, 49, 51, 53, 57, 59, 61, 63, 65, 69, 71, 73, 75, or 77. In some embodiments, such methods may further comprise selecting a progeny tobacco plant that exhibits reduced axillary bud growth relative to a plant lacking the mutation.

In yet another aspect, there is provided a tobacco product comprising dried leaves from a tobacco plant having a mutation in one or more nucleic acids having a sequence shown in each of: SEQ ID NO: 1. 3, 5,7, 9, 11, 13, 15, 17, 19, 21, 23, 25, 27, 29, 31, 33, 35, 37, 39, 41, 43, 45, 47, 49, 51, 53, 57, 59, 61, 63, 65, 69, 71, 73, 75, or 77. In some embodiments, the tobacco plant exhibits reduced axillary bud growth relative to a leaf from a plant lacking the mutation. In some embodiments, the tobacco plant exhibits reduced MH residues relative to leaves from a plant lacking the mutation.

In yet another aspect, a method of producing a tobacco product is provided. Such methods typically comprise providing dry leaves from a tobacco plant having a mutation in one or more nucleic acids having a sequence shown in: SEQ ID NO: 1. 3, 5,7, 9, 11, 13, 15, 17, 19, 21, 23, 25, 27, 29, 31, 33, 35, 37, 39, 41, 43, 45, 47, 49, 51, 53, 57, 59, 61, 63, 65, 69, 71, 73, 75, or 77; and using the dried leaves to make a tobacco product. In some embodiments, the tobacco plant exhibits reduced axillary bud growth relative to dry leaves from a plant lacking the mutation.

As used herein, mutations may be point mutations, insertions, deletions and substitutions.

In one aspect, a transgenic tobacco is provided comprising a plant expression vector comprising a nucleic acid molecule that is at least 25 nucleotides in length and has at least 91% sequence identity to a sequence shown in: SEQ ID NO: 1. 3, 5,7, 9, 11, 13, 15, 17, 19, 21, 23, 25, 27, 29, 31, 33, 35, 37, 39, 41, 43, 45, 47, 49, 51, 53, 55, 57, 59, 61, 63, 65, 67, 69, 71, 73, 75, 77, 79 or 81. In some embodiments, the nucleic acid molecule has at least 91% sequence identity to a sequence shown in seq id no: SEQ ID NO: 1. 3, 5,7, 9, 11, 13, 15, 17, 19, 21, 23, 25, 27, 29, 31, 33, 35, 37, 39, 41, 43, 45, 47, 49, 51, 53, 55, 57, 59, 61, 63, 65, 67, 69, 71, 73, 75, 77, 79 or 81. In some embodiments, expression of the nucleic acid molecule results in a plant that exhibits reduced axillary bud growth relative to a tobacco plant that does not express the nucleic acid molecule.

In another aspect, there is provided a seed produced by any of the transgenic tobacco plants described herein, wherein the seed comprises the expression vector.

In another aspect, a transgenic tobacco plant is provided comprising a heterologous nucleic acid molecule of at least 25 nucleotides in length, wherein the heterologous nucleic acid molecule hybridizes under stringent conditions to a nucleic acid sequence shown in seq id no: SEQ ID NO: 1. 3, 5,7, 9, 11, 13, 15, 17, 19, 21, 23, 25, 27, 29, 31, 33, 35, 37, 39, 41, 43, 45, 47, 49, 51, 53, 55, 57, 59, 61, 63, 65, 67, 69, 71, 73, 75, 77, 79 or 81. In some embodiments, the heterologous nucleic acid molecule hybridizes under stringent conditions to a nucleic acid sequence shown in seq id no: SEQ ID NO: 1. 3, 5,7, 9, 11, 13, 15, 17, 19, 21, 23, 25, 27, 29, 31, 33, 35, 37, 39, 41, 43, 45, 47, 49, 51, 53, 55, 57, 59, 61, 63, 65, 67, 69, 71, 73, 75, 77, 79 or 81. In some embodiments, expression of the heterologous nucleic acid molecule results in a plant that exhibits reduced axillary bud growth relative to a tobacco plant not expressing the nucleic acid molecule.

In some aspects, provided is a seed produced by any of the transgenic tobacco plants described herein, wherein the seed comprises the heterologous nucleic acid molecule.

In yet another aspect, methods of making transgenic plants are provided. Such methods typically include expressing a transgene encoding a double-stranded RNA molecule that inhibits expression of a nucleic acid sequence shown from: SEQ ID NO: 1. 3, 5,7, 9, 11, 13, 15, 17, 19, 21, 23, 25, 27, 29, 31, 33, 35, 37, 39, 41, 43, 45, 47, 49, 51, 53, 57, 59, 61, 63, 65, 69, 71, 73, 75, or 77, wherein the double stranded RNA molecule comprises at least 25 contiguous nucleotides having 91% or greater sequence identity to a sequence set forth in: SEQ ID NO: 1. 3, 5,7, 9, 11, 13, 15, 17, 19, 21, 23, 25, 27, 29, 31, 33, 35, 37, 39, 41, 43, 45, 47, 49, 51, 53, 57, 59, 61, 63, 65, 69, 71, 73, 75, or 77. In some embodiments, the transgenic plant is a plant that exhibits reduced axillary bud growth relative to a plant not expressing the transgene.

In another aspect, there is provided a tobacco product comprising dried leaves from any of the transgenic tobacco plants described herein.

In yet another aspect, there is provided a method of producing a tobacco product, the method comprising providing dried leaves from any of the transgenic tobacco plants described herein; and using the dried leaves to make tobacco products.

In yet another aspect, a method of reducing axillary bud growth in a tobacco plant is provided. Such methods generally comprise introducing a heterologous nucleic acid molecule operably linked to a promoter into a tobacco cell to produce a transgenic tobacco cell, and regenerating a transgenic tobacco plant from the transgenic tobacco cell. Typically, the heterologous nucleic acid molecule comprises a length of at least 25 nucleotides and has at least 91% sequence identity to a nucleic acid sequence shown in: SEQ ID NO: 1. 3, 5,7, 9, 11, 13, 15, 17, 19, 21, 23, 25, 27, 29, 31, 33, 35, 37, 39, 41, 43, 45, 47, 49, 51, 53, 55, 57, 59, 61, 63, 65, 67, 69, 71, 73, 75, 77, 79 or 81. Such transgenic tobacco plants exhibit reduced axillary bud growth. In some embodiments, the heterologous nucleic acid molecule has at least 91% sequence identity to a nucleic acid sequence as shown in seq id no: SEQ ID NO: 1. 3, 5,7, 9, 11, 13, 15, 17, 19, 21, 23, 25, 27, 29, 31, 33, 35, 37, 39, 41, 43, 45, 47, 49, 51, 53, 55, 57, 59, 61, 63, 65, 67, 69, 71, 73, 75, 77, 79 or 81. In some embodiments, expression of the nucleic acid molecule results in a plant that exhibits reduced axillary bud growth relative to a tobacco plant not expressing the nucleic acid molecule. Such methods may further comprise selecting at least one transgenic tobacco plant that exhibits reduced axillary bud growth relative to a tobacco plant that does not express the heterologous nucleic acid molecule.

In one embodiment, the nucleic acid is in the sense orientation. In some embodiments, the nucleic acid is in an antisense orientation. In some embodiments, the nucleic acid molecule is introduced into the tobacco cell using particle bombardment, Agrobacterium (Agrobacterium) -mediated transformation, microinjection, polyethylene glycol-mediated transformation, liposome-mediated DNA uptake, or electroporation. In some embodiments, the tobacco plant is selected from the group consisting of: burley tyPe, dark tyPe (dark tyPe), roast tyPe (blue-cured tyPe Pe), Maryland tyPe, and Oriental tyPe. In some embodiments, the tobacco plant is a variety selected from the group consisting of: BU 64, CC 101, CC 200, CC13, CC27, CC33, CC35, CC37, CC65, CC 67, CC 301, CC 400, CC 500, CC 600, CC 700, CC 800, CC 900, CC 1063, Coker 176, Coker 319, Coker371Gold, Coker48, CU263, DF911, Galpao tobacco, GL26H, GL338, GL350, GL395, GL600, GL737, GL939, GL973, GF157, GF318, RJR901, HB04P, K149, K326, K346, K358, K394, K399, K730, NC 196, NC NF, NC471, NC55, NC 92, NC2326, NC 95, NC KT, PVH 1118, PVH 1452, PVH 2110, PVH 2254, PVH 2275, VA 116, VA 119, NC 959, NC 16, NC2326, NC 95, NC KT, NC 18, NC KY 33, KY 3, KY 102, Nartenky 463, GL 944, Narden 32, GL 944, NartyK 3, GL 944, Nartne 33, GL 373, Nartne 32, NartyK 3, GL 150, Na 3, K32, K3, K32, K3, K32, Na < K3, K32, Na < TM < K < TM < K < TM < K > K < K > K < K > K < K > K <, NC 291, NC 297, NC 299, NC3, NC4, NC5, NC 6, NC7, NC 606, NC 71, NC 72, NC 810, NC BH 129, NC 2002, Neal Smith Madole, OxFORMED 207, ` Perique ` tobacco, PVH03, PVH09, PVH19, PVH50, PVH51, R610, R630, R7-11, R7-12, RG 17, RG 81, RG H51, RGH 51, RS 1410, Speight 168, Speight 172, Speight 179, Speight 210, Speight 220, Speight 225, Speight 227, Speight 234, Speight G-28, Speight G-70, Speight H-6, Speight H20, Speight 24, Speight 12686, Speight TN9, TN 11, TN9, and TN9, or TN9 (RossVA 9, TN9, and VA 9 (VA) 309 (VA) 309).

Unless defined otherwise, all technical and scientific terms used herein have the same meaning as commonly understood by one of ordinary skill in the art to which methods and compositions of matter belong. Although methods and materials similar or equivalent to those described herein can be used in the practice or testing of the methods and material compositions, suitable methods and materials are described below. In addition, the materials, methods, and examples are illustrative only and not intended to be limiting. All publications, patent applications, patents, and other references mentioned herein are incorporated by reference in their entirety.

Brief Description of Drawings

Fig. 1A is a graph showing the analysis of SEQ ID NO: 2 was confirmed for gene expression. AB 0: axillary buds before truncation; AB 2: axillary buds 2 hours after truncation; AB 6: axillary buds 6 hours after truncation; AB 12: axillary buds 12 hours after truncation; AB 48: axillary buds 48 hours after truncation; AB 72: axillary buds 72 hours after topping; RT 0: root before truncation; RT 24: root 24 hours after truncation; YL 0: young leaves before cutting; YL 24: young leaves 24 hours after topping; ML: mature leaves; MID midrib; SK 0: stem before truncation; SK 24: stem 24 hours after truncation; SAM: shoot apical meristem and SCL: aged leaves.

Fig. 1B is a graph showing the analysis of SEQ ID NO: 19 was confirmed for gene expression. AB 0: axillary buds before truncation; AB 2: axillary buds 2 hours after truncation; AB 6: axillary buds 6 hours after truncation; AB 12: axillary buds 12 hours after truncation; AB 48: axillary buds 48 hours after truncation; AB 72: axillary buds 72 hours after topping; RT 0: root before truncation; RT 24: root 24 hours after truncation; YL 0: young leaves before cutting; YL 24: young leaves 24 hours after topping; ML: mature leaves; MID midrib; SK 0: stem before truncation; SK 24: stem 24 hours after truncation; SAM: shoot apical meristem and SCL: aged leaves.

Fig. 1C is a graph showing the results of real-time PCR analysis on SEQ ID NO: 29 was confirmed for gene expression. AB 0: axillary buds before truncation; AB 2: axillary buds 2 hours after truncation; AB 6: axillary buds 6 hours after truncation; AB 12: axillary buds 12 hours after truncation; AB 48: axillary buds 48 hours after truncation; AB 72: axillary buds 72 hours after topping; RT 0: root before truncation; RT 24: root 24 hours after truncation; YL 0: young leaves before cutting; YL 24: young leaves 24 hours after topping; ML: mature leaves; MID midrib; SK 0: stem before truncation; SK 24: stem 24 hours after truncation; SAM: shoot apical meristem and SCL: aged leaves.

Fig. 1D is a graph showing the results of real-time PCR analysis on SEQ ID NO: 35 was confirmed. AB 0: axillary buds before truncation; AB 2: axillary buds 2 hours after truncation; AB 6: axillary buds 6 hours after truncation; AB 12: axillary buds 12 hours after truncation; AB 48: axillary buds 48 hours after truncation; AB 72: axillary buds 72 hours after topping; RT 0: root before truncation; RT 24: root 24 hours after truncation; YL 0: young leaves before cutting; YL 24: young leaves 24 hours after topping; ML: mature leaves; MID midrib; SK 0: stem before truncation; SK 24: stem 24 hours after truncation; SAM: shoot apical meristem and SCL: aged leaves.

Fig. 1E is a graph showing the results of real-time PCR analysis on SEQ ID NO: 37 was confirmed for gene expression. AB 0: axillary buds before truncation; AB 2: axillary buds 2 hours after truncation; AB 6: axillary buds 6 hours after truncation; AB 12: axillary buds 12 hours after truncation; AB 48: axillary buds 48 hours after truncation; AB 72: axillary buds 72 hours after topping; RT 0: root before truncation; RT 24: root 24 hours after truncation; YL 0: young leaves before cutting; YL 24: young leaves 24 hours after topping; ML: mature leaves; MID midrib; SK 0: stem before truncation; SK 24: stem 24 hours after truncation; SAM: shoot apical meristem and SCL: aged leaves.

Fig. 1F is a graph showing the results of real-time PCR analysis on SEQ ID NO: 45 was confirmed. AB 0: axillary buds before truncation; AB 2: axillary buds 2 hours after truncation; AB 6: axillary buds 6 hours after truncation; AB 12: axillary buds 12 hours after truncation; AB 48: axillary buds 48 hours after truncation; AB 72: axillary buds 72 hours after topping; RT 0: root before truncation; RT 24: root 24 hours after truncation; YL 0: young leaves before cutting; YL 24: young leaves 24 hours after topping; ML: mature leaves; MID midrib; SK 0: stem before truncation; SK 24: stem 24 hours after truncation; SAM: shoot apical meristem and SCL: aged leaves.

FIG. 2 is a schematic representation of a map of Agrobacterium transformation vector p 45-2-7.

FIG. 3A shows various nucleic acid alignments (SEQ ID NOS: 1, 13, 33, 35, 37, and 55, top to bottom).

FIG. 3B shows various nucleic acid alignments (SEQ ID NOS: 2,14, 34, 36, 38, and 56, top to bottom).

FIG. 4A is a photograph of a wild type tobacco plant before truncation (left) and a tobacco plant transformed with RNA construct #1(SEQ ID NO: 29; right).

FIG. 4B is a photograph of wild type plants (top) and plants transformed with RNA construct #1 (bottom) at the indicated times after truncation.

Fig. 4C is a photograph showing T1 generations generated from wild type plants (left) and plants transformed with RNA construct #1 (right).

FIG. 5A shows GUS staining from expression of the axillary meristem-specific promoter P1 (promoter from the sequence shown in SEQ ID NO: 31) and promoter P7(SEQ ID NO: 32).

FIG. 5B shows GUS staining of expression from promoter P1 (P1: GUS expression vector) before (0 hours) and after (24 hours, 48 hours, and 144 hours) truncation.

FIG. 6A are photographs showing the phenotype of T0 generation of transgenic lines (RNAi _ 1(SEQ ID NO: 83 for the BRANCH tobacco homolog); right) at 0h (top) and 1 week after truncation (bottom) compared to wild type plants (left).

FIG. 6B are photographs showing the phenotype of T0 generation of transgenic lines (RNAi _ 1(SEQ ID NO: 86 for the BRANCH tobacco homolog); right) at 0h (top) and 1 week after truncation (bottom) compared to wild type plants (left).

FIG. 6C are photographs showing the phenotype of T1 transgenic plants (RNAi _ 1; upper right, lower right) compared to wild type plants (upper left and lower left) 2 weeks after truncation.

Figure 6D is a graph showing that the fresh weight of axillary shoots of RNAi _1 plants is twice that of wild type plants, indicating that silencing of the BRANCH1 homologue in tobacco results in enhanced shoot outgrowth.

Fig. 7A is a photograph showing that overexpression of an arabidopsis BRANCH1 nucleic acid results in reduced shoot outgrowth (right) within 1 week after truncation (top) relative to wild type plants (left).

FIG. 7B are photographs showing that overexpression of an Arabidopsis BRANCH1 nucleic acid generally affects plant growth relative to wild type plants (left) (right).

FIG. 8 is a photograph showing the nucleotide sequence of SEQ ID NO: overexpression of the nucleic acid sequence shown in 11 resulted in enhanced shoot outgrowth after truncation (right). Illustratively, the phenotype is for one transgenic line compared to the wild type (left) at 0 hours (top) and 1 week after truncation (bottom).

The photograph of FIG. 9 (close-up, top; whole plant, bottom) shows that RNAi _ CET2 overexpression in three different transgenic lines down regulated root growth and resulted in reduced shoot outgrowth. Phenotypes of the three line transgenes for RNAi _ CET2 compared to wild type plants (left) 1 week after truncation are shown.

FIG. 10 is a photograph taken 7 days after truncation, showing that expression of RNAi _26 reduces root-sucking growth relative to wild-type plants (top left) (close-up, top right; whole plant, bottom).

FIG. 11 is a photograph showing the presence of a peptide having SEQ ID NO: 116 under the control of a promoter for the sequence shown in seq id no. As noted: no expression was observed in seedlings in the absence of SAM; in seedlings, blue color was seen in the presence of SAM; weak expression on axillary buds was seen before truncation; strong expression was observed 3 days after truncation; GUS expression faded out within 5 days after truncation; and GUS expression was absent by 7 days after truncation.

FIG. 12 is a photograph showing the presence of a peptide having SEQ ID NO: under the control of the promoter for the sequence shown in 117, axillary bud specific expression of GUS. As noted: no expression was observed in seedlings in the absence of SAM; GUS expression was observed in axillary buds in the presence of SAM; in mature plants, GUS expression was observed in the basal and in the lateral buds; no GUS expression was observed in flower buds; and strong GUS expression was observed in axillary buds before and after truncation for up to 15 days.

FIG. 13 is a photograph showing meristem-specific GUS expression under the control of the P1 promoter. GUS expression was observed, but was down-regulated after truncation (at 0 hours).

Detailed Description

Methods of producing tobacco without or with reduced root take growth are described. For example, the description includes: axillary bud growth gene profiling to discover genes critical to axillary bud development; up-regulation of axillary bud growth and/or root uptake inhibitory genes; down-regulation of axillary bud and/or root uptake activating genes; and regulation of regulatory components of root-sucking growth; or using axillary bud specific promoters to initiate or induce cell death mechanisms in the axillary buds.

The present disclosure is based on the discovery of nucleic acids encoding polypeptides from tobacco (n. tabacum), Arabidopsis (Arabidopsis thaliana) and Bacillus amyloliquefaciens (Bacillus amyloliquefaciens) involved in axillary bud growth and regulation thereof. Such nucleic acids are described and characterized herein as SEQ ID NOs: 1. 3, 5,7, 9, 11, 13, 15, 17, 19, 21, 23, 25, 27, 29, 31, 33, 35, 37, 39, 41, 43, 45, 47, 49, 51, 53, 55, 57, 59, 61, 63, 65, 67, 69, 71, 73, 75, 77, 79 or 81, and the polypeptide encoded thereby SEQ ID NO: 2. 4,6, 8, 10, 12, 14, 16, 18, 20, 22, 24, 26, 28, 30, 32, 34, 36, 38, 40, 42, 44, 46, 48, 50, 52, 54, 56, 58, 60, 62, 64, 66, 68, 70, 72, 74, 76, 78, 80, or 82. Based on this finding, it is possible to modulate the expression level of such nucleic acid sequences and/or the function of such polypeptides in Nicotiana species (Nicotiana species), in particular, for example, tobacco. Modulation of polypeptide function and/or gene expression may allow for improved control of axillary bud growth.

Nucleic acids and polypeptides

Provided herein are nucleic acids (see, e.g., SEQ ID NOs: 1,3, 5,7, 9, 11, 13, 15, 17, 19, 21, 23, 25, 27, 29, 31, 33, 35, 37, 39, 41, 43, 45, 47, 49, 51, 53, 55, 57, 59, 61, 63, 65, 67, 69, 71, 73, 75, 77, 79, or 81). As used herein, nucleic acids may include DNA and RNA, and include nucleic acids that contain one or more nucleotide analogs or backbone modifications. Nucleic acids may be single-stranded or double-stranded, depending generally on their intended use. Nucleic acids provided herein encode polypeptides (see, e.g., SEQ ID NOs: 2, 4,6, 8, 10, 12, 14, 16, 18, 20, 22, 24, 26, 28, 30, 32, 34, 36, 38, 40, 42, 44, 46, 48, 50, 52, 54, 56, 58, 60, 62, 64, 66, 68, 70, 72, 74, 76, 78, 80, or 82).

Also provided are polypeptides corresponding to SEQ ID NOs: 1. 3, 5,7, 9, 11, 13, 15, 17, 19, 21, 23, 25, 27, 29, 31, 33, 35, 37, 39, 41, 43, 45, 47, 49, 51, 53, 55, 57, 59, 61, 63, 65, 67, 69, 71, 73, 75, 77, 79, or 81, and SEQ ID NO: 2. 4,6, 8, 10, 12, 14, 16, 18, 20, 22, 24, 26, 28, 30, 32, 34, 36, 38, 40, 42, 44, 46, 48, 50, 52, 54, 56, 58, 60, 62, 64, 66, 68, 70, 72, 74, 76, 78, 80, or 82. Is identical in sequence to SEQ ID NO: 1. 3, 5,7, 9, 11, 13, 15, 17, 19, 21, 23, 25, 27, 29, 31, 33, 35, 37, 39, 41, 43, 45, 47, 49, 51, 53, 55, 57, 59, 61, 63, 65, 67, 69, 71, 73, 75, 77, 79, or 81, and SEQ ID NO: 2. 4,6, 8, 10, 12, 14, 16, 18, 20, 22, 24, 26, 28, 30, 32, 34, 36, 38, 40, 42, 44, 46, 48, 50, 52, or 54, may differ from SEQ ID NOs: 1. 3, 5,7, 9, 11, 13, 15, 17, 19, 21, 23, 25, 27, 29, 31, 33, 35, 37, 39, 41, 43, 45, 47, 49, 51, 53, 55, 57, 59, 61, 63, 65, 67, 69, 71, 73, 75, 77, 79, or 81, and SEQ ID NO: 2. 4,6, 8, 10, 12, 14, 16, 18, 20, 22, 24, 26, 28, 30, 32, 34, 36, 38, 40, 42, 44, 46, 48, 50, 52, 54, 56, 58, 60, 62, 64, 66, 68, 70, 72, 74, 76, 78, 80, or 82 have at least 50% sequence identity (e.g., at least 55%, 60%, 65%, 70%, 75%, 80%, 81%, 82%, 83%, 84%, 85%, 86%, 87%, 88%, 89%, 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, or 99% sequence identity).

In calculating percent sequence identity, two sequences are aligned and the number of identical matches of nucleotides or amino acid residues between the two sequences is determined. The number of identical matches is divided by the length of the aligned region (i.e., the number of aligned nucleotides or amino acid residues) and multiplied by 100 to obtain a percent sequence identity value. It will be appreciated that the length of the aligned regions may be a fraction of one or both sequences up to the full length of the shortest sequence. It will also be appreciated that a single sequence may be aligned with more than one other sequence and therefore may have different percent sequence identity values over each aligned region.

The computer program ClustalW and default parameters can be used to perform an alignment of two or more sequences to determine percent sequence identity, which allows the nucleic acid or polypeptide sequences to be aligned over their entire length (global alignment). Chenna et al, 2003, Nucleic Acids res, 31 (13): 3497-500. ClustalW calculates the best match between the query and one or more subject sequences and aligns them so that identity, similarity, and differences can be determined. Gaps in one or more residues may be inserted into the query sequence, the subject sequence, or both to maximize sequence alignment. For rapid alignment of nucleic acid sequences, default parameters (i.e., word size: 2; window size: 4; scoring method: percentage; number of top diagonals; 4; and gap penalty: 5) can be used; to align multiple nucleic acid sequences, the following parameters can be used: gap opening penalty: 10.0; gap extension penalty: 5.0; and weight transformation (weight transition): is. For rapid pairwise alignment of polypeptide sequences, the following parameters may be used: word size: 1; window size: 5; the scoring method comprises the following steps: percent; number of top diagonal lines: 5; and gap penalties: 3. for multiple alignments of polypeptide sequences, the following parameters may be used: the weight matrix is: blosum; gap opening penalty: 10.0; gap extension penalty: 0.05; hydrophilic notch: opening; hydrophilic residue: gly, Pro, Ser, Asn, Asp, Gln, Glu, Arg and Lys; and residual specific gap penalties: and (4) opening. ClustalW can be run, for example, on the world Wide Web at the Beller institute of Medicine Search initiator web site (Baylor College of Medicine Search Launcher site) or the European bioinformatics institute web site.

Changes can be introduced into a nucleic acid molecule (e.g., SEQ ID NOs: 1,3, 5,7, 9, 11, 13, 15, 17, 19, 21, 23, 25, 27, 29, 31, 33, 35, 37, 39, 41, 43, 45, 47, 49, 51, 53, 55, 57, 59, 61, 63, 65, 67, 69, 71, 73, 75, 77, 79, or 81) resulting in a change in the amino acid sequence (e.g., SEQ ID NOs: 2, 4,6, 8, 10, 12, 14, 16, 18, 20, 22, 24, 26, 28, 30, 32, 34, 36, 38, 40, 42, 44, 46, 48, 50, 52, 54, 56, 58, 60, 62, 64, 66, 68, 70, 72, 74, 76, 78, 80, or 82) of the encoded polypeptide. For example, changes can be introduced into a nucleic acid coding sequence using mutagenesis (e.g., site-directed mutagenesis, transcription activator-like effector nuclease (TALEN), PCR-mediated mutagenesis, Clustered Regularly Interspersed Short Palindromic Repeats (CRISPR) mutagenesis), or by chemically synthesizing nucleic acid molecules with such changes. Such nucleic acid changes may result in conservative and/or non-conservative amino acid substitutions at one or more amino acid residues. "conservative amino acid substitutions" are substitutions in which one amino acid residue is replaced with a different amino acid residue having a similar side chain (see, e.g., Dayhoff et al (1978, in Atlas of protein Sequence and Structure, 5(suppl. 3): 345-352), which provides a frequency table for amino acid substitutions), and non-conservative substitutions are substitutions in which an amino acid residue is replaced with an amino acid residue that does not have a similar side chain.

As used herein, an "isolated" nucleic acid molecule is a nucleic acid molecule that does not contain sequences that naturally flank one or both ends of the nucleic acid in the genome of the organism from which the isolated nucleic acid molecule is derived (e.g., cDNA or genomic DNA fragments produced by PCR or restriction endonuclease digestion). Such isolated nucleic acid molecules are typically introduced into a vector (e.g., a cloning vector or an expression vector) to facilitate manipulation or generation of a fusion nucleic acid molecule, as discussed in more detail below. In addition, an isolated nucleic acid molecule can include an engineered nucleic acid molecule, such as a recombinant or synthetic nucleic acid molecule.

As used herein, a "purified" polypeptide is a polypeptide that has been isolated or purified from the cellular components with which it naturally accompanies. Generally, a polypeptide is considered "purified" when it is at least 70% (e.g., at least 75%, 80%, 85%, 90%, 95%, or 99%) (by dry weight) free of the polypeptide and naturally-occurring molecule with which it is naturally associated. A synthetic polypeptide is "purified" in that the chemically synthesized polypeptide is essentially separated from the components that naturally accompany it.

Nucleic acids can be isolated using techniques conventional in the art. For example, nucleic acids can be isolated using any method, including but not limited to recombinant nucleic acid techniques and/or Polymerase Chain Reaction (PCR). General PCR techniques are described, for example, in PCR Primer: a Laboratory Manual, Dieffenbach & Dveksler, eds., Cold Spring Harbor Laboratory Press, 1995. Recombinant nucleic acid techniques include, for example, restriction enzyme digestion and ligation, which may possess isolated nucleic acids. An isolated nucleic acid can also be chemically synthesized as a single nucleic acid molecule or as a series of oligonucleotides.

The polypeptide can be purified from a natural source (e.g., a biological sample) by known methods such as DEAE ion exchange, gel filtration, and hydroxyapatite chromatography. The polypeptide may also be purified, for example, by expressing the nucleic acid in an expression vector. In addition, purified polypeptides can be obtained by chemical synthesis. The purity of the polypeptide may be measured using any suitable method, such as column chromatography, polyacrylamide gel electrophoresis, or HPLC analysis.

Vectors containing the nucleic acids (e.g., nucleic acids encoding polypeptides) are also provided. Vectors (including expression vectors) are commercially available or may be produced by recombinant DNA techniques conventional in the art. Vectors containing nucleic acids can have expression elements operably linked to such nucleic acids, and can also include sequences, such as sequences encoding selectable markers (e.g., antibiotic resistance genes). The vector containing the nucleic acid may encode a chimeric or fused polypeptide (i.e., a polypeptide operably linked to a heterologous polypeptide, which may be at the N-terminus or C-terminus of the polypeptide). Representative heterologous polypeptides are those that can be used to purify the encoded polypeptide (e.g., 6XHis tag, glutathione S-transferase (GST)).

Expression elements include nucleic acid sequences that direct and regulate the expression of a nucleic acid coding sequence. An example of an expression element is a promoter sequence. Expression elements may also include introns, enhancer sequences, response elements or induction elements that regulate expression of the nucleic acid. The expression element may be of bacterial, yeast, insect, mammalian or viral origin, and the vector may comprise a combination of elements from different origins. As used herein, operably linked means that the promoter or other expression element is positioned in the vector relative to the nucleic acid in a manner (e.g., in-frame) such that it directs or modulates expression of the nucleic acid.

Additionally or alternatively, the vector can include sequences that direct homologous recombination of a nucleic acid (e.g., SEQ ID NOs: 1,3, 5,7, 9, 11, 13, 15, 17, 19, 21, 23, 25, 27, 29, 31, 33, 35, 37, 39, 41, 43, 45, 47, 49, 51, 53, 55, 57, 59, 61, 63, 65, 67, 69, 71, 73, 75, 77, 79, or 81) into the genome. Representative sequences that can direct homologous recombination of a nucleic acid into the genome are known in the art and include TALEN sequences (e.g., Cermak et al, 2011, nuc.acids res, 39: e82), CRISPR sequences (Jiang et al, 2013, nuc.acids res, 41: e188), or zinc finger nucleases (Guo et al, 2010, j.mol.biol., 400: 96).

A vector as described herein can be introduced into a host cell. As used herein, a "host cell" is a particular cell into which a nucleic acid is directed, and also includes progeny of such a cell that carry the vector. The host cell may be any prokaryotic or eukaryotic cell. For example, the nucleic acid may be expressed in bacterial cells such as e.coli (e.coli), or insect, yeast or mammalian cells such as Chinese Hamster Ovary (CHO) or COS cells. Other suitable host cells are known to those skilled in the art and include plant cells. Many methods of introducing nucleic acids into host cells in vivo and in vitro are well known to those skilled in the art, including but not limited to electroporation, calcium phosphate precipitation, polyethylene glycol (PEG) transformation, heat shock, lipofection, microinjection, and virus-mediated nucleic acid transfer.

Nucleic acids can be detected using any number of amplification techniques using appropriate oligonucleotide (e.g., Primer) pairs (see, e.g., PCR Primer: A Laboratory Manual, 1995, ediffenbach & Dveksler, Cold Spring Harbor Laboratory Press, Cold Spring Harbor, NY; and U.S. Pat. Nos.4,683,195; 4,683,202; 4,800,159; and 4,965,188). Many modifications to the initial PCR have been developed and can be used to detect nucleic acids.

Nucleic acids can also be detected using hybridization. Hybridization between nucleic acids is discussed in detail in Sambrook et al (1989, Molecular Cloning: A Laboratory Manual, 2nd Ed., Cold Spring Harbor Laboratory Press, Cold Spring Harbor, NY; Sections 7.37-7.57, 9.47-9.57, 11.7-11.8, and 11.45-11.57). Suitable Southern blotting conditions for oligonucleotide probes of less than about 100 nucleotides are disclosed in Sambrook et al (sections 11.45-11.46). The Tm between a sequence less than 100 nucleotides in length and a second sequence can be calculated using the formula provided in section 11.46. Southern blotting conditions for oligonucleotide probes greater than about 100 nucleotides are additionally disclosed by Sambrook et al (see sections 9.47-9.54). The Tm between a sequence greater than 100 nucleotides in length and a second sequence can be calculated using the formula provided in sections 9.50-9.51 of Sambrook et al.

The conditions for pre-hybridization and hybridization of nucleic acid-containing membranes, as well as the conditions for washing nucleic acid-containing membranes to remove excess and non-specifically bound probes, can play an important role in the stringency of hybridization. Such hybridization and washing may be carried out under moderate or high stringency conditions, where appropriate. For example, the washing conditions may be made more stringent by reducing the salt concentration in the washing solution and/or by increasing the temperature at which washing is carried out. By way of example only, high stringency conditions typically include washing the membrane in 0.2X SSC at 65 ℃.

Furthermore, the amount of hybridization may be explained by, for example, the specific activity of the labeled oligonucleotide probe, the number of probe-binding sites on the template nucleic acid to which the probe has hybridized, and the amount of exposure to an autoradiogram or other detection medium. One of ordinary skill in the art will readily appreciate that while any number of hybridization and wash conditions can be used to check for hybridization of a probe nucleic acid molecule to an immobilized target nucleic acid, it is more important to check for hybridization of a probe to a target nucleic acid under the same hybridization, wash, and exposure conditions. Preferably, the target nucleic acids are on the same membrane.

A nucleic acid molecule is considered to hybridize to a nucleic acid but not to another nucleic acid if hybridization to the nucleic acid is at least 5-fold (e.g., at least 6-fold, 7-fold, 8-fold, 9-fold, 10-fold, 20-fold, 50-fold, or 100-fold) greater than hybridization to another nucleic acid. The amount of hybridization can be quantified using, for example, a phosphoimager or densitometer (Molecular Dynamics, Sunnyvale, Calif.) either directly on the membrane or from autoradiographs.

The polypeptide may be detected using an antibody. Techniques for detecting polypeptides using antibodies include enzyme-linked immunosorbent assays (ELISA), Western blots, immunoprecipitations, and immunofluorescence. The antibody may be a polyclonal or monoclonal antibody. Antibodies having specific binding affinity for the polypeptide can be generated using methods well known in the art. The antibodies can be attached to a solid support, such as a microtiter plate, using methods known in the art. In the presence of the polypeptide, an antibody-polypeptide complex is formed.

Detection (e.g., amplification product, hybridization complex, or polypeptide) is typically accomplished using a detectable label. The term "label" is intended to encompass the use of direct labels as well as indirect labels. Detectable labels include enzymes, prosthetic groups, fluorescent materials, luminescent materials, bioluminescent materials, and radioactive materials.

Plants having reduced axillary bud growth and methods of making

Tobacco hybrids, variants, lines, or cultivars are provided having a mutation in one or more nucleic acids described herein (e.g., SEQ ID NOs: 1,3, 5,7, 9, 11, 13, 15, 17, 19, 21, 23, 25, 27, 29, 31, 33, 35, 37, 39, 41, 43, 45, 47, 49, 51, 53, 57, 59, 61, 63, 65, 69, 71, 73, 75, or 77). As described herein, a stem of a plant having a mutation in one or more of the nucleic acids described herein (e.g., SEQ ID NOs: 1,3, 5,7, 9, 11, 13, 15, 17, 19, 21, 23, 25, 27, 29, 31, 33, 35, 37, 39, 41, 43, 45, 47, 49, 51, 53, 57, 59, 61, 63, 65, 69, 71, 73, 75, or 77) can exhibit reduced axillary bud growth (e.g., as compared to a stem of a plant lacking the mutation). In some examples, the nucleic acid having a mutation can be an endogenous nucleic acid; in some instances, nucleic acids having mutations can be recombinantly introduced.

As used herein, axillary bud growth (or "into root take") describes the production of lateral buds (or "root take") that grow between the leaves and the stem after truncation of a tobacco plant, as is generally understood in the art. Truncation refers to the removal of the stem apex, including flowers and up to several adjacent leaves, as the plant approaches maturity and results in a loss of apical dominance. If axillary bud growth is adequately controlled, truncation will increase yield and value of harvest per acre (value-per-acre) and produce the desired modification of the physical and chemical properties of the leaves.

Methods of making tobacco plants having mutations are known in the art. The mutation may be a random mutation or a targeted mutation. For random mutagenesis, cells (e.g., tobacco cells) can be mutagenized using, for example, chemical mutagens, ionizing radiation, or fast neutron bombardment (see, e.g., Li et al, 2001, Plant j., 27: 235-42). Representative chemical mutagens include, but are not limited to, nitrous acid, sodium azide, acridine orange, ethidium bromide, and Ethyl Methanesulfonate (EMS), while representative ionizing radiation includes, but is not limited to, x-ray, gamma (gamma) ray, fast neutron irradiation, and ultraviolet irradiation. For each type of plant tissue, the dose of mutagenic chemical or radiation is determined experimentally so as to obtain a level below a threshold level characterized by lethality or reproductive sterilityThe frequency of mutation. Estimation of M produced by mutagenesis treatment based on expected frequency of mutation₁Number of seed generations or M₁Size of the plant population. For targeted mutagenesis, representative techniques include TALENs (see, e.g., Li et al, 2011, Nucleic Acids res., 39 (14): 6315-25) or The use of zinc finger nucleases (see, e.g., Wright et al, 2005, The Plant j., 44: 693-. Whether random or targeted, the mutation may be a point mutation, insertion, deletion, substitution, or a combination thereof.

As discussed herein, one or more nucleotides can be mutated to alter the expression and/or function of an encoded polypeptide relative to the expression and/or function of a corresponding wild-type polypeptide. It is understood that, for example, mutations in one or more highly conserved regions may alter polypeptide function, while mutations outside those conserved regions may have little to no effect on polypeptide function. Furthermore, mutations in a single nucleotide may result in a stop codon, which will result in a truncated polypeptide and, depending on the degree of truncation, loss of function.

Preferably, a mutation in one of the novel nucleic acids disclosed herein results in a reduction or even a complete elimination of axillary bud growth after truncation in a tobacco plant comprising the mutation. Suitable types of mutations in a coding sequence include, but are not limited to, insertions of nucleotides, deletions of nucleotides, or transitions or transversions in the wild-type coding sequence. Mutations in the coding sequence may result in the insertion of one or more amino acids, the deletion of one or more amino acids, and/or non-conservative amino acid substitutions in the encoded polypeptide. In some cases, the coding sequence comprises more than one mutation or more than one type of mutation.

Insertions or deletions of amino acids in the coding sequence may, for example, disrupt the conformation of the encoded polypeptide. Amino acid insertions or deletions may also disrupt sites important for recognition of binding partners or polypeptide activity. It is known in the art that insertions or deletions of a larger number of consecutive amino acids are more likely to render the gene product non-functional than a smaller number of inserted or deleted amino acids. In addition, one or more mutations (e.g., point mutations) can alter the positioning of a polypeptide, introduce stop codons to produce a truncated polypeptide, or disrupt an active site or domain (e.g., catalytic site or domain, binding site or domain) within a polypeptide. In addition, can mutation of target or signal sequence, thereby destroying or changing the protein in the cell position.

Non-conservative amino acid substitutions may replace one class of amino acid with a different class of amino acid. Non-conservative substitutions may result in substantial changes in the charge or hydrophobicity of the gene product. Non-conservative amino acid substitutions may also result in substantial changes in the bulk of the side chain of the residue, such as the substitution of an isoleucine residue with an alanine residue. Examples of non-conservative substitutions include a basic amino acid in place of a non-polar amino acid or a polar amino acid in place of an acidic amino acid.

After mutagenesis, M₀Plants are regenerated from the mutagenized cells and those plants or subsequent generations of the plants (e.g., M)₁、M₂、M₃Etc.) screening sequences of interest (e.g., SEQ ID NO: 1. 3, 5,7, 9, 11, 13, 15, 17, 19, 21, 23, 25, 27, 29, 31, 33, 35, 37, 39, 41, 43, 45, 47, 49, 51, 53, 57, 59, 61, 63, 65, 69, 71, 73, 75, or 77). Screening of plants carrying mutations in the sequence of interest can be performed using methods routine in the art (e.g., hybridization, amplification, combinations thereof) or by assessing phenotype (e.g., detecting and/or determining axillary bud growth). Typically, the presence of a mutation in one or more of the nucleic acid sequences disclosed herein (e.g., SEQ ID NOs: 1,3, 5,7, 9, 11, 13, 15, 17, 19, 21, 23, 25, 27, 29, 31, 33, 35, 37, 39, 41, 43, 45, 47, 49, 51, 53, 57, 59, 61, 63, 65, 69, 71, 73, 75, or 77) results in a reduction in axillary bud growth in the mutant plant as compared to a corresponding plant lacking the mutation (e.g., having the same variety background).

As used herein, reduced axillary bud growth (also referred to as reduced shoot growth) refers to a reduction in the number of axillary buds (e.g., a statistically significant reduction), a reduction in the size of the axillary buds (e.g., a statistically significant reduction) as compared to a control plant, and/or a reduction in the impact of the axillary buds on agronomic performance (e.g., yield, quality and overall productivity of the plant) (e.g., a statistically significant reduction). The effect may be evidenced by the need to hinder and/or eliminate axillary bud growth after truncation, or to reduce and/or eliminate the application of chemicals (e.g., MH and/or flumetralin) after truncation. As used herein, statistically significant refers to a p-value of less than 0.05, e.g., a p-value of less than 0.025 or a p-value of less than 0.01, using an appropriate measure of statistical significance, e.g., a one-tailed two sample t-test.

M₁The tobacco plant may be heterozygous for the mutant allele and exhibit a wild-type phenotype. In such cases, at least a portion of the first self-pollinated progeny of such plants exhibit a wild-type phenotype. Or, M₁The tobacco plant may have mutant alleles and exhibit mutant phenotypes. Despite the presence of wild-type alleles, such plants may be heterozygous and exhibit mutant phenotypes due to phenomena such as dominant negative suppression (dominant negative suppression), or the plants may be heterozygous due to different independently induced mutations in different alleles.

Tobacco plants carrying mutant alleles can be used in plant breeding programs to create novel useful cultivars, lines, varieties, and hybrids. Thus, in some embodiments, M will contain at least one mutation₁、M₂、M₃Or a later generation tobacco plant is crossed with a second tobacco plant and progeny of the cross are identified for the presence of the mutation. It is to be understood that the second tobacco plant may be one of the species and varieties described herein. It is also understood that the second tobacco plant may contain the same mutation, a different mutation, or be wild-type at the locus as the plant with which it is crossed. Additionally or alternatively, the second tobacco line may exhibit phenotypic traits such as, for example, disease resistance, high yield, high grade index (high grade index), curability (curability), quality of dry treatment (curability), mechanical harvest, retention (ho1ding ability), leaf quality, height, plant maturity (e.g., early maturing), early maturing to medium maturing (medium maturing), medium maturing)Mature, medium to late mature (late maturing), or late maturing), stem size (e.g., small, medium, large), and/or the number of leaves per plant (e.g., small (e.g., 5-10 leaves), medium (e.g., 11-15 leaves), or large (e.g., 16-21) number of leaves).

Breeding is performed using known procedures. As described herein, DNA fingerprinting, SNP, or similar techniques may be used in Marker Assisted Selection (MAS) breeding programs to transfer or breed mutant alleles into other tobacco. Progeny of the crosses can be screened for mutations using the methods described herein, and plants having a mutation in a nucleic acid sequence disclosed herein (e.g., SEQ ID NOs: 1,3, 5,7, 9, 11, 13, 15, 17, 19, 21, 23, 25, 27, 29, 31, 33, 35, 37, 39, 41, 43, 45, 47, 49, 51, 53, 57, 59, 61, 63, 65, 69, 71, 73, 75, or 77) can be selected. For example, F can be screened using one of the techniques listed herein using a marker developed from a sequence described herein or a fragment thereof₂Or plants in backcross generations. Progeny plants can also be screened for axillary bud growth, and plants can be selected that have reduced axillary bud growth as compared to a corresponding plant lacking the mutation. Plants identified as possessing mutant alleles and/or mutant phenotypes can be backcrossed or self-pollinated to produce a second population to be screened. Backcrossing or other breeding procedures may be repeated until the desired phenotype of the parent is recovered.

Successful hybridization yields F₁Plants which are fertile and, if desired, can be backcrossed to a parental line. In some embodiments, F is screened using standard methods (e.g., PCR with primers based on the nucleic acid sequences disclosed herein)₂Mutant or variant gene expression of a population of plants in a generation. The selected plants are then crossed with one of the parents and a first Backcross (BC) is performed₁) Self-pollination of progeny plants to produce BC₁F₂Population of the BC₁F₂The population is again screened for variant gene expression. The process of backcrossing, self-pollination, and screening is repeated, for example, at least four times, until the final screening yields a plant that is fertile and reasonably similar to the recurrent parent. If so desired, the user may then proceed to,this plant was self-pollinated and the progeny were then screened again to confirm that the plant contained the mutation and exhibited variant gene expression. Breeder seeds of the selected plants can be produced using standard methods including, for example, field testing, validation of null conditions, and/or planting to assess axillary bud growth.

The result of plant breeding programs using the mutant tobacco plants described herein are novel useful cultivars, varieties, lines, and hybrids. As used herein, the term "variety" refers to a population of plants that share the characteristic of being isolated from other plants of the same species. Varieties are often, but not always, sold commercially. While possessing one or more unique characteristics, the cultivar is further characterized by very small overall variation between individuals within the cultivar. "inbred" varieties can be produced by self-pollination and selection over several generations, or vegetative propagation from a single parent using tissue or cell culture techniques. As distinguished from a variety, a "line" more generally refers to a group of plants that are not commercially used, for example, in plant research. Lines typically exhibit little overall variation among individuals in one or more characteristics of interest, although there may be some variation in other traits among individuals.

The breed may be substantially derived from another line or breed. According to the definition of the International Convention for the Protection of New Varieties of Plants (International Convention of the Protection of New Varieties of Plants) (Geneva 2.12.1961, such as Geneva amendment at 11.10.1972, 10.23.1978, and 3.19.1991), the variety "substantially originates from" the original variety in the following cases: a) it is derived primarily from the original variety, or from an expressed variety derived primarily from the original variety, while retaining the essential characteristics resulting from the genotype or combination of genotypes of the original variety; b) it is clearly distinguishable from the original variety; and c) it is consistent with the original variety in the expression of the essential characteristic produced by the genotype or combination of genotypes of the original variety, except for differences resulting from the deriving behaviour. The substantially derived varieties may be obtained, for example, by selection of natural or induced mutants, somaclonal variants (somaclonal variants), individual plants of the variants from the original variety, backcrossing or transformation.

Tobacco hybrids can be produced as follows: preventing self-pollination of a female parent plant (i.e., the seed parent) of a first variety, allowing pollen from a male parent plant of a second variety to pollinate the female parent plant, and allowing F₁Hybrid seed is formed on female plants. Self-pollination of female flower plants can be prevented by emasculating the flowers at an early stage of flower development. Alternatively, a form of male sterility may be used to prevent pollen formation on the female parent plant. For example, male sterility can be produced by Cytoplasmic Male Sterility (CMS)/nuclear male sterility, genetic male sterility, molecular male sterility (where the transgene inhibits microsporogenesis and/or pollen formation), or self-incompatibility. Female parent plants containing CMS are particularly useful. In embodiments where the female parent plant is the CMS, the male parent plant will typically contain a fertility recovery gene to ensure that F₁The hybrid is fertile. In other embodiments where the female parent is CMS, the male parent may be used without a fertility restorer line. F produced by such parents₁The hybrid is male sterile. The male sterile hybrid seed can be intercropped with male fertile seed to provide pollen on the resulting male sterile plant for seed set.

The varieties, lines, and cultivars described herein can be used to form monohybrid tobacco F₁And (4) hybrid. In such embodiments, plants of the parent variety may be grown into a substantially uniform contiguous population to promote natural cross-pollination from male parent plants to female parent plants. Selectively harvesting F formed on female parent plant by conventional means₂And (4) seeds. It is also possible to plant two parent plant species in bulk and harvest the F formed on the female parent₁A mixture of hybrid seed and seed formed on the male parent due to self-pollination. Alternatively, three-way crosses (three-way crosses) may be performed, in which a single cross F is used₁The hybrid serves as the female parent and is crossed with a different male parent. As another alternative, two-hybrid hybrids can be produced in which two different monohybridized F's are combined₁The progeny cross themselves. Self-incompatibility can be used to a particular advantage in preventing self-pollination of the female parent when forming a two-hybrid.

The tobacco plants used in the methods described herein can be of the Burley type, dark type, flue-cured type, Maryland type, and Oriental type. The tobacco plants used in the methods described herein are typically from tobacco, and can be from any number of tobacco varieties. The variety can be BU 64, CC 101, CC 200, CC13, CC27, CC33, CC35, CC37, CC65, CC 67, CC 301, CC 400, CC 500, CC 600, CC 700, CC 800, CC 900, CC 1063, Coker 176, Coker 319, Coker371Gold, Coker48, CU263, DF911, Galpao tobacco, GL26H, GL, GL350, GL395, GL600, GL737, GL939, GL973, GF157, GF318, RJR901, HB04P, K, K326, K346, K358, K394, K399, K730, NC 196, NC37NF, NC471, NC55, NC 92, NC2326, NC 95, NC 925, PVH 1118, PVH 1452, PVH 2110, PVH 2254, PVH 2275, VA 116, VA 119, KDH 639, 200, KY 9552, KY 10, KY 925, VB 204, K10, K35, GL 9552, GL 10, K35, GL 57, GL 3360, GL 87, GL60, GL 371, GL 87, and the like, KY14, KY 160, KY 17, KY 171, KY907LC, KTY14 x L8 LC, Little Crittenden, McNairr 373, McNairr 944, msKY 14xL8, Narrow LeafMadole, NC 100, NC 102, NC 2000, NC 291, NC 297, NC 299, NC3, NC4, NC5, NC 6, NC7, NC 606, NC 71, NC 72, NC 810, NC BH 129, NC 2002, Neal Smith MadOlOXORD 207, ` Perique' tobacco, PVH03, PVH09, PVH19, PVH50, PVH51, R610, R630, R7-11, R7-12, RG 17, RG 81, RGH 3, RGH 4, RGH 51, RGRS 1410, Spehtt 1406, Spehtg 179, Spehtg 84, Spehtg 179, Spehtg 210, Spehtg 179, Spehtg 210, Spehtg 220, Spehtg 210, Spehtg 220, Spehtg 32, Spehtt 32, Spehtg 32, Spehte, TI 1269, TN86LC, TN90LC, TN97LC, TN D94, TN D950, TR (Tom Rosson) Madole, VA 309, or VA 359.

In addition to mutations, another method that can reduce axillary bud growth in tobacco is the use of inhibitory RNA (e.g., RNAi). Thus, transgenic tobacco plants are provided that contain a transgene encoding at least one RNAi molecule that, when expressed, silences at least one endogenous nucleic acid described herein (e.g., SEQ ID NOs: 1,3, 5,7, 9, 11, 13, 15, 17, 19, 21, 23, 25, 27, 29, 31, 33, 35, 37, 39, 41, 43, 45, 47, 49, 51, 53, 57, 59, 61, 63, 65, 69, 71, 73, 75, or 77). As described herein, such transgenic plants exhibit reduced axillary bud growth (e.g., as compared to a plant lacking or not expressing RNAi).

RNAi techniques are known in the art and are a very effective form of post-transcriptional gene silencing. RNAi molecules typically contain nucleotide sequences that are complementary to the target gene in both sense and antisense orientations (e.g., about 18 nucleotides in length (e.g., about 19 or 20 nucleotides in length) up to about 700 nucleotides in length). The sense and antisense strands can be joined by short "loop" sequences (e.g., from about 5 nucleotides in length up to about 800 nucleotides in length) and expressed in a single transcript, or the sense and antisense strands can be delivered to and expressed in a target cell on separate vectors or constructs. Many companies offer RNAi design and integrated services (e.g., Life Technologies, Applied Biosystems).

RNAi molecules can be expressed using plant expression vectors. RNAi molecules are typically at least 25 nucleotides in length and have at least 91% sequence identity (e.g., at least 95%, 96%, 97%, 98% or 99% sequence identity) to one of the nucleic acid sequences disclosed herein (e.g., SEQ ID NOs: 1,3, 5,7, 9, 11, 13, 15, 17, 19, 21, 23, 25, 27, 29, 31, 33, 35, 37, 39, 41, 43, 45, 47, 49, 51, 53, 57, 59, 61, 63, 65, 69, 71, 73, 75 or 77) or are identical under stringent conditions to one of the nucleic acid sequences disclosed herein (e.g., SEQ ID NOs: 1,3, 5,7, 9, 11, 13, 15, 17, 19, 21, 23, 25, 27, 29, 31, 33, 35, 37, 39, 41, 43, 45, 47, 49, 51, 53, 57, 59, 61, 63, 65, 69, 71, 73, 47, 49, 25, 27, 29, 31, 33, 35, 37, 39, 41, 43, 45, 47, or combinations thereof, 75 or 77). Hybridization under stringent conditions is described above.

In addition, certain sequences described herein can be overexpressed in plants to reduce axillary bud growth. Thus, transgenic tobacco plants transformed with a nucleic acid molecule described herein (e.g., SEQ ID NOs: 1,3, 5,7, 9, 11, 13, 15, 17, 19, 21, 23, 25, 27, 29, 31, 33, 35, 37, 39, 41, 43, 45, 47, 49, 51, 53, 55, 57, 59, 61, 63, 65, 67, 69, 71, 73, 75, 77, 79, or 81) or a functional fragment thereof, under the control of a promoter capable of driving expression in a plant are provided. As discussed herein, the nucleic acid molecules used in the plant expression vectors can have sequences that differ from the sequences described herein, which can be expressed in percent sequence identity (e.g., relative to SEQ ID NOs: 1,3, 5,7, 9, 11, 13, 15, 17, 19, 21, 23, 25, 27, 29, 31, 33, 35, 37, 39, 41, 43, 45, 47, 49, 51, 53, 55, 57, 59, 61, 63, 65, 67, 69, 71, 73, 75, 77, 79, or 81), or based on the sequence and SEQ ID NO: 1. 3, 5,7, 9, 11, 13, 15, 17, 19, 21, 23, 25, 27, 29, 31, 33, 35, 37, 39, 41, 43, 45, 47, 49, 51, 53, 55, 57, 59, 61, 63, 65, 67, 69, 71, 73, 75, 77, 79 or 81.

As an alternative to using a full-length sequence, a portion of the sequence encoding a polypeptide fragment having the desired functionality (referred to herein as a "functional fragment") may be used. When used in reference to a nucleic acid, it is to be understood that it is not a nucleic acid fragment which possesses functionality, but rather an encoded polypeptide fragment. Based on the disclosure herein and the alignment shown in fig. 3, one skilled in the art can predict the portion (e.g., one or more domains) of a polypeptide that can confer the desired functionality.

Promoters which drive expression of a coding sequence in a plant are known in the art. Representative promoters include, for example, CaMV 35S promoter, actin promoter, ubiquitin promoter, phaseolin (phaseolin) promoter, rubisco promoter, zein promoter, ACEI system promoter, In2 promoter, or H3 histone promoter. In addition, tissue or development specific promoter sequences associated with axillary bud growth are described herein and can be used to express or overexpress nucleic acid coding sequences. Representative tissue or development specific promoter sequences associated with axillary bud growth are shown in SEQ ID NO: 113. 114, 115, 116, 117 or 118. As described herein, the coding sequence can be any of the nucleic acid coding sequences described herein (e.g., SEQ ID NOs: 1,3, 5,7, 9, 11, 13, 15, 17, 19, 21, 23, 25, 27, 29, 31, 33, 35, 37, 39, 41, 43, 45, 47, 49, 51, 53, 55, 57, 59, 61, 63, 65, 67, 69, 71, 73, 75, 77, 79, or 81); alternatively, the coding sequence may be derived from a gene that causes programmed cell death (e.g., a nucleic acid molecule encoding a ribosome inactivating protein, a nucleic acid molecule encoding a protein involved in the hypersensitive response initiated in plants when faced with a pathogen (e.g., a fungus or a bacterium)). By way of example only, tissue or development specific promoter sequences associated with axillary bud growth as described herein may be used to express or over-express coding sequences whose expression is reduced after truncation or coding sequences involved in apoptosis.

Methods for introducing nucleic acids (e.g., heterologous nucleic acids) into plant cells are known in the art and include, for example, particle bombardment, agrobacterium-mediated transformation, microinjection, polyethylene glycol-mediated transformation (e.g., of protoplasts, see, e.g., Yoo et al (2007, Nature Protocols, 2 (7): 1565-72)), liposome-mediated DNA uptake, or electroporation. After transformation, the transgenic plant cell can be regenerated into a transgenic tobacco plant. As described herein, expression of a transgene results in a plant that exhibits reduced axillary bud growth relative to a plant that does not express the transgene. Regenerated transgenic plants can be screened for axillary bud growth, and plants with reduced axillary bud growth compared to corresponding non-transgenic plants can be used, for example, in breeding programs as discussed herein.

In addition to the overexpression or down-regulation of coding sequences associated with axillary bud growth, axillary bud growth can be controlled using any of the following methods:

a. altering the expression of axillary bud growth-related regulatory genes essential for axillary bud development (as described in examples 7 and 8);

b. using an axillary bud-specific promoter to alter a meristem development-specific gene;

c. alter hormone signaling, leading to axillary bud growth inhibition. This can be achieved by overexpression or downregulation of hormone synthesis or transporter genes driven by tissue-or timing-specific (e.g., truncated) promoters; and

d. an axillary bud-specific promoter driving a cell suicide or virulence gene is used to initiate the cell death mechanism in the axillary bud.

Nucleic acids that confer traits such as herbicide resistance (sometimes referred to as herbicide tolerance), insect resistance or stress tolerance may also be present in the novel tobacco plants described herein. Genes conferring resistance to herbicides that inhibit the growing point or meristem, such as imidazolinones or sulfonylureas, may be suitable. Exemplary genes in this category encode mutant ALS and AHAS enzymes as described, for example, in U.S. patent nos. 5,767,366 and 5,928,937. U.S. Pat. Nos.4,761,373 and 5,013,659 relate to plants that are resistant to various imidazolinone or sulfonamide herbicides. U.S. Pat. No.4,975,374 relates to plant cells and plants containing a gene encoding a mutant Glutamine Synthetase (GS) that is resistant to inhibition by herbicides known to inhibit GS, such as phosphinothricin and methionine sulfimide. U.S. Pat. No.5,162,602 discloses plants resistant to inhibition by cyclohexanedione and aryloxyphenoxypropionic acid (aryloxyphenoxypropanoic acid) herbicides.

Genes for resistance to glyphosate (glyphosate) are also suitable. See, for example, U.S. Pat. Nos.4,940,835 and 4,769,061. Such genes may confer resistance to glyphosate herbicide compositions, including but not limited to glyphosate salts, such as trimethylsulfonium salt (trimethallylphosphonium salt), isopropylamine salt (isopropylamine salt), sodium, potassium and ammonium salts. See, for example, U.S. patent nos. 6,451,735 and 6,451,732. Genes for resistance to phosphono compounds such as glufosinate ammonium or phosphinothricin and pyridyloxy or phenoxypropionic acid and cyclohexanone are also suitable. See, e.g., U.S. Pat. Nos. 5,879,903; 5,276,268; and 5,561,236; and European application No. 0242246.

Other suitable herbicides include those that inhibit photosynthesis, such as triazines (triazones) and benzonitriles (nitrilases). See U.S. Pat. No.4,810,648. Other suitable herbicides include 2, 2-dichloropropionic acid, sethoxydim (sethoxydim), haloxyfop (haloxyfop), imidazolinone herbicides, sulfonylurea herbicides, triazolopyrimidine (triazolopyrimidine) herbicides, s-triazine herbicides, and bromoxynil (bromoxynil). Herbicides which confer resistance to protox enzymes are also suitable. See, for example, U.S. patent No.6,084,155 and US 20010016956.

A number of genes are available which confer resistance to insects, for example in the Lepidoptera (Lepidoptera). Exemplary genes include genes encoding truncated Cry1A (b) and Cry1A (c) toxins. See, e.g., U.S. patent nos. 5,545,565; 6,166,302, respectively; and 5,164,180. See also Vaeck et al, 1997, Nature, 328: 33-37 and Fischhoff et al, 1987, Nature Biotechnology, 5: 807-813. Particularly useful are the codes for the resistance to tobacco hornworm (Manduca sexta) (tobacco hornworm); genes of toxins that exhibit insecticidal activity against Heliothis virescens Fabricius (tobacco aphid) and/or Spodoptera litura Fabricius (tobacco cutworm).

Tobacco product and method of making

Leaves from tobacco plants having reduced axillary bud growth may be dry treated (cured), aged (aged), conditioned (conditioned) and/or fermented. Methods of dry processing tobacco are well known and include, for example, air drying (air curing), fire curing (fire curing), flue curing (tobacco curing), and sun drying. Aging is also known and is typically carried out under pressure in wooden barrels (e.g., vats) or cartons for years (e.g., 2 to 5 years) with moisture contents of about 10% to about 25% (see, e.g., U.S. patent nos.4,516,590 and 5,372,149). Conditioning includes a heating, sweating (sweating) or pasteurization step, for example as described in US 2004/0118422 or US 2005/0178398, while fermentation is generally characterized by a high initial moisture content, heat production, and a 10% to 20% dry weight loss. See, for example, U.S. patent nos.4,528,993, 4,660,577, 4,848,373, and 5,372,149. The tobacco can also be further processed (e.g., cut, expanded, blended, ground, or comminuted), if desired, and used in tobacco products.

Tobacco products are known in the art and include products made from or derived from tobacco intended for human consumption, including any component, portion, or accessory of a tobacco product. Representative tobacco products include, but are not limited to, smokeless tobacco products, tobacco-derived nicotine products, cigarillos (cigrilos), non-ventilated recess filter cigarettes (non-ventilated recess cigarettes), ventilated recess filter cigarettes (ventilated recess cigarettes), cigars (cigars), snuff (snuff), pipe tobacco (pipe tobaco), cigar tobacco, cigarette tobacco, chewing tobacco, leaf tobacco, shredded tobacco (shredded tobaco), and cut tobacco (cut tobaco). Representative smokeless tobacco products include, for example, chewing tobacco, snuff, long cut moist smokeless tobacco (1ong-cut tobacco chewing tobacco), snus, pouches (pouches), films, tablets, coated dowels, rods, and the like. Representative cigarettes and other smoking articles include, for example, smoking articles that include a filter element or rod element, wherein the rod element of smokable material may include dry tobacco within a tobacco mixture. In addition to the tobacco described herein, the tobacco product may include other ingredients such as, but not limited to, binders, plasticizers, stabilizers, and/or flavoring agents (flavors). For examples of tobacco products, see e.g. US 2005/0244521; US 2006/0191548; US 2012/0024301; US 2012/0031414; and US 2012/0031416.

The invention will be further described in the following examples, which do not limit the scope of the methods and compositions of matter described in the claims.

Examples

Example 1: sampling, RNA preparation and sequencing

Tobacco seeds from TN90(Burley variety) were germinated. After 4 weeks, the seedlings were transferred to 4-inch pots. At shelf life (8-10 fully expanded leaves), a total of 10 different samples were collected, including pre-truncated axillary buds (Aa), post-truncated axillary buds (Ab, Ac, Ad and Ae (2 h, 6h, 24h and 72h, respectively), pre-truncated roots (Ra), post-truncated roots (Rb, Rc (24h and 72h)), truncated Young Leaves (YL), and branch apical meristem (ST) for next generation sequencing analysis.

RNA from the above samples was isolated using RNeasy Plant mini kit (Qiagen, MA) and tested for quality using Agilent Plant RNA Nano kit and 2100 Bioanalyzer (Agilent Technologies, Calif.). 30 cDNA libraries were constructed and indexed (indexing) using TrueSeq RNA library preparation kit v.2 (Illumina). cDNA libraries prepared from the same biological replicates were pooled together and each pooled replicate, 100bp single read, with a minimum of 3000 ten thousand reads per sample was analyzed on an Illumina HiSeq 2000. Two samples were labeled per lane for a total of 15 sequencing lanes. Axillary bud-specific gene expression in TN90 tobacco was determined by RNA deep sequencing by ArrayXpress (Raleigh, NC).

Example 2: RNA sequence analysis

Gene expression data from 5 axillary buds, 3 roots and 1 each of the shoot and shoot apical meristems were analyzed to identify axillary bud development-associated genes compared to other tissues. Gene reads were mapped to our internal tobacco encyclopedia (tobacopedia) genomic database (table 1). The EdgeR in the CLC genomic workstation was used to implement differential gene expression. Gene expression data was filtered for axillary bud specific expression from other tissues. FDR adjustments were made for all p-values and a cutoff of < 0.05 FDR corrected p-value was used. The results were then filtered against high axillary bud expression. A list of differentially expressed candidate genes for root control is listed in table 2.

Table 1: localization of next generation sequencing reads using an internal tobacco encyclopedia database

Sample (I)	Positioning read	% location	Sample (I)	Positioning read	% location
						Aa1	23,920,938	92.03	Ra1	39,732,686	92.02
Aa2	49,392,444	91.21	Ra2	40,262,611	91.16
						Aa3	28,288,803	86.23	Ra3	33,248,092	92.13
Ab1	24,848,558	92.2	Rb1	35,937,062	93.06
						Ab2	35,727,478	92.23	Rb2	40,036,265	92.43
Ab3	34,000,094	92.25	Rb3	46,268,788	92.34
						Ac1	45,951,075	92.04	Rc1	35,595,122	92.84
Ac2	48,242,863	92.15	Rc2	37,925,157	92.25
						Ac3	41,733,418	91.67	Rc3	34,832,062	92.18
Ad1	33,474,960	92.08	ST1	48,115,555	92.45
						Ad2	31,891,377	92.35	ST2	41,373,361	92.41
Ad3	40,791,919	92.23	ST3	31,760,672	91.85
						Ae1	28,758,337	92.04	YL1	41,811,850	92.63
Ae2	38,369,793	92.26	YL2	51,356,432	91.82
						Ae3	40,552,134	92.45	YL3	40,252,190	91.95

Example 3: confirmation of expression of selected candidate genes

To confirm the expression pattern of the selected candidate genes, relative changes in transcripts from 10-16 different tissue samples (6 axillary bud samples (2 hours before and after truncation, 6 hours, 12 hours, 24 hours, and 72 hours), 24 hours after truncation young leaves, mature leaves, senescent leaves, midvein, stem before truncation, stem 24 hours after truncation, stem apical meristem, root before truncation and 24 hours after truncation) were measured. Briefly, total RNA was isolated using TRI reagent (Sigma-Aldritch, st. To remove DNA impurities, purified RNA was treated with RNase-free DNase (without Turbo DNA, Ambion, Austin, TX). To synthesize the first cDNA strand, about 10. mu.g of total RNA was transcribed using the High Capacity cDNA Kit (Applied Biosystems, Foster City, Calif.). To measure the level of selected gene transcripts in the samples, RT-PCR was performed using SYBR Green PCR Master Mix (Applied Biosystems, Foster City, Calif.) and the gene-specific primers listed in Table 3. Real-time gene expression validation of representative candidate genes is presented in FIGS. 1A-1F.

Example 4: full-Length candidate Gene cloning, analysis and use for validation of selected real-time PCR

Candidate genes predicted to be involved in axillary bud initiation and growth were identified and annotated (table 4), and RNA from axillary bud tissue of TN90 plants before, and 12, 24, and 48 hours after, truncation was collected. A cDNA library was generated from RNA using the In-Fusion SMARTER directed cDNA library construction kit from Clontech (Cat # 634933). The full-length candidate gene was cloned using gene-specific primers designed from the predicted full-length cDNA sequence. The full-length coding sequence was confirmed by sequencing and is shown in SEQ ID NO:1, 3, 5,7, 9, 11, 13, 15, 17, 19, 21, 23, 25, 27, 29, 31, 33, 35, 37, 57, 59, or 69. The predicted protein sequence is shown in SEQ ID NO: 2, 4,6, 8, 10, 12, 14, 16, 18, 20, 22, 24, 26, 28, 30, 32, 34, 36, 38, 58, 60, or 70.

Table 4: selected candidate genes

From the RNA sequence analysis and RT-PCR confirmation, candidate putative full-length gene sequences were selected for RNAi and full-length Agrobacterium transformation analysis. Candidate sequences are listed in table 5 and shown in SEQ ID NO: 39, 41, 43, 45, 47, 49, 51, 53, 61, 63, 65, 71, 73, 75 or 77. The predicted protein sequence is shown in SEQ ID NO: 40, 42, 44, 46, 48, 50, 52, 54, 62, 64, 66, 72, 74, 76 or 78.

Based on the presence of a conserved domain (TCP domain), six of the candidate genes are members of the transcription factor gene family. The nucleotide and protein sequence alignment is shown in figure 3. Members of this family are involved in plant growth and development regulation. The conserved domain is thought to be responsible for DNA binding to cis-elements in the promoter to regulate downstream genes.

Table 5: selected candidate putative Gene sequences

Example 5: development and efficacy testing of transgenic plants containing RNAi or overexpression constructs

To investigate the function of candidate genes, three sets of transgenic plants were generated; the first group used full length coding sequences from tobacco (Table 4, SEQ ID NO:1, 3, 5,7, 9, 11, 13, 15, 17, 19, 21, 23, 25, 27, 29, 31, 33, 35, 37, 39, 41, 43, 45, 47, 49, 51, 53, 57, 59, or 69), the second group used full length genes from non-tobacco sources (Table 4, SEQ ID NO: 55, 67, 79, or 81); and a third group using RNAi sequences (SEQ ID NO: 83, 84, 85, 86, 87, 88, 89, 90, 91, 92, 93, 94, 95, 96, 97, 98, 99, 100 or 101). An expression vector p45-2-7(SEQ ID NO: 112; FIG. 2) was used, with the CsVMV promoter and the NOS terminator, and a cassette with the kanamycin selection marker (NPT II) under the direction of the actin 2 promoter and the NOS terminator. The nucleic acid construct carrying the transgene of interest is introduced into tobacco leaves using the agrobacterium transformation method. See, e.g., Mayo et al, 2006, Nat protoc, 1 (3): 1105-11 and Horsch et al, 1985, Science 227: 1229-1231.

Briefly, tobacco plants (Narrow leaf madole (NLM)) were grown from a magenta box and leaf discs were cut into 15x150mm plates. The Agrobacterium tumefaciens containing the target plasmid was collected by centrifuging 20ml of the cell suspension in a 50ml centrifuge tube at 3500rpm for 10 minutes. The supernatant was removed and the Agrobacterium cell pellet was resuspended in 40ml of liquid resuspension medium. Approximately 25ml of the solution was transferred to each 15x100mm petri dish. In those 15x150mm plates, tobacco leaves (avoiding the midvein) were cut into 0.6cm disks. The leaf discs were placed upside down, a thin layer of MS/B5 liquid resuspension medium was added, and sliced with a #15 razor blade. The leaf discs were evenly poked with a fine point needle. In each regeneration board (15x100mm) 8 discs were placed upside down. The agrobacterium tumefaciens suspension was added and the leaf discs were incubated for 10 minutes.

The leaf disks were transferred to a co-cultivation plate (1/2MS medium) and the disks were placed upside down in contact with filter paper overlaid on co-cultivation TOM medium (MS medium with 20g sucrose/L; 1mg/L IAA and 2.5mg/L BAP). Plates were sealed with parafilm and appropriately marked. The plates were incubated at 24 ℃ for three days in dim light (60-80 mE/ms) and 18/6 photoperiod. Leaf disks were transferred to regeneration/selection TOM K medium plates (TOM medium with 300mg/l kanamycin) and subcultured twice a week to the same fresh medium in dim light at 24 ℃ until shoots became excisable. Shoots from leaves were removed with tweezers and inserted for rooting in MS basal medium with 100mg/L kanamycin at 24 ℃ and 18/6 photoperiod at a light intensity of 6080 mE/MS.

When plantlets with branches and roots grew large enough (e.g., more than half of the GA7 box), they were transferred to soil for acclimation. During transfer, the gel was washed from the root tissue with tap water. The established seedlings were transferred to a greenhouse for further analysis and seed set.

Efficacy testing of the root-sucking growth phenotype was performed by planting plants to the shelve (laybe) stage. These plants were truncated and axillary bud growth was observed at a specific time point after truncation.

FIG. 4A shows wild type tobacco plants before truncation (left) and plants transformed with RNA construct #1(SEQ ID NO: 55; right), and FIG. 4B shows wild type plants at the indicated time after truncation (top) and plants transformed with RNA construct #1 (bottom). Fig. 4C shows T1 generations of wild type plants (left) and plants transformed with RNA construct #1 (right). The growth of axillary buds after truncation is substantially increased in the transgenic plant relative to the wild-type plant. Initiation of axillary bud growth in transgenic plants has been initiated before the plant was truncated and growth rate increased up to 1 week after truncation. These results demonstrate that expression of RNA construct #1 may cause shoot dormancy and that down-regulation of the gene is a factor in the initiation and growth of root take.

The sequence of the expression cassette is shown in SEQ ID NO: in 111, the relevant part is indicated on the left.

Example 6: promoter cloning, transformation and analysis

The expression patterns of 41 candidate genes were analyzed, and promoters of genes having high expression levels in axillary buds but low expression levels in other tissues were selected (Table 6). The expression pattern of these clones was confirmed by real-time PCR analysis (figure 1). 6 axillary meristem-specific promoters were cloned by PCR from TN90 genomic DNA using gene-specific primers. The sequence of the promoter is shown in SEQ ID NO:113, and 118.

By using chimeric candidate promoters with the same cassettes described in example 5: : tobacco transformation of the β -Glucuronidase (GUS) reporter gene to analyze expression of the candidate promoter. The chimeric gene was introduced into the NLM line by agrobacterium-mediated transformation. According to Crone et al, 2001, Plant Cell environ, 24: 869-874, Gus staining was used to localize promoter expression. Transgenic tobacco tissue was placed in cold 90% acetone on ice. When all samples were collected, the samples were left at room temperature for 20 minutes. Acetone was removed from the sample and staining buffer (0.2% Triton X-100; 50mM NaHPO4 buffer, pH 7.2; 2mM potassium ferricyanide) was added to the sample, all while holding the sample on ice. X-Gluc was added to the staining buffer to a final concentration of 2mM from a 100mM X-Gluc stock solution in DMF, which had to be kept in the dark at-20 ℃. The staining buffer was removed from the sample and fresh staining buffer with X-Gluc was added. The sample was diafiltered on ice under vacuum for 15 to 20 minutes. The samples were incubated at 37 ℃ for 2 hours to overnight. The sample was removed from the incubator and the staining buffer was removed. The samples were washed by shading to a 95% ethanol series (i.e. from 10%, 30%, 50%, 70%; samples could be heated to 60 ℃ if desired to remove chloroplasts) for 30 minutes each step. Finally, the samples were stored in 100% ethanol.

GUS positive plant tissues were examined at low magnification using a brightfield microscope (Leica Q500MC, Cambridge, England) and photographed with a digital camera. See fig. 5A and 5B. The results of the experiments using the two different promoters described herein (SEQ ID NOS: 113 and 115) are shown in FIG. 5. The young seedlings were stained. GUS expression, indicated by blue staining, was concentrated in the axillary buds, indicating that both promoters were active in the axillary buds, but not in the stem or leaf (fig. 5A). In SEQ ID NO: the expression of GUS under the direction of the 113 promoter was also reduced after truncation, consistent with the gene expression pattern observed for endogenous genes normally regulated by this promoter (fig. 5B). These promoter sequences can be used to express genes only or mainly in the axillary buds while limiting expression in the remainder of the plant.

Table 6: selection cloning of promoter analysis

Contig numbering	Promoter length	SEQ ID NO
			C5787	2248	113
C7651	2800	114
			C26207	3356	115
C12866	3150	116
			C41568	2964	117
C16249	941	118

Example 7: efficacy testing of promoter and Gene combinations

Use of promoters in transgenic plants: : after GUS fusion analysis examined the tissue-specific expression pattern of the candidate promoter, we constructed a continuous vector to express the candidate gene only in the axillary buds. Transgenic plants containing these constructs were generated using agrobacterium-mediated transformation. Expression of the candidate gene in the transgenic plant can result in a plant that inhibits axillary bud growth, resulting from inhibition or overexpression of the candidate gene.

Some examples are shown below:

construct 1: promoter (SEQ ID NO: 113) and Gene (SEQ ID NO: 17)

Construct 2: promoter (SEQ ID NO: 113) and Gene (SEQ ID NO: 104)

Construct 3: promoter (SEQ ID NO: 113) and Gene (SEQ ID NO: 7)

Construct 4: promoter (SEQ ID NO: 113) and Gene (SEQ ID NO: 41)

Construct 5: promoter (SEQ ID NO: 113) and Gene (SEQ ID NO)：5)

Construct 6: promoter (SEQ ID NO: 118) and Gene (SEQ ID NO: 17)

Construct 7: promoter (SEQ ID NO: 118) and Gene (SEQ ID NO: 104)

Construct 8: promoter (SEQ ID NO: 118) and Gene (SEQ ID NO: 7)

Construct 9: promoter (SEQ ID NO: 118) and Gene (SEQ ID NO: 41)

Construct 10: promoter (SEQ ID NO: 118) and Gene (SEQ ID NO: 5)

Construct 11: promoter (SEQ ID NO: 115) and Gene (SEQ ID NO: 17)

Construct 12: promoter (SEQ ID NO: 115) and Gene (SEQ ID NO: 104)

Construct 13: promoter (SEQ ID NO: 115) and Gene (SEQ ID NO: 7)

Construct 14: promoter (SEQ ID NO: 115) and Gene (SEQ ID NO: 41)

Construct 15: promoter (SEQ ID NO: 115) and Gene (SEQ ID NO: 5)

Construct 16: promoter (SEQ ID NO: 117) and Gene (SEQ ID NO: 17)

Construct 17: promoter (SEQ ID NO: 117) and Gene (SEQ ID NO: 104)

Construct 18: promoter (SEQ ID NO: 117) and Gene (SEQ ID NO: 7)

Construct 19: promoter (SEQ ID NO: 117) and Gene (SEQ ID NO: 41)

Construct 20: promoter (SEQ ID NO: 117) and Gene (SEQ ID NO: 5)

Efficacy testing of the effect of constructs 1-20 will be performed under greenhouse and field conditions. Transgenic plants and matched wild type controls were planted to the shelve stage and truncated. The root growth was measured using metrics including the total number of roots, the rate of root growth, and the appearance of new roots after root removal. These measurements will be made by manual or digital imaging techniques. The field effect test will also determine the type and range of root control chemical applications required under normal agronomic practices. Using this metric, the effect of gene expression constructs on axillary bud initiation and growth was compared to wild type plants of the same variety. At the same time, the effect of this technique on the costs associated with root control and the chemical residue changes found in the final dry leaves will be quantified.

Example 8: TALEN-mediated mutagenesis

Transcription activator-like effector nucleases (TALEN) technology is used for genome modification in commercial tobacco varieties such as TN90, K326, and Narrow Leaf Madole. TALENs achieve genetic modification by inducing Double Strand Breaks (DSBs) in the DNA target sequence. Subsequent repair of DNA breaks by non-homologous end joining (NHEJ) or Homology Directed Repair (HDR) -mediated pathways can be used to introduce desired modifications (e.g., gene disruption, gene correction, or gene insertion).

To introduce TALENs and donor DNA into plant cells, PEG-mediated protoplast transformation was used. Tobacco leaves from 4-8 week old tobacco plants from sterile cultures were cut into small pieces and transferred to petri dishes containing sterile enzyme solution with 1.0% cellulase onuzuka R10 and 0.5% macrozym. Leaf strips in the petri dish were vacuum infiltrated in the dark for 30 minutes using a desiccator. After incubation, the digested leaves were resuspended with shaking at 45rpm for 230 minutes and then filtered through a sterile nylon filter (100 μm pore size) by collection in a 50ml centrifuge tube. The solution placed on Lymphoprep was separated at 100g for 10 minutes by a centrifuge. The protoplast bands were collected using a Pasteur pipette and used with equal volumes of NaCl, CaCl₂Purified protoplasts were washed with a W5n solution of KCl, MES and glucose and centrifuged at 2000rpm for 5 minutes. Protoplast pellet was pelleted at 2X10 in W5n solution⁵Resuspend in/ml and let stand on ice for 30 min. Then, the supernatant was removed and the protoplast pellet was resuspended in a filter-sterilized solution containing mannitol, MgCl₂And MES in MMM.

PEG transfection of tobacco protoplasts was performed according to the method described by Zhang et al (2012) with minor modifications. A500. mu.l aliquot of the protoplast suspension was transferred to a 10ml culture tube, and 25. mu.l (10. mu.g) of plasmid DNA was slowly added to the protoplast suspension. To the protoplast DNA solution, 525. mu.l of PEG solution was added and mixed carefully by tapping the tube. The tube was incubated for 20 minutes and then 2.5ml of W5n solution was added to stop the reaction. The solution was centrifuged at 100g for 5 minutes and washed with protoplast culture medium. PEG-treated protoplasts were resuspended in 1ml of medium containing 0.1mg/l NAA and 0.5mg/l BAP and mixed with 1ml of low melting agar to prepare protoplast beads. Protoplast beads were cultured in liquid medium and calli grown from the protoplast beads were transferred to solid germination medium. When the branches developed well, the branches were transferred to a magenta box for root formation. When the root system has developed completely and the branch growth has been restored, the plant is transplanted into the soil.

TALEN methods useful for preventing or reducing root-sucking growth include: (1) for targeted genomic integration in tobacco varieties, gene-specific TALENs and recombinant (HDR) donor DNA with homology derivation were designed; (2) for the root-sucking specific promoter and target gene insertion in the tobacco genome; and (3) for target gene disruption, directing the TALEN to the target gene disruption using a gene-specific TALEN (with, e.g., non-homologous end joining (NHEJ)).

(1) Targeted genomic integration:

(A) targeted genomic integration of the coding sequence into the promoter region of genes with highly specific expression in axillary buds:

instead of random gene insertion using conventional transformation methods, targeted genomic integration of coding sequences into the promoter region of genes with highly specific expression in axillary buds can be used to control expression of coding sequences by endogenous promoter activity. An example of a targeted genomic integration approach is the combination of a promoter (SEQ ID NO: 118) and a coding sequence (SEQ ID NO: 1). Using such constructs, the coding sequence (or more than one coding sequence) is homologously recombined into the genomic region of the promoter sequence and controlled by the promoter.

TALEN donor sequences are shown in SEQ ID NO: 119 (promoter and target sequences are underlined and the target gene sequence is in bold), and the TALEN target sequence is shown in SEQ ID NO: 120 (target sequence underlined).

(B) Targeted genomic integration of promoters and coding sequences to the promoter region of genes with highly specific expression in axillary buds:

to effectively provide dual doses of promoter control, a haustorium-specific promoter and coding sequences can be inserted into the promoter region of a gene that is highly expressed in axillary buds. In this method, two promoters work together to control one or more coding sequences. For example, in one end of the promoter (SEQ ID NO: 118), a construct comprising the promoter (SEQ ID NO: 113) and the coding sequence (SEQ ID NO: 13) is inserted using TALEN technology, so that expression of the coding sequence is directed by both promoters (SEQ ID NO: 118 and 113).

TALEN donor sequences are shown in SEQ ID NO: 121 (endogenous promoter underlined, and exogenous promoter italicized, and target gene bold).

(C) Root-suction specific promoter and coding sequence insertion

Another option for targeted gene integration is to insert the selected tobacco promoter and coding sequence into a significant position of the tobacco genome via TALENs.

(2) Target gene disruption

To disrupt the function of a candidate gene without the use of an RNAi construct, gene-specific TALENs are designed and introduced into tobacco cells, resulting in deletions or insertions to knock out one or more endogenous genes. For example, potential TALEN target sites in the coding sequence (SEQ ID NO: 104) were identified and homologous recombination sites within the coding sequence of the gene were selected.

TALEN target sequences are shown in SEQ ID NO: 122 (target sequence underlined).

Example 9: alternative transgenic strategies

The following strategy to regulate the root outgrowth is described herein.

The first strategy applied was to modulate axillary bud outgrowth gene expression.Mutant studies in Arabidopsis, rice and barley suggest that the genetic pathways regulating the branches are complex. There are two broad classes of genes that regulate branching. One class of genes limits shoot outgrowth and is defined by mutants with increased branching. See, e.g., the Arabidopsis BRANCHED1 gene (e.g., SEQ ID NO: 81 and possible tobacco homologs as shown in SEQ ID NOS: 13, 35, 37, 39) and more axillary branches of Arabidopsis (R) ((R))More Axill branch, MAX) gene. Another class of genes promotes axillary meristem development and is defined by mutants with reduced branching. See, e.g., Arabidopsis thaliana lateral body inhibitors (Lateral SThe uppressor, LAS) gene and possible homologues in tobacco (e.g., SEQ ID NO: 71 or 73) and Arabidopsis thaliana axillary meristem regulator: (Regulator of Axillary MAmericans, RAX) and possible tobacco homologues (e.g., SEQ ID NO: 75 and 77).

The second strategy applied was to modulate the synthesis and distribution of tobacco cytokinins.As a phytohormone, cytokinins exert many regulatory roles in shoot growth, leaf senescence delay, root growth inhibition, seed germination and stress response. Cytokinins are known to promote axillary bud growth. When cytokinins are applied directly to axillary buds or are provided by xylem flow, collateral branches increase. Cytokinin oxidase/dehydrogenase (CKX) is an enzyme that degrades cytokinin. Overexpression of a single CKX gene establishes cytokinin deficient plants and reveals that cytokinin is a positive regulator of shoot meristem activity. On the other hand, decreased expression of CKX in rice results in cytokinin accumulation in shoot meristems, thereby increasing the number of buds (such as flower buds), ultimately resulting in increased grain yield (grain yield). Based on these results, CKX expression in axillary buds can inhibit or delay axillary bud outgrowth in tobacco after truncating the shoot apical meristem.

Truncating the shoot apex releases the axillary buds from their dormancy and they begin to grow out. Auxin originating from the top of intact branches inhibits the outgrowth of axillary buds, while cytokinins induced by truncating the top of branches stimulate the outgrowth of axillary buds. The depletion of cytokinins in the axillary bud region by overexpression of the relevant enzyme under the control of an axillary bud specific promoter can be used to inhibit the outgrowth of axillary meristems. Candidate genes involved in this strategy are Arabidopsis cytokinin oxidase (CKX; SEQ ID NO: 55 encoding SEQ ID NO: 56); tobacco CKX (SEQ ID NO: 57, 59 or 61); and tobacco adenosine phosphoprenyltransferase (IPT) (SEQ ID NO: 61).

A third strategy applied is to control axillary bud outgrowth by disrupting the development of the axillary apical meristem.There are two types of transgene expression in transgenic plants: constitutive expression and tissue-specific expression. Constitutive gene expression can cause unexpected problems if genes of critical significance in one tissue are under-expressed in other tissues. Unlike constitutive expression of a gene, tissue-specific expression is the result of gene regulation in the target tissue. For tissue-specific expression, a promoter may control the expression of a given gene in a tissue-dependent manner and depending on the developmental stage of the plant. In our case, the promoter is obtained from a gene specifically expressed in the axillary bud, and the promoter is defined to regulate gene expression in the bud. To control shoot growth of shoot apical meristems, promoters (or modified promoters) may be used to direct expression of heterologous genes in tobacco plants. As a result of axillary bud specific expression, a heterologous gene (or transgene) operably linked to a promoter is expressed in the axillary bud, wherein expression of the transgene is desired, leaving the remainder of the plant unaffected by expression of the transgene.

The shoot meristems of plants consist of stem cells that are continuously complemented by a classical feedback pathway involving the signaling pathways of the homeobox wuschel (wus) gene and the clavata (clv) gene. Targeting of the WUSHEL sequence or overexpression of the CLAVATA gene in the axillary buds alters the pathway and causes defects in shoot meristem development and inhibits shoot outgrowth. Candidate genes were WUS (SEQ ID NO: 63 and 65) and CLV3(SEQ ID NO: 67).

The CENTRORADIALIS (CEN) gene, which is the meristem of the middle branch of the genus Antirrhinum (Antirrhinum), was cloned and characterizedRequired for unlimited growth of tissue. When the gene is expressed in tobacco, the tobacco plant exhibits an extended vegetative phase, delaying the transition to flowering. In tobacco, the CET gene (derived from "CEN-like gene of tobaccoCEN-like genes from tobacco) ") is not expressed in the meristem of the main branch; its expression is restricted to vegetative axillary meristems. It is evident that the CET genes play a role in the development of vegetative axillary meristems to the growth of axillary buds, but their actual function is still unknown. When their expression was silenced using the RNAi CET construct, the transgenic plants showed slow shoot growth after truncation.

Example 10: experimental data

Plant tissue was stained for GUS by immersion in staining solution (50mM sodium phosphate buffer, pH 7.0, 1mM EDTA, 0.5mg/mL 5-bromo-4-chloro-3-indolyl-D GlcUA [ X-Gluc; Biosynth AG ], 0.4% Triton X-100, and 5mM ferric/ferrous cyanide each) and incubated at 37 ℃ for 6-24 hours.

It has been shown that SEQ ID NO: the promoter shown in 117 is a good candidate for specific expression in axillary buds before and 15 days after truncation. No expression was observed in the apical meristematic region of the shoot before truncation. SEQ ID NO: the promoter shown in 117 (about 2.5kb) is SEQ ID NO: 27, which encodes a component of the eukaryotic translation initiation factor 3, subunit a (eIF-3A), i.e., the eukaryotic translation initiation factor 3(eIF-3) complex, which is essential for several steps in the initiation of protein synthesis.

Several genes were stacked by co-transformation overexpression and/or knock-down (using e.g. RNAi, under the control of the promoter shown in SEQ ID NO: 117). The following are constructs and genes stacked together by co-transformation.

a) Promoter SEQ ID NO: 117-RNAi _ CET2-26-6 targeting CET2, SEQ ID NO:11 and SEQ ID NO: 49;

b) promoter SEQ ID NO: 117-RNAi _ CET2-26-6, to the promoter SEQ ID NO: 117-AtBRC1(SEQ ID NO: 81);

c) promoter SEQ ID NO: 117-RNAi _ CET2-26-6, to the promoter SEQ ID NO: 117-SEQ ID NO:1, co-transformation; and

d) promoter SEQ ID NO: 117-SEQ ID NO:1, and the promoter SEQ ID NO: 117-AtBRC1(SEQ ID NO: 81).

It should be understood that while the methods and compositions of matter have been described herein in connection with a number of different aspects, the foregoing description of the various aspects is intended to illustrate and not limit the scope of the methods and compositions of matter. Other aspects, advantages, and modifications are within the scope of the following claims.

Appendix A

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RNAi_1(SEQ ID NO：83)

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RNAi_63 and 65(SEQ ID No：98)

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RNAi_75 and 77(SEQ ID No：100)

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45-2-7-TDNA-145337-RI(SEQ ID NO：102)

45-2-7-TDNA-348CDS-RI(SEQ ID NO：103)

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45-2-7-TDNA-22266-RI (SEQ ID NO：105)

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Transformation cassette sequence (SEQ ID NO: 111)

Agrobacterium transformation plasmid p45-2-7 sequence

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