Compositions and Methods for Manipulating the Development of Plants

Abstract

The invention provides a methods and materials for producing and selecting plants with at least one dwarfing-associated phenotype. The methods and materials relate to altering the expression, or activity, of an ARF3 poypeptide in the plant, and selecting plants with altered the expression, or activity, of an ARF3 poypeptide. The invention also provides plants produced or selected by the methods. The methods also involve crossing plants of the invention with other plants to produce further plants with at least one dwarfing-associated phenotype.

1 - 47 . (canceled) 
     
     
         48 . A method for producing a plant with at least one dwarfing-associated phenotype the method comprising altering the expression, or activity, of an ARF3 poypeptide in the plant, wherein the dwarfing-associated phenotype is selected from:
 i) one of the following phenotypes in the plant:
 a) altered auxin transport, 
 b) slower auxin transport, 
 c) reduced apical dominance, 
 d) an altered xylem/phloem ratio, 
 e) an increased number of phloem elements, 
 f) smaller phloem elements, 
 g) thicker bark, 
 h) a bushier habit, 
 i) reduced root mass, and 
   ii) competence to induce one of the following phenotypes in a scion grafted on to the plant:
 j) reduced vigour, 
 k) less vegetative growth, 
 l) earlier termination of shoot growth, 
 m) earlier competence to flower, 
 n) precocity, 
 o) earlier phase change, 
 p) smaller canopy, 
 q) reduced stem circumference, 
 r) reduced branch diameter, 
 s) fewer sylleptic branches, 
 t) shorter sylleptic branches, 
 u) more axillary flowers, 
 v) an earlier teminating primary axis, 
 w) earlier teminating secondary axes, and 
 x) shorter intenode length 
 y) reduced scion mass. 
   
     
     
         49 . The method of  claim 48  comprising increasing the expression of the ARF3 poypeptide in the plant. 
     
     
         50 . The method of  claim 48  comprising transforming the plant to express the ARF3 poypeptide in the plant. 
     
     
         51 . The method of  claim 50  comprising transforming the plant with polynucleotide encoding the ARF3 polypeptide. 
     
     
         52 . The method of  claim 51  wherein polynucleotide is operably linked to a heterologous promoter. 
     
     
         53 . The method of  claim 48  comprising modifying the sequence of an endogenous polynucleotide encoding the ARF3 polypeptide in the plant. 
     
     
         54 . The method of  claim 53  wherein modifying the endogenous polynucleotide alters the activity of the ARF3 polypeptide in the plant to induce the dwarfing-associated phenotype. 
     
     
         55 . The method of  claim 48  wherein the dwarfing-associated phenotype in the plant is at least one of reduced apical dominance, a bushier habit, an altered xylem/phloem ratio, an increased number of phloem elements and reduced root mass. 
     
     
         56 . The method of  claim 48  wherein the dwarfing-associated phenotype is the competence to induce at least one of: reduced vigour, less vegetative growth, earlier termination of shoot growth, a smaller canopy, reduced stem circumference, and reduced scion mass, in a scion grafted on to the plant. 
     
     
         57 . The method of  claim 48  wherein the method includes the step of grafting a scion on to a plant produced by the method. 
     
     
         58 . A method for producing a plant with at least one dwarfing-associated phenotype selected from:
 j) reduced vigour,   k) less vegetative growth   l) earlier termination of shoot growth   m) earlier competence to flower   n) precocity   o) earlier phase change   p) smaller canopy,   q) reduced stem circumference   r) reduced branch diameter   s) fewer sylleptic branches   t) shorter sylleptic branches   u) more axillary flowers   v) an earlier teminating primary axis,   w) earlier teminating secondary axes,   x) shorter intenode length   y) reduced scion mass   
       the method comprising the steps:
 A. providing a plant with altered the expression or activity of a ARF3 poypeptide produced by the method of  claim 48 , 
 B. grafting a scion onto the plant in A 
 
       wherein at least one of j) to y) is exhibited in the scion grafted on to the plant in A. 
     
     
         59 . The method of  claim 58  wherein the phenotype exhibited in the scion is at least one of: reduced vigour, less vegetative growth, earlier termination of shoot growth, a smaller canopy, reduced stem circumference, and reduced scion mass. 
     
     
         60 . The method of  claim 48  in which the ARF3 polypeptide has a sequence with at least 70% identity to any one of SEQ ID NO:1 to 11, 28 and 29. 
     
     
         61 . The method of  claim 60  in which the ARF3 polypeptide has a sequence with at least 70% identity to SEQ ID NO:1 or 28 (MdARF3). 
     
     
         62 . The method of  claim 60  in which the ARF3 polypeptide comprises a Leucine residue at the position corresponding amino acid residue 72 in SEQ ID NO:1 or 28 (MdARF3). 
     
     
         63 . The method of  claim 60  in which the ARF3 polypeptide comprises the sequence of SEQ ID NO:2 or 29 (M9 MdARF3) 
     
     
         64 . The method of  claim 48  in which the alteration results in expression of an ARF3 polypeptide with a Leucine residue at a position corresponding the amino acid residue 72 in SEQ ID NO:1 or 28 (MdARF3). 
     
     
         65 . A construct, cell or plant comprising a polynucleotide encoding an ARF3 polypeptide, or a fragment or variant thereof with ARF3 activity, comprising a Leucine residue at a position corresponding the amino acid residue 72 in SEQ ID NO:1 or 28 (MdARF3). 
     
     
         66 . The construct, cell or plant of  claim 65  wherein the ARF3 polypeptide comprises at least 70% identity to SEQ ID NO:2 or 29 (MdARF3). 
     
     
         67 . The construct, cell or plant of  claim 65  wherein the polypeptide comprises the sequence of SEQ ID NO:2 or 29 (M9 MdARF3). 
     
     
         68 . The construct, cell or plant of  claim 65  wherein the polynucleotide has at least 70% identity to at least one of SEQ ID NO:14 and 15. 
     
     
         69 . An isolated polynucleotide comprising the sequence with at least 70% identity to at least one of SEQ ID NO:14 or 15, or a fragment thereof, encoding a polypeptide with ARF3 activity. 
     
     
         70 . An isolated ARF3 polypeptide encoded by the polynucleotide of  claim 65 , or a fragment thereof with ARF3 activity, comprising a Leucine residue at a position corresponding the amino acid residue 72 in SEQ ID NO:1 or 28. 
     
     
         71 . A construct comprising the polynucleotide of  claim 65  operably linked to a heterologous promoter. 
     
     
         72 . A construct comprising the polynucleotide of  claim 69  operably linked to a heterologous promoter. 
     
     
         73 . A cell plant, plant part, propagule or progeny comprising the polynucleotide of  claim 65 . 
     
     
         74 . A cell plant, plant part, propagule or progeny comprising the polynucleotide of  claim 69 . 
     
     
         75 . A method for identifying a plant with a genotype indicative of at least one dwarfing-associated phenotype, the method comprising testing a plant for at least one of:
 a) altered expression of at least one ARF3 polypeptide,   b) altered expression of at least one ARF3 polynucleotide,   c) presence of a marker associated with altered expression of at least one ARF3 polypeptide,   d) presence of a marker associated with altered expression of at least one ARF3 polynucleotide,   e) presence of a marker associated with altered activity of at least one ARF3 polypeptide,   
       wherein presence of any of A) to E) indicates that the plant has at least one dwarfing—associated phenotype, and wherein the dwarfing-associated phenotype is selected from:
 i) one of the following phenotypes in the plant:
 a) altered auxin transport, 
 b) slower auxin transport, 
 c) reduced apical dominance, 
 d) an altered xylem/phloem ratio, 
 e) an increased number of phloem elements, 
 f) smaller phloem elements, 
 g) thicker bark, 
 h) a bushier habit, 
 i) reduced root mass, and 
 
 ii) competence to induce one of the following phenotypes in a scion grafted on to the plant:
 j) reduced vigour, 
 k) less vegetative growth, 
 l) earlier termination of shoot growth, 
 m) earlier competence to flower, 
 n) precocity, 
 o) earlier phase change, 
 p) smaller canopy, 
 q) reduced stem circumference, 
 r) reduced branch diameter, 
 s) fewer sylleptic branches, 
 t) shorter sylleptic branches, 
 u) more axillary flowers, 
 v) an earlier teminating primary axis, 
 w) earlier teminating secondary axes, and 
 x) shorter intenode length 
 y) reduced scion mass. 
 
 
     
     
         76 . The method of  claim 75  in which the marker associated with altered activity of at least one ARF3 polypeptide is presence of a Leucine residue at a position corresponding the amino acid residue 72 in SEQ ID NO:1 or 28 (MdARF3). 
     
     
         77 . The method of  claim 76  in which the method involves detection of a polynucleotide encoding the Leucine residue at a position corresponding the amino acid residue 72 in SEQ ID NO:1 or 28 (MdARF3). 
     
     
         78 . The method of  claim 75  including an additional step of at least one of:
 a) cultivating the identified plant, and 
 b) breeding from the identified plant. 
 
     
     
         79 . A method for producing a plant with at least one dwarfing-associated phenotype, the method comprising crossing a plant produced by a method of  claim 48  with another plant, wherein the off-spring produced by the crossing is a plant with at least one dwarfing-associated phenotype. 
     
     
         80 . A method of producing a plant with at least one dwarfing-associated phenotype selected from:
 j) reduced vigour,   k) less vegetative growth,   l) earlier termination of shoot growth,   m) earlier competence to flower,   n) precocity,   o) earlier phase change,   p) smaller canopy,   q) reduced stem circumference,   r) reduced branch diameter,   s) fewer sylleptic branches,   t) shorter sylleptic branches,   u) more axillary flowers,   v) an earlier teminating primary axis,   w) earlier teminating secondary axes,   x) shorter intenode length,   y) reduced scion mass,   
       the method comprising grafting a scion onto a plant produced by a method of  claim 48 . 
     
     
         81 . The method of  claim 80  in which the at least one dwarfing associated phenotype is exhibited in the grafted scion. 
     
     
         82 . The method of  claim 81  in which the grafted scion exhibits at least one of reduced vigour, less vegetative growth, earlier termination of shoot growth, a smaller canopy, reduced stem circumference and reduced scion mass. 
     
     
         83 . A plant that has been altered from the wild type to include a Leucine residue at the position corresponding to amino acid residue 72 in SEQ ID NO: 1 or 28. 
     
     
         84 . The plant of  claim 83  that has at least one dwarfing associated phenotype selected from:
 i) one of the following phenotypes in the plant:
 a) altered auxin transport, 
 b) slower auxin transport, 
 c) reduced apical dominance, 
 d) an altered xylem/phloem ratio, 
 e) an increased number of phloem elements, 
 f) smaller phloem elements, 
 g) thicker bark, 
 h) a bushier habit, 
 i) reduced root mass, and 
 
 ii) competence to induce one of the following phenotypes in a scion grafted on to the plant:
 j) reduced vigour, 
 k) less vegetative growth, 
 l) earlier termination of shoot growth, 
 m) earlier competence to flower, 
 n) precocity, 
 o) earlier phase change, 
 p) smaller canopy, 
 q) reduced stem circumference, 
 r) reduced branch diameter, 
 s) fewer sylleptic branches, 
 t) shorter sylleptic branches, 
 u) more axillary flowers, 
 v) an earlier teminating primary axis, 
 w) earlier teminating secondary axes, and 
 x) shorter intenode length 
 y) reduced scion mass.