Compositions and Methods for Increasing Plant Tolerance to High Population Density

Abstract

Compositions and methods for suppressing the shade-avoidance response of plants and improving plant yield are provided. Compositions of the invention include an early flowering 3 (ELF3) maize gene, the promoter for this gene, an Arabidopsis basic helix-loop-helix transcription factor (bHLH-041), and fragments and variants thereof. The ELF3 promoter sequence is useful for driving expression of polynucleotides of interest in a plant. The ELF3 and bHLH-041 sequences of the invention, or variants and fragments thereof, are provided in expression cassettes for use in manipulating expression of the ELF3 and bHLH-041 genes. By increasing expression of ELF3 and/or suppressing expression of bHLH-041, the methods of the invention provide for altered response of a plant to light quality and suppression of the high-density-invoked survival mode of development. The invention thus provides methods for growing crop plants at high population densities for yield enhancement. Transformed plants having the altered shade-avoidance phenotype of the invention, and seeds of said plants, are also provided.

1 . A method for improving performance of a plant grown in high population density conditions, comprising:
 a) transforming a plant cell with a construct comprising an ELF3 polynucleotide; and   b) regenerating a plant from said transformed cell   
       wherein expression of the polypeptide encoded by the ELF3 polynucleotide is increased in the regenerated plant or its transformed progeny, relative to expression in a control plant. 
     
     
         2 . The method of  claim 1 , wherein improved performance is measured in increased grain yield, relative to a control plant. 
     
     
         3 . The method of  claim 1 , wherein improved performance is measured in increased biomass production, relative to a control plant. 
     
     
         4 . The method of  claim 1 , wherein the ELF3 polynucleotide is selected from the group consisting of:
 (a) the nucleotide sequence set forth in SEQ ID NO: 1 or SEQ ID NO: 2;   (b) a nucleotide sequence encoding a polypeptide comprising the amino acid sequence of SEQ ID NO: 3;   (c) a nucleotide sequence comprising at least 90% sequence identity to the sequence set forth in SEQ ID NO: 1 or SEQ ID NO: 2, wherein said polynucleotide encodes a polypeptide having ELF3 protein activity; and   (d) a nucleotide sequence encoding a polypeptide with an amino acid sequence at least 90% identical to SEQ ID NO: 3, wherein said encoded polypeptide has ELF3 protein activity.   
     
     
         5 . The method of  claim 1 , wherein said polynucleotide is operably linked to a promoter selected from the group consisting of a constitutive promoter, a leaf-preferred promoter, a light-regulated promoter, and a circadian-clock-regulated promoter. 
     
     
         6 . A method for improving performance of a plant grown in high population density conditions, comprising:
 (a) transforming a plant cell with an expression cassette which reduces the level or activity of a native bHLH-041 polynucleotide or its encoded polypeptide; and   (b) regenerating a plant from said transformed cell,   
       wherein the level or activity of the polypeptide encoded by the native bHLH-041 polynucleotide is reduced in the regenerated plant or its transformed progeny, relative to expression in a control plant. 
     
     
         7 . The method of  claim 6 , wherein improved performance is measured in increased grain yield, relative to a control plant. 
     
     
         8 . The method of  claim 6 , wherein improved performance is measured in increased biomass production, relative to a control plant. 
     
     
         9 . The method of  claim 6 , wherein said expression cassette comprises a sequence selected from the group consisting of:
 (a) the nucleotide sequence set forth in SEQ ID NO: 5, or its complement;   (b) a nucleotide sequence encoding a polypeptide comprising the amino acid sequence of SEQ ID NO: 6;   (c) a nucleotide sequence comprising at least 90% sequence identity to the sequence set forth in SEQ ID NO: 5, or its complement;   (d) a nucleotide sequence comprising at least 10 consecutive nucleotides of a sequence of (a), (b) or (c); and   (e) a nucleotide sequence comprising at least 10 consecutive nucleotides of a sequence of (a), (b) or (c), and the nucleotides complementary thereto.   
     
     
         10 . The method of  claim 6 , wherein said polynucleotide is operably linked to a promoter selected from the group consisting of a constitutive promoter, a leaf-preferred promoter, a light-regulated promoter and a circadian-clock-regulated promoter. 
     
     
         11 . The method of  claim 6 , wherein said expression cassette comprises:
 (a) a sense sequence comprising at least 19 nucleotides corresponding to an mRNA encoding said bHLH-041 polypeptide;   (b) a sequence having at least 94% identity to the complement of the sense sequence of (a); and   (c) an operably linked promoter that drives expression in a plant cell.   
     
     
         12 . The method of  claim 6 , wherein said expression cassette comprises a polynucleotide which encodes a polypeptide with an incomplete bHLH domain. 
     
     
         13 . The method of  claim 12 , wherein the basic region of the bHLH domain is retained. 
     
     
         14 . The method of  claim 6 , further comprising increasing the level or activity of an ELF3 polypeptide in said plant. 
     
     
         15 . An isolated polynucleotide comprising a nucleotide sequence selected from the group consisting of:
 (a) the nucleotide sequence set forth in SEQ ID NO: 1 or SEQ ID NO: 2;   (b) the nucleotide sequence set forth in SEQ ID NO:5;   (c) a nucleotide sequence encoding a polypeptide comprising the amino acid sequence of SEQ ID NO: 3 or SEQ ID NO: 6;   (d) a nucleotide sequence comprising at least 90% sequence identity to the sequence set forth in SEQ ID NO: 1 or SEQ ID NO: 2, wherein said polynucleotide encodes a polypeptide having ELF3 protein activity;   (e) a nucleotide sequence comprising at least 90% sequence identity to the sequence set forth in SEQ ID NO: 5, wherein said polynucleotide encodes a polypeptide having bHLH-041 protein activity;   (f) a nucleotide sequence comprising at least 15 consecutive nucleotides of   SEQ ID NO: 1, SEQ ID NO: 2, or SEQ ID NO: 5 or a complement thereof;   (g) a nucleotide sequence encoding a polypeptide with an amino acid sequence at least 90% identical to SEQ ID NO: 3, wherein said encoded polypeptide has ELF3 protein activity; and   (h) a nucleotide sequence encoding a polypeptide with an amino acid sequence at least 90% identical to SEQ ID NO: 6, wherein said polypeptide has bHLH-041 protein activity.   
     
     
         16 . An expression cassette comprising the polynucleotide of  claim 15  operably linked to a promoter that drives expression in a plant cell. 
     
     
         17 . A plant comprising the expression cassette of  claim 16 . 
     
     
         18 . The plant of  claim 17 , wherein said plant is a monocot. 
     
     
         19 . The plant of  claim 18 , wherein said monocot is maize, wheat, rice, barley, sorghum, or rye. 
     
     
         20 . The plant of  claim 17 , wherein said plant is a dicot. 
     
     
         21 . The plant of  claim 20 , wherein said dicot is soybean,  Brassica , sunflower, cotton, or alfalfa. 
     
     
         22 . A seed of the plant of  claim 17 , wherein said seed comprises said expression cassette. 
     
     
         23 . A polynucleotide of SEQ ID NO: 4. 
     
     
         24 . A method for modulating expression of a polynucleotide of interest in a plant, comprising
 (a) transforming a plant cell with an expression cassette comprising the polynucleotide of interest operably linked to a polynucleotide of SEQ ID NO: 4 or an operable fragment thereof; and   (b) regenerating a plant from said transformed plant cell,   
       wherein expression of the polynucleotide of interest is modulated.