Plants Having Enhanced Yield-Related Traits and a Method for Making the Same

Abstract

The present invention relates generally to the field of molecular biology and concerns a method for enhancing various economically important yield-related traits in plants. More specifically, the present invention concerns a method for enhancing yield-related traits in plants by modulating expression in a plant of a nucleic acid encoding a Harpin-associated Factor G polypeptide (hereinafter termed HpaG”). The present invention also concerns plants having modulated expression of a nucleic acid encoding an HpaG polypeptide, which plants have enhanced yield-related traits relative to control plants. The invention also provides constructs comprising HpaG-encoding nucleic acids, useful in performing the methods of the invention. The present invention also provides a method for enhancing yield-related traits in plants relative to control plants, by modulating (preferably increasing) expression in a plant of a nucleic acid sequence encoding a SWITCH 2/SUCROSE NON-FERMENTING 2 (SWI2/SNF2) polypeptide. The present invention also concerns plants having modulated expression of a nucleic acid sequence encoding a SWI2/SNF2 polypeptide, which plants have enhanced yield-related traits relative to control plants. The invention also provides constructs useful in performing the methods of the invention.

1 . A method for enhancing yield-related traits in plants relative to control plants, comprising modulating expression in a plant of a nucleic acid encoding an HpaG polypeptide comprising:
 23) in increasing order of preference, at least 35%, 40%, 45%, 50%, 55%, 60%, 65%, 70%, 75%, 80%, 85%, 90%, 95% or more sequence identity to the HpaG polypeptide sequence represented by SEQ ID NO: 2; and   24) an amino acid composition wherein the glycine content ranges between 13% and 25%, the glutamine content ranges between 13% and 20%, the cysteine content ranges between 0% and 1%, the histidine content ranges between 0% and 1%, and wherein tryptophan is absent.   
     
     
         2 . Method according to  claim 1 , wherein said HpaG polypeptide further comprises one or more of the following motifs:
 (i) (motif 1): G(G/E/D)(N/E)X(Q/R/P)Q(A/S)GX(N/D)G (SEQ ID NO: 3), wherein X on position 4 may be any amino acid, preferably one of S, N, P, R, or Q, and wherein X on position 9 may be any amino acid, preferably one of Q, E, S, or P; and   (ii) (motif 2): (P/A/V)S(P/Q/A)(F/L/Y)TQ(M/A)LM(H/N/Q)IV(G/M)(E/D/Q) (SEQ ID NO: 4),   
     
     
         3 . Method according to  claim 1  or  2 , wherein said modulated expression is effected by introducing and expressing in a plant a nucleic acid encoding an HpaG polypeptide. 
     
     
         4 . Method according to any preceding claim, wherein said nucleic acid encoding an Hpag polypeptide is represented by any one of the nucleic acids listed in Table A or a portion thereof, or a sequence capable of hybridising with any one of the nucleic acids given in Table A. 
     
     
         5 . Method according to any preceding claim, wherein said nucleic acid sequence encodes an orthologue or paralogue of any of the proteins given in Table A. 
     
     
         6 . Method according to any preceding claim, wherein said enhanced yield-related traits comprise increased yield, preferably increased biomass and/or increased seed yield relative to control plants. 
     
     
         7 . Method according to any one of  claims 1  to  6 , wherein said enhanced yield-related traits are obtained under non-stress conditions. 
     
     
         8 . Method according to any one of  claims 1  to  6 , wherein said enhanced yield-related traits are obtained under abiotic stress conditions. 
     
     
         9 . Method according to any one of  claims 3  to  8 , wherein said nucleic acid is operably linked to a constitutive promoter, preferably to a GOS2 promoter, most preferably to a GOS2 promoter from rice. 
     
     
         10 . Method according to any one of  claims 3  to  8 , wherein said nucleic acid is operably linked to a green tissue-specific promoter, preferably to a protochlorophyllide reductase promoter, most preferably to a protochlorophyllide reductase promoter from rice. 
     
     
         11 . Method according to any preceding claim, wherein said nucleic acid encoding an HpaG polypeptide is of prokaryotic origin, preferably from a plant pathogenic bacterium possessing a Type Three Secretion System (TTSS), further preferably from the family Pseudomonaceae, more preferably from the genus  Xanthomonas , most preferably from  Xanthomonas axonopodis.    
     
     
         12 . Plant or part thereof, including seeds, obtainable by a method according to any preceding claim, wherein said plant or part thereof comprises a recombinant nucleic acid encoding an HpaG polypeptide. 
     
     
         13 . Construct comprising:
 (a) nucleic acid encoding an HpaG polypeptide as defined in  claim 1  or  2 ;   (b) one or more control sequences capable of driving expression of the nucleic acid sequence of (a); and optionally   (c) a transcription termination sequence.   
     
     
         14 . Construct according to  claim 13 , wherein said one of said control sequences is selected from:
 (i) a constitutive promoter, preferably a GOS2 promoter, most preferably to a GOS2 promoter from rice; or   (ii) a green tissue-specific promoter, preferably a protochlorophyllide reductase promoter, most preferably a protochlorophyllide reductase promoter from rice.   
     
     
         15 . Use of a construct according to  claim 13  or  14  in a method for making plants having increased yield, particularly increased biomass and/or increased seed yield relative to control plants. 
     
     
         16 . Plant, plant part or plant cell transformed with a construct according to any of  claim 13  or  14 . 
     
     
         17 . Method for the production of a transgenic plant having increased yield, particularly increased biomass and/or increased seed yield relative to control plants, comprising:
 (i) introducing and expressing in a plant a nucleic acid encoding an HpaG polypeptide as defined in  claim 1  or  2 ; and   (ii) cultivating the plant cell under conditions promoting plant growth and development.   
     
     
         18 . Transgenic plant having increased yield, particularly increased biomass and/or increased seed yield, relative to control plants, resulting from increased expression of a nucleic acid encoding an HpaG polypeptide as defined in  claim 1  or  2 , or a transgenic plant cell derived from said transgenic plant. 
     
     
         19 . Transgenic plant according to  claim 12 ,  16  or  18 , or a transgenic plant cell derived thereof, wherein said plant is a crop plant or a monocot or a cereal, such as rice, maize, wheat, barley, millet, rye, sorghum and oats. 
     
     
         20 . Harvestable parts of a plant according to  claim 19 , wherein said harvestable parts are preferably seeds. 
     
     
         21 . Products derived from a plant according to  claim 19  and/or from harvestable parts of a plant according to  claim 18 . 
     
     
         22 . Use of a nucleic acid encoding HpaG polypeptide in increasing yield, particularly in increasing seed yield, in plants relative to control plants. 
     
     
         23 . A method for enhancing yield-related traits in plants relative to control plants, comprising increasing expression in a plant of a nucleic acid sequence encoding a SWITCH 2/SUCROSE NON-FERMENTING 2 (SWI2/SNF2) polypeptide, which SWI2/SNF2 polypeptide comprises an ATPase domain comprising from N-terminus to C-terminus at least five, preferably six, more preferably seven, most preferably eight of the following motifs:
 (i) Motif I LADDMGLGK(T/S), as represented by SEQ ID NO: 103 or a motif having in increasing order of preference at least 50%, 55%, 60%, 65%, 70%, 75%, 80%, 85%, 90%, 95%, 98%, 99% or more sequence identity to the sequence of Motif I;   (ii) Motif Ia L(L/V/I)(V/I/L)(A/C)P(T/M/V)S(V/I/L)(V/I/L)XNW, as represented by SEQ ID NO: 104 or a motif having in increasing order of preference at least 50%, 55%, 60%, 65%, 70%, 75%, 80%, 85%, 90%, 95%, 98%, 99% or more sequence identity to the sequence of Motif Ia;   (iii) Motif II DEAQ(N/A/H)(V/I/L)KN, as represented by SEQ ID NO: 105 or a motif having in increasing order of preference at least 50%, 55%, 60%, 65%, 70%, 75%, 80%, 85%, 90%, 95%, 98%, 99% or more sequence identity to the sequence of Motif II;   (iv) Motif III A(L/M)TGTPXEN, as represented by SEQ ID NO: 106 or a motif having in increasing order of preference at least 50%, 55%, 60%, 65%, 70%, 75%, 80%, 85%, 90%, 95%, 98%, 99% or more sequence identity to the sequence of Motif III;   (v) Motif IV (L/I)XF(T/S)Q(F/Y), as represented by SEQ ID NO: 107 or a motif having in increasing order of preference at least 50%, 55%, 60%, 65%, 70%, 75%, 80%, 85%, 90%, 95%, 98%, 99% or more sequence identity to the sequence of Motif IV;   (vi) Motif V S(L/V)KAGG(V/T/L)G(L/I)(N/T)LTXA(N/S/T)HV, as represented by SEQ ID NO: 108 or a motif having in increasing order of preference at least 50%, 55%, 60%, 65%, 70%, 75%, 80%, 85%, 90%, 95%, 98%, 99% or more sequence identity to the sequence of Motif V;   (vii) Motif Va DRWWNPAVE, as represented by SEQ ID NO: 109 or a motif having in increasing order of preference at least 50%, 55%, 60%, 65%, 70%, 75%, 80%, 85%, 90%, 95%, 98%, 99% or more sequence identity to the sequence of Motif Va; and   (viii) Motif VI QA(T/S)DR(A/T/V)(F/Y)R(I/L)GQ, as represented by SEQ ID NO: 110 or a motif having in increasing order of preference at least 50%, 55%, 60%, 65%, 70%, 75%, 80%, 85%, 90%, 95%, 98%, 99% or more sequence identity to the sequence of Motif VI,   where X in Motif Ia, Motif III, Motif IV, and Motif V, is any amino acid.   
     
     
         24 . Method according to  claim 23 , wherein said SWI2/SNF2 polypeptide, when used in the construction of a phylogenetic tree, such as the one depicted in  FIG. 7 , tends to cluster with the SSO1653 clade of SWI2/SNF2 polypeptides comprising the polypeptide sequence as represented by SEQ ID NO: 30 rather than with any other SWI2/SNF2 clade. 
     
     
         25 . Method according to  claim 23  or  24 , wherein said SWI2/SNF2 polypeptide comprises an ATPase domain having in increasing order of preference at least 45%, 50%, 55%, 60%, 65%, 70%, 75%, 80%, 85%, 90%, 95%, 98%, 99% or more sequence identity to the ATPase domain as represented by SEQ ID NO: 111, comprised in SEQ ID NO: 30. 
     
     
         26 . Method according to any one of  claims 23  to  25 , wherein said SWI2/SNF2 polypeptide has in increasing order of preference at least 30%, 35%, 40%, 45%, 50%, 55%, 60%, 65%, 70%, 75%, 80%, 85%, 90%, 95%, 98%, 99% or more sequence identity to the SWI2/SNF2 polypeptide as represented by SEQ ID NO: 30 or to any of the polypeptide sequences given in Table E herein. 
     
     
         27 . Method according to any one of  claims 23  to  26 , wherein said nucleic acid sequence encoding a SWI2/SNF2 polypeptide is represented by any one of the nucleic acid sequence SEQ ID NOs given in Table E or a portion thereof, or a sequence capable of hybridising with any one of the nucleic acid sequences SEQ ID NOs given in Table E. 
     
     
         28 . Method according to any one of  claims 23  to  27 , wherein said nucleic acid sequence encodes an orthologue or paralogue of any of the SEQ ID NOs given in Table E. 
     
     
         29 . Method according to any one of  claims 23  to  28 , wherein said increased expression is effected by introducing and expressing in a plant a nucleic acid sequence encoding a SWI2/SNF2 polypeptide. 
     
     
         30 . Method according to any one of  claims 23  to  29 , wherein said yield-related traits are one or more of: (i) increased number of flowers per panicle; (ii) increased total seed weight per plant; (iii) increased number of (filled) seeds; or (iv) increased harvest index. 
     
     
         31 . Method according to any one of  claims 23  to  30 , wherein said yield-related traits are enhanced in plants grown under abiotic stress conditions, preferably under water stress conditions, most preferably under drought stress conditions, relative to control plants grown under comparable stress conditions. 
     
     
         32 . Method according to  claim 31 , wherein said enhanced yield-related traits are one or more of: (i) increased aboveground area; (ii) increased total root biomass; (iii) increased thick root biomass; (iv) increased thin root biomass; (v) increased number of flowers per panicle; (vi) increased seed fill rate; (vii) increased total seed weight per plant; (viii) increased number of (filled) seeds; or (ix) increased harvest index. 
     
     
         33 . Method according to any one of  claims 23  to  32 , wherein said nucleic acid sequence is operably linked to a tissue-specific promoter, preferably to a promoter capable of preferentially expressing the nucleic acid sequence in young expanding tissues, most preferably to a beta-expansin promoter. 
     
     
         34 . Method according to any one of  claims 23  to  33 , wherein said nucleic acid sequence encoding a SWI2/SNF2 polypeptide is from a microbial genome, further preferably from archea or bacteria, more preferably from cyanobacteria, such as  Synechocystis  sp.,  Nostoc  sp.,  Synechococcus  sp.,  Prochlorococcus  sp.,  Anaebena  sp.,  Gloeobacter  sp., or  Thermosynechococcus  sp., more preferably from  Synechocystis  sp., most preferably from  Synechocystis  sp. PCC6803. 
     
     
         35 . Plants, parts thereof (including seeds), or plant cells obtainable by a method according to any one of  claims 23  to  34 , wherein said plant, part or cell thereof comprises an isolated nucleic acid transgene encoding a SWI2/SNF2 polypeptide. 
     
     
         36 . Construct comprising:
 (a) A nucleic acid sequence encoding a SWI2/SNF2 polypeptide as defined in any one of  claims 23  to  28 ;   (b) one or more control sequences capable of driving expression of the nucleic acid sequence of (a); and optionally   (c) a transcription termination sequence.   
     
     
         37 . Construct according to  claim 36 , wherein said one of said control sequences is a tissue-specific promoter, preferably a promoter for expression in young expanding tissues, most preferably a beta-expansin promoter. 
     
     
         38 . Use of a construct according to  claim 36  or  37  in a method for making plants having enhanced yield-related traits relative to control plants. 
     
     
         39 . Plant, plant part or plant cell transformed with a construct according to  claim 36  or  37 . 
     
     
         40 . Method for the production of transgenic plants having enhanced yield-related traits relative to control plants, comprising:
 (i) introducing and expressing in a plant a nucleic acid sequence encoding a SWI2/SNF2 polypeptide as defined in any one of  claims 23  to  28 ; and   (ii) cultivating the plant cell under conditions promoting plant growth and development.   
     
     
         41 . Transgenic plant having enhanced yield-related traits relative to control plants, resulting from increased expression of a nucleic acid sequence encoding a SWI2/SNF2 polypeptide as defined in any one of  claims 23  to  28 , or a transgenic plant cell derived from said transgenic plant. 
     
     
         42 . Transgenic plant according to  claim 35 ,  39  or  41 , wherein said plant is a crop plant or a monocot or a cereal, such as rice, maize, wheat, barley, millet, rye, triticale, sorghum and oats, or a transgenic plant cell derived from said transgenic plant. 
     
     
         43 . Harvestable parts of a plant according to  claim 42 , wherein said harvestable parts are preferably seeds. 
     
     
         44 . Products derived from a plant according to  claim 42  and/or from harvestable parts of a plant according to  claim 43 . 
     
     
         45 . Use of a nucleic acid sequence encoding a SWI2/SNF2 polypeptide as defined in any one of  claims 23  to  28  in enhancing yield-related traits in plants, preferably in increasing one or more of: (i) increased number of flowers per panicle; (ii) increased total seed weight per plant; (iii) increased number of (filled) seeds; or (iv) increased harvest index. 
     
     
         46 . Use of a nucleic acid sequence encoding a SWI2/SNF2 polypeptide as defined in any one of  claims 23  to  28  in enhancing yield-related traits in plants, wherein said yield-related traits are enhanced in plants grown under abiotic stress conditions, preferably under water stress conditions, most preferably under drought stress conditions, relative to control plants grown under comparable stress conditions. 
     
     
         47 . Use of a nucleic acid sequence according to  claim 45 , wherein said enhanced yield-related traits are one or more of: (i) increased aboveground area; (ii) increased total root biomass; (iii) increased thick root biomass; (iv) increased thin root biomass; (v) increased number of flowers per panicle; (vi) increased seed fill rate; (vii) increased total seed weight per plant; (viii) increased number of (filled) seeds; or (ix) increased harvest index.