Methods and Compositions for Obtaining Useful Plant Traits

Abstract

The present disclosure provides methods for obtaining plants that exhibit useful traits by perturbation of organellar function in plants. Methods for identifying genetic loci that provide for useful traits in plants and plants produced with those loci are also provided. In addition, plants and grafted plants that exhibit, contain, or harbor the useful traits, parts of the plants including seeds, and products of the plants are provided as well as methods of using the plants. Recombinant DNA vectors and transgenic plants comprising those vectors that provide for organellar perturbation are also provided.

What is claimed is: 
     
         1 . A method for producing a plant having a useful trait that exhibits nuclear inheritance comprising the steps of:
 (a) selfing a first plant wherein said plant or a parent plant thereof is or had been subjected to perturbation of organellar function;   (b) screening a population of progeny plants obtained from the selfed plant of step (a) for the useful trait; and,   (c) selecting one or more progeny plants having the useful trait that exhibits nuclear inheritance and having recovered organellar function, thereby producing a plant having a useful trait that exhibits nuclear inheritance.   
     
     
         2 . The method of  claim 1 , wherein organellar function has been recovered in any of: (i) the selfed first plant in step (a); (ii) at least a portion of the progeny plants of step (b); or (iii) one or more of the selected progeny plants in step (c). 
     
     
         3 . The method of  claim 1 , wherein the selfed first plant of step (a) exhibits a wild type phenotype or an improvement in a useful trait in comparison to a control plant. 
     
     
         4 . The method of  claim 1 , wherein the selfed first plant of step (a) exhibits one or more MSH1-dr phenotypes. 
     
     
         5 . The method of  claim 1  wherein the perturbed organellar function is a plastid function selected from the group consisting of a sensor, photosystem I, photosystem II, NAD(P)H dehydrogenase (NDH) complex, cytochrome b6f complex, and plastocyanin function. 
     
     
         6 . The method of  claim 5 , wherein the photosystem II function and/or sensor function is perturbed by suppressing expression of a gene selected from the group consisting of an MSH1, PPD3, a PsbO-1, a PsbO-2, PsbY, PsbW, PsbX, PsbR, PsbTn, PsbP1, PsbP2, PsbS, PsbQ-1, PsbQ-2, PPL1, PSAE-1, LPA2, PQL1, PQL2, and a PQL3 gene. 
     
     
         7 . The method of  claim 1 , wherein said selfed plant in step (a) is an inbred plant. 
     
     
         8 . The method of  claim 1 , wherein about 1% to about 45% of the population of progeny plants in step (b) are selected for the useful trait in step (c). 
     
     
         9 . The method of any one of  claims 1 - 8 , wherein the method further comprises making a first cross of the selected progeny plant(s) of step (c) to one or more second plant(s). 
     
     
         10 . The method of  claim 9 , wherein the selected progeny plant(s) and the second plant(s) are in a single heterotic group. 
     
     
         11 . The method of  claim 9 , wherein the second plant is isogenic to the plant or parent plant of step (a). 
     
     
         12 . The method of  claim 9 , wherein the second plant and the selected plant are in distinct heterotic groups. 
     
     
         13 . The method of  claim 9 , further comprising the step of selecting of one or more progeny of the first cross that exhibit an improvement in a useful trait in comparison to progeny of a control cross. 
     
     
         14 . The method of  claim 13 , wherein the selected progeny of the first cross comprise about 1.0% to about 45% of the population of progeny plants obtained from the first cross. 
     
     
         15 . The method of  claim 13 , wherein plants used in the control cross are of the same heterotic group as the selected progeny plant(s) and the second plant(s), but had not been subjected to organellar perturbation. 
     
     
         16 . The method of  claim 13 , wherein plants used in the control cross are isogenic to the selected plant and the second plant, but had not been subjected to organellar perturbation. 
     
     
         17 . The method of  claim 13 , further comprising the step of making a second cross of the one or more of the selected progeny plant(s) of the first cross to one or more third plants. 
     
     
         18 . The method of  claim 17 , further comprising the step of selecting of one or more progeny of the second cross that exhibit an improvement in a useful trait in comparison to progeny of a control cross. 
     
     
         19 . The method of  claim 9 , wherein the second plant or a parent plant thereof had been subjected to perturbation of organellar function. 
     
     
         20 . The method of any one of  claims 1 - 19 , wherein the organellar function is a plastid function or a mitochondrial function. 
     
     
         21 . The method of any one of  claims 1 - 20 , wherein the useful trait is transmitted by using selected progeny plant(s) or progeny thereof as pollen donors. 
     
     
         22 . A plant or progeny thereof that exhibits a useful trait that is made by the method of any one of  claims 1 - 21 . 
     
     
         23 . A plant part obtained from the plant or progeny thereof of  claim 22 . 
     
     
         24 . The plant part of  claim 23 , wherein said part is selected from the group consisting of a seed, leaf, stem, fruit, and a root. 
     
     
         25 . A processed plant product obtained from the plant part of  claim 23 . 
     
     
         26 . A clonal propagate obtained from the plant of  claim 22  or from the plant part of  claim 23 . 
     
     
         27 . A method for producing a plant having a useful trait that exhibits nuclear inheritance comprising the steps of:
 (a) crossing one or more first plant(s) to one or more second plant(s), wherein at least said first plant(s) or a parent plant thereof is or had been subjected to perturbation of organellar function and wherein either: (i) the first plant or a parent plant thereof does not exhibit any MSH1-dr phenotypes; or (ii) wherein the first plant or a parent plant thereof exhibits one or more MSH1-dr phenotype(s) and the perturbation of does not comprise direct suppression of MSH 1 gene expression;   (b) screening a population of progeny plants obtained from the cross of step (a) for the useful trait; and,   (c) selecting one or more progeny plants having the useful trait that exhibits nuclear inheritance and having recovered organellar function, thereby producing a plant exhibiting a useful trait that exhibits nuclear inheritance.   
     
     
         28 . The method of  claim 27 , wherein organellar function has been recovered in any of: (i) the first plant in step (a); (ii) at least a portion of the population of progeny plants of step (b); or (iii) one or more of the selected progeny plants in step (c). 
     
     
         29 . The method of  claim 27 , wherein the first plant(s) of step (a) exhibit a wild type phenotype or an improvement in a useful trait in comparison to a control plant. 
     
     
         30 . The method of  claim 27 , wherein about 1% to about 45% of the population of progeny plants in step (b) are selected for the useful trait in step (c). 
     
     
         31 . The method of  claim 27  wherein the perturbed organellar function is a plastid function selected from the group consisting of a sensor, photosystem I, photosystem II, NAD(P)H dehydrogenase (NDH) complex, cytochrome b6f complex, and plastocyanin function. 
     
     
         32 . The method of  claim 31 , wherein the photosystem II function and/or sensor function is perturbed by suppressing expression of a gene selected from the group consisting of an MSH1, PPD3, a PsbO-1, a PsbO-2, PsbY, PsbW, PsbX, PsbR, PsbTn, PsbP1, PsbP2, PsbS, PsbQ-1, PsbQ-2, PPL1, PSAE-1, LPA2, PQL1, PQL2, and a PQL3 gene, with the proviso that the gene is not MSH1 when first plant or a parent plant thereof exhibits an MSH1-dr phenotype. 
     
     
         33 . The method of  claim 27 , wherein said first plant in step (a) is an inbred plant. 
     
     
         34 . The method of any one of  claims 27 - 33 , wherein the method further comprises making a second cross of the selected progeny plant(s) of step (c) to one or more third plant(s). 
     
     
         35 . The method of  claim 34 , wherein the selected progeny plant(s) and the third plant are in a single heterotic group. 
     
     
         36 . The method of  claim 34 , wherein the third plant is isogenic to the first plant or parent plant of step (a). 
     
     
         37 . The method of any one of  claims 34 - 36 , further comprising the step of selecting of one or more progeny of the second cross that exhibit an improvement in a useful trait in comparison to progeny of a control cross. 
     
     
         38 . The method of  claim 37 , wherein the selected progeny of the second cross comprise about 1% to about 45% of the population of progeny plants obtained from the second cross. 
     
     
         39 . The method of  claim 38 , further comprising the step of making a third cross of the one or more of the selected progeny plants of the second cross to one or more fourth plants. 
     
     
         40 . The method of  claim 27 , wherein the second plants or a parent plant thereof had been subjected to perturbation of organellar function. 
     
     
         41 . The method of  claim 34 , wherein the third plants or a parent plant thereof had been subjected to perturbation of organellar function. 
     
     
         42 . The method of any one of  claims 27 - 41 , wherein the organellar function is a plastid or a mitochondrial function. 
     
     
         43 . The method of any one of  claims 27 - 42 , wherein the useful trait is transmitted by using selected progeny plant(s) or progeny thereof as pollen donors. 
     
     
         44 . A plant or progeny thereof that exhibits a useful trait that is made by the method of any one of  claims 27 - 43 . 
     
     
         45 . A plant part obtained from the plant or progeny thereof of  claim 44 . 
     
     
         46 . The plant part of  claim 45 , wherein said part is selected from the group consisting of a seed, leaf, stem, fruit, and a root. 
     
     
         47 . A processed plant product obtained from the plant part of  claim 45 . 
     
     
         48 . A clonal propagate obtained from the plant of  claim 44  or from the plant part of  claim 45 . 
     
     
         49 . A method of identifying a organellar perturbation agent that comprises: (a) assaying one or more candidate agents for inhibition of an interaction of an MSH-1 protein or fragment thereof with at least one assistant protein selected from the group consisting of PPD3, PsbA (D1), a PsbO-1, a PsbO-2, PetC, CAD9, KAB1, GOS12, ELI3-1, STT3B, a fragment thereof and combinations thereof; and, (b) selecting an agent that inhibits the interaction of MSH-1 or fragment thereof with the assistant protein, thereby identifying a organellar perturbation agent. 
     
     
         50 . The method of  claim 49 , wherein the fragment of MSH-1 comprises a peptide of at least about 10 amino acids located within Domain 2, 3, or 6 of MSH-1. 
     
     
         51 . The method of  claim 50 , wherein the agent is selected from the group consisting of a compound, a peptide, and a peptidomimetic compound. 
     
     
         52 . The method of  claim 51 , wherein said peptide is comprises a peptide of a peptide of at least about 10 amino acids located within Domain 2, 3, or 6 of MSH-1. 
     
     
         53 . A method of identifying a plant harboring a useful trait comprising the steps of:
 (a) crossing a candidate plant to a second plant, wherein the candidate plant is progeny of: (i) a selfed plant wherein said plant or a parent plant thereof is or had been subjected to perturbation of organellar function; or of (ii) a cross wherein at least one crossed plant or a parent plant thereof is or had been subjected to perturbation of organellar function; and,   (b) identifying one or more progeny plants from the cross in step (a) that exhibit a useful trait to a greater extent than the candidate plant, the second plant, or a control plant, thereby identifying the candidate plant as a plant that harbors a useful trait.   
     
     
         54 . The method of  claim 53 , wherein the control plant is progeny of a cross between; (i) a plant that is not progeny of a selfed plant, a crossed plant, or parent thereof that is or had been subjected to organellar perturbation; and (ii) a plant that is isogenic to the second plant. 
     
     
         55 . The method of  claim 53 , wherein the selfed plant or a parent plant thereof in (i) or the crossed plant or parent plant thereof in (ii) does not exhibit any MSH1-dr phenotypes. 
     
     
         56 . The method of  claim 55 , wherein the selfed plant or a parent plant thereof in (i) or the crossed plant or parent plant thereof in (ii) exhibits one or more MSH1-dr phenotypes. 
     
     
         57 . The method of  claim 56 , wherein the perturbation does not comprise direct suppression of MSH 1 gene expression. 
     
     
         58 . The method of any one of  claims 53 - 57 , wherein the candidate plant is used as a pollen donor in the crossing step (a). 
     
     
         59 . The method of any one of  claims 53 - 58 , wherein the identifying further comprises showing that the harbored trait exhibits nuclear inheritance. 
     
     
         60 . A plant, progeny thereof or seed thereof that harbors a useful trait, wherein said plant, progeny thereof, or seed thereof is identified or identifiable by the method of any one of  claims 53 - 59 . 
     
     
         61 . A method for producing a seed lot comprising:
 (i) growing a population of plants, wherein said population comprises two or more of the plants or progeny thereof of  claim 22 ,  44 , or  60 ;   (ii) selecting a first sub-population of plants exhibiting a useful trait; and,   (ii) obtaining a seed lot from the first selected sub-population of step (i) or, optionally, repeating steps (i) and (ii) on a second population of plants grown from the seed obtained from the first selected sub-population of plants.   
     
     
         62 . A seed lot produced by the method of  claim 61 . 
     
     
         63 . A method for producing a seed lot comprising:
 (i) growing a population of plants, wherein said population comprises two or more of the plants or progeny thereof of  claim 22 ,  44 , or  60 ; and,   (ii) obtaining a seed lot from the population.   
     
     
         64 . A seed lot produced by the method of  claim 63 .