# US 2014/0157452 A1 · Plants with Useful Traits and Related Methods

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- Number: US 2014/0157452 A1
- Document ID: US20140157452A1
- Status: Published application
- Kind: A1
- Application number: 14/114,945
- Filed: 2012-05-02
- Published: 2014-06-05
- Earliest claimed: 2011-05-02
- Assignees: Board of Regents of the University of Nebraska
- Inventors: Sally Ann Mackenzie; Roberto De la Rosa Santamaria
- Web page: https://patentgrep.com/patent/US20140157452A1

## CPC

- C12N 15/8241: {Phenotypically and genetically modified plants via recombinant DNA technology}
- C12N 15/113: Non-coding nucleic acids modulating the expression of genes, e.g. antisense oligonucleotides; {Antisense DNA or RNA; Triplex- forming oligonucleotides; Catalytic nucleic acids, e.g. ribozymes; Nucleic acids used in co-suppression or gene silencing (when used in plants C12N15/8218)}
- C12N 15/8218: {Antisense, co-suppression, viral induced gene silencing [VIGS], post-transcriptional induced gene silencing [PTGS]}
- C12N 15/8261: {with agronomic (input) traits, e.g. crop yield}
- C12Q 1/6895: for plants, fungi or algae
- C12Q 2600/13: Plant traits
- C12Q 2600/154: Methylation markers
- C12Q 2600/156: Polymorphic or mutational markers
- C12Q 2600/158: Expression markers
- Y02A 40/146: Genetically Modified [GMO] plants, e.g. transgenic plants
- C12N: MICROORGANISMS OR ENZYMES; COMPOSITIONS THEREOF; PROPAGATING, PRESERVING, OR MAINTAINING MICROORGANISMS; MUTATION OR GENETIC ENGINEERING; CULTURE MEDIA (microbiological testing media C12Q1/00)
- C12Q: MEASURING OR TESTING PROCESSES INVOLVING ENZYMES, NUCLEIC ACIDS OR MICROORGANISMS (immunoassay G01N33/53); COMPOSITIONS OR TEST PAPERS THEREFOR; PROCESSES OF PREPARING SUCH COMPOSITIONS; CONDITION-RESPONSIVE CONTROL IN MICROBIOLOGICAL OR ENZYMOLOGICAL PROCESSES
- Y02A: TECHNOLOGIES FOR ADAPTATION TO CLIMATE CHANGE

## Abstract

The present invention provides methods for obtaining plants that exhibit useful traits by transient suppression of the MSH1 gene of the 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 that exhibit the useful traits, parts of the plants including seeds, and products of the plants are provided as well as methods of using the plants.

## Claims

### Claim 1

A method for producing a plant exhibiting a useful trait comprising the steps of:
a. suppressing expression of MSH1 gene(s) in a first parental plant or plant cell;
b. outcrossing the parental plant of step (a), progeny of said parental plant of step (a), a plant obtained from said plant cell of step (a), or progeny of a plant obtained from said plant cell of step (a) to a second plant wherein MSH1 had not been suppressed;
c. screening a population of progeny plants obtained from said outcross of step (b) for at least one useful trait, wherein a portion of said population of progeny plants express MSH1; and,
d. selecting a progeny plant having a useful trait that exhibits nuclear inheritance, wherein said trait is not caused by substoichiometric shifting (SSS) in mitochondria of the selected progeny plant and wherein said selected progeny plant expresses MSH1, thereby producing a plant exhibiting a useful trait.

### Claim 2 (depends on 1)

The method of claim 1, further comprising the step of comparing methylation status of chromosomal DNA of one or more altered chromosomal loci in the nucleus of plant cells of said progeny plant of step (d) and a reference plant that does not exhibit the useful trait.

### Claim 3 (depends on 1)

The method of claim 1, wherein suppression of MSH1 expression is effected with a MSH1 nucleic acid fragment of 21 or more nucleotides.

### Claim 4 (depends on 1)

The method of claim 1, wherein said method further comprises the step of producing seed from: i) a selfed progeny plant of step (d), ii) an out-crossed progeny plant of step (d), or, iii) from both of a selfed and an out-crossed progeny plant of step (d).

### Claim 5 (depends on 4)

The method of claim 4, wherein said method further comprises the step of assaying said seed or plants grown from said seed for the presence of said trait.

### Claim 6 (depends on 1)

The method of claim 1, wherein said first parental plant or plant cell comprises a transgene that can suppress expression of MSH1.

### Claim 7 (depends on 6)

The method of claim 6, wherein said transgene is selected from the group of transgenes that suppress expression of MSH1 by producing a small inhibitory RNA (siRNA), a microRNA (miRNA), a co-suppressing sense RNA, and/or an anti-sense RNA.

### Claim 8 (depends on 1)

The method of claim 1, wherein said first parental plant or plant cell is obtained by crossing an female plant with a distinct male plant, wherein at least one of said female or male plants comprise a transgene that suppresses expression of the endogenous MSH1 gene of said parental plant(s).

### Claim 9 (depends on 1)

The method of claim 1, wherein said first parental plant or plant cell was isogenic to said second parental plant prior to suppression of MSH1 in said first parental plant or plant cell.

### Claim 10 (depends on 1)

The method of claim 1, wherein said trait is selected from the group consisting of yield, male sterility, non-flowering, biotic stress, and abiotic stress.

### Claim 11 (depends on 1)

The method of claim 1, wherein suppression of MSH1 expression is effected with a MSH1 nucleic acid fragment of 18 nucleotides to about 500 nucleotides.

### Claim 12 (depends on 140)

The method of claim 140, wherein said trait is male sterility.

### Claim 13 (depends on 1)

The method of claim 1, wherein said progeny plant in step (d) or progeny thereof exhibit an improvement in said trait in comparison to a plant that had not been subjected to suppression of MSH1 expression but was otherwise isogenic to said first parental plant or plant cell.

### Claim 14 (depends on 1)

The method of claim 1, wherein said plant is a crop plant.

### Claim 15 (depends on 14)

The method of claim 14, wherein said crop plant is selected from the group consisting of corn, soybean, cotton, canola, wheat, rice, tomato, tobacco, millet, and sorghum.

### Claim 16 (depends on 15)

The method of claim 15, wherein said crop is sorghum.

### Claim 17 (depends on 16)

The method of claim 16, wherein said trait is selected from the group consisting of panicle length, panicle weight, dry biomass, and combinations thereof.

### Claim 18 (depends on 1)

A plant produced by the method of claim 1, wherein said plant exhibits an improvement in at least one useful trait in comparison to a plant that had not been subjected to suppression of MSH1 expression but was otherwise isogenic to said first parental plant or plant cell and wherein the plant comprises one or more altered chromosomal loci having an altered methylation status in comparison to a reference plant that does not exhibit the useful trait.

### Claim 19 (depends on 18)

The plant of claim 18 wherein said plant is inbred.

### Claim 20 (depends on 18)

Seed obtained from the plant of claim 18, wherein the seed or a plant obtained therefrom exhibits the improvement in at least one useful trait and wherein the seed comprises the one or more altered chromosomal loci.

### Claim 21 (depends on 18)

A processed product from the plant of claim 18 or from the seed therefrom, wherein said product comprises a detectable amount of a nuclear chromosomal DNA comprising one or more chromosomal loci having an altered methylation status in comparison to a reference plant that does not exhibit the useful trait.

### Claim 22 (depends on 21)

The processed product of claim 21, wherein said product is oil, meal, lint, hulls, or a pressed cake.

### Claim 23 (depends on 18)

A method for producing a lot of seed, comprising the steps of selfing a population of plants of claim 18, and harvesting seed therefrom, wherein the harvested seed or a plant obtained therefrom exhibits the improvement in at least one useful trait.

### Claim at position 24

-43. (canceled)