# US 12,180,497 B2 · Resistance genes associated with disease resistance in soybeans

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- Number: US 12,180,497 B2
- Document ID: US12180497B2
- Status: Granted
- Kind: B2
- Application number: 17/631,174
- Filed: 2020-07-30
- Published: 2022-08-25
- Granted: 2024-12-31
- Earliest claimed: 2019-08-01
- Assignees: Syngenta Crop Protection AG
- Applicants: Syngenta Crop Protection AG
- Inventors: Qingli Liu; Robert Arthur Dietrich; Thomas Joseph Curley, Jr.; Becky Welsh Breitinger; John Daniel Hipskind; John Luther Dawson; Xiaoping Tan; Andrew David Farmer
- Web page: https://patentgrep.com/patent/US12180497B2

## CPC

- A01N 65/00: Biocides, pest repellants or attractants, or plant growth regulators containing material from algae, lichens, bryophyta, multi-cellular fungi or plants, or extracts thereof (containing compounds of determined constitution A01N27/00 - A01N59/00)
- C12N 15/8282: {for fungal resistance}
- A01H 1/045: {using molecular markers}
- A01H 1/1255: {for fungal resistance}
- A01H 5/10: Seeds
- A01H 6/542: {Glycine max [soybean]}
- A01N 63/50: Isolated enzymes; Isolated proteins (peptides A01N37/46)
- C07K 14/415: from plants
- C12Q 1/6895: for plants, fungi or algae
- C12Q 2600/13: Plant traits
- Y02A 40/146: Genetically Modified [GMO] plants, e.g. transgenic plants
- A01N: PRESERVATION OF BODIES OF HUMANS OR ANIMALS OR PLANTS OR PARTS THEREOF (preservation of food or foodstuff A23); BIOCIDES, e.g. AS DISINFECTANTS, AS PESTICIDES OR AS HERBICIDES (preparations for medical, dental or toiletry purposes which kill or prevent the growth or proliferation of unwanted organisms A61K); PEST REPELLANTS OR ATTRACTANTS; PLANT GROWTH REGULATORS
- C12N: MICROORGANISMS OR ENZYMES; COMPOSITIONS THEREOF; PROPAGATING, PRESERVING, OR MAINTAINING MICROORGANISMS; MUTATION OR GENETIC ENGINEERING; CULTURE MEDIA (microbiological testing media C12Q1/00)
- A01H: NEW PLANTS OR {NON-TRANSGENIC} PROCESSES FOR OBTAINING THEM; PLANT REPRODUCTION BY TISSUE CULTURE TECHNIQUES
- C07K: PEPTIDES (peptides in foodstuffs A23; obtaining protein compositions for foodstuffs, working-up proteins for foodstuffs A23J; preparations for medicinal purposes A61K; peptides containing beta-lactam rings C07D; cyclic dipeptides not having in their molecule any other peptide link than those which form their ring, e.g. piperazine-2,5-diones, C07D; ergot alkaloids of the cyclic peptide type C07D519/02; macromolecular compounds having statistically distributed amino acid units in their molecules, i.e. when the preparation does not provide for a specific; but for a random sequence of the amino acid units, homopolyamides and block copolyamides derived from amino acids C08G69/00; macromolecular products derived from proteins C08H1/00; preparation of glue or gelatine C09H; single cell proteins, enzymes C12N; genetic engineering processes for obtaining peptides C12N15/00; compositions for measuring or testing processes involving enzymes C12Q; investigation or analysis of biological material G01N33/00)
- 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 relates to methods and compositions for identifying, selecting and/or producing a Disease resistant soybean plant or germplasm using genes derived from Glycine canescens, Glycine clandestina, Glycine tomentella. A soybean plant or germplasm that has been identified, selected and/or produced by any of the methods of the present invention is also provided. Disease resistant soybean seeds, plants and germplasms are also provided.

## Claims

### Claim 1

A nucleic acid molecule comprising a polynucleotide operably linked to a heterologous promoter, wherein said polynucleotide encodes a polypeptide having at least 95% sequence identity to the full length of SEQ ID NO: 11, wherein co-expression of said polypeptide with a polypeptide having at least 90% sequence identity to the full length of SEQ ID NO: 16, in a soybean plant, enhances resistance of the plant to Asian Soybean Rust (ASR) compared to a control plant.

### Claim 2 (depends on 1)

The nucleic acid molecule of claim 1, wherein the polynucleotide comprises:
(a) the nucleotide sequence of any one of SEQ ID NOs: 7, or 8; or
(b) a nucleotide sequence having at least 90% sequence identity to the full length of any one of SEQ ID NOS: 7, or 8.

### Claim 3 (depends on 1)

The nucleic acid molecule of claim 1, wherein the heterologous promoter is a plant expressible promoter.

### Claim 4 (depends on 3)

The nucleic acid molecule of claim 3, wherein the heterologous promoter comprises SEQ ID NO: 9.

### Claim 5 (depends on 1)

A vector comprising the nucleic acid molecule of claim 1.

### Claim 6 (depends on 1)

A transgenic cell comprising the nucleic acid molecule of claim 1.

### Claim 7

A method of producing a transgenic soybean plant with increased resistance to a soybean pathogen, the method comprising:
introducing into the genome of a soybean plant, a nucleic acid molecule comprising a first expression cassette comprising a first polynucleotide encoding a polypeptide having at least 95% sequence identity to the full length of SEQ ID NO: 11 operably coupled to a first heterologous, plant active promoter, and a second expression cassette comprising a second polynucleotide encoding a polypeptide having at least 95% sequence identity to the full length of SEQ ID NO: 16 operably coupled to a second heterologous, plant active promoter, wherein the polypeptide having at least 95% sequence identity to the full length of SEQ ID NO: 11 is co-expressed with the polypeptide having at least 95% sequence identity to the full length of SEQ ID NO: 16 in the plant, thereby producing a transgenic soybean plant with increased resistance to a soybean pathogen, wherein the soybean pathogen is Asian Soy Rust.

### Claim 8 (depends on 7)

The method according to claim 7, wherein the introducing step comprises:
(i) transforming a soybean plant cell with the nucleic acid molecule, thereby incorporating said nucleic acid molecule into the genome of the soybean plant cell, and regenerating a transgenic soybean plant from the transformed soybean plant cell; or
(ii) crossing a first soybean plant comprising the nucleic acid molecule with a second, different soybean plant.

### Claim 9 (depends on 8)

The method according to claim 8, wherein the method further comprises obtaining a progeny soybean plant for one or more generations from the transgenic soybean plant, wherein the progeny soybean plant comprises the nucleic acid molecule in the genome of the plant and has increased resistance to the soybean pathogen.

### Claim 10

A transgenic soybean plant comprising in its genome a first expression cassette comprising a polynucleotide encoding a protein having at least 95% sequence identity to the full length of SEQ ID NO: 11 operably coupled to a first heterologous plant expressible promoter, and a second expression cassette comprising a polynucleotide encoding a protein having at least 95% sequence identity to the full length of SEQ ID NO: 16 operably coupled to a second heterologous plant expressible promoter, wherein said transgenic soybean plant has increased pathogen resistance to Asian Soy Rust (ASR) relative to a soybean plant not comprising the first and second expression cassette.

### Claim 11 (depends on 10)

The transgenic soybean plant of claim 10, wherein the soybean plant further has increased resistance to any one of the following: soy cyst nematode, bacterial pustule, root knot nematode, frog eye leaf spot, phytopthora, brown stem rot, nematode, smut, Golovinomyces cichoracearum, Erysiphe cichoracearum, Blumeria graminis, Podosphaera xanthii, Sphaerotheca fuliginea, Pythium ultimum, Uncinula necator, Mycosphaerella pinodes, Magnaporthe grisea, Bipolaris oryzae, Magnaporthe grisea, Rhizoctonia solani, Phytophthora sojae, Schizaphis graminum, Bemisia tabaci, Rhopalosiphum maidis, Deroceras reticulatum, Diatraea saccharalis, Schizaphis graminum or Myzus persicae.

### Claim 12

A nucleic acid molecule comprising a polynucleotide operably linked to a heterologous promoter, wherein said polynucleotide encodes a polypeptide having at least 95% sequence identity to the full length of SEQ ID NO: 16, wherein co-expression of said polypeptide, with a polypeptide having at least 95% sequence identity to the full length of SEQ ID NO: 11, in a soybean plant, enhances resistance of the plant to Asian Soybean Rust (ASR) compared to a control plant.

### Claim 13 (depends on 12)

The nucleic acid molecule of claim 12, wherein the polynucleotide comprises:
(i) the nucleotide sequence of any one of SEQ ID NOs: 12-13; or
(ii) a nucleotide sequence having at least 90% sequence identity to the full length of any one of SEQ ID NOs: 12-13.

### Claim 14 (depends on 12)

A vector comprising the nucleic acid molecule of claim 12.

### Claim 15 (depends on 1)

The nucleic acid molecule of claim 1, wherein said polynucleotide encodes a polypeptide having at least 98% sequence identity to the full length of SEQ ID NO: 11.

### Claim 16 (depends on 1)

The nucleic acid molecule of claim 1, wherein said polynucleotide encodes a polypeptide having at least 99% sequence identity to the full length of SEQ ID NO: 11.

### Claim 17 (depends on 16)

The nucleic acid molecule of claim 16, wherein said polynucleotide encodes a polypeptide comprising SEQ ID NO:11.

### Claim 18 (depends on 12)

The nucleic acid molecule of claim 12, wherein said polynucleotide encodes a polypeptide having at least 98% sequence identity to the full length of SEQ ID NO: 16.

### Claim 19 (depends on 12)

The nucleic acid molecule of claim 12, wherein said polynucleotide encodes a polypeptide having at least 99% sequence identity to the full length of SEQ ID NO: 16.

### Claim 20 (depends on 19)

The nucleic acid molecule of claim 19, wherein said polynucleotide encodes a polypeptide comprising SEQ ID NO: 16.

### Claim 21 (depends on 10)

The transgenic soybean plant of claim 10, wherein the polynucleotide in the first expression cassette encodes a protein having at least 98% sequence identity to the full length of SEQ ID NO: 11, and the polynucleotide in the second expression cassette encodes a protein having at least 98% sequence identity to the full length of a SEQ ID NO: 16.

### Claim 22 (depends on 21)

The transgenic soybean plant of claim 21, wherein the polynucleotide in the first expression cassette encodes a protein comprising SEQ ID NO: 11, and the polynucleotide in the second expression cassette encodes a protein comprising SEQ ID NO: 16.

### Claim 23 (depends on 10)

The transgenic soybean plant of claim 10, wherein the polynucleotide in the first expression cassette comprises SEQ ID NO: 7 or 8, and the polynucleotide in the second expression cassette comprises SEQ ID NO: 12 or 13.

### Claim 24 (depends on 10)

The transgenic soybean plant of claim 10, wherein the plant is an elite soybean plant.

### Claim 25

A seed of a transgenic soybean plant having increased resistance to Asian Soy Rust, wherein the seed comprises, in its genome, a first expression cassette comprising a polynucleotide encoding a protein having at least 95% sequence identity to the full length of SEQ ID NO: 11 operably coupled to a first heterologous plant expressible promoter, and a second expression cassette comprising a polynucleotide encoding a protein having at least 95% sequence identity to the full length of SEQ ID NO: 16 operably coupled to a second heterologous plant expressible promoter.

### Claim 26 (depends on 25)

The seed of claim 25, wherein the polynucleotide in the first expression cassette encodes a protein having at least 98% sequence identity to the full length of SEQ ID NO: 11, and the polynucleotide in the second expression cassette encodes a protein having at least 98% sequence identity to the full length of SEQ ID NO: 16.

### Claim 27 (depends on 26)

The seed of claim 26, wherein the polynucleotide in the first expression cassette encodes a protein comprising SEQ ID NO: 11, and the polynucleotide in the second expression cassette encodes a protein comprising SEQ ID NO: 16.

### Claim 28 (depends on 25)

The seed of claim 25, wherein the polynucleotide in the first expression cassette comprises SEQ ID NO: 7 or 8, and the polynucleotide in the second expression cassette comprises SEQ ID NO: 12 or 13.

### Claim 29 (depends on 25)

The seed of claim 25, wherein the transgenic soybean plant is an elite soybean plant.

### Claim 30 (depends on 7)

The method of claim 7, wherein the polynucleotide in the first expression cassette encodes a polypeptide having at least 98% sequence identity to the full length of SEQ ID NO: 11, and the polynucleotide in the second expression cassette encodes a polypeptide having at least 98% sequence identity to the full length of SEQ ID NO: 16.

### Claim 31 (depends on 30)

The method of claim 30, wherein the polynucleotide in the first expression cassette encodes a polypeptide having at least 99% sequence identity to the full length of SEQ ID NO: 11, and the polynucleotide in the second expression cassette encodes a polypeptide having at least 99% sequence identity to the full length of SEQ ID NO: 16.

### Claim 32 (depends on 30)

The method of claim 30, wherein the polynucleotide in the first expression cassette encodes a polypeptide comprising SEQ ID NO: 11, and the polynucleotide in the second expression cassette encodes a polypeptide comprising SEQ ID NO: 16.

### Claim 33 (depends on 3)

The nucleic acid molecule of claim 3, wherein the heterologous promoter comprises SEQ ID NO: 14.

### Claim 34 (depends on 3)

The nucleic acid molecule of claim 3, wherein the heterologous promoter comprises SEQ ID NO: 19.

### Claim 35 (depends on 3)

The nucleic acid molecule of claim 3, wherein the heterologous promoter comprises SEQ ID. NO: 20.

### Claim 36 (depends on 3)

The nucleic acid molecule of claim 3, wherein the heterologous promoter comprises SEQ ID NO: 21.

### Claim 37 (depends on 3)

The nucleic acid molecule of claim 3, wherein the heterologous promoter comprises SEQ ID NO: 22.