# US 2019/0166779 A1 · Markers associated with soybean rust resistance and methods of use therefor

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- Number: US 2019/0166779 A1
- Document ID: US20190166779A1
- Status: Published application
- Kind: A1
- Application number: 16/053,639
- Filed: 2018-08-02
- Published: 2019-06-06
- Earliest claimed: 2008-07-18
- Assignees: Syngenta Participations AG
- Applicants: Syngenta Participations AG
- Inventors: Glenn R. Bowers; Ju-Kyung Yu; Becky Welsh Breitinger; Nanda Chakraborty
- Web page: https://patentgrep.com/patent/US20190166779A1

## CPC

- A01H 1/045: {using molecular markers}
- A01H 5/10: Seeds
- A01H 6/542: {Glycine max [soybean]}
- C12N 15/8282: {for fungal resistance}
- C12Q 1/6895: for plants, fungi or algae
- C12Q 2600/13: Plant traits
- C12Q 2600/156: Polymorphic or mutational markers
- Y10T 436/143333: Saccharide [e.g., DNA, etc.]
- A01H: NEW PLANTS OR {NON-TRANSGENIC} PROCESSES FOR OBTAINING THEM; PLANT REPRODUCTION BY TISSUE CULTURE TECHNIQUES
- 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
- Y10T: TECHNICAL SUBJECTS COVERED BY FORMER US CLASSIFICATION

## Abstract

Methods for conveying soybean rust (SBR) resistance into non-resistant soybean germplasm are provided. In some embodiments, the methods include introgressing SBR resistance into a non-resistant soybean using one or more nucleic acid markers for marker-assisted breeding among soybean lines to be used in a soybean breeding program, wherein the markers are linked to and/or associated with SBR resistance. Also provided are single nucleotide polymorphisms (SNPs) associated with resistance to SBR; soybean plants, seeds, and tissue cultures produced by any of the disclosed methods; seed produced by the disclosed soybean plants; and compositions including amplification primer pairs capable of initiating DNA polymerization by a DNA polymerase on soybean nucleic acid templates to generate soybean marker amplicons.

## Claims

### Claim 1

A method for producing a soybean rust (SBR) resistant soybean plant, the method comprising the steps of:
(a) isolating one or more nucleic acids from a plurality of soybean plants;
(b) genotyping said one or more nucleic acid for the presence of a marker associated with SBR resistance located within a chromosome interval, wherein said chromosome interval is located on soybean LG N and is defined by and comprises map positions 34.26 cM to 38.8 cM and wherein said chromosome interval further comprises a an A at position 102 at SEQ ID NO: 11; A T at position 159 of SEQ ID NO: 12; and/or a G at position 357 of SEQ ID NO: 13;
(c) selecting a first soybean plant on the basis of the presence of the marker genotyped in (b);
(d) crossing the first soybean plant of (c) with a second soybean plant not having said chromosome interval;
(e) collecting seed from the cross of (d); and
(f) growing a progeny soybean plant from the seed of (e), wherein said progeny soybean plant comprises in its genome said chromosome interval thereby producing a SBR resistant soybean plant.

### Claim 2 (depends on 1)

The method of claim 1, wherein the marker detected in (c) comprises an A at position 102 at SEQ ID NO: 11; A Tat position 159 of SEQ ID NO: 12; and/or a G at position 357 of SEQ ID NO: 13.

### Claim 3 (depends on 1)

The method of claim 1, wherein the genotyping in (b) comprises amplifying a marker locus or a portion of the marker locus and detecting the resulting amplified marker amplicon.

### Claim 4 (depends on 3)

The method of claim 3, wherein the amplifying comprises: (a) admixing an amplification primer or amplification primer pair with a nucleic acid isolated from the first Glycine max plant or germplasm, wherein the primer or primer pair is complementary or partially complementary to at least a portion of the marker locus, and is capable of initiating DNA polymerization by a DNA polymerase using the soybean nucleic acid as a template; and (b) extending the primer or primer pair in a DNA polymerization reaction comprising a DNA polymerase and a template nucleic acid to generate at least one amplicon.

### Claim 5 (depends on 4)

The method of claim 4, wherein the nucleic acid is selected from DNA and RNA.

### Claim 6 (depends on 4)

The method of claim 4, wherein the amplifying comprises employing a polymerase chain reaction (PCR) or ligase chain reaction (LCR) using a nucleic acid isolated from the first soybean plant or germplasm as a template in the PCR or LCR.

### Claim 7 (depends on 6)

The method of claim 6, wherein the amplifying is a PCR and the primers comprise any one of SEQ ID Nos: 70-81.

### Claim 8

A composition comprising any one of SEQ ID Nos: 70-81