# US 10,373,706 B2 · Variety identification-encoding system and encoding method using the same

> Agents: this data is available as JSON from the patentgrep API and MCP server — see https://patentgrep.com/llms.txt

- Number: US 10,373,706 B2
- Document ID: US10373706B2
- Status: Granted
- Kind: B2
- Application number: 14/901,922
- Filed: 2013-10-30
- Published: 2016-07-07
- Granted: 2019-08-06
- Earliest claimed: 2013-09-26
- Assignees: Republic of Korea (Management: Rural Development Administration)
- Applicants: Republic of Korea (Mngmnt: Rural Devel. Admin.)
- Inventors: Yul Ho Kim; Hyang Mi Park; Tae Young Hwang; Sun Lim Kim; Seong Bum Baek; Young Up Kwon; Wook Hwan Kim; Sang Jong Lim
- Web page: https://patentgrep.com/patent/US10373706B2

## CPC

- G16B 20/20: Allele or variant detection, e.g. single nucleotide polymorphism [SNP] detection
- C12Q 1/6895: for plants, fungi or algae
- G16B 30/00: ICT specially adapted for sequence analysis involving nucleotides or amino acids
- C12Q 2600/13: Plant traits
- C12Q 2600/156: Polymorphic or mutational markers
- G16B: BIOINFORMATICS, i.e. INFORMATION AND COMMUNICATION TECHNOLOGY [ICT] SPECIALLY ADAPTED FOR GENETIC OR PROTEIN-RELATED DATA PROCESSING IN COMPUTATIONAL MOLECULAR BIOLOGY
- 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

## Abstract

Provided is a variety identification-encoding system, including: a chromosome-decoding module decoding a chromosome of a reference genome variety and a chromosome of a target variety; a variation region-detecting module detecting a variation region in the decoded chromosome through single nucleotide variation dense region analysis; an amplification result-acquiring module setting an indel marker in the detected variation region and amplifying the indel marker by a polymerase chain reaction (PCR) to acquire an amplification result; and an encoding module encoding the amplification result.

## Claims

### Claim 1

A variety identification-encoding method, comprising the steps of:
(a) extracting DNA of a reference genome variety and a target variety by pulverization, centrifugation, and precipitation of tissue of a reference genome variety and a target variety;
(b) decoding a base sequence of extracted DNA of the reference genome variety and a base sequence of extracted DNA of the target variety;
(c) detecting a plurality of variation regions through single nucleotide variation dense region analysis, wherein a variation region is detected when the base sequence of the target variety is compared with the base sequence of the reference genome variety in units of 10 kb and a single nucleotide variation is more than 4 per 10 kb;
(d) setting a plurality of indel markers having nucleotide sequence specific to the detected plurality of variation regions and amplifying the DNA of the reference genome variety and the target variety by a polymerase chain reaction (PCR) using the set indel markers to acquire an amplification result;
(e) encoding the amplification result; and
(f) outputting an encoded result for each of the plurality of variation regions for each DNA of each target variety for two or more target varieties by a two-dimensional expression,
wherein, in the step (d), the amplification result is represented by “a” when the band size of an amplification result of the reference genome variety is the same as the band size of an amplification result of the target variety, and is represented by “b” when the band size of the amplification result of the reference genome variety is different from the band size of the amplification result of the target variety,
wherein the step (e) includes the step of:
(e1) converting the amplification result “a” into a digital signal “0” to be marked with white, and converting the amplification result “b” into a digital signal “1” to be marked with black,
wherein the two or more encoded results are represented by the two-dimensional expression and information about a female or male variety thereof is outputted as a lineage tree.

### Claim 2 (depends on 1)

The method according to claim 1, wherein the step (f) includes the step of: outputting the phenotype of the target variety together with the encoded result.

### Claim 3 (depends on 1)

The method according to claim 1, wherein the step (f) includes the steps of:
detecting regions having the differences between the two or more two-dimensional expressions; and
marking the detected regions with colors other than white and black to distinguish backcrossed varieties and recurrent parent varieties and output these varieties.

### Claim 4 (depends on 1)

The method according to claim 1, wherein the step (f) includes the steps of:
detecting hetero regions; and
marking the hetero regions with colors other than white and black to distinguish a degree of immobilization of varieties and output these varieties.

### Claim 5

A variety identification-encoding system, comprising:
a pulverizer pulverizing tissue of a reference genome variety and a target variety;
a centrifuge centrifuging the pulverized tissue;
a tube in which DNA is precipitated from supernatant obtained by the centrifuge,
a chromosome-decoder decoding a base sequence of precipitated DNA of the reference genome variety and a base sequence of precipitated DNA of the target variety;
a variation region-detector detecting a plurality of variation regions through single nucleotide variation dense region analysis, wherein a variation region is detected when the base sequence of the target variety is compared with the base sequence of the reference genome variety in units of 10 kb and a single nucleotide variation is more than 4 per 10 kb,
wherein the system is operable to set a plurality of indel markers having a nucleotide sequence specific to the detected plurality of variation regions and amplify the DNA of the reference genome variety and the target variety by a polymerase chain reaction (PCR) using the set indel markers to acquire an amplification result; and
an encoder encoding the amplification result,
wherein the system is operable to acquire the amplification result as “a” when the band size of an amplification result of the reference genome variety is the same as the band size of an amplification result of the target variety, and acquire the amplification result as “b” when the band size of an amplification result of the reference genome variety is different from the band size of an amplification result of the target variety,
wherein the encoder converts the amplification result “a” into a digital signal “0” to be marked with white, and converts the amplification result “b” into a digital signal “1” to be marked with black,
wherein the system is further operable to output an encoded result for each of the plurality of variation regions for each DNA of each target variety for two or more target varieties encoded by the encoder by a two-dimensional expression, and output information about a female or male variety thereof as a lineage tree.

### Claim 6 (depends on 5)

The system according to claim 5, wherein the system is further operable to receive a phenotype of the target variety and output the phenotype thereof.

### Claim 7 (depends on 5)

The system according to claim 5, wherein the system is further operable to output the two or more encoded results by a two-dimensional expression, and detect regions having the differences between the two or more two-dimensional expressions to mark the detected regions with colors other than white and black.

### Claim 8 (depends on 5)

The system according to claim 5, wherein the system is operable to output the two or more encoded results by a two-dimensional expression, and detect hetero regions to mark the hetero regions with colors other than white and black.