Method for identifying racehorse using microsatellite marker

Provided is a method for identifying a racehorse including amplifying a target gene by a multiplex PCR using a microsatellite marker obtained by combining one or more sets selected from a first set consisting of AHT4, AHT5, ASB2, HMS3, HMS6, HMS7, HTG4, HTG10, VHL20, ASB17, ASB23, HMS1, LEX3, CA425, HMS2, HTG6, HTG7, LEX033, AMEL, HMS18, LEX27, SRY, and LEX020 and a second set consisting of HTG21, COR089, TKY279, TKY287, TKY294, TKY297, TKY301, TKY312, TKY321, TKY325, TKY333, TKY337, TKY341, TKY343, TKY344, TKY374, and TKY394; detecting alleles in the product amplified in the multiplex PCR amplification step and analyzing the sizes of the alleles using an electrophoresis apparatus to determine a genotype of the racehorse; and summarizing the sizes of the alleles analyzed using the electrophoresis apparatus according to the population and breed of racehorses to plot the number and a frequency distribution of the alleles based on the summarized results.

CROSS-REFERENCE TO RELATED APPLICATION

This application claims priority to and the benefit of Korean Patent Application No. 2021-0002808, filed Jan. 8, 2021, the disclosure of which is incorporated herein by reference in its entirety.

BACKGROUND

1. Field of the Invention

The present invention relates to a method for identifying a racehorse using a microsatellite marker, and more particularly, to a method for identifying a racehorse using a microsatellite marker capable of performing a multiplex polymerase chain reaction (PCR) using a microsatellite marker to more rapidly, accurately and economically distinguish a population of racehorses and stably perform paternity tests, and the like, compared to existing techniques.

2. Discussion of Related Art

In recent years, much interest and effort have been put into the characterization and use of genetic resources as well as attainment, preservation, and management of the genetic resources with the recognized importance of their future value of utility. In particular, the evaluation of molecular biological characterization for understanding the genetic characteristics (such as the origin, variety formation, genetic diversity, taxonomic relationships with other varieties, and the like) of possessed resources using various genetic markers based on DNA polymorphism has been actively performed (Groeneveld et al., (2010) Anim Genet. 41: 6-31).

Microsatellites (MSs) have a structure in which a DNA sequence of 2 to 6 bases is repeated, and is present widely throughout the non-coding regions on eukaryotic DNA (Tautz and Renz, (1984) Nucleic Acids Res. 12: 4127-4138).

Also, there is a lot of polymorphic information because approximately 10 alleles are present per locus of one microsatellite, and DNA extracted from various samples such as blood, hair roots, skin, and the like may be easily amplified due to its small size. In particular, the microsatellites have an advantage in that it is possible to easily analyze allelotypes at low cost because a multiplex PCR technique in which the PCR reaction and amplification may be performed at one time using two or more microsatellite-specific primers is applicable to the microsatellites (Butler, (2007) Biotechniques 43: Sii-Sv).

Such advantages of the microsatellites have been used to analyze the genetic traits and taxonomic relationships of human beings and animals (including domestic animals) since the 1990s, and thus the microsatellites have been used as the most efficient genetic markers (Naidoo and Chetty, (1998) Pathol Oncol Res. 4: 310-315).

To date, the microsatellites have also been used to identify the genetic diversity and quantitative genetic loci of the varieties or groups, distinguish a population of the varieties or groups, and perform paternity tests (Gutierrez-Gil et al., (2010) Meat Sci. 85: 721-729; Costa et al., (2012) BMC Res Notes. 5: 479). In Korea, various academic and industrial outcomes have also been deduced through the analysis of microsatellites, and the development of a method of distinguishing between Korean beef and imported beef, a beef history management system, and the like have been promoted.

Meanwhile, a genetic testing technique using genetic markers (microsatellite markers) developed to conserve the genes of racehorses, study the genetic diversity between varieties, and perform a paternity test has been used, but has drawbacks in that it has its poor utility and accuracy, and it requires relatively high inspection costs and a longer analysis time.

Patent Documents

SUMMARY OF THE INVENTION

The present invention is directed to providing a method for identifying a racehorse using a microsatellite marker capable of performing a multiplex polymerase chain reaction (Multiplex PCR) using a microsatellite marker to more rapidly, accurately and economically distinguish a population of racehorses and stably perform paternity tests, and the like, compared to existing techniques.

Also, the present invention is directed to providing a method for identifying a racehorse using a microsatellite marker capable of deducing more accurate outcomes at lower costs when compared to conventional markers to reduce a recall rate and minimize inspection time and inspection manpower, and also distinguishing a population of general horses, donkeys, and the like and performing paternity tests, thereby enhancing compatibility.

The technical subjects to be achieved by the present invention are not limited to the aforementioned technical subjects, and other subjects which are not mentioned above will be clearly understood from the following detailed description by those skilled in the art to which the present invention belongs.

One aspect of the present invention provides a method for identifying a racehorse using a microsatellite marker, which includes amplifying a target gene by a multiplex polymerase chain reaction (multiplex PCR) using a microsatellite marker obtained by combining one or more sets selected from a first set consisting of AHT4, AHT5, ASB2, HMS3, HMS6, HMS7, HTG4, HTG10, VHL20, ASB17, ASB23, HMS1, LEX3, CA425, HMS2, HTG6, HTG7, LEX033, AMEL, HMS18, LEX27, SRY, and LEX020 and a second set consisting of HTG21, COR089, TKY279, TKY287, TKY294, TKY297, TKY301, TKY312, TKY321, TKY325, TKY333, TKY337, TKY341, TKY343, TKY344, TKY374, and TKY394; detecting alleles in the product amplified in the multiplex PCR amplification step and analyzing the sizes of the alleles using an electrophoresis apparatus to determine a genotype of the racehorse; and summarizing the sizes of the alleles analyzed using the electrophoresis apparatus according to the population and breed of racehorses to plot the number and a frequency distribution of the alleles based on the summarized results.

In the multiplex PCR amplification step, the microsatellite marker may consist of the first set and the second set.

In the multiplex PCR amplification step, the multiplex PCR amplification conditions may include maintenance at 95° C. for 2 minutes, followed by repeating 33 cycles of denaturation at 95° C. for 30 seconds, annealing at 56.5° C. for 90 seconds and extension at 72° C. for 60 seconds, and the final extension at 72° C. for 30 minutes and maintenance at 4° C.

The specific contents of the other embodiments fall within the detailed description of the present invention.

DETAILED DESCRIPTION OF EXEMPLARY EMBODIMENTS

Advantages and features of the present invention and methods for achieving them will be made clear from the embodiments described below in detail with reference to the accompanying drawings. However, it should be understood that the present invention may be embodied in many different forms and may not be construed as being limited to the embodiments set forth herein. Rather, the embodiments disclosed herein are provided so that this disclosure will be thorough and complete and will fully convey the scope of the present invention to those of ordinary skill in the art.

Unless otherwise defined, all the terms including technical and scientific terms used herein have the same meaning as commonly understood by one of ordinary skill in the art to which the present invention pertains. Furthermore, generally used terms defined in most dictionaries are interpreted to have a meaning corresponding to the meaning in the context of the related art, but are not interpreted in an ideal or excessively formal manner unless otherwise defined.

Hereinafter, a method for identifying a racehorse using a microsatellite marker according to the present invention will be described in detail with reference to preferred embodiments thereof.

Meanwhile, the case of the method for identifying a racehorse using a microsatellite marker according to the present invention, which may be used to perform a multiplex polymerase chain reaction (multiplex PCR) using a microsatellite marker to distinguish a population of racehorses or perform paternity tests, is described as one example. However, it should be understood that the technical idea of the present invention is not limited to racehorses as described above, and is also applied to different types of animals including general horses, donkeys, and the like in addition to the racehorses.

In the present invention, the term “microsatellite” refers to a short tandem repeat (STR) having structure in which a DNA sequence of 2 to 6 bases is repeated. Such microsatellites are known to be uniformly distributed in most eukaryotic genomes. In particular, the microsatellites are mainly present in non-coding DNA.

In the present invention, the term “microsatellite marker” refers to a polymorphism that occurs due to a variation in the repeat copies of the microsatellite repeats.

Such a microsatellite marker has various repeat copies of the microsatellite repeats according to the population and species. Therefore, a genetically unique sequence in base pairs present in both ends of a repeated region of a microsatellite may be designed as a primer sequence, and may be subjected to PCR amplification. Then, the sizes of the resulting PCR products may be compared to distinguish the population or species.

In the present invention, the term “primer” refers to a nucleic acid sequence that has a short free 3′-terminal hydroxyl group, that is, a short nucleic acid sequence that may form base pairs with a complementary template and functions as an initiation point for duplication of template strands.

In the present invention, the term “polymerase chain reaction (PCR)” refers to a molecular biological technique that is used to replicate and amplify a desired region of DNA. Specifically, the PCR includes a series of three steps. The first step of PCR is to denature DNA and separate two DNA strands by heating. Each of the separated DNA strands serves as a template.

The second step of PCR is to anneal the DNA strands. In this step, primers for a microsatellite marker bind to the template DNA. The annealing temperature is an important factor that determines the accuracy of the reaction. In this case, when the temperature is too high, a very small amount of the amplified DNA product may be obtained because the primers are very weakly bound to the template DNA. On the other hand, when the temperature is too low, unwanted DNA may be amplified because the primers are non-specifically bound to the template. Therefore, the annealing temperature should be properly adjusted according to the type of the primers used, and the like.

The third step of PCR is an extension step. In this step, when the primers are bound to the template, a heat-resistant DNA polymerase forms new DNA from the template DNA.

When the analysis is performed on several microsatellite markers as in the present invention, multiplex PCR may be used.

In the present invention, the term “multiplex PCR” refers to a PCR technique that amplifies a variety of genes at the same time unlike single PCR that amplifies one gene on one template DNA. In the multiplex PCR, various primer pairs are included in a single PCR mix. In this case, different DNA sequences have a specific range of sizes of amplified product. Therefore, it is desirable that the sizes of the DNA sequences do not overlap each other.

In the multiplex PCR technique, inhibition between the primers may occur because various types of different primer pairs are put into one tube and reacted. Therefore, it is important to select primers for a gene to be amplified when the primers are applied to the multiplex PCR.

Also, the annealing temperature may vary depending on the various primers included in the PCR reaction. Therefore, when PCR primer pairs are applied to the multiplex PCR, it is necessary to optimize the annealing temperature suitable for multiplex PCR so that all of the PCR primer pairs included in the single PCR reaction can effectively bind to the template DNA.

After the PCR is performed as described above, the PCR-amplified products may be identified using a technique capable of classifying the PCR-amplified products depending on the size of the PCR-amplified products, such as SDS-PAGE or capillary electrophoresis.

Specifically, the PCR-amplified products may be subjected to an electrophoresis method, and the like so that the PCR-amplified products can classified according to the size of the PCR-amplified products. Based on the results of size determination, it may be determined how many repeats are included in each allele. Therefore, the populations may be identified by separately constructing a database in which the data on such genotypes and the data of the verified racehorse are recorded or using the established information to compare the data obtained by experiments with such information.

According to the present invention, the microsatellite markers selected as a genetic identification method using a multiplex polymerase chain reaction (multiplex PCR) for identifying genes of a racehorse may be selected based on the microsatellite markers of racehorses reported in the database of the International Society for Animal Genetics (ISAG). Ultimately, a total of 40 microsatellite markers may be divided into two sets in consideration of specific selection conditions such as allele frequency, the annealing temperature of primers, the size of the amplified product, a fluorescent material (a dye), and the like, and then combined to perform a multiplex polymerase chain reaction (multiplex PCR).

Further, the method for identifying a racehorse using a microsatellite marker according to the present invention includes amplifying a target gene by a multiplex polymerase chain reaction (multiplex PCR) using a microsatellite marker obtained by combining one or more sets selected from a first set consisting of AHT4, AHT5, ASB2, HMS3, HMS6, HMS7, HTG4, HTG10, VHL20, ASB17, ASB23, HMS1, LEX3, CA425, HMS2, HTG6, HTG7, LEX033, AMEL, HMS18, LEX27, SRY, and LEX020 and a second set consisting of HTG21, COR089, TKY279, TKY287, TKY294, TKY297, TKY301, TKY312, TKY321, TKY325, TKY333, TKY337, TKY341, TKY343, TKY344, TKY374, and TKY394; detecting alleles in the product amplified in the multiplex PCR amplification step and analyzing the sizes of the alleles using an electrophoresis apparatus to determine a genotype of the racehorse; and summarizing the sizes of the alleles analyzed using the electrophoresis apparatus according to the population and breed of racehorses to plot the number and a frequency distribution of the alleles based on the summarized results.

In the multiplex PCR amplification step, a reagent for the microsatellite marker may consist of 25 μL of a Platinum Multiplex PCR Master mix, 5 μL of a GC enhancer, 10 μL of a primer mix, 4 μL of genomic DNA, and 6 μL of deionized water 6.

In the multiplex PCR amplification step, the reagent for the microsatellite marker may also consist of 12.5 μL of a Platinum Multiplex PCR Master mix, 2.5 μL of a GC enhancer, 5 μL of a primer mix, 2 μL of genomic DNA, and 3 μL of deionized water.

Also, the multiplex PCR amplification conditions in the multiplex PCR amplification step may include maintenance at 95° C. for 2 minutes, followed by repeating 33 cycles of denaturation at 95° C. for 30 seconds, annealing at 56.5° C. for 90 seconds and extension at 72° C. for 60 seconds, and the final extension at 72° C. for 30 minutes and final maintenance at 4° C.

Hereinafter, the method for identifying a racehorse using a microsatellite marker according to the present invention will be described in further detail with reference to the accompanying drawings.

EXAMPLES

1: Selection of Microsatellite Marker for Identifying Racehorse

To select a microsatellite marker which is able to be effectively used to identify a racehorse, microsatellite markers were selected based on the microsatellite markers of the racehorses reported in a database. That is, a total of 40 microsatellite markers were finally selected and divided into two sets in consideration of the specific selection conditions such as allele frequency, the annealing temperature of primers, the size of the amplified product, a fluorescent material (a dye), and the like.

The microsatellite markers are as follows.

2: Analytical Equipment

An analytical apparatus and an auxiliary apparatus as shown in [Table 1] below were used as the analytical equipment.

3: Conditions for Analytical Equipment

This experiment was performed under the conditions for analytical equipment as shown in [Table 2] below.

4: Analysis Software3130 Data collection version 3.0: 3130xL Instrument Inspection and Running3500 Data collection version 3.0: 3500xL Instrument Inspection and RunningGeneMapper version 4.0): 3130xL Result AnalysisGeneMapper version 5.0: 3500xL Result Analysis

5: Analytical Reagents and Compositions

As the first set, the analytical reagents and compositions as listed in [Table 3] below were used.

Meanwhile, in the case of the second set, the analytical reagents and compositions as listed in [Table 3] above were used for DNA extraction and DNA amplification, but the GeneScan 400HD ROX Size standard was used instead of the GeneScan 500LIZ Size standard for DNA analysis.

That is, Filter Set: D, Dye Primer Matrix standard set: DS-30, and the reagents were used in the same amounts.

(1) Platinum Multiplex PCR MasterMix Gene Test Kit

A known product as shown in [Table 4] below was used as the Platinum Multiplex PCR MasterMix gene test kit shown in [Table 3] above.

(2) Detailed Composition of Reagents for Microsatellite Marker

A reagent for a microsatellite marker blended as shown in [Table 5] below was used as a composition of reagents for DNA amplification as shown in [Table 3] above.

6: PCR Conditions

This experiment was performed under the PCR conditions as shown in [Table 6] below.

7: PCR Pretreatment Conditions

This experiment was performed under the PCR pretreatment conditions as shown in [Table 7] below.

PCR Products: The PCR products were diluted with deionized water (D.W) at a weight ratio of 1:20, and used in this experiment.

The racehorse gene (DNA) reading results as shown inFIGS.1to9were obtained.

FIGS.1to9are graphs illustrating the racehorse gene (DNA) reading results obtained by the method for identifying a racehorse using a microsatellite marker according to the present invention.

Referring toFIGS.1to9, it can be seen that the method for identifying a racehorse using a microsatellite marker according to the present invention was able to be used to easily and accurately identify a racehorse.

The method for identifying a racehorse using a microsatellite marker according to the present invention can perform a multiplex polymerase chain reaction (Multiplex PCR) using a microsatellite marker to more rapidly, accurately and economically distinguish a population of racehorses and stably perform paternity tests, and the like, compared to existing techniques.

Also, the method for identifying a racehorse using a microsatellite marker according to the present invention can deduce more accurate outcomes at lower costs when compared to conventional markers to reduce a recall rate and minimize the inspection time and inspection manpower, and can also distinguish a population of general horses, donkeys, and the like and perform paternity tests, thereby enhancing compatibility.

It should be understood that embodiments of the technical idea of the present invention may provide various effects which are not specifically mentioned herein.

While the invention has been shown and described with reference to certain exemplary embodiments thereof, it will be understood by those skilled in the art that various changes in form and details may be made therein without departing from the spirit and scope of the invention as defined by the appended claims. Therefore, it should be understood that the embodiments disclosed herein are only for illustrative purposes and are not intended to be limitative for all aspects.