CN114959069A - Specific molecular identity card for identifying Hexi black pig variety and application thereof - Google Patents

Specific molecular identity card for identifying Hexi black pig variety and application thereof Download PDF

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CN114959069A
CN114959069A CN202210816818.5A CN202210816818A CN114959069A CN 114959069 A CN114959069 A CN 114959069A CN 202210816818 A CN202210816818 A CN 202210816818A CN 114959069 A CN114959069 A CN 114959069A
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mutant
pig
hexi
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李新建
李秀领
李聪
段栋栋
韩雪蕾
王克君
乔瑞敏
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Henan Agricultural University
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    • C—CHEMISTRY; METALLURGY
    • C12—BIOCHEMISTRY; BEER; SPIRITS; WINE; VINEGAR; MICROBIOLOGY; ENZYMOLOGY; MUTATION OR GENETIC ENGINEERING
    • C12Q—MEASURING OR TESTING PROCESSES INVOLVING ENZYMES, NUCLEIC ACIDS OR MICROORGANISMS; COMPOSITIONS OR TEST PAPERS THEREFOR; PROCESSES OF PREPARING SUCH COMPOSITIONS; CONDITION-RESPONSIVE CONTROL IN MICROBIOLOGICAL OR ENZYMOLOGICAL PROCESSES
    • C12Q1/00—Measuring or testing processes involving enzymes, nucleic acids or microorganisms; Compositions therefor; Processes of preparing such compositions
    • C12Q1/68—Measuring or testing processes involving enzymes, nucleic acids or microorganisms; Compositions therefor; Processes of preparing such compositions involving nucleic acids
    • C12Q1/6876—Nucleic acid products used in the analysis of nucleic acids, e.g. primers or probes
    • C12Q1/6888—Nucleic acid products used in the analysis of nucleic acids, e.g. primers or probes for detection or identification of organisms
    • G—PHYSICS
    • G16—INFORMATION AND COMMUNICATION TECHNOLOGY [ICT] SPECIALLY ADAPTED FOR SPECIFIC APPLICATION FIELDS
    • G16B—BIOINFORMATICS, i.e. INFORMATION AND COMMUNICATION TECHNOLOGY [ICT] SPECIALLY ADAPTED FOR GENETIC OR PROTEIN-RELATED DATA PROCESSING IN COMPUTATIONAL MOLECULAR BIOLOGY
    • G16B20/00—ICT specially adapted for functional genomics or proteomics, e.g. genotype-phenotype associations
    • G16B20/20—Allele or variant detection, e.g. single nucleotide polymorphism [SNP] detection
    • G—PHYSICS
    • G16—INFORMATION AND COMMUNICATION TECHNOLOGY [ICT] SPECIALLY ADAPTED FOR SPECIFIC APPLICATION FIELDS
    • G16B—BIOINFORMATICS, i.e. INFORMATION AND COMMUNICATION TECHNOLOGY [ICT] SPECIALLY ADAPTED FOR GENETIC OR PROTEIN-RELATED DATA PROCESSING IN COMPUTATIONAL MOLECULAR BIOLOGY
    • G16B20/00—ICT specially adapted for functional genomics or proteomics, e.g. genotype-phenotype associations
    • G16B20/50—Mutagenesis
    • G—PHYSICS
    • G16—INFORMATION AND COMMUNICATION TECHNOLOGY [ICT] SPECIALLY ADAPTED FOR SPECIFIC APPLICATION FIELDS
    • G16B—BIOINFORMATICS, i.e. INFORMATION AND COMMUNICATION TECHNOLOGY [ICT] SPECIALLY ADAPTED FOR GENETIC OR PROTEIN-RELATED DATA PROCESSING IN COMPUTATIONAL MOLECULAR BIOLOGY
    • G16B30/00—ICT specially adapted for sequence analysis involving nucleotides or amino acids
    • G—PHYSICS
    • G16—INFORMATION AND COMMUNICATION TECHNOLOGY [ICT] SPECIALLY ADAPTED FOR SPECIFIC APPLICATION FIELDS
    • G16B—BIOINFORMATICS, i.e. INFORMATION AND COMMUNICATION TECHNOLOGY [ICT] SPECIALLY ADAPTED FOR GENETIC OR PROTEIN-RELATED DATA PROCESSING IN COMPUTATIONAL MOLECULAR BIOLOGY
    • G16B40/00—ICT specially adapted for biostatistics; ICT specially adapted for bioinformatics-related machine learning or data mining, e.g. knowledge discovery or pattern finding
    • G—PHYSICS
    • G16—INFORMATION AND COMMUNICATION TECHNOLOGY [ICT] SPECIALLY ADAPTED FOR SPECIFIC APPLICATION FIELDS
    • G16B—BIOINFORMATICS, i.e. INFORMATION AND COMMUNICATION TECHNOLOGY [ICT] SPECIALLY ADAPTED FOR GENETIC OR PROTEIN-RELATED DATA PROCESSING IN COMPUTATIONAL MOLECULAR BIOLOGY
    • G16B45/00—ICT specially adapted for bioinformatics-related data visualisation, e.g. displaying of maps or networks
    • C—CHEMISTRY; METALLURGY
    • C12—BIOCHEMISTRY; BEER; SPIRITS; WINE; VINEGAR; MICROBIOLOGY; ENZYMOLOGY; MUTATION OR GENETIC ENGINEERING
    • C12Q—MEASURING OR TESTING PROCESSES INVOLVING ENZYMES, NUCLEIC ACIDS OR MICROORGANISMS; COMPOSITIONS OR TEST PAPERS THEREFOR; PROCESSES OF PREPARING SUCH COMPOSITIONS; CONDITION-RESPONSIVE CONTROL IN MICROBIOLOGICAL OR ENZYMOLOGICAL PROCESSES
    • C12Q2600/00—Oligonucleotides characterized by their use
    • C12Q2600/156—Polymorphic or mutational markers

Abstract

The invention belongs to the field of pig breed identification, relates to Yuxi black pig germplasm resources, and particularly relates to a specific molecular identity card for identifying Yuxi black pig breeds and application thereof. The variety of the black pig in the west Henan province is researched by the SNP molecular marker, the bioinformatics technology is adopted for comprehensive analysis, the research result is preliminarily verified, and the variety specific molecular marker of the black pig in the Henan province is constructed, so that the difference between the black pig in the Henan province and the variety of the other local pig can be simply and clearly distinguished, the method can be used for the authenticity identification and genetic relationship analysis of the black pig variety in the Henan province, and an effective scientific basis is provided for the intellectual property protection of the black pig variety in the Henan province. When the variety of the black pig in Hexi is identified and evaluated, whether the variety of the black pig in Hexi is the variety of the black pig in Hexi can be determined only by comparing and analyzing the variety of the black pig in Hexi with the existing specific molecular identity card. The time and the cost for identifying and evaluating the germplasm resources of the Hexi black pig are greatly reduced, and the efficiency for identifying and evaluating the variety of the Hexi black pig is improved.

Description

Specific molecular identity card for identifying Henan black pig variety and application thereof
Technical Field
The invention belongs to the field of pig breed identification, relates to Yuxi black pig germplasm resources, and particularly relates to a specific molecular identity card for identifying Yuxi black pig breeds and application thereof.
Background
Black pigs in western Henan province are distributed in the three gorges city in Henan province and are superior local pigs: black southern yang pigs, blackish mount pigs, leuw pigs and western commercial pigs: the Duroc pigs are used as basic herds and are bred in generations, and have the excellent characteristics of strong fertility, good meat quality, high disease resistance, coarse feeding resistance and the like. In the process of breeding dominant varieties, new technologies and means need to be explored to provide guarantee for the cultivation of superior varieties. How to quickly and efficiently carry out molecular identification and variety identification on livestock and poultry varieties becomes a key for the development and utilization and sustainable development of the varieties in production. The effective protection and reasonable development of local varieties are beneficial to the sustainable development of the pig industry in Henan province and the abundance of livestock resource diversity. Particularly, the research on the specific genetic structure and the characteristics of the local pig breed is helpful for making a protection plan for each breed according to the genetic condition of the breed, and promoting the specific protection of the local pig breed. Preserving the unique variations, genes and characteristics of each variety is extremely important for maintaining biodiversity and adapting to future environmental changes. Therefore, the identification of the unique genetic characteristics of the local pig breed in Henan by using the bioinformatics technology is an important part for accurately protecting the genetic resources of the local pig breed.
With the development of sequencing technology, chip sequencing technology becomes a powerful tool for high-throughput SNP typing. At the same time, when animals are subjected to long-term natural and artificial selection, corresponding genetic imprints are left on their genomes. These genetic imprints are commonly referred to as selection signals. The study of selection signals is a research strategy based on the concept of genome-to-phenotype. Due to the lack of local pig species phenotype records and small population scale in China, the analysis of the germplasm characteristics of livestock increasingly becomes an important method. In order to realize batch detection of Hexi black pigs, the subject group has been long-term explored.
Disclosure of Invention
In order to realize the purpose, the invention provides a specific molecular identity card for identifying Hexi black pig breeds and application thereof.
The technical scheme of the invention is realized as follows:
the specific molecular identity card for identifying the Hexi black pig breed is characterized in that the SNP loci are a SNP locus set with higher allele frequency among the Hexi black pig breeds.
Preferably, the SNP site is located in the porcine reference genome EnsemblScrofa version 11.1.
The set of SNP sites includes CNC10013894 site G/A, CNC10014056 site C/T, CNC10020115 site T/C, CNC10020130 site a/C, CNC10020514 site C/T, CNC10023146 site, CNC10023149 site, CNC10031517 site, CNC10031852 site, CNC10032441 site, CNC 10042042061 site, CNC10042622 site, CNC10050243 site, CNC10050264 site, CNC10050750 site, CNC10050761 site, CNC10061222 site, CNC10061407 site, CNC10062206 site, CNC10062339 site, CNC10062741 site, CNC10070087 site, CNC10071263 site, CNC10081973 site, CNC 1009082066 site, CNC 100100634 site, CNC 100100641 100641, CNC10090931 site, CNC 1009102 site, CNC10130645 site, CNC 100333333474 site, CNC 101904034130 site, CNC 10110110110187524 site, CNC 10151515151229 site, CNC 10051515152229 site, CNC 10032124 site and CNC 1003262 site.
The mutant of the CNC10013894 site is a G/A, CNC10014056 site, the mutant is a C/T, CNC10020115 site, the mutant is a T/C, CNC10020130 site, the mutant is a A/C, CNC10020514 site, the mutant is a C/T, CNC10023146 site, the mutant is a C/T, CNC10023149 site, the mutant is a G/A, CNC10031517 site, the mutant is a T/C, CNC10031852 site, the mutant is a T/A, CNC10032441 site, the mutant is a C/T, CNC10042061 site, the mutant is a G/T, CNC10042622 site, the mutant is a C/T, CNC10050243 site, the mutant is a C/A, CNC10050264 site, the mutant is a T/C, CNC10050761 site, the mutant is a T/586126 10061222 site, the mutant is a C/5810061407 site, the mutant is a G/A, CNC 100206 site, and the mutant is a C/T1005048 10050761 site, The mutation type of the CNC10062339 site is A/G, CNC10062741 site, the mutation type is A/C, CNC10070087 site, the mutation type is C/G, CNC10071263 3 site, the mutation type is T/C, CNC10082066 site, the mutation type is C/T, CNC10090634 site, the mutation type is G/A, CNC10090641 site, the mutation type is C/A, CNC10090931 site, the mutation type is A/C, CNC10091691 site, the mutation type is G/T, CNC10111302 site, the mutation type is C/T, CNC10130645 site, the mutation type is C/T, CNC10133474 site, the mutation type is C/T, CNC10134130 site, the mutation type is T/C, CNC10140524 site, the mutation type is A/G, CNC10140877 site, the mutation type is C/5851220 site, the mutation type is A/5851229 site, the mutation type is A/G, CNC,231 site, the mutation type is A/6351231 site, The mutant of the CNC10152118 site is G/A and the mutant of the CNC10171124 site is T/C.
The gene chip is used for identifying the specific molecular identity card.
The gene chip is applied to identifying the Yuxi black pig variety.
Preferably, the steps are as follows:
(1) collecting a tissue sample of a pig to be detected, and extracting genome DNA;
(2) carrying out SNP typing on the genome DNA in the step (1) by using a gene chip to obtain the genotype data of the pig to be detected;
(3) and combining the genotype data of the pig to be detected with the genotype of the SNP locus on the specific molecular identity card by utilizing PLINK software, and then carrying out principal component analysis.
Further, in the step (1), the light absorption ratio of the genome DNA at A260/280 is between 1.8 and 2.0, and the concentration is more than or equal to 50 ng/microliter.
Further, the result of the main component analysis of the SNP typing in the step (3) is close to the genetic distance of the Hexi black pig group, and the Hexi black pigs are obtained when the result is gathered into a cluster.
The invention has the following beneficial effects:
1. and combining the significant SNPs of the group A and the group B by utilizing PLINK software, calculating the allele frequency of each SNP in 11 varieties, and screening SNP sets with the allele frequencies distributed higher than those of other 10 varieties in a test group as specific molecular identity cards of the Hexi black pig variety.
2. The method combines the whole genome correlation analysis and the analysis method of the selection signal, determines the specific molecular identity card of the Hexi black pig breed, and lays a foundation for the development, utilization and identification of the Hexi black pig breed. The variety of the black pig in Hexi is researched by the SNP molecular marker, the bioinformatics technology is adopted for comprehensive analysis, the research result is preliminarily verified, and the variety specific molecular marker of the black pig in Hexi is constructed, so that the difference between the black pig in Hexi and other local pig varieties can be simply and clearly distinguished, the method can be used for authenticity identification and genetic relationship analysis of the black pig variety in Hexi, and an effective scientific basis is provided for intellectual property protection of the black pig variety in Hexi. When the variety of the black pig in Hexi is identified and evaluated, whether the variety of the black pig in Hexi is the variety of the black pig in Hexi can be determined only by comparing and analyzing the variety of the black pig in Hexi with the existing specific molecular identity card. The time and the cost for identifying and evaluating the germplasm resources of the Hexi black pig are greatly reduced, and the efficiency for identifying and evaluating the variety of the Hexi black pig is improved.
Drawings
In order to more clearly illustrate the embodiments of the present invention or the technical solutions in the prior art, the drawings used in the description of the embodiments or the prior art will be briefly described below, it is obvious that the drawings in the following description are only some embodiments of the present invention, and for those skilled in the art, other drawings can be obtained according to the drawings without creative efforts.
Fig. 1 is a manhattan diagram and a QQ diagram of the GWAS analysis result of the black yuxi pig of the present invention.
FIG. 2 is a Manhattan diagram showing the analysis results of the selection signal of Hexi black pig according to the present invention.
FIG. 3 is a main component analysis and verification diagram of the Yuxi black pig breed specific molecular identity card of the present invention.
Detailed Description
The technical solutions of the present invention will be described clearly and completely with reference to the following embodiments of the present invention, and it should be understood that the described embodiments are only a part of the embodiments of the present invention, and not all of the embodiments. All other embodiments, which can be obtained by a person skilled in the art without inventive effort based on the embodiments of the present invention, are within the scope of the present invention.
Examples
A method for screening specific molecular identity cards of Yuxi black pig germplasm resources comprises the following steps:
(1) ear sample collection
The experimental population was 1144 pigs, for a total of 11 pig breeds, including 8 chinese pig breeds: black yuxi pigs (n =27, YX), black southern yang pigs (n =10, NY), huainan pigs (n =10, HN), black yunong pigs (n =1036, YN), black genshan pigs (n =10, QS), lekuwa pigs (n =10, LWH), erhualian pigs (n =10, EHL), MIN pigs (n =6, MIN); 3 commercial western pig breeds: duroc pigs (n =10, DU), large white pigs (n =10, LW), long white pigs (n =5, LR). The ears of the pigs were cleaned with 75% alcohol, a small amount of ear tissue was cut with an ear-like forceps, placed in a 2mL centrifuge tube containing 75% alcohol, and stored in a freezer at-20 ℃.
(2) Total DNA extraction, quality detection and genotyping
Extracting total DNA by using an animal tissue genome DNA extraction kit;
detecting with DYY-6C electrophoresis apparatus by 1% agarose gel electrophoresis;
the method adopts a Nanodrop-2000 ultraviolet spectrophotometer to detect the concentration of DNA, reserves a genome DNA sample with the light absorption ratio (A260/280) between 1.8 and 2.0 and the concentration more than or equal to 50 ng/microliter, and is used for carrying out whole genome chip typing on Illumina Portine SNP50 Beadchip.
(3) Genotype data fill and quality control
A total of 1,144 SNPs of 51,315 were obtained by chip sequencing. Quality control is carried out on chip data by using PLINK software. The genotype data was filtered by the following parameters: the detection rate of individual genotypes (-mind) is more than 90%, the detection rate of marker genotypes (-gene) is more than 95%, the minimum allele frequency (-maf) is more than 1%, and the minimum Hawth Winberg balance (-hwe) is 1.0E-6, and is located in autosomes. The filling of the missing genotypes is performed in the BEAGLE software using the Hidden Markov Model (HMM) algorithm.
(4) Whole genome correlation analysis and screening of SNP specific sites
The GEMMA software was used to perform the whole genome association analysis, and the test group was 27 Yuxi black pigs (case), and the control group was the remaining 10 breeds (control). Identifying SNPs significantly related to the breed by using a Bankshire correction method, wherein a Manhattan graph of a Yuxi black pig is shown in the left of a graph 1 and a QQ graph is shown in the right of the graph 1, and two threshold lines are arranged in the Manhattan graph, wherein the threshold value of a solid line is 0.05/N (N is the number of used chip sites), the site above the solid line is the significant level of the whole genome, the threshold value of a dotted line is 1/N, the site above the dotted line is the significant level of a chromosome, and the more close the lambda value in the QQ graph is to 1, which indicates that the result of the correlation analysis of the whole genome is more reliable; identifying SNPs significantly related to the breed using a Bancost correction method, the set of significant SNPs being group A.
(5) Selection signal analysis for screening SNP specific sites
As shown in fig. 2, VCFtools software is used to calculate the genetic differentiation index (Fst), and a calculation method of taking the mean value by a sliding window is used, and specific parameters are as follows: the size of the sliding window (- -fst-window-size) is 100,000 bp, and the step size of the sliding window (- -fst-window-step) is 40,000 bp. Sorting the windows according to the Fst value from large to small, defining the first 1 percent of windows as significant windows, and extracting the SNPs in the significant windows by utilizing PLINK software, wherein the set of the significant SNPs is a B group.
(6) Allele frequency screening of SNP specific sites
And combining the significant SNPs of the group A and the group B by utilizing PLINK software, calculating the allele frequency of each SNP in 11 varieties, and screening SNP sets with the allele frequencies distributed higher than those of other 10 varieties in a test group as specific molecular identity cards of the Hexi black pig variety.
TABLE 1 specific molecular marker set for Hexi black pig breeds
Figure 411877DEST_PATH_IMAGE001
(7) The 40 SNPs of 11 varieties were extracted by PLINK software, and principal component analysis and verification were performed.
(8) The application of the 40 SNP loci in identifying Hexi black pig breeds is that the SNP loci are positioned in genome version EnsemblSsccrofa 11.1.
Application example
The identification method of the pig breed to be detected specifically comprises the following steps:
1. extracting an ear tissue sample of the pig to be detected, extracting the genome DNA of the tissue sample, and typing the above 40 sites through a chip. The genomic DNA was sent to Beijing Congpson Biotechnology Ltd for SNP typing on the "center-in-the-core No. (Axiom) chip of the local pig. The principle of the SNP typing assay using the chip is based on a ligation reaction in which two probes are used. The first is capture probes on a chip, which serve to immobilize target DNA fragments to the chip surface. The second is a chromogenic probe, responsible for staining the SNP chip (red and green fluorescence). The assay was run in two rounds of hybridization. The first round of hybridization is that the target DNA is hybridized with the chip, and the capture probe can grab the matched target DNA fragment; the chromogenic probe hybridizes to the DNA fragment in a second round of hybridization. Then, only the chromogenic probe complementary to the target DNA fragment is ligated to the capture probe by the recognition of the ligase. And carrying out SNP typing under laser scanning by dyeing of a fluorescent marker to obtain the genotype data of the pig to be detected.
2. And combining the genotype data of the pig to be detected and the genotype data of the 11 varieties by using PLINK software, then carrying out principal component analysis and visualizing the result by using R language, and when the individual pig to be detected is close to the genetic distance of the black pig population in Hexi and is gathered into a cluster, referring to figure 3, judging that the pig to be detected is the black pig in Hexi.
The variety of the black pig in Hexi is researched by the SNP molecular marker, the bioinformatics technology is adopted for comprehensive analysis, the research result is preliminarily verified, and the variety specific molecular marker of the black pig in Hexi is constructed, so that the difference between the black pig in Hexi and other local pig varieties can be simply and clearly distinguished, the method can be used for authenticity identification and genetic relationship analysis of the black pig variety in Hexi, and an effective scientific basis is provided for intellectual property protection of the black pig variety in Hexi. When the variety of the black pig in Hexi is identified and evaluated, whether the variety of the black pig in Hexi is the variety of the black pig in Hexi can be determined only by comparing and analyzing the variety of the black pig in Hexi with the existing specific molecular identity card. The time and the cost for identifying and evaluating the germplasm resources of the Hexi black pig are greatly reduced, and the efficiency for identifying and evaluating the variety of the Hexi black pig is improved.
The above description is only for the purpose of illustrating the preferred embodiments of the present invention and is not to be construed as limiting the invention, and any modifications, equivalents, improvements and the like that fall within the spirit and principle of the present invention are intended to be included therein.

Claims (9)

1. A specific molecular identity card for identifying Henan black pig breeds is characterized in that: the SNP loci are a SNP locus set with higher allele frequency among Hexi black pig breeds.
2. The specific molecular identification card for identifying black-skinned pig breeds in Hexi, as claimed in claim 1, wherein: the SNP site is located in the porcine reference genome EnsemblScrofa version 11.1.
3. The specific molecular identification card for identifying black-skinned pig breeds in Hexi, as claimed in claim 2, wherein: the set of SNP sites includes CNC10013894 site G/A, CNC10014056 site C/T, CNC10020115 site T/C, CNC10020130 site a/C, CNC10020514 site C/T, CNC10023146 site, CNC10023149 site, CNC10031517 site, CNC10031852 site, CNC10032441 site, CNC 10042042061 site, CNC10042622 site, CNC10050243 site, CNC10050264 site, CNC10050750 site, CNC10050761 site, CNC10061222 site, CNC10061407 site, CNC10062206 site, CNC10062339 site, CNC10062741 site, CNC10070087 site, CNC10071263 site, CNC10081973 site, CNC 1009082066 site, CNC 100100634 site, CNC 100100641 100641, CNC10090931 site, CNC 1009102 site, CNC10130645 site, CNC 100333333474 site, CNC 101904034130 site, CNC 10110110110187524 site, CNC 10151515151229 site, CNC 10051515152229 site, CNC 10032124 site and CNC 1003262 site.
4. The specific molecular identity card for identifying black-pig breeds in western Henan according to claim 3, wherein: the mutant of the CNC10013894 site is a G/A, CNC10014056 site, the mutant is a C/T, CNC10020115 site, the mutant is a T/C, CNC10020130 site, the mutant is a A/C, CNC10020514 site, the mutant is a C/T, CNC10023146 site, the mutant is a C/T, CNC10023149 site, the mutant is a G/A, CNC10031517 site, the mutant is a T/C, CNC10031852 site, the mutant is a T/A, CNC10032441 site, the mutant is a C/T, CNC10042061 site, the mutant is a G/T, CNC10042622 site, the mutant is a C/T, CNC10050243 site, the mutant is a C/A, CNC10050264 site, the mutant is a T/C, CNC10050761 site, the mutant is a T/586126 10061222 site, the mutant is a C/5810061407 site, the mutant is a G/A, CNC 100206 site, and the mutant is a C/T1005048 10050761 site, The mutation type of the CNC10062339 site is A/G, CNC10062741 site, the mutation type is A/C, CNC10070087 site, the mutation type is C/G, CNC10071263 3 site, the mutation type is T/C, CNC10082066 site, the mutation type is C/T, CNC10090634 site, the mutation type is G/A, CNC10090641 site, the mutation type is C/A, CNC10090931 site, the mutation type is A/C, CNC10091691 site, the mutation type is G/T, CNC10111302 site, the mutation type is C/T, CNC10130645 site, the mutation type is C/T, CNC10133474 site, the mutation type is C/T, CNC10134130 site, the mutation type is T/C, CNC10140524 site, the mutation type is A/G, CNC10140877 site, the mutation type is C/5851220 site, the mutation type is A/5851229 site, the mutation type is A/G, CNC,231 site, the mutation type is A/6351231 site, The mutant of the CNC10152118 site is G/A and the mutant of the CNC10171124 site is T/C.
5. A gene chip for identifying the specific molecular identity card of any one of claims 1 to 4.
6. The use of the gene chip of claim 5 in the identification of black-pig breeds in Hexi.
7. Use according to claim 6, characterized in that the steps are:
(1) collecting a tissue sample of a pig to be detected, and extracting genome DNA;
(2) carrying out SNP typing on the genome DNA in the step (1) by using a gene chip to obtain the genotype data of the pig to be detected;
(3) and combining the genotype data of the pig to be detected with the genotype of the SNP locus on the specific molecular identity card by utilizing PLINK software, and then carrying out principal component analysis.
8. Use according to claim 7, characterized in that: in the step (1), the light absorption ratio of the genome DNA at A260/280 is between 1.8 and 2.0, and the concentration is more than or equal to 50 ng/microliter.
9. Use according to claim 7, characterized in that: and (4) obtaining the result of the SNP typing principal component analysis in the step (3) which is close to the genetic distance of the Henan black pig group and is a cluster of Henan black pigs.
CN202210816818.5A 2022-07-12 2022-07-12 Specific molecular identity card for identifying Hexi black pig variety and application thereof Pending CN114959069A (en)

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