CN114959068A - Specific molecular identity card for identifying Yunong black pig germplasm resources and application thereof - Google Patents

Specific molecular identity card for identifying Yunong black pig germplasm resources and application thereof Download PDF

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CN114959068A
CN114959068A CN202210816333.6A CN202210816333A CN114959068A CN 114959068 A CN114959068 A CN 114959068A CN 202210816333 A CN202210816333 A CN 202210816333A CN 114959068 A CN114959068 A CN 114959068A
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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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Abstract

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

Description

Specific molecular identity card for identifying Yunong black pig germplasm resources and application thereof
Technical Field
The invention belongs to the field of pig breed identification, relates to Yunong black pig germplasm resources, and particularly relates to a specific molecular identity card for identifying Yunong black pig breeds and application thereof.
Background
Henan province black pigs are distributed in the three gorges city of 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. This group of subjects has conducted a long-term investigation in order to realize the batch detection of Henong black pigs.
Disclosure of Invention
In order to achieve the purpose, the invention provides a specific molecular identity card for identifying Yunong black pig germplasm resources and application thereof.
The technical scheme of the invention is realized as follows:
the specific molecular identity card is used for identifying the germplasm resources of Henan nong black pigs, and the SNP loci are a SNP locus set with higher allele frequency among Henan nong black pig breeds.
Preferably, the SNP site is located in the porcine reference genome EnsemblScrofa version 11.1.
Preferably, the set of SNP sites includes CNC10010909 locus, CNC10011130 locus, CNC10011533 locus, CNC10012476 locus, CNC10012481 locus, CNC10012482 locus, CNC10012483 locus, CNC10013609 locus, CNC10013901 locus, CNC10013912 locus, CNC10014023 locus, CNC10014056 locus, CNC10014645 locus, CNC10020600 locus, CNC10021264 locus, CNC10021414 locus, CNC10021534 locus, CNC 10010010010076 locus, CNC 10021821861 locus, CNC10022664 locus, CNC 1003030303030888 locus, CNC10031341 locus, CNC 10032132139 locus, CNC 32433 locus, CNC 40140140140140140109 locus, CNC 10141731 locus, 10042349 locus, 50024 locus, CNC10050222 locus, CNC10050620 locus, CNC 100515151515194 locus, CNC 60060034 locus, CNC 8110181101811017795 locus, CNC 1011011011017295 locus, CNC 10010010010010010010010010010032 locus, CNC 1001001001001001001001001008110032 locus, CNC 8110032 locus, CNC 1001001001001001001001001001008110094 locus, CNC 811008110094 locus, CNC 8110094 locus, CNC 81100811008110094 locus, CNC 811008110094 locus, CNC 811008110032 locus, CNC10032 locus, CNC 100100811008110032 locus, CNC 10081100811008110094 locus, CNC10032 locus, CNC 10010010010032 locus, CNC 10010010051511008110032 locus, CNC 10010010032 locus, CNC 10010010010032 locus, CNC 10010010032 locus, CNC 100100811008110010010032 locus, CNC 1001008110032 locus, CNC 10010032 locus, CNC 10010010032 locus, CNC 1001001001008110010010010010032 locus, CNC 1001001001001001008110081100811001001008110032 locus, CNC 1008110032 locus, CNC 10010032 locus, CNC 1001001001001001001001008120 locus, CNC 10010010010010010010010010010010010010010010010010010010010010010010010010010010010010032 locus, CNC 10010010010 locus, CNC 1001001001001001001001001001001001001008120 locus, CNC 1001001001001001001001001001001001001001001008120 locus, CNC 10010010010010010010 locus, CNC10010 locus, CNC 10029 locus, CNC10010 locus, CNC 1001001001001001001001001001001001001001001001001001008120 locus, CNC 10010010010010010010010010010010010010010010010010010010 locus, CNC 10010010010010010010010 locus, CNC 10010010010 locus, CNC 10010010010010 locus, CNC10010 locus, CNC 10010010010010010010010010010010010029 locus, CNC 10010010010010010010010010010010 locus, CNC10010 locus, CNC 10010010029 locus, CNC 10010010010 locus, CNC 10010010 locus, CNC 10010010010 locus, CNC 10010010 locus, CNC 10010010010 locus, CNC 10010010 locus, CNC 10010010010010 locus, CNC 10010010 locus, CNC10010 locus, CNC 10010010010010 locus, CNC 10010010 locus, CNC 10010010010 locus, CNC 10010010010010 locus, CNC 10010010010, CNC10130479 site, CNC10132801 site, CNC10133069 site, CNC10133411 site, CNC10133517 site, CNC10133915 site, CNC10134173 site, CNC10140073 site, CNC10140089 site, CNC10140088 site, CNC10140503 site, CNC10140928 site, CNC10142200 site, CNC10070140 site, CNC10142598 site, CNC10150082 site, CNC10150342 site, CNC10150857 site, CNC10150887 site, CNC10151225 site, CNC10151534 site, CNC10152380 site, CNC10152716 site, CNC10160964 site, CNC10161348 site, CNC10170850 site, CNC10180332 site.
Further, the mutant of the CNC10010909 site is the mutant of the A/G, CNC10011130 site which is T/C, CNC10011533 site which is mutant of the G/A, CNC10012476 site which is mutant of the T/C, CNC10012481 site which is mutant of the T/G, CNC10012482 site which is mutant of the G/T, CNC10012483 site which is mutant of the G/A, CNC10013609 site which is mutant of the G/T, CNC10013901 site which is mutant of the A/G, CNC10013912 site which is mutant of the A/G, CNC10014023 site which is mutant of the A/G, CNC10014056 site which is mutant of the T/C, CNC10014645 site which is mutant of the G/C, CNC10020600 site which is mutant of the C/A, CNC10021264 site which is mutant of the A/G, CNC 21414 site which is mutant of the T/C, CNC 21534 site which is mutant of the C/100G, CNC site which is the A/T100G, CNC site, The site of CNC10021861 is mutated into the site of A/C, CNC10022664, the site of T/C, CNC10030888 is mutated into the site of A/G, CNC10031341, the site of T/G, CNC10032433 is mutated into the site of C/G, CNC10040109, the site of T/C, CNC10041731 is mutated into the site of G/T, CNC10042349, the site of A/G, CNC10050024 is mutated into the site of C/T, CNC10050222, the site of T/C, CNC10050620 is mutated into the site of A/G, CNC 1005134, the site of C/A, CNC10060034 is mutated into the site of G/A, CNC 30010065, the site of T/C, CNC10060366 is mutated into the site of A/G, CNC10061519, the site of T/100C, CNC 519 is mutated into the site of C/36100612, the site of T/C6328 10061560 is mutated into the site of T/C/A, CNC 10061703, Mutation of CNC10061562 locus as T/C, CNC10061603 locus, mutation of T/C, CNC10061804 locus as C/G, CNC10070094 locus, mutation of C/T, CNC10070095 locus as A/G, CNC10070970 locus, mutation of C/G, CNC10072223 locus as C/T, CNC10072406 locus, mutation of G/A, CNC10081349 locus as G/A, CNC10081350 locus, mutation of G/C, CNC10081506 locus as G/A, CNC10081507 locus, mutation of G/A, CNC10081568 locus as G/A, CNC10082853 locus as T/A, CNC10090805 locus as T/C, CNC10091776 locus as G/A, CNC10091860 locus as G/59672 locus as C/T10072 locus, The mutant at the CNC10100994 site is T/G, CNC10111342 site, the mutant at the A/G, CNC10120314 site is G/T, CNC10120395 site, the mutant at the G/T, CNC10130054 site is G/A, CNC10130479 site, the mutant at the T/C, CNC10132801 site is G/T, CNC10133069 site, the mutant at the A/G, CNC10133411 site is C/T, CNC10133517 site, the mutant at the C/T, CNC10133915 site, the mutant at the A/G, CNC 1019673 site is C/G, CNC10140073 site, the mutant at the C/T, CNC10140089 site is A/3910140088 site, the mutant at the G/A, CNC10140503 site is C/5840926 site, the mutant at the T/5842200 site, the mutant at the G/1002 70140 site, and the mutant at the A/C/10010029, The mutation type of the CNC10142598 site is G/A, CNC10150082 site, the mutation type of the G/T, CNC10150342 site is A/G, CNC10150857 site, the mutation type of the A/G, CNC10150887 site is C/T, CNC10151225 site, the mutation type of the G/T, CNC10151534 site is A/G, CNC10152380 site, the mutation type of the G/A, CNC10152716 site is G/A, CNC10160964 site, the mutation type of the C/A, CNC10161348 site is C/T, CNC10170850 site, and the mutation type of the A/G, CNC10180332 site is T/C.
The gene chip is used for identifying the specific molecular identity card.
The gene chip is applied to identifying Yunong black pig breeds.
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 Yunong black pig group, and the Yunong black pigs are obtained when the result is gathered into a cluster.
The invention has the following beneficial effects:
1. according to the application, significant SNPs of the group A and the group B are combined by utilizing PLINK software, allele frequency of each SNP in 10 varieties is calculated, and SNP sets with allele frequency higher than that of other 9 varieties in a test group are screened to serve as specific molecular identity cards of Henan nong black pig varieties.
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 Henan nong black pig variety, and lays a foundation for the development, utilization and identification of the Henan nong black pig variety. The Henan nong black pig variety is researched through the SNP molecular marker, the bioinformatics technology is adopted for comprehensive analysis, the research result is preliminarily verified, and the variety specificity molecular marker of the Henan nong black pig is constructed, so that the difference between the Henan nong black pig and other local pig varieties can be simply and clearly distinguished, the method can be used for the authenticity identification and genetic relationship analysis of the Henan nong black pig variety, and an effective scientific basis is provided for the intellectual property protection of the Henan nong black pig variety. When the Yunong black pig breed is identified and evaluated, whether the Yunong black pig breed is the Yunong black pig breed can be determined only by comparing and analyzing the Yunong black pig breed and the existing specific molecular identity card. The time and the cost for identifying and evaluating the Yunong black pig germplasm resources are greatly reduced, and the efficiency for identifying and evaluating the Yunong black pig breeds 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 shows a Manhattan diagram and a QQ diagram of the results of GWAS analysis of Henan nong black pigs according to the present invention.
FIG. 2 is a Manhattan chart showing the results of analysis of selection signals of Yunong black pigs according to the present invention.
FIG. 3 is a main component analysis and verification diagram of the Yunong 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 a specific molecular identity card of Yunong black pig germplasm resources comprises the following steps:
(1) ear sample collection
The test population is 1117 pigs, and the total number of the pig breeds is 10, including 7 Chinese pig breeds: black southern yang pigs (n =10, NY), huai nan pigs (n =10, HN), yunong black pigs (n =1036, YN), chun black pigs (n =10, QS), lekuwa pigs (n =10, LWH), dihedral face 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). Cleaning pig ear with 75% alcohol, cutting a small amount of ear tissue with ear-like forceps, placing in 2ml centrifuge tube filled with 75% alcohol, and storing in-20 deg.C refrigerator.
(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 of more than or equal to 50 ng/microliter, is used for carrying out whole genome chip typing on Illumina Portine SNP50 Beadchip (Beijing Congpson biotechnology, Inc., center core I), and has the specific operation that:
a. a gene library is established for the sample pig by using Tn5 transposase, and 50K gene chip scanning is carried out.
b. And (3) carrying out genotype filling on the 50K chip and the whole genome re-sequencing result in the step (1) by using Beagle.
c. And c, performing genome-wide association analysis and selection signal analysis on the genotype filling data obtained by the step b on all individuals.
d. And c, calculating the allele frequency among the breeds of the remarkable loci obtained in the step c, reserving SNP loci with higher allele frequency of Henan nong black pigs, and taking the set of the SNP loci as the Henan nong black pig breed specific molecular identity card.
(3) Genotype data fill and quality control
A total of 1,117 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: detection rate of individual genotype (- -mind)>90% detection Rate of marker genotype (- -geno)>95%, minimum allele frequency (- -maf)>1% with a minimum Hami Weinberg balance (- -hwe) of 10 -6 Located in an autosomal chromosome. 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, the test group was 10 Yunong black pigs (case), and the control group was the remaining 9 breeds (control). The Manhattan graph of the Henon black pig is shown in the left side of figure 1 and the QQ graph is shown in the right side of figure 1, 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 a 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 the lambda value in the QQ graph is close to 1, the more credible the result of the whole genome association analysis is shown; 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
The VCFtools software is used to calculate the genetic differentiation index (Fst), and a calculation method of averaging with a sliding window is used, and the result is shown in fig. 2, where the threshold line in fig. 2 is the first 1% of the Fst value after sorting, and the sites above the threshold line are significant sites (red marks). The 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 10 varieties, and screening SNP sets with higher distribution of the allele frequency in a test group than other 9 varieties as specific molecular identity cards of Yunong black pig varieties.
TABLE 1 set of specific molecular markers for Henan nong black pig breeds
Figure 304684DEST_PATH_IMAGE002
Figure 159507DEST_PATH_IMAGE004
(7) The 88 SNPs of 10 varieties were extracted by PLINK software, and principal component analysis and verification were performed.
(8) The 88 SNP loci are applied to the identification of Henong black pig breeds, and are positioned in the genome version EnsemblSscrofa 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 a pig to be detected, extracting the genome DNA of the tissue sample, and typing the 88 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 segment; 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 to-be-detected pig and the genotype data of the 10 varieties by using PLINK software, then performing principal component analysis and visualizing the result by using R language, and when the individual to-be-detected pig is close to the genetic distance of the Henan dark pig group and is gathered into a cluster, referring to fig. 3, judging that the to-be-detected pig is the Henan dark pig.
The Henan nong black pig variety is researched through the SNP molecular marker, the bioinformatics technology is adopted for comprehensive analysis, the research result is preliminarily verified, and the variety specificity molecular marker of the Henan nong black pig is constructed, so that the difference between the Henan nong black pig and other local pig varieties can be simply and clearly distinguished, the method can be used for the authenticity identification and genetic relationship analysis of the Henan nong black pig variety, and an effective scientific basis is provided for the intellectual property protection of the Henan nong black pig variety. When the Yunong black pig breed is identified and evaluated, whether the Yunong black pig breed is the Yunong black pig breed can be determined only by comparing and analyzing the Yunong black pig breed and the existing specific molecular identity card. The time and the cost for identifying and evaluating the Yunong black pig germplasm resources are greatly reduced, and the efficiency for identifying and evaluating the Yunong black pig breeds 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. The specific molecular identity card for identifying the Yunong black pig germplasm resources is characterized by comprising the following steps: the SNP loci are a SNP locus set with higher allele frequency among Henan nong black pig breeds.
2. The specific molecular identity card for identifying the germplasm resources of Henong black pigs according to claim 1, wherein: the SNP site is located in the porcine reference genome EnsemblScrofa version 11.1.
3. The specific molecular identity card for identifying the germplasm resources of Henong black pigs according to claim 2, wherein: the set of CNC loci includes CNC10010909 locus, CNC10011130 locus, CNC10011533 locus, CNC10012476 locus, CNC10012481 locus, CNC10012482 locus, CNC10012483 locus, CNC10013609 locus, CNC10013901 locus, CNC10013912 locus, CNC10014023 locus, CNC 10014014014056 locus, CNC10014645 locus, CNC10020600 locus, CNC10021264 locus, CNC10021414 locus, CNC10021534 locus, CNC 10010010010021776 locus, CNC 10010022664 locus, CNC10030888 locus, CNC10031341 locus, CNC10032139 locus, CNC10032433 locus, CNC 40109 locus, CNC10041731 locus, CNC10042349 locus, CNC 10010110010110010110010110010122 locus, CNC 10020385620 locus, CNC 10051562 locus, CNC 60034 locus, CNC 10010030010030065 locus, CNC 30030030030030030030030030065 locus, CNC 300100419104418180 locus, CNC 61616161616142349 locus, CNC 10010110010010010010110010010010010010110020 locus, CNC 1001001001001001001001008120 locus, CNC 1001001001001001001001001008120 locus, CNC 100100100811001001001001008120 locus, CNC 1001001001001001001001001008120 locus, CNC 1001001001001001001008180 locus, CNC 1001008180 locus, CNC 1001001001001001001001008180 locus, CNC 1008180 locus, CNC 1001001001001001008180, CNC 1008195 locus, CNC 1001001001001001001008180 locus, CNC 1001001001001001001001008195 locus, CNC 1001001001001001001001001008195 locus, CNC 1001001001001001001001001008180, CNC 1001001008180, CNC 1001008195 locus, CNC 1001001001001001001001001001001001001001001008195 locus, CNC 1001001001001001001001001008180, CNC 1008180 locus, CNC 1001001008195 locus, CNC 1001008195 locus, CNC 1001001001001001001011008180, CNC 1001001001008180, CNC 1001001001001008180, CNC 1001001001011008180 locus, CNC 1008180, CNC 1001001008195, CNC 1008180, CNC 1001011008180, CNC 1008180, CNC 1008195 locus, CNC 1001001001011001011008180 locus, CNC 1008195 locus, CNC 1001008195, CNC 1008195, CNC 1001001001008180, CNC 1001001001001001001001008195, CNC 1008180, CNC 1008195, CNC 1001001001001001001001001001008180, CNC 1001011001001001001001011008180, CNC 1008180, CNC 10095, CNC 1008180, CNC 1008195, CNC 1001001001008180, CNC 1001001008195, CNC 1008195, CNC 10010010095, CNC 10010010010095, CNC 1001001001008195, CNC 1001008195, CNC 1001001011008195, CNC 10095, CNC 1008195, CNC 10095, CNC 10010095, CNC 10010010010010095, CNC 10095, CNC 4295, CNC 10095, CNC, CNC10132801 site, CNC10133069 site, CNC10133411 site, CNC10133517 site, CNC10133915 site, CNC10134173 site, CNC10140073 site, CNC10140089 site, CNC10140088 site, CNC10140503 site, CNC10140928 site, CNC10142200 site, CNC10070140 site, CNC10142598 site, CNC10150082 site, CNC10150342 site, CNC10150857 site, CNC10150887 site, CNC10151225 site, CNC10151534 site, CNC10152380 site, CNC10152716 site, CNC10160964 site, CNC10161348 site, CNC 70850 site and CNC10180332 site.
4. The specific molecular identity card for identifying the germplasm resources of Henong black pigs according to claim 3, wherein: the CNC10010909 site is mutated into the site A/G, CNC10011130, the T/C, CNC10011533 site is mutated into the site T/A, CNC10012476, the T/C, CNC10012481 site is mutated into the site T/G, CNC10012482, the G/T, CNC10012483 site is mutated into the site G/A, CNC10013609, the G/T, CNC10013901 site is mutated into the site A/G, CNC10013912, the A/G, CNC10014023 site is mutated into the site A/G, CNC10014056, the T/C, CNC10014645 site is mutated into the site G/C, CNC10020600, the C/A, CNC10021264 site is mutated into the site A/3910021414, the T/C, CNC10021534 site is mutated into the site C/G, CNC 21776 site, the A/1002172 site is mutated into the site A/10059661, the A/C10010010021761 site is mutated into the site, The mutant site of CNC10022664 is T/C, CNC10030888, the mutant site of A/G, CNC10031341 is T/C, CNC10032139, the mutant site of A/G, CNC10032433 is C/G, CNC10040109, the mutant site of T/C, CNC10041731, the mutant site of G/T, CNC10042349, the mutant site of A/G, CNC10050024, the mutant site of C/T, CNC10050222, the mutant site of T/C, CNC10050620, the mutant site of C/G, CNC10051703, the mutant site of C/A, CNC10060034, the mutant site of G/A, CNC10030065, the mutant site of T/C, CNC 60366, the mutant site of A/G, CNC10061501, the mutant site of T/C, CNC10061519, the mutant site of C/10058560,562, the mutant site of T/100562, C, CNC, the mutant site of T/6361562, Mutation of CNC10061603 locus into T/C, CNC10061804 locus mutation into A/G, CNC10070094 locus mutation into C/T, CNC10070095 locus mutation into A/G, CNC10070970 locus mutation into A/G, CNC10072223 locus mutation into C/T, CNC10072406 locus mutation into G/A, CNC10081349 locus mutation into G/A, CNC10081350 locus mutation into T/C, CNC10081506 locus mutation into G/A, CNC10081507 locus mutation into G/A, CNC10081568 locus mutation into G/A, CNC10082853 locus mutation into T/A, CNC10090019 locus mutation into T/C, CNC 100805 locus mutation into G/C, CNC10091776 locus mutation into G/A, CNC10091860 860 72 locus mutation into C/T, CNC 0099994 locus mutation into T/C, CNC 1009995 locus mutation into T/6395, CNC10111342 site mutant is G/G, CNC10120314 site mutant is G/T, CNC10120395 site mutant is G/T, CNC10130054 site mutant is G/A, CNC10130479 site mutant is T/C, CNC10132801 site mutant is G/T, CNC10133069 site mutant is C/G, CNC10133411 site mutant is C/T, CNC10133517 site mutant is C/T, CNC10133915 site mutant is A/G, CNC 10173 site mutant is C/G, CNC10140073 site mutant is C/T, CNC10140089 site mutant is G/G, CNC10140088 site mutant is G/A, CNC10140503 site mutant is C/T, CNC10140928 site mutant is T/C, CNC10142200 site mutant is G/5870140 site mutant is A/10042598 site mutant is G/A10142598 site mutant is G/A/1012039, The mutation type of the CNC10150082 site is G/T, CNC10150342 site, the mutation type of the A/G, CNC10150857 site is A/G, CNC10150887 site, the mutation type of the C/T, CNC10151225 site is G/T, CNC10151534 site, the mutation type of the A/G, CNC10152380 site is G/A, CNC10152716 site, the mutation type of the G/A, CNC10160964 site is C/A, CNC10161348 site, the mutation type of the C/T, CNC10170850 site is A/G, and the mutation type of the CNC10180332 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 identifying Henong black pig breeds.
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 utilizing 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) the result of the SNP typing principal component analysis in the step (3) is close to the genetic distance of the Henan nong black pig group, and the Henan nong black pigs are obtained when the result is gathered into a cluster.
CN202210816333.6A 2022-07-12 2022-07-12 Specific molecular identity card for identifying Yunong black pig germplasm resources and application thereof Pending CN114959068A (en)

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