A SNP locus combination and its application for identifying Ding'an pig breeds

Abstract

The present invention belongs to the field of molecular biological identification, and specifically relates to a SNP site combination and application for identifying Ding'an pig breeds. The SNP site combination for identifying Ding'an pig breeds includes 53 SNP sites, whose physical locations are based on the reference genome of the pig. Sscrofa11 .1 The SNP locus combination was screened based on the whole genome association analysis combined with the selection signal analysis method, which can quickly realize the accurate identification of Ding'an pig breed at the gene level, and has significant application value in the accurate protection of genetic resources and breed utilization of Hainan Ding'an pig.

Description

Technical Field

[0001] The invention belongs to the field of molecular biological identification, and specifically relates to a SNP site combination and application for identifying Ding'an pig breeds. Background Art

[0002] Ding'an pigs are mainly distributed in Leiming, Longmen and other towns in Ding'an County, Hainan Province. They are precious pig germplasm resources left over from a century of natural breeding. They belong to one of the four major groups of Hainan pigs and are one of the special pig breeds in Hainan Province. Ding'an pigs are fatty pigs that are resistant to high temperatures and roughage. They have delicate meat and are a well-known brand of pork with a unique flavor in Hainan Province. They have been selected as a high-quality local pig breed in my country and included in the Hainan Province Livestock and Poultry Genetic Resources Protection List.

[0003] In recent years, due to the impact of foreign local pig breeds on Hainan's pig market and the impact of African swine fever and other factors, the number of purebred Ding'an pigs has continued to decrease. Research on the characteristic genetic resources of Ding'an pigs and promoting the group protection of purebred Ding'an pigs are of great significance to the characteristic development of my country's pig breeding industry and the maintenance of the diversity of germplasm resource banks. Among them, the use of bioinformatics to carry out the mining of Ding'an pig characteristic variety sites and realize the accurate identification of the unique genetic characteristics of Ding'an pigs at the gene level is an important part of the accurate protection of Hainan Ding'an pig genetic resources.

[0004] Single nucleotide polymorphism (SNP) is one of the most common forms of genetic variation, widely present in biological genomes, and is also the most common genetic marker in the genome. It has important application value in genetic relationship analysis, genetic structure analysis, pathogenic gene mining, and many other aspects of biological populations.

[0005] In the long-term breeding of Chinese local pig breeds, a large number of selection marks are usually left in the genome. These selection marks can be used as unique gene markers of the breed in the genome and applied to the purity identification of the breed. Genome wide association study (GWAS) and selection signal analysis are effective methods for screening differential loci. The combination of the two can further ensure the reliability of screening differential loci between populations. Summary of the invention

[0006] In order to overcome the deficiencies and shortcomings of the prior art, the primary purpose of the present invention is to provide a SNP site combination for identifying the Ding'an pig breed.

[0007] Another object of the present invention is to provide an application of the above-mentioned SNP site combination for identifying the Ding'an pig breed.

[0008] Another object of the present invention is to provide a method for quickly identifying the Ding'an purebred pig breed.

[0009] The purpose of the present invention is achieved through the following technical solutions:

[0010] A SNP site combination for identifying Ding'an pig breeds, comprising 53 SNP sites, named SNP sites 1-53, the physical positions of the 53 SNP sites are determined based on sequence comparison of the reference genome Sscrofa11.1 of the pig, and the positions and variation information of the 53 SNP sites are as follows:

[0011] SNP site 1 is located on chromosome 1, its physical position is 34353526, and the mutation type is A / G;

[0012] SNP site 2 is located on chromosome 1, its physical position is 34355278, and the mutation type is A / C;

[0013] SNP site 3 is located on chromosome 1, its physical position is 63703594, and the mutation type is G / A;

[0014] SNP site 4 is located on chromosome 1, its physical position is 78237435, and the mutation type is A / G;

[0015] SNP site 5 is located on chromosome 1, with a physical position of 126776991 and a mutation type of C / T;

[0016] SNP site 6 is located on chromosome 1, its physical position is 126816640, and the mutation type is T / C;

[0017] SNP site 7 is located on chromosome 1, its physical position is 226858077, and the mutation type is C / A;

[0018] SNP site 8 is located on chromosome 1, its physical position is 236235017, and the mutation type is A / C;

[0019] SNP site 9 is located on chromosome 1, its physical position is 236244731, and the mutation type is C / T;

[0020] SNP site 10 is located on chromosome 1, its physical position is 264711037, and the mutation type is C / A;

[0021] SNP site 11 is located on chromosome 2, its physical position is 1569508, and the mutation type is T / C;

[0022] SNP site 12 is located on chromosome 2, with a physical position of 59443211 and a mutation type of G / A;

[0023] SNP site 13 is located on chromosome 2, with a physical position of 62411060 and a mutation type of A / G;

[0024] SNP site 14 is located on chromosome 2, its physical position is 65269914, and the mutation type is T / C;

[0025] SNP site 15 is located on chromosome 2, its physical position is 72770530, and the mutation type is T / C;

[0026] SNP site 16 is located on chromosome 2, its physical position is 78142302, and the mutation type is A / G;

[0027] SNP site 17 is located on chromosome 2, its physical position is 78144554, and the mutation type is C / A;

[0028] SNP site 18 is located on chromosome 2, its physical position is 78175365, and the mutation type is G / C;

[0029] SNP site 19 is located on chromosome 2, its physical position is 95419435, and the mutation type is C / T;

[0030] SNP site 20 is located on chromosome 2, its physical position is 125112690, and the mutation type is A / G;

[0031] SNP site 21 is located on chromosome 2, its physical position is 132247545, and the mutation type is G / A;

[0032] SNP site 22 is located on chromosome 3, its physical position is 131466475, and the mutation type is T / C;

[0033] SNP site 23 is located on chromosome 4, its physical position is 29593079, and the mutation type is T / G;

[0034] SNP site 24 is located on chromosome 4, its physical position is 29594502, and the mutation type is C / A;

[0035] SNP site 25 is located on chromosome 4, its physical position is 29601230, and the mutation type is A / C;

[0036] SNP site 26 is located on chromosome 4, its physical position is 29605058, and the mutation type is T / C;

[0037] SNP site 27 is located on chromosome 4, its physical position is 29638456, and the mutation type is C / A;

[0038] SNP site 28 is located on chromosome 4, its physical position is 29901127, and the mutation type is A / G;

[0039] SNP site 29 is located on chromosome 5, its physical position is 1965872, and the mutation type is A / C;

[0040] SNP site 30 is located on chromosome 6, its physical position is 144225798, and the mutation type is G / A;

[0041] SNP site 31 is located on chromosome 8, its physical position is 45952780, and the mutation type is C / T;

[0042] SNP site 32 is located on chromosome 8, its physical position is 53146129, and the mutation type is A / G;

[0043] SNP site 33 is located on chromosome 8, its physical position is 113435311, and the mutation type is T / G;

[0044] SNP site 34 is located on chromosome 9, its physical position is 7865891, and the mutation type is T / C;

[0045] SNP site 35 is located on chromosome 10, its physical position is 6251171, and the mutation type is C / T;

[0046] SNP site 36 is located on chromosome 12, its physical position is 5189400, and the mutation type is T / C;

[0047] SNP site 37 is located on chromosome 13, its physical position is 37675655, and the mutation type is C / T;

[0048] SNP site 38 is located on chromosome 13, its physical position is 38684319, and the mutation type is A / G;

[0049] SNP site 39 is located on chromosome 13, its physical position is 76623007, and the mutation type is A / G;

[0050] SNP site 40 is located on chromosome 13, its physical position is 77372992, and the mutation type is T / C;

[0051] SNP site 41 is located on chromosome 13, its physical position is 78021287, and the mutation type is C / A;

[0052] SNP site 42 is located on chromosome 13, its physical position is 125841898, and the mutation type is A / G;

[0053] SNP site 43 is located on chromosome 14, its physical position is 29917816, and the mutation type is C / T;

[0054] SNP site 44 is located on chromosome 14, its physical position is 127191168, and the mutation type is A / G;

[0055] SNP site 45 is located on chromosome 14, its physical position is 127209414, and the mutation type is T / C;

[0056] SNP site 46 is located on chromosome 15, its physical position is 22437509, and the mutation type is C / T;

[0057] SNP site 47 is located on chromosome 15, its physical position is 31262323, and the mutation type is T / C;

[0058] SNP site 48 is located on chromosome 15, its physical position is 55589883, and the mutation type is T / C;

[0059] SNP site 49 is located on chromosome 15, its physical position is 59503271, and the mutation type is T / C;

[0060] SNP site 50 is located on chromosome 17, its physical position is 22751640, and the mutation type is C / T;

[0061] SNP site 51 is located on chromosome 18, its physical position is 21405530, and the mutation type is C / A;

[0062] SNP site 52 is located on chromosome 18, its physical position is 45056206, and the mutation type is G / C;

[0063] SNP site 53 is located on chromosome 18, its physical position is 45871389, and the mutation type is G / A;

[0064] Application of the SNP locus combination in identifying Dingan pig breeds;

[0065] An application of a product for detecting the above SNP locus combination in identifying Dingan pig breeds;

[0066] The product is a reagent, a kit or a gene chip, etc.;

[0067] The reagents include at least one of primers, probes, etc.;

[0068] A molecular probe combination for identifying Ding'an pig breeds, the molecular probe combination targets the above-mentioned SNP site combination and is used to detect the above-mentioned SNP site combination;

[0069] A gene chip for identifying the Ding'an pig breed, the chip being loaded with the above molecular probe combination;

[0070] A method for quickly identifying Ding'an pig breeds preferably comprises the following steps:

[0071] (1) Collecting tissue samples from the pigs to be tested, extracting DNA from the tissue samples, and obtaining DNA samples from the pigs to be tested;

[0072] (2) performing gene sequencing on the DNA sample of the pig to be tested obtained in step (1) to obtain genotype data of the pig to be tested;

[0073] (3) The genotype data of the pig to be tested obtained in step (2) are combined with the genotype data of the known Ding'an pig group and the control group, and the genotype data of the above-mentioned SNP site combination (53 SNP sites) are extracted. The combined and extracted genotype data are subjected to principal component analysis, and the principal component analysis graph is visualized by the R language ggplot2 package to determine whether the pig to be tested is a Ding'an pig;

[0074] The DNA sample described in step (2) must first undergo quality inspection, and then undergo gene sequencing after passing the quality inspection;

[0075] The DNA sample nucleic acid purity test in step (2) has an A260 / 280 light absorption ratio between 1.8 and 2.0, and a concentration of ≥50 ng / μl;

[0076] The known Ding'an pig group described in step (3) is a group consisting of multiple (≥15) purebred Ding'an pigs, which may be the group of Ding'an pigs in the embodiment, or a group of Ding'an pigs selected by oneself, or a group of Ding'an pigs in a public database;

[0077] The control group described in step (3) is a group of other pigs of multiple pigs (≥5 pigs in a single breed group, ≥30 pigs in the whole group) other than Ding'an pigs, which can be the non-Ding'an pig group in the embodiment, or other non-Ding'an pig groups selected by themselves, or non-Ding'an pig groups in a public database;

[0078] The control group is preferably at least one of Lingao pig, Tunchang pig, Wuzhishan pig, Bama Xiang pig, Diannan small-eared pig, Erhua pig, Meishan pig, Anqing pig, Min pig, Tibetan Xiang pig, Landrace pig, Large White pig, Duroc pig and Asian wild boar;

[0079] The extraction and merging described in step (3) are preferably performed using Plink software;

[0080] The judgment method described in step (3) is:

[0081] When the results of principal component analysis show that the genetic distance between the pig to be tested and the known Ding'an pig population is close, that is, they are clustered in one cluster, the pig to be tested is a Ding'an pig; otherwise, it is a pig of other breeds.

[0082] Compared with the prior art, the present invention has the following advantages and effects:

[0083] (1) Based on resequencing data, the present invention obtains a SNP site combination for specific identification of Ding'an pig breed by combining whole genome association analysis with selection signal analysis. This method further improves the accuracy of identifying specific SNP site combinations, and the screened SNP site combination is more reliable in the identification of Ding'an pig breed.

[0084] (2) The SNP locus combination provided by the present invention has strong specificity and can be used for the scientific and accurate identification and genetic relationship analysis of Ding'an purebred pigs, which is conducive to promoting the protection and development and utilization of Hainan's characteristic local pig varieties.

[0085] (3) The present invention provides a method for rapidly identifying the Ding'an pig breed. The method utilizes genomics and bioinformatics techniques to accurately identify purebred Ding'an pigs, providing an effective scientific basis for the protection of the Ding'an pig breed at the genetic level. BRIEF DESCRIPTION OF THE DRAWINGS

[0086] Figure 1 It is a Manhattan plot of the GWAS analysis results of Dingan pig of the present invention.

[0087] Figure 2 It is a Manhattan plot of the selection signal analysis results of Dingan pig of the present invention.

[0088] Figure 3 It is a distribution diagram of each specific SNP site disclosed in the present invention in each chromosome.

[0089] Figure 4 It is a genotype comparison diagram of different groups at each specific SNP site disclosed in the present invention.

[0090] Figure 5 It is a verification result diagram of the SNP site combination disclosed in the present invention and the principal component analysis of other varieties. DETAILED DESCRIPTION

[0091] The present invention is further described in detail below in conjunction with embodiments and drawings, but the embodiments of the present invention are not limited thereto.

[0092] Example 1 Screening of Ding'an pig-specific SNP sites

[0093] 1. Genotype data acquisition

[0094] (1) The experimental population included 809 pigs of 15 breeds, including 11 local Chinese breeds, including 4 Hainan local breeds, Ding'an pig (n=24, DA), Lingao pig (n=27, LG), Tunchang pig (n=29, TC), and Wuzhishan pig (n=26, WZS); 2 South China breeds, Bama Xiang pig (n=6, BMX) and Diannan small-eared pig (n=33, DNXE); 2 Jianghai pig breeds, Erhualian pig (n=24, EHL) and Meishan pig (n=43, MS); 1 East China breed, Anqing pig (n=18, AQ); 1 North China breed, Min pig (n=18, MIN); 1 plateau breed, Tibetan Xiang pig (n=118, ZX). There are three Western pig breeds, including Landrace (n=52, LR), Large White (n=177, LW), and Duroc (n=172, DU), and one wild boar breed, the Asian wild boar (n=42, AWB).

[0095] Table 1 Statistical table of species, types and numbers of experimental populations

[0096] Serial number variety type Quantity (head) 1 Dingan Pig Hainan local pig 24 2 Lingao Pig Hainan local pig 27 3 Tunchang Pig Hainan local pig 29 4 Wuzhishan Pig Hainan local pig 26 5 Bama Xiang pig South China Pig 6 6 Yunnan Small-eared Pig South China Pig 33 7 Two-faced pig Jianghai Pig 24 8 Meishan Pig Jianghai Pig 43 9 Anqing Pig East China Pig 18 10 Minzhu North China Pig 18 11 Tibetan Pig Plateau Pig 118 12 Landrace Pig Western breed pigs 52 13 Large White Pig Western breed pigs 177 14 Duroc pig Western breed pigs 172 15 Asian wild boar Wild Boar 42

[0097] (2) The genotype data of Ding'an pig, Lingao pig, Tunchang pig and Wuzhishan pig populations were directly obtained by resequencing. The specific method is as follows:

[0098] Ear tissue samples were collected from Ding'an pigs, Lingao pigs, Tunchang pigs, and Wuzhishan pigs, and the total DNA of the samples was extracted using the Omega tissue DNA extraction kit. The integrity and purity of the DNA of each sample were inspected by agarose gel electrophoresis and UV spectrophotometer. The DNA sample light absorption ratio (A260 / 280) was required to be between 1.8 and 2.0, and the concentration was ≥50 ng / μL. The DNA samples that passed the quality inspection were genotyped using the DNBSEQ sequencing platform (Shenzhen BGI Genomics Service Co., Ltd.) to obtain whole-genome genotype (SNP) data. The sequencing depth was 10×, and a total of 40,201,194 SNP sites were obtained for 106 samples.

[0099] (3) The genotype data of other pigs were obtained from the PGIDB database.

[0100] 2. Genotype data processing

[0101] (1) The genotype data of each group were merged according to the conventional method using Plink software (command: --bmerge), and the merged genetic data were quality controlled. SNPs with a site detection rate lower than 95% (command: --geno0.05) and individuals with an individual detection rate lower than 90% (command: --mind 0.1) were removed. A total of 12,633,058 SNP sites shared by 809 individuals were obtained.

[0102] (2) A secondary quality control was then performed. Based on the original quality control conditions, loci with a minimum allele frequency of less than 1% and sex chromosome loci were removed (command: --maf 0.1 --chr 1-18). Finally, 12,631,911 high-quality SNP loci from 809 individuals were used for subsequent analysis.

[0103] 3. Screening of Ding'an pig-specific loci by genome-wide association analysis

[0104] On the basis of step 2, GEMMA software was used to conduct genome-wide association analysis based on a mixed linear model. The specific method was as follows: Ding'an pigs were used as the experimental group, and other breeds were uniformly set as the control group. Association analysis was carried out, and the threshold of significant sites was set to 1e-20.

[0105] like Figure 1 As shown, the significant SNP sites above the threshold line were selected as Ding'an pig breed-specific SNP site group A.

[0106] 4. Select signal analysis to screen Dingan pig-specific loci

[0107] Based on step 2, Plink software was used to convert the quality-controlled genotype data into vcf format (command: --recode vcf-iid), and VCFtools software was used to calculate the genetic differentiation index (Fst). The specific method was as follows: Ding'an pigs were used as the experimental group, and other breeds were uniformly set as the control group. The sliding window size was set to 50,000 bp (command: --fst-window-size 50,000), and the sliding step was set to 10,000 bp (command: --fst-window-step 10,000), and the Fst values ​​of the analysis results were sorted from large to small.

[0108] like Figure 2 As shown, the sites in the top 1% window with the largest Fst value are Ding'an pig breed-specific SNP site group B.

[0109] 5. Screening of common specific SNP loci for whole genome association analysis and genetic differentiation index

[0110] The common SNP sites of group A and group B were retained as group C. The SNP sites of group C were sorted according to their position in the genome, and the SNP sites with a distance of less than 1Mb were regarded as a significant QTL region. The top 1-8 sites with the most significant P value (obtained from the whole genome association analysis in step 3) in each QTL region were retained as the specific SNP sites of Ding'an pigs.

[0111] The distribution of each specific SNP site screened in the genome is as follows Figure 3 The specific site information is shown in Table 2. The genotypes of different populations at each specific SNP site are shown in Figure 4 As shown, the rows in the figure represent different specific SNP sites, the columns represent all individuals used for analysis, and different breeds are represented by different colors above each column. The higher the frequency of the major allele of each SNP site, the closer it is to red. Figure 4 The results showed that the genotypes of the specific SNP loci of Ding'an pigs were significantly different from those of other populations.

[0112] Table 2 Combination of 53 specific SNP molecular markers of Dingan pig

[0113] Serial number chromosome Physical Location Mutation type 1 1 34353526 A / G 2 1 34355278 A / C 3 1 63703594 G / A 4 1 78237435 A / G 5 1 126776991 C / T 6 1 126816640 T / C 7 1 226858077 C / A 8 1 236235017 A / C 9 1 236244731 C / T 10 1 264711037 C / A 11 2 1569508 T / C 12 2 59443211 G / A 13 2 62411060 A / G 14 2 65269914 T / C 15 2 72770530 T / C 16 2 78142302 A / G 17 2 78144554 C / A 18 2 78175365 G / C 19 2 95419435 C / T 20 2 125112690 A / G 21 2 132247545 G / A 22 3 131466475 T / C 23 4 29593079 T / G 24 4 29594502 C / A 25 4 29601230 A / C 26 4 29605058 T / C 27 4 29638456 C / A 28 4 29901127 A / G 29 5 1965872 A / C 30 6 144225798 G / A 31 8 45952780 C / T 32 8 53146129 A / G 33 8 113435311 T / G 34 9 7865891 T / C 35 10 6251171 C / T 36 12 5189400 T / C 37 13 37675655 C / T 38 13 38684319 A / G 39 13 76623007 A / G 40 13 77372992 T / C 41 13 78021287 C / A 42 13 125841898 A / G 43 14 29917816 C / T 44 14 127191168 A / G 45 14 127209414 T / C 46 15 22437509 C / T 47 15 31262323 T / C 48 15 55589883 T / C 49 15 59503271 T / C 50 17 22751640 C / T 51 18 21405530 C / A 52 18 45056206 G / C 53 18 45871389 G / A

[0114] Example 2 PCA visualization analysis of specific SNP loci combination identification of Dingan pigs

[0115] 1. Processing of genotype data

[0116] Referring to Example 1, the genotype data of 15 pig breeds in Example 1 (data of 809 individuals merged in step 2) were extracted according to Table 2 to obtain genotype data corresponding to 53 specific SNP sites (named: D) using Plink software according to conventional methods.

[0117] 2. Variety identification application

[0118] (1) Principal component analysis (PCA)

[0119] Use Plink software to perform PCA analysis on the genotype data D. The output result prefix is ​​named dapca, and two files ending with .eigenval and .eigenvec are obtained. Among them, .eigenval represents the proportion of each PCA, and the other records the eigenvector for drawing the PCA graph. The relevant code is as follows:

[0120] plink --bfile D --pca 3 --out dapca

[0121] plink: used to start Plink;

[0122] --bfile D: used to read the genotype file D in binary format;

[0123] --pca 3: used to perform principal component analysis and obtain the first three columns of eigenvector values;

[0124] --out dapca: Output principal component analysis results, the file prefix is ​​named dapca.

[0125] (2) Visualization

[0126] The output of step (1) is sorted in data format through Excel. Specifically, the first column is set as breed (Breed), the second column is eigenvector value 1 (PC1), and the third column is eigenvector value 2 (PC2). The sorted data (the read data is named pca) is read into R language, and the ggplot2 package is used to draw a PCA analysis chart based on the eigenvector values ​​of the principal component analysis of the first two columns (PC1 and PC2). The X-axis is set as PC1 and the Y-axis is set as PC2. Different breeds are represented by different colors. The relevant code is as follows:

[0127] ggplot(pca,aes(x=PC1,y=PC2,color=Breed))+

[0128] geom_point(size=3)+

[0129] theme_bw() +

[0130] theme(panel.border=element_blank(), panel.grid.major=element_blank(), panel.grid.minor=element_blank(), axis.line=element_line(colour="black"))

[0131] ggplot(pca, aes(x=PC1, y=PC2, color=Breed)):

[0132] ggplot(): The function of the ggplot2 library is used to create graphic objects;

[0133] pca: object / data frame defining the data, containing the result data of principal component analysis;

[0134] aes(x=PC1, y=PC2, color=Breed): Aesthetic mapping function aes(), specifies how to map data to graphic attributes; x=PC1: maps the PC1 column in the data to the x-axis; y=PC2: maps the PC2 column in the data to the y-axis; color=Breed: uses the Breed column in the data to determine the color of the scatter points.

[0135] geom_point(size=3):

[0136] geom_point(): This is a function that adds a scatter point layer to the graph; size=3: sets the size of the scatter points to 3.

[0137] theme_bw():

[0138] Apply a theme, theme_bw() represents the "black and white" theme, which is a simple theme with a white background and grid lines;

[0139] theme(panel.border=element_blank(), panel.grid.major=element_blank(), panel.grid.minor=element_blank(), axis.line=element_line(colour="black")):

[0140] theme(): used to set or adjust non-data elements of the graphic; panel.border=element_blank(): removes the border of the graphic panel; panel.grid.major=element_blank(): removes major grid lines; panel.grid.minor=element_blank(): removes minor grid lines; axis.line=element_line(colour="black"): sets the axis line to black.

[0141] The results are as follows Figure 5 As shown, the 24 Ding'an pigs in Table 1 clustered into one cluster, showing a close genetic distance, and a long genetic distance with the other 14 pig breeds, indicating that Ding'an pigs can be accurately identified by combining the 53 specific SNP sites in Table 2 with PCA analysis. Therefore, the 53 specific SNP site combinations provided by the present invention can be used to identify the breed of Ding'an pigs.

[0142] Example 3 Application of Ding'an pig-specific SNP locus combination in identification of purebred Ding'an pigs

[0143] 1. Genotype data acquisition

[0144] Referring to Example 1, a tissue sample of the pig to be tested is collected, and DNA of the tissue sample is extracted to obtain a DNA sample of the pig to be tested.

[0145] 2. Obtaining genotype data of the pigs to be tested

[0146] Referring to Example 1, the DNA samples of the pigs to be tested are subjected to quality inspection, and after passing the quality inspection, they are sent to a gene sequencing company for gene sequencing to obtain the genotype data of the pigs to be tested.

[0147] 3. Processing of genotype data

[0148] Referring to Example 1, the genotype data of the pig to be tested obtained in step 2 was merged with the genotype data of the known Ding'an pig population (Table 1) and the control population (non-Ding'an pig population in Table 1) through Plink software according to conventional methods, and combined with Table 2, the genotype data corresponding to 53 specific SNP sites were extracted.

[0149] 4. Variety identification application

[0150] (1) Principal component analysis (PCA)

[0151] The specific method is the same as in Example 2;

[0152] (2) Visualization

[0153] The specific method is the same as Example 2.

[0154] (3) Result determination

[0155] When the principal component analysis results show that the genetic distance between the pig to be tested and the known Ding'an pig population (Ding'an pig population in Table 1) is close, that is, they are clustered in one cluster, the pig to be tested is Ding'an pig; otherwise, it is another breed of pig.

[0156] The above embodiments are preferred implementation modes of the present invention, but the implementation modes of the present invention are not limited to the above embodiments. Any other changes, modifications, substitutions, combinations, and simplifications that do not deviate from the spirit and principles of the present invention should be equivalent replacement methods and are included in the protection scope of the present invention.

Claims

1. Application of a product for detecting a specific SNP locus combination in identifying Ding'an pig breeds, characterized in that The specific SNP locus combination consists of 53 SNP loci, and the physical positions of the 53 SNP loci are based on the reference genome of the pig Sscrofa11.1 The positions and variation information of the 53 SNP sites were determined by sequence comparison as follows: SNP site 1 is located on chromosome 1, its physical position is 34353526bp, and the mutation type is A / G; SNP site 2 is located on chromosome 1, its physical position is 34355278 bp, and the mutation type is A / C; SNP site 3 is located on chromosome 1, its physical position is 63703594 bp, and the mutation type is G / A; SNP site 4 is located on chromosome 1, its physical position is 78237435 bp, and the mutation type is A / G; SNP site 5 is located on chromosome 1, its physical position is 126776991 bp, and the mutation type is C / T; SNP site 6 is located on chromosome 1, its physical position is 126816640 bp, and the mutation type is T / C; SNP site 7 is located on chromosome 1, its physical position is 226858077 bp, and the mutation type is C / A; SNP site 8 is located on chromosome 1, its physical position is 236235017 bp, and the mutation type is A / C; SNP site 9 is located on chromosome 1, its physical position is 236244731 bp, and the mutation type is C / T; SNP site 10 is located on chromosome 1, its physical position is 264711037 bp, and the mutation type is C / A; SNP site 11 is located on chromosome 2, its physical position is 1569508 bp, and the mutation type is T / C; SNP site 12 is located on chromosome 2, its physical position is 59443211 bp, and the mutation type is G / A; SNP site 13 is located on chromosome 2, its physical position is 62411060 bp, and the mutation type is A / G; SNP site 14 is located on chromosome 2, its physical position is 65269914 bp, and the mutation type is T / C; SNP site 15 is located on chromosome 2, its physical position is 72770530 bp, and the mutation type is T / C; SNP site 16 is located on chromosome 2, its physical position is 78142302 bp, and the mutation type is A / G; SNP site 17 is located on chromosome 2, its physical position is 78144554 bp, and the mutation type is C / A; SNP site 18 is located on chromosome 2, its physical position is 78175365 bp, and the mutation type is G / C; SNP site 19 is located on chromosome 2, its physical position is 95419435 bp, and the mutation type is C / T; SNP site 20 is located on chromosome 2, its physical position is 125112690 bp, and the mutation type is A / G; SNP site 21 is located on chromosome 2, its physical position is 132247545 bp, and the mutation type is G / A; SNP site 22 is located on chromosome 3, its physical position is 131466475 bp, and the mutation type is T / C; SNP site 23 is located on chromosome 4, its physical position is 29593079 bp, and the mutation type is T / G; SNP site 24 is located on chromosome 4, its physical position is 29594502 bp, and the mutation type is C / A; SNP site 25 is located on chromosome 4, its physical position is 29601230 bp, and the mutation type is A / C; SNP site 26 is located on chromosome 4, its physical position is 29605058 bp, and the mutation type is T / C; SNP site 27 is located on chromosome 4, its physical position is 29638456 bp, and the mutation type is C / A; SNP site 28 is located on chromosome 4, its physical position is 29901127 bp, and the mutation type is A / G; SNP site 29 is located on chromosome 5, its physical position is 1965872 bp, and the mutation type is A / C; SNP site 30 is located on chromosome 6, its physical position is 144225798 bp, and the mutation type is G / A; SNP site 31 is located on chromosome 8, its physical position is 45952780 bp, and the mutation type is C / T; SNP site 32 is located on chromosome 8, its physical position is 53146129 bp, and the mutation type is A / G; SNP site 33 is located on chromosome 8, its physical position is 113435311 bp, and the mutation type is T / G; SNP site 34 is located on chromosome 9, its physical position is 7865891 bp, and the mutation type is T / C; SNP site 35 is located on chromosome 10, its physical position is 6251171 bp, and the mutation type is C / T; SNP site 36 is located on chromosome 12, its physical position is 5189400 bp, and the mutation type is T / C; SNP site 37 is located on chromosome 13, its physical position is 37675655 bp, and the mutation type is C / T; SNP site 38 is located on chromosome 13, its physical position is 38684319 bp, and the mutation type is A / G; SNP site 39 is located on chromosome 13, its physical position is 76623007 bp, and the mutation type is A / G; SNP site 40 is located on chromosome 13, its physical position is 77372992 bp, and the mutation type is T / C; SNP site 41 is located on chromosome 13, its physical position is 78021287 bp, and the mutation type is C / A; SNP site 42 is located on chromosome 13, its physical position is 125841898 bp, and the mutation type is A / G; SNP site 43 is located on chromosome 14, its physical position is 29917816 bp, and the mutation type is C / T; SNP site 44 is located on chromosome 14, its physical position is 127191168 bp, and the mutation type is A / G; SNP site 45 is located on chromosome 14, its physical position is 127209414 bp, and the mutation type is T / C; SNP site 46 is located on chromosome 15, its physical position is 22437509 bp, and the mutation type is C / T; SNP site 47 is located on chromosome 15, its physical position is 31262323 bp, and the mutation type is T / C; SNP site 48 is located on chromosome 15, its physical position is 55589883 bp, and the mutation type is T / C; SNP site 49 is located on chromosome 15, its physical position is 59503271 bp, and the mutation type is T / C; SNP site 50 is located on chromosome 17, its physical position is 22751640 bp, and the mutation type is C / T; SNP site 51 is located on chromosome 18, its physical position is 21405530 bp, and the mutation type is C / A; SNP site 52 is located on chromosome 18, its physical position is 45056206 bp, and the mutation type is G / C; SNP site 53 is located on chromosome 18, its physical position is 45871389 bp, and the mutation type is G / A.

2. The use according to claim 1, characterized in that: The product is a kit or a gene chip.

3. The use according to claim 1, characterized in that: The product described is a reagent; The reagent is at least one of a primer and a probe.

4. A method for quickly identifying Dingan pig breeds, characterized in that The following steps are included: (1) Collecting tissue samples from the pigs to be tested, extracting DNA from the tissue samples, and obtaining DNA samples from the pigs to be tested; (2) performing gene sequencing on the DNA sample of the pig to be tested obtained in step (1) to obtain genotype data of the pig to be tested; (3) merging the genotype data of the pig to be tested obtained in step (2) with the genotype data of the known Ding'an pig population and the control population, and extracting the genotype data of the specific SNP site combination described in claim 1, performing principal component analysis on the combined and extracted genotype data, and visualizing the principal component analysis graph using the R language ggplot2 package to determine whether the pig to be tested is a Ding'an pig; The judgment method described in step (3) is: When the principal component analysis results show that the genetic distance between the pig to be tested and the known Ding'an pig group is close, that is, they are clustered together, the pig to be tested is a Ding'an pig; otherwise, it is a pig of other breeds; the known Ding'an pig group is a group composed of multiple purebred Ding'an pigs; the control group is a group of other pigs that are not Ding'an pigs.

5. The method for rapid identification of Ding'an pig breed according to claim 4, characterized in that: The control group is at least one of Lingao pig, Tunchang pig, Wuzhishan pig, Bama Xiang pig, Diannan small-eared pig, Erhualian pig, Meishan pig, Anqing pig, Min pig, Tibetan Xiang pig, Landrace pig, Large White pig, Duroc pig and Asian wild boar.

6. The method for rapid identification of Ding'an pig breeds according to claim 4, characterized in that: The extraction and merging described in step (3) are preferably performed using Plink software.

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