CN118480613A

CN118480613A - Pig whole genome low-density 5K SNP chip and application

Info

Publication number: CN118480613A
Application number: CN202410717765.0A
Authority: CN
Inventors: 武建亮; 周磊; 孟庆利; 许光勇; 刘剑锋; 闫田田; 李智; 马小军; 张博; 刘永乐; 王朝军; 徐利
Original assignee: Beijing Zhongyu Pig Co ltd
Current assignee: Beijing Zhongyu Pig Co ltd
Priority date: 2024-06-04
Filing date: 2024-06-04
Publication date: 2024-08-13

Abstract

The invention relates to the technical fields of animal genomics, molecular biology, bioinformatics and genome breeding, in particular to a pig whole genome low-density 5K SNP chip and application thereof, comprising the following steps: the 5K SNP chip comprises SNP molecular markers shown as SEQ ID NO. 1-5,311, the SNP markers on the chip are fixed by a microarray technology, and high-throughput and high-precision genotyping is realized by utilizing hybridization and fluorescence detection technologies. The pig whole genome low-density 5K SNP chip establishes a breeding value prediction model by combining genotype data and phenotype data acquired by the chip, and remarkably improves the accuracy of genetic evaluation. For example, genetic evaluation using the dual trait GBLUP method, the accuracy of breeding value estimation using low density chip filling to the original site approaches or even exceeds the original high density data. The method effectively supports the realization of different breeding targets, optimizes the breeding strategy and accelerates the genetic progress.

Description

Pig whole genome low-density 5K SNP chip and application

Technical Field

The invention relates to the technical fields of animal genomics, molecular biology, bioinformatics and genome breeding, in particular to a pig whole genome low-density 5K SNP chip and application thereof.

Background

SNP (Single Nucleotide Polymorphism) refers to the variation of single nucleotide at genome level, including single base deletion, insertion, transition, transversion and other molecular markers, and has the characteristics of large number and wide distribution. SNPs, which are genetic markers, contribute to genetic variation of complex traits, and are thus widely used in genetic research. The SNP chip is prepared by fixing a DNA probe with a fluorescent label on a silicon wafer, and then carrying out SNP typing by hybridization of the probe DNA and the genome DNA. SNPs bind to probes on the surface of a silicon wafer instead of genomic sequences, which allows DNA of a large number of individuals to be immobilized on a single chip for analysis.

The genome selection (Genomic selection, GS) technology is one of the current efficient and accurate breeding technologies, and has the advantages of early selection, generation interval shortening, breeding process acceleration and the like compared with the conventional breeding method. The technical implementation process involves SNP breeding chips, big data, high-performance calculation and the like, wherein the breeding chips are important factors influencing the cost effectiveness of the SNP breeding chips. Because of the high price of high-density SNP chips, the application of genome selection technology to livestock and poultry such as pigs, chickens and sheep has not been popularized in China.

The gene chip is relatively expensive for the value of pigs, so that researchers in recent years propose that a low-density SNP chip can be designed based on the current commercial medium-high-density SNP chip, and the low-density SNP chip is filled to medium-high density by utilizing group linkage disequilibrium (Linkage Disequilibrium, LD) information so as to be used for genome selection, thereby reducing the breeding cost and being convenient for the application of a gene selection technology in livestock production practice.

Disclosure of Invention

In view of the above drawbacks of the prior art, a first objective of the present invention is to provide a low-density 5K SNP chip with whole genome of pigs and an application thereof, which solve the above problems in the prior art.

In order to achieve the above purpose, the present invention provides the following technical solutions:

A pig whole genome low-density 5K SNP chip and application, comprising: the 5K SNP chip comprises SNP molecular markers shown as SEQ ID NO. 1-5,311, the SNP markers on the chip are fixed by a microarray technology, and high-throughput and high-precision genotyping is realized by utilizing hybridization and fluorescence detection technologies; the 5K SNP chip expands genome association research by increasing the density of SNP markers, and identifies gene loci related to important economic traits; the 5K SNP chip establishes a breeding value prediction model by carrying out high-density genotyping on pig individuals and combining phenotype data; the 5K SNP chip establishes a breeding value prediction model by genotyping a large number of pig individuals and combining phenotype data and environmental factors; the 5K SNP chip can optimize breeding strategies according to different breeding targets by utilizing whole genome selection.

The invention is further provided with: the application of the 5K SNP chip in high-density chip filling in pigs; the whole genome selection can be utilized to optimize breeding strategies according to different breeding targets (such as improving meat yield, improving meat quality, enhancing disease resistance and the like); the 5K SNP chip improves the efficient acquisition and integration efficiency of the data, and realizes the efficient management and utilization of the data by constructing a comprehensive database; the 5K SNP chip can construct genome finger-prints of different varieties by genotyping different pig varieties, thereby accurately identifying the variety sources of pigs.

The invention is further provided with: the application of the 5K SNP chip in pig whole genome selective breeding; the 5K SNP chip can evaluate the genetic structure and variation level of pig groups through genetic diversity analysis.

The invention is further provided with: the 5K SNP chip can perform early selection of target characters by selecting SNP markers related to important economic characters; the 5K SNP chip utilizes SNP markers to carry out genome background selection.

The invention is further provided with: the application of the 5K SNP chip in identifying pig breeds and genetic relationship identification of pigs; the 5K SNP chip can be used for early selection by utilizing SNP markers, and can be used for screening when the breeding pigs do not show target characters, and the breeding direction can be determined in advance.

The invention is further provided with: SNP markers on the 5K SNP chip are fixed by a microarray technology, and high-throughput and high-precision genotyping 5 is realized by utilizing hybridization and fluorescence detection technologies.

Advantageous effects

Compared with the known public technology, the technical scheme provided by the invention has the following beneficial effects:

The pig whole genome low-density 5K SNP chip has obvious beneficial effects in the practical application process. Firstly, the chip greatly improves the accuracy and the integrity of genotype data through an efficient genotype filling technology. And filling the low-density chip data by using the high-density genotype data of the reference population and Beagle software, wherein the accuracy is more than 90%. The high-precision filling technology not only saves cost, but also improves the quality of genotype data, and provides a solid data basis for subsequent genome selection and breeding. In addition, by combining genotype data and phenotype data obtained by the chip, a breeding value prediction model is established, and the accuracy of genetic evaluation is remarkably improved. For example, genetic evaluation using the dual trait GBLUP method, the accuracy of breeding value estimation using low density chip filling to the original site approaches or even exceeds the original high density data. The method effectively supports the realization of different breeding targets, optimizes the breeding strategy and accelerates the genetic progress.

Secondly, the application effect of the 5K SNP chip in the whole genome association research is remarkable, and the gene locus related to important economic traits is identified by increasing the density of SNP markers, so that the early selection and gene positioning of target traits are performed. The high-efficiency genome association analysis method not only improves the breeding accuracy, but also provides powerful support for subsequent molecular verification and gene function research. In addition, the 5K SNP chip is utilized to establish a genetic relationship matrix, so that genetic relationship identification, population inbreeding coefficient calculation and genealogy error detection can be effectively carried out. For example, genome fingerprints of different varieties are constructed by detecting genotypes of different pig varieties, so that the variety sources of the pigs can be accurately identified, and the accuracy and scientificity of the breeding process are ensured. The genetic relationship analysis method based on genotype information can also be used for detecting errors in genealogy records, and improves the efficiency and precision of breeding management. Through genetic diversity analysis, the genetic structure and variation level of pig groups can be evaluated, so that genome background selection is performed, and a breeding strategy is optimized. In the comprehensive view, the practical application of the 5K SNP chip in pig whole genome selective breeding greatly promotes the improvement of genetic improvement and breeding efficiency, and has remarkable economic benefit and application prospect. These effects not only promote the accuracy and efficiency of breeding, but also provide powerful support for genetic improvement, promoting the rapid development of pig breeding and genome research.

Drawings

FIG. 1 is a diagram showing the distribution of a low-density 5K SNP chip and the applied sites of the whole genome of a pig in the whole genome range;

FIG. 2 is a schematic diagram of MAF of a low-density 5K SNP chip of whole pig genome and SNP sites on each chromosome applied in the invention;

FIG. 3 is a schematic diagram showing the horizontal distribution of SNP loci of a low-density 5K SNP chip and application of the whole genome of a pig in the invention;

FIG. 4 is a schematic diagram of the distance between adjacent SNP markers of the SNP molecular markers of the low-density 5K SNP chip and the application of the whole genome of the pig;

FIG. 5 is a schematic diagram of a low-density 5K SNP chip of a whole genome of a pig and four pig group principal component analysis and clustering results applied.

Detailed Description

In order to make the objects, technical solutions and advantages of the embodiments of the present invention more clear, the technical solutions in the embodiments of the present invention will be clearly and completely described below. It will be apparent that the described embodiments are some, but not all, embodiments of the invention. All other embodiments, which can be made by those skilled in the art based on the embodiments of the invention without making any inventive effort, are intended to be within the scope of the invention.

The invention is further described below with reference to examples.

Example 1

A pig whole genome low-density 5K SNP chip and application, comprising: the 5K SNP chip comprises SNP molecular markers shown as SEQ ID NO. 1-5,311, the SNP markers on the chip are fixed by a microarray technology, and high-throughput and high-precision genotyping is realized by utilizing hybridization and fluorescence detection technologies; the 5K SNP chip expands genome association research by increasing the density of SNP markers, and identifies gene loci related to important economic traits; the 5K SNP chip establishes a breeding value prediction model by carrying out high-density genotyping on pig individuals and combining phenotype data; the 5K SNP chip establishes a breeding value prediction model by genotyping a large number of pig individuals and combining phenotype data and environmental factors; the 5K SNP chip can optimize breeding strategies according to different breeding targets (such as improving meat yield, improving meat quality, enhancing disease resistance and the like) by utilizing whole genome selection.

In this embodiment: the SNP molecular marker is obtained by the following three steps:

The first step: the Duroc, changbai and Dabai pigs from breeding farm A and Dabai pigs from breeding farm B were used for genotype data, genotype detection chip model KPSISUS50 0-V1 (CAU 50K), number of primary chip sites 43,832, distributed on 20 pairs (18 pairs autosomal+XY chromosome) of whole genome. Quality control is respectively carried out on the original data of the four groups, the quality control standard is carried out according to the conventional genome selection genotype processing flow in production, and the set parameters are as follows: MAF (minimum allele frequency) > 0.05, hwe (Hartmania temperature balance) > 1e-5, call rate (genotyping detection rate) > 95%, individual detection rate > 95% and removal of sites on all sex chromosomes, leaving only 18 pairs of sites on autosomes, obtaining genotype data of 1,270 doloque, 1,475 long white pigs, 4,173 white pigs from breeding farm A and 5,037 white pigs from breeding farm B, containing 25,454, 30,681, 31,945, 32,049 SNP sites respectively, as original sites of high density chips in four populations, for subsequent genotype filling and genome breeding value estimation.

And a second step of: intersection of the high quality loci of the four populations was taken and the final 18,365 SNP loci were used as the primary loci for low density chip design.

And a third step of: in this study, the heterozygosity score (heterozygosity score) was defined as the sum of the heterozygosity of the loci in the 4 populations previously described, and for the ith SNP, the heterozygosity score hetscore was calculated as:

wherein p _ij is the Minimum Allele Frequency (MAF) of the ith SNP in the jth variety.

Sliding windows are arranged to slide on 18 autosomes of the genome respectively, the highest locus of hetscore in each window is selected, and in order to ensure that the designed low-density chips are consistent with the original locus distribution uniformity, the locus number and the window length on each chromosome are set according to the following formula:

num_i＝num_5k_all/num_row_all*num_raw_i

Wherein num _i is the number of sites on the ith chromosome of the low-density chip=num_5k _all is the number of total sites of the 5K low-density chip/num_raw _all chip design primitive total number of sites (num_raw _i is the number of chip design primitive sites on the ith chromosome)

len_window_i＝len_chr_i/num_chr_i

Wherein len_window _i is the window length on the ith chromosome, len_chr _i is the length of the ith chromosome, num_chr _i is the number of sites on the ith chromosome of the low-density chip

In addition, to ensure genotype filling accuracy, sufficient flanking information was provided, the first and last sites on each chromosome were retained, and a total of 5,311 sites were retained as a 5k low density chip for this study, the site distribution of which is shown in table 1.

The identified SNP loci were submitted to the Illumina company and scored by the Infmium iSelect scoring system (http:// www.illumina.com /), and loci with intra-gene scores <0.7 and inter-gene <0.9 were removed. For deleted disqualified SNP sites, the SNP site nearest to it is selected for supplementation and scoring again. And identifying and screening according to the steps, and finally obtaining 5,311 label SNP loci. 5,311 microbeads (beads) were required according to Illumina Infmium ISELECT HD design requirements. All 5,311 tag SNP loci are 5,311 DNA sequences shown in SEQ ID NO. 1-5,311. These tag sequences were submitted to Illumina corporation design fabrication Infmium SNP chips.

The low-density 5K SNP chip provided by the invention has the following advantages:

The low-density SNP chip provided by the invention has low preparation cost, contains few sites, has strict quality control in the design process, integrates group information of a plurality of varieties, has high polymorphism and heterozygosity of the sites, contains large information quantity, can measure more individuals with low cost, has no group specificity, and can be used for a plurality of pig breeds in production. The low-density SNP chip provided by the invention can effectively reduce the cost of acquiring genotype information, provide more data volume for genome selection and improve evaluation accuracy. The SNP molecular marker provided by the invention has the characteristics of uniform distribution and high whole genome coverage rate, and test results show that the SNP molecular marker has higher genotype filling accuracy, can be filled to medium-high density by using population information and is further used for genome selection, so that early seed selection is realized, the generation interval is shortened, and the genetic progress is accelerated. In addition, the SNP molecular marker provided by the invention can be used as one of the basis of genetic identification, variety identification, pedigree error correction and the like.

TABLE 1 distribution of SNP loci of 5k Low Density chips on genome

Chromosome number	Number of SNP loci	Chromosome number	Number of SNP loci
				1	485	10	183
2	417	11	160
				3	283	12	151
4	335	13	487
				5	245	14	386
6	377	15	352
				7	293	16	195
8	317	17	174
				9	316	18	155

Example 2

A pig whole genome low-density 5K SNP chip and application, the application that the said 5K SNP chip fills in high-density chip in pig; the whole genome selection can be utilized to optimize breeding strategies according to different breeding targets (such as improving meat yield, improving meat quality, enhancing disease resistance and the like); the 5K SNP chip improves the efficient acquisition and integration efficiency of the data, and realizes the efficient management and utilization of the data by constructing a comprehensive database; the 5K SNP chip can construct genome finger-prints of different varieties by genotyping different pig varieties, thereby accurately identifying the variety sources of pigs.

In this embodiment: the conventional quality control was used to obtain four populations of original sites (hereinafter referred to as "original sites") containing 25,454, 30,681, 31,945, 32,049 SNP sites, and genotype test was performed on the four populations using the 5K chip pairs of the present invention, followed by genotype filling of the 5K low density chip data. The method comprises the following specific steps:

According to the birth year of pigs, four groups are subjected to reference group and verification group division, so that subsequent genotype filling and genome breeding value estimation accuracy research are facilitated.

And filling 5K chip data of verification group individuals of four groups of A, B pig farms into original site data by using Beagle software according to reference group information, wherein the obtained accuracy is more than 90% compared with the actual original site data, and the detailed results are shown in Table 3.

TABLE 3 filling accuracy of 5k low density chips

A number of individuals genotype tested and routinely quality controlled using the original 50k chip.

B filling the low-density chip into the individual number of the 50k chip genotype after quality control.

Example 3

A pig whole genome low-density 5K SNP chip and application, the application of the 5K SNP chip in pig whole genome selective breeding; the 5K SNP chip can evaluate the genetic structure and variation level of pig groups through genetic diversity analysis.

In this embodiment: genetic evaluation was performed using the actual original site data and the data filled into the original site using the 5K low density chip of the present invention, respectively. Two large white pig populations of A, B pig farms were used for practical data, a "GBLUP" method was used to build a dual-trait animal model, and genetic evaluation was performed for up to 100kg body weight corrected AGE of day (AGE)/up to 100kg corrected backfat thickness (BF). The method comprises the following specific steps:

(1) DNA from two pig farm large white pigs was extracted for SNP chip detection as described in example 2.

(2) As described in example 2, the reference population uses genotype information contained in the original sites after quality control of the CAU 50K chip, and the validation population uses the original sites and the 5K chip filled in the original sites, respectively, to provide genotype information. The two-trait GBLUP was used for the heavy white pigs of A, B pig farms for the AGE of 100kg body weight per day (AGE)/backfat thickness (BF) trait, and the DMU software was used for genetic evaluation.

Wherein y1 and y2 are phenotypic observations of AGE and BF traits, mu 1 and mu 2 are averages of AGE and BF traits, g1 and g2 are additive breeding values of AGE and BF traits, and e1 and e2 are residuals of AGE and BF traits, respectively.

(3) Results

The specific evaluation accuracy is shown in table 4.

TABLE 4 accuracy of estimation of breeding values for data calculations on different chips

Example 4

A pig whole genome low-density 5K SNP chip and application, said 5K SNP chip can carry on the early selection of the goal trait through choosing the SNP marker correlated with important economic trait; the 5K SNP chip utilizes SNP markers to carry out genome background selection, and the 5K SNP chip is applied to the identification of pig varieties and genetic relationship identification of pigs; the 5K SNP chip can be used for early selection by utilizing SNP markers, and can be used for screening when the breeding pigs do not show target characters, and the breeding direction can be determined in advance.

In this embodiment: the genotype detection is carried out on the DNA extracted from the four groups of pigs by using the 5K pig whole genome SNP chip provided by the invention, the Principal Component Analysis (PCA) is carried out by using GCTA software, and the first and second principal components are mapped, so that the result is shown in figure 4. The results show that pigs of different breeds can be obviously distinguished, wherein large white pig groups of A, B pig farms are respectively from breeding farms of two different areas and still gather together, which shows that the low-density chip has a certain identification and distinguishing effect on pig breeds, but cannot be used as the only standard for identifying pig groups.

Example 5

A low-density 5K SNP chip of pig whole genome and application thereof, SNP mark on the 5K SNP chip is fixed by microarray technology, and high-flux and high-precision genotyping is realized by hybridization and fluorescence detection technology.

In this embodiment: the 5K pig whole genome SNP chip provided in the embodiment 1 of the invention is used for screening and identifying major genes of important economic traits of pig groups. The method comprises the following steps: firstly, genotype detection is carried out on pig groups by using the SNP chip, whole genome association analysis is carried out by combining phenotype data of pig target characters recorded in actual production, and SNP loci which are obviously related to the target characters are selected from the SNP chips according to the result of the saliency detection. Functional genes within 500kb upstream and downstream of the remarkable SNP are annotated as candidate genes, and the functions of the genes are queried by combining with the existing database, so that the purposes of target trait gene positioning and mining are achieved, and theoretical support is provided for subsequent molecular verification.

Genetic relationship identification was performed using the 5K porcine whole genome SNP chip provided in example 1 of the invention. The method comprises the following steps: firstly, genotype detection is carried out on a target individual by using the SNP chip, then, a genetic relationship matrix is established by using genotype information, and genetic relationship identification is carried out according to genetic relationship between individuals and a genealogy record (for example, the genetic relationship coefficient between parents and isotactic cells is about 0.5, and the genetic relationship coefficient between half-siblings is about 0.25). In addition, based on the result of the genetic relationship matrix, the calculation of the population inbreeding coefficient, the genealogy error detection and the like can be performed subsequently.

Working principle:

As shown in figures 1-5, the whole genome low-density 5K SNP chip of the pig fixes SNP markers by a microarray technology, and high-throughput and high-precision genotyping is realized by hybridization and fluorescence detection technologies. 5311 SNP markers contained in the chip are strictly controlled in quality, so that polymorphism and heterozygosity are ensured. The working principle comprises the following steps: first, the acquisition of SNP molecular markers involves the use of various porcine genotyping data from different breeding farms, through quality control steps such as Minimum Allele Frequency (MAF), hardy-Wenberg equilibrium (HWE) and genotyping detection rate screening, and finally 18365 SNP loci are selected as the primary loci for low density chip design. Then, the heterozygosity score of each SNP locus is calculated, the locus with the highest score is selected through a sliding window technology, the uniformity of locus distribution is ensured, and 5311 loci are finally determined as SNP loci of a 5K low-density chip. These sites were chip designed and fabricated by Illumina corporation via Infinium ISELECT HD technology.

The chip has wide application, including genotype filling, breeding value prediction, whole genome association research, genetic relationship identification and genome background selection. The specific application is as follows: genotype filling is performed by using Beagle software by using genotype data of a reference group, and low-density chip data is filled into original site data, so that filling accuracy is more than 90%. And by combining phenotype data and environmental factors, genetic evaluation is carried out by a dual-character GBLUP method, a breeding value is predicted, and the evaluation accuracy is improved. The whole genome association study is used for identifying gene loci related to important economic traits and carrying out early selection and gene positioning of target traits. And establishing a genetic relationship matrix through the SNP chip, and carrying out genetic relationship identification, population inbreeding coefficient calculation and genealogy error detection. Genome background selection is carried out through SNP markers, a breeding strategy is optimized, early seed selection is realized, generation intervals are shortened, and genetic progress is accelerated.

In addition, the 5K SNP chip has remarkable advantages: the low-cost preparation is suitable for large-scale genotype detection, integrates population information of a plurality of varieties, ensures high site polymorphism and heterozygosity, has no population specificity, and is suitable for a plurality of pig breeds. The application of the chip effectively reduces the cost of acquiring genotype information and improves the evaluation accuracy. The SNP molecular marker provided by the method has the characteristics of uniform distribution and high whole genome coverage rate, and the test result shows that the SNP molecular marker has high genotype filling accuracy. The population information is utilized, and the software is used for filling to medium-high density and can be used for genome selection, so that early seed selection is realized, the generation interval is shortened, and the genetic progress is accelerated. SNP molecular markers can also be used for paternity test, variety identification and pedigree error correction.

Through the working principles and the application, the whole genome low-density 5K SNP chip of the pig provides a reliable and economic tool for genome selection and breeding, and accelerates the progress of genetic improvement. The chip not only can reduce the cost of acquiring genotype information, but also can improve data accuracy through an efficient genotype filling technology, so that a breeding strategy is optimized, early seed selection is realized, and genetic progress is accelerated. Through whole genome association research and genetic relationship identification, important economic character related gene loci are identified, and important roles are played in population genetic structure analysis. In a word, the application of the 5K SNP chip not only improves the accuracy and efficiency of breeding, but also provides powerful support for genetic improvement.

The above embodiments are only for illustrating the technical solution of the present invention, and are not limiting; although the invention has been described in detail with reference to the foregoing embodiments, it will be understood by those of ordinary skill in the art that: the technical scheme described in the foregoing embodiments can be modified or some technical features thereof can be replaced by equivalents; such modifications and substitutions do not depart from the spirit and scope of the technical solutions of the embodiments of the present invention.

Claims

1. A pig whole genome low-density 5K SNP chip and application, characterized by comprising: the 5K SNP chip comprises SNP molecular markers shown as SEQ ID NO. 1-5,311, the SNP markers on the chip are fixed by a microarray technology, and high-throughput and high-precision genotyping is realized by utilizing hybridization and fluorescence detection technologies; the 5KSNP chip expands genome association research by increasing the density of SNP markers, and identifies gene loci related to important economic traits; the 5K SNP chip establishes a breeding value prediction model by carrying out high-density genotyping on pig individuals and combining phenotype data; the 5K SNP chip establishes a breeding value prediction model by genotyping a large number of pig individuals and combining phenotype data and environmental factors; the 5K SNP chip can optimize breeding strategies according to different breeding targets by utilizing whole genome selection.

2. The porcine whole genome low-density 5K SNP chip and the application thereof according to claim 1, wherein the SNP chip is characterized by: the application of the 5K SNP chip in high-density chip filling in pigs; the whole genome selection can be utilized to optimize breeding strategies according to different breeding targets (such as improving meat yield, improving meat quality, enhancing disease resistance and the like); the 5K SNP chip improves the efficient acquisition and integration efficiency of the data, and realizes the efficient management and utilization of the data by constructing a comprehensive database; the 5K SNP chip can construct genome finger-prints of different varieties by genotyping different pig varieties, thereby accurately identifying the variety sources of pigs.

3. The porcine whole genome low-density 5K SNP chip and the application thereof according to claim 1, wherein the SNP chip is characterized by: the application of the 5K SNP chip in pig whole genome selective breeding; the 5K SNP chip can evaluate the genetic structure and variation level of pig groups through genetic diversity analysis.

4. The porcine whole genome low-density 5K SNP chip and the application thereof according to claim 1, wherein the SNP chip is characterized by: the 5K SNP chip can perform early selection of target characters by selecting SNP markers related to important economic characters; the 5K SNP chip utilizes SNP markers to carry out genome background selection.

5. The porcine whole genome low-density 5K SNP chip and the application thereof according to claim 1, wherein the SNP chip is characterized by: the application of the 5K SNP chip in identifying pig breeds and genetic relationship identification of pigs; the 5K SNP chip can be used for early selection by utilizing SNP markers, and can be used for screening when the breeding pigs do not show target characters, and the breeding direction can be determined in advance.

6. The low-density 5K SNP chip and the application thereof of the whole genome of the pig, which are disclosed in claim 5, are characterized in that SNP markers on the 5K SNP chip are fixed by a microarray technology, and high-throughput and high-precision genotyping is realized by utilizing hybridization and fluorescence detection technologies.