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

Abstract

The invention discloses a pig whole genome low-density 5K SNP (Single Nucleotide Polymorphism) chip. The chip contains 5311 SNP loci. The SNP marker on the chip is fixed by a microarray technology, and high-throughput and high-precision genetic typing is realized by using hybridization and fluorescence detection technologies. According to the pig whole genome low-density 5K SNP chip disclosed by the invention, a breeding value prediction model is established by combining genotype data and phenotype data obtained by the chip, so that the accuracy of genetic evaluation is remarkably improved, different breeding targets can be realized, a breeding strategy can be optimized, and the progress of pig breeding and genome research can be accelerated.

Description

[0001] This application claims priority to the Chinese patent application with application number 202410717765.0, application date June 4, 2024, and invention name “A pig whole genome low-density 5K SNP chip and its application”. Technical Field

[0002] The present invention relates to the fields of animal genomics, molecular biology, bioinformatics and genome breeding technology, and in particular to a pig whole genome low-density 5K SNP chip and its application. Background Art

[0003] Single nucleotide polymorphisms (SNPs) refer to variations in a single nucleotide at the genomic level, including single-base deletions, insertions, transitions, and transversions, forming molecular markers. These are characterized by their large number and wide distribution. As genetic markers, SNPs contribute to the genetic variation of complex traits and are therefore widely used in genetic research. SNP chips are fabricated by affixing fluorescently labeled DNA probes to a silicon wafer, and then SNP typing is performed by hybridizing the probe DNA with genomic DNA. SNPs bind to the probes on the silicon wafer surface rather than to the genomic sequence, allowing the DNA of a large number of individuals to be affixed and analyzed on a single chip.

[0004] Genomic selection (GS) technology is currently one of the most efficient and precise breeding techniques. Compared with conventional breeding methods, it offers advantages such as enabling earlier selection, shortening generation intervals, and accelerating the breeding process. The implementation of this technology involves SNP breeding microarrays, big data, and high-performance computing, with the breeding microarray being a key factor influencing its cost-effectiveness. However, due to the high cost of high-density SNP microarrays, the application of genomic selection technology in livestock and poultry such as pigs, sheep, and chickens has not yet been widespread in my country.

[0005] Gene chips are relatively expensive compared to the value of the pigs themselves. Therefore, in recent years, researchers have proposed that low-density SNP chips can be designed based on the current commercial medium- and high-density SNP chips, and the population linkage disequilibrium (LD) information can be used to fill them to medium- and high-density, and then used for genomic selection, thereby reducing breeding costs and facilitating the application of gene selection technology in livestock production practices.

[0006] Therefore, it is necessary to develop a pig whole-genome low-density SNP chip. Summary of the Invention

[0007] In order to solve the above problems existing in the prior art, the present invention provides a pig whole genome low-density 5K SNP chip and its application.

[0008] To achieve the above objectives, the present invention provides the following technical solutions.

[0009] In a first aspect, the present invention provides a SNP molecular marker for the whole pig genome, wherein the SNP molecular marker is selected from at least one of the markers shown in Table 2.

[0010] In a second aspect, the present invention provides a molecular probe for specifically identifying the SNP molecular marker described in the first aspect.

[0011] In a third aspect, the present invention provides a pig whole-genome SNP chip, wherein the SNP chip comprises probes targeting the SNP molecular markers described in the first aspect.

[0012] In some embodiments, the porcine whole-genome SNP chip of the present invention contains 5311 SNP sites.

[0013] In some embodiments, the molecular marker is associated with an economic trait.

[0014] In some embodiments, the economic traits include one or more of meat yield, meat quality, and disease resistance, such as age corrected to 100 kg (AGE), backfat thickness corrected to 100 kg (BF), and the like.

[0015] In a fourth aspect, the present invention provides a kit comprising the molecular probe described in the second aspect, or the SNP chip described in the third aspect.

[0016] In a fifth aspect, the present invention provides use of the molecular probe, or the SNP chip, or the kit in pig genotyping detection.

[0017] In some embodiments, the SNP markers on the SNP chip of the present invention are fixed by microarray technology, and high-throughput and high-precision genotyping can be achieved using hybridization and fluorescence detection technology.

[0018] In some embodiments, the SNP chip of the present invention can achieve efficient acquisition and integration of genetic analysis data, and achieve efficient management and utilization of data by constructing a comprehensive database.

[0019] In a sixth aspect, the present invention provides the use of the molecular probe, or the SNP chip, or the kit in pig whole genome breeding.

[0020] In some embodiments, the application in pig whole genome breeding includes using the SNP chip of the present invention to fill medium- and high-density chips of pigs.

[0021] In some embodiments, the SNP chip of the present invention establishes a breeding value prediction model by performing high-density genotyping on individual pigs and combining phenotypic data.

[0022] In some embodiments, the SNP chip of the present invention establishes a breeding value prediction model by genotyping a large number of pig individuals and combining phenotypic data with environmental factors.

[0023] In some embodiments, the SNP chip of the present invention utilizes SNP markers for genomic background selection.

[0024] In some embodiments, the SNP array of the present invention expands genome-wide association studies by increasing the density of SNP markers and identifying gene loci associated with economically important traits.

[0025] In some embodiments, the SNP chip of the present invention can be used for early selection of target traits by selecting SNP markers associated with important economic traits.

[0026] In some embodiments, the SNP chip of the present invention can be used to perform early selection using SNP markers, and can be used to screen sows before they exhibit target traits, thereby determining the breeding direction in advance.

[0027] In some embodiments, the SNP chip of the present invention utilizes genome-wide selection to optimize breeding strategies according to different breeding goals.

[0028] In some embodiments, the use of whole genome selection can optimize breeding strategies according to different breeding goals, such as increasing meat yield, improving meat quality, and enhancing disease resistance.

[0029] In a seventh aspect, the present invention provides use of the molecular probe, or the SNP chip, or the kit in pig breed identification.

[0030] In some embodiments, the SNP chip of the present invention can construct genomic fingerprints of different pig breeds by performing genotyping on different pig breeds, thereby accurately identifying the breed origin of the pigs.

[0031] In an eighth aspect, the present invention provides use of the molecular probe, or the SNP chip, or the kit in pig kinship identification.

[0032] In a ninth aspect, the present invention provides use of the molecular probe, or the SNP chip, or the kit in analyzing genetic diversity of pig populations.

[0033] In some embodiments, the SNP chip of the present invention can be used to assess the genetic structure and variation level of a pig population through genetic diversity analysis.

[0034] Beneficial effects

[0035] The porcine whole genome low-density 5K SNP chip of the present invention has demonstrated significant beneficial effects in practical applications.

[0036] First, through efficient genotype filling technology, the chip greatly improves the accuracy and completeness of genotype data. Using the high-density genotype data of the reference population, Beagle software is used to fill the low-density chip data, and the accuracy is over 90%. This high-precision filling technology not only saves costs, but also improves the quality of genotype data, providing a solid data foundation for subsequent genomic selection and breeding. In addition, by combining the genotype data and phenotypic data obtained by the chip, a breeding value prediction model is established, which significantly improves the accuracy of genetic evaluation. For example, using the double-trait GBLUP method for genetic evaluation, the accuracy of breeding value estimation using the low-density chip of the present invention filled to the original site is close to or even exceeds the original high-density data. This method effectively supports the realization of different breeding goals, optimizes breeding strategies, and accelerates genetic progress.

[0037] Secondly, the 5K SNP array has demonstrated significant success in genome-wide association studies. By increasing the density of SNP markers, it identifies loci associated with economically important traits, enabling early selection and gene mapping for target traits. This highly efficient genomic association analysis method not only improves breeding accuracy but also provides strong support for subsequent molecular validation and gene function studies. Furthermore, the use of the 5K SNP array to construct kinship matrices effectively identifies kinship relationships, calculates population inbreeding coefficients, and detects pedigree errors. For example, by genotyping different pig breeds, genomic fingerprints have been constructed, enabling accurate identification of pig breed origin and ensuring the accuracy and scientific integrity of the breeding process. This genotype-based kinship analysis method can also be used to detect errors in pedigree records, improving the efficiency and precision of breeding management. Genetic diversity analysis can assess the genetic structure and variation levels of pig populations, enabling genomic background selection and optimizing breeding strategies.

[0038] Overall, the practical application of the 5K SNP array in whole-genome selective pig breeding has greatly promoted genetic improvement and increased breeding efficiency, with significant economic benefits and application prospects. These results not only enhance the accuracy and efficiency of breeding, but also provide strong support for genetic improvement and promote the rapid development of pig breeding and genomic research. BRIEF DESCRIPTION OF THE DRAWINGS

[0039] Figure 1This is a genome-wide distribution diagram of the sites of the pig whole-genome low-density 5K SNP chip of the present invention.

[0040] Figure 2 Schematic diagram of the MAF of SNP sites on each chromosome of the pig whole genome low-density 5K SNP chip of the present invention.

[0041] Figure 3 This is a schematic diagram of the distribution of SNP sites at the whole genome level of the pig whole genome low-density 5K SNP chip of the present invention.

[0042] Figure 4 Schematic diagram of the distance between adjacent SNPs of the SNP molecular markers of the pig whole genome low-density 5K SNP chip of the present invention.

[0043] Figure 5 This is a schematic diagram of the clustering results of principal component analysis of four breeding pig populations based on the pig whole genome low-density 5K SNP chip of the present invention. DETAILED DESCRIPTION

[0044] To make the objectives, technical solutions, and advantages of the embodiments of the present invention more clear, the technical solutions in the embodiments of the present invention are described clearly and completely below. Obviously, the described embodiments are only part of the embodiments of the present invention, not all of them. Based on the embodiments of the present invention, all other embodiments obtained by ordinary technicians in this field without making any creative efforts are within the scope of protection of the present invention.

[0045] The present invention will be further described below with reference to the embodiments.

[0046] Example 1. Preparation of a low-density 5K SNP chip for the entire pig genome

[0047] This example provides the preparation of a low-density 5K SNP chip for the entire pig genome.

[0048] In this embodiment, the SNP molecular marker is prepared by the following steps:

[0049] Step 1: Use the genotype data of Duroc pigs, Landrace pigs and Large White pigs from breeding farm A, and the Large White pigs from breeding farm B. The genotype detection chip model is KPSISUS50-V1 (CAU 50K), and the number of original chip sites is 43,832, distributed on 20 pairs of chromosomes (18 pairs of autosomes + XY sex chromosomes) in the whole genome. The raw data from the four populations were quality controlled separately according to the conventional genomic selection genotyping process used in production. The parameters were set as follows: MAF (minimum allele frequency) > 0.05, hwe (Hardy-Weinberg equilibrium) > 1e-5, and call rate (genotyping detection rate) > 95%. The individual detection rate was controlled to be > 95%. All loci on the sex chromosomes were removed, and only loci on 18 pairs of autosomes were retained. Genotyping data for 1,270 Duroc pigs from breeding farm A, 1,475 Landrace pigs, 4,173 Large White pigs from breeding farm A, and 5,037 Large White pigs from breeding farm B were obtained, containing 25,454, 30,681, 31,945, and 32,049 SNP loci, respectively. These loci were used as the raw loci for high-density microarrays in the four populations for subsequent genotype filling and genomic breeding value estimation.

[0050] Step 2: The high-quality sites of the four groups were intersected, and the final 18,365 SNP sites were used as preliminary sites for low-density chip design.

[0051] Step 3: In this study, the heterozygosity score (hetscore) is defined as the sum of the heterozygosities of the sites in the four populations mentioned above. For the i-th SNP, the heterozygosity score is calculated as:

[0052]

[0053] where p ij is the minimum allele frequency (MAF) of the ith SNP in the jth variety.

[0054] Set the sliding window to slide across the 18 autosomes of the genome, and select the site with the highest hetscore in each window. To ensure that the designed low-density chip has the same uniformity of distribution as the original sites, the number of sites on each chromosome and the window length are set according to the following formula:

[0055] num i =num_5k all / num_raw all *num_raw i

[0056] Among them, num i is the number of sites on chromosome i on the low-density chip; num_5k all The total number of sites on the 5K low-density chip; num_raw all The total number of raw sites designed for the chip; num_raw i The original number of sites designed for the chip on chromosome i;

[0057] len_window i =len_chr i / num_chr i

[0058] Among them, len_window i is the window length on chromosome i, len_chr i is the length of chromosome i, num_chr i is the number of sites on chromosome i in the low-density chip.

[0059] In addition, to ensure the accuracy of genotype filling and provide sufficient flanking information, the first and last sites on each chromosome were retained, and a total of 5,311 sites were retained as the 5K low-density array for this study. The site distribution is shown in Table 1.

[0060] Table 1. Distribution of SNP sites on the genome using 5K low-density microarray

[0061] chromosome number Number of SNP sites chromosome number Number of SNP sites 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

[0062] The identified SNP sites were scored using the Infmium iSelect scoring system (http: / / www.illumina.com / ), and sites with intragenic scores <0.7 and intergenic scores <0.9 were removed. For the deleted unqualified SNP sites, the nearest SNP sites were selected to supplement them and score them again. Following the above steps for identification and screening, a total of 5,311 tag SNP sites were obtained. According to the Illumina Infmium iSelect HD design requirements, 5,311 beads are required. These tag sequences were designed to produce the Infmium SNP chip, resulting in a low-density 5K SNP chip for the entire porcine genome.

[0063] The distribution of the sites of the pig whole genome low density 5K SNP chip in the whole genome is as follows: Figure 1 The MAF diagram of the SNP sites on each chromosome of the 5K SNP chip is shown as follows: Figure 2The schematic diagram of the distribution of SNP sites at the whole genome level is shown in Figure 3 As shown, the distance diagram of adjacent SNPs of SNP molecular markers is as follows Figure 4 shown.

[0064] The position information of the SNP chip obtained by the present invention is shown in Table 2.

[0065] Table 2. Location information of SNP chips

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[0101] The low-density 5K SNP chip provided by the present invention has the following advantages:

[0102] The SNP markers on the chip of the present invention are fixed by microarray technology, and high-throughput and high-precision genotyping is achieved by hybridization and fluorescence detection technology; the 5K SNP chip expands genome association studies by increasing the density of SNP markers and identifies gene loci associated with important economic traits; the 5K SNP chip establishes a breeding value prediction model by performing high-density genotyping on pig individuals and combining phenotypic data; the 5K SNP chip establishes a breeding value prediction model by performing genotyping on a large number of pig individuals and combining phenotypic data and environmental factors; the 5K SNP chip uses whole-genome selection to optimize breeding strategies according to different breeding goals (such as increasing meat production, improving meat quality, enhancing disease resistance, etc.).

[0103] The low-density SNP chip provided by the present invention has low preparation cost, strict quality control during the design process, and integrates population information of multiple breeds. The polymorphism and heterozygosity of the sites are high, and the amount of information contained is large. A large number of individuals can be measured at a very low cost, and there is no population specificity. It can be used for multiple pig breeds in production. The use of the low-density SNP chip provided by the present invention can effectively reduce the cost of obtaining genotype information, provide more data for genome selection, and improve evaluation accuracy. The SNP molecular markers provided by the present invention have the characteristics of uniform distribution and high whole-genome coverage. The test results show that they have high genotype filling accuracy, can utilize population information, use software to fill to medium and high density, and then be used for genome selection, thereby achieving early seed selection, shortening the generation interval, and accelerating genetic progress. In addition, the SNP molecular markers provided by the present invention can also be used as one of the bases for kinship identification, breed identification, pedigree error correction, etc.

[0104] Example 2. Application of 5K SNP Chip in High-Density Chip Population in Pigs

[0105] In this example, the 25,454, 30,681, 31,945, and 32,049 SNPs described in step 3 of Example 1, after routine quality control, were used as the original sites for four populations (hereinafter referred to as "original sites"). Genotypes were then tested for the four populations using the 5K chip described in the present invention, and the genotype filling was then performed on the 5K low-density chip data. The specific steps are as follows:

[0106] According to the year of birth of the pigs, the four groups were divided into reference group and verification group to facilitate subsequent genotype filling and genomic breeding value estimation accuracy research.

[0107] Using the reference group information and Beagle software, the 5K chip data of the validation group individuals from the four groups in farms A and B were filled into the original site data. Compared with their actual original site data, the accuracy obtained exceeded 90%. The detailed results are shown in Table 3.

[0108] Table 3. Accuracy of low-density 5K SNP array filling

[0109]

[0110] Note: a. Number of individuals genotyped using the original 50K chip and routine quality control; b. Number of individuals genotyped using the 50K chip after quality control using the low-density 5K SNP chip.

[0111] The results of this example demonstrate the high accuracy of the 5K SNP chip for high-density pig chip filling. Using whole-genome selection, breeding strategies can be optimized based on different breeding goals (e.g., increasing meat yield, improving meat quality, enhancing disease resistance, etc.); the 5K SNP chip can improve the efficient acquisition and integration of this data, enabling efficient data management and utilization through the construction of a comprehensive database. By genotyping different pig breeds, the 5K SNP chip can also construct genomic fingerprints for different breeds, thereby accurately identifying the breed origin of pigs.

[0112] Example 3. Application of 5K SNP Chip in Whole Genome Selection Breeding of Pigs

[0113] This embodiment provides the application of the 5K SNP chip in whole-genome selective breeding of pigs. The 5K SNP chip can evaluate the genetic structure and variation level of a pig population through genetic diversity analysis.

[0114] In this example, genetic evaluation was performed using both real original site data and data populated into the original sites using the 5K low-density chip described in the present invention. Using actual data from two Large White pig populations from farms A and B, a dual-trait animal model was established using the "GBLUP" method. Genetic evaluation was performed on age corrected to 100 kg (AGE) and backfat thickness corrected to 100 kg (BF). The specific steps are as follows:

[0115] (1) As described in Example 2, DNA was extracted from Large White pigs in farms A and B for SNP chip detection.

[0116] (2) As described in Example 2, the reference population used genotype information from the original sites after quality control using the CAU 50K chip, and the validation population used genotype information from both the original sites and the 5K chip populated with the original sites. Genetic evaluation of the corrected age (AGE) to 100 kg / corrected backfat thickness (BF) traits of Large White pigs from farms A and B was performed using the dual-trait GBLUP and DMU software.

[0117]

[0118] Among them, y1 and y2 are the phenotypic observation values of AGE and BF traits, μ1 and μ2 are the mean values of AGE and BF traits, g1 and g2 are the additive breeding values of AGE and BF traits, and e1 and e2 are the residuals of AGE and BF traits, respectively.

[0119] (3) Results

[0120] The specific evaluation accuracy is shown in Table 4.

[0121] Table 4. Accuracy of breeding value estimates calculated from different chip data

[0122]

[0123] From the results in Table 4, it can be seen that the low-density 5K SNP chip of the present application has a high accuracy in estimating breeding values.

[0124] Example 4. Application of 5K SNP Chip in Identifying Pig Breeds

[0125] In this example, the porcine whole genome 5K SNP chip provided by the present invention was used to perform genotyping on the DNA extracted from the four groups of pigs mentioned above. Principal component analysis (PCA) was performed using GCTA software, and the first and second principal components were plotted. The results are shown in Figure 2. Figure 5 The results show that different breeds of pigs can be clearly distinguished. Specifically, the Large White pigs from farms A and B, although originating from breeding farms in different regions, were still clustered together. This demonstrates that the low-density chip of the present invention has a certain ability to identify and differentiate pig breeds and can serve as a reference for identifying pig populations.

[0126] The 5K SNP chip of the present invention can also perform early selection of target traits by selecting SNP markers associated with important economic traits; the 5K SNP chip uses SNP markers to select genomic backgrounds and can be used for pig breed identification and kinship identification; the 5K SNP chip can use SNP markers for early selection, and can screen breeding pigs before they show target traits, thereby determining the breeding direction in advance.

[0127] Example 5.5K SNP chip screening and identification of important economic traits

[0128] The pig whole genome 5K SNP chip provided in Example 1 of the present invention was used to screen and identify major effect genes of important economic traits in pig populations.

[0129] In this example, the SNP chip of the present invention was used to genotype a pig population. Combined with phenotypic data for target pig traits recorded in actual production, such as meat yield, meat quality, and disease resistance, a genome-wide association analysis was performed. Based on the results of the significance test, SNP sites significantly associated with the target traits were selected. Functional genes within 500 kb upstream and downstream of the significantly associated SNP sites were annotated as candidate genes. Gene function was then queried against existing databases to locate and identify genes associated with the target traits, providing theoretical support for subsequent molecular validation.

[0130] Example 6. Application of 5K SNP Chip in Phylogenetic Identification

[0131] Phylogenetic relationship identification was performed using the porcine whole-genome 5K SNP chip provided in Example 1 of the present invention. Specifically, the SNP chip of the present invention was used to perform genotyping on target individuals. A kinship matrix was then constructed using the genotype information. Phylogenetic relationship identification was performed based on the kinship coefficients between individuals combined with pedigree records. The kinship coefficients between parents and children and full siblings were approximately 0.5, and between half siblings were approximately 0.25. Furthermore, the kinship matrix results were used to subsequently calculate the population inbreeding coefficient and detect pedigree errors.

[0132] Working principle:

[0133] like Figure 1-5 As shown, this porcine whole-genome low-density 5K SNP array utilizes microarray technology to immobilize SNP markers and hybridization and fluorescence detection techniques for high-throughput, high-precision genotyping. The 5,311 SNP markers included in the array undergo rigorous quality control to ensure polymorphism and heterozygosity. Its working principle includes the following: First, SNP molecular markers are obtained using genotype data from multiple pig breeds across different breeding farms. Through quality control steps such as minimum allele frequency (MAF), Hardy-Weinberg equilibrium (HWE), and genotyping call rate screening, 18,365 SNP loci were ultimately selected as preliminary loci for low-density array design. Next, heterozygosity scores were calculated for each SNP locus, and the highest-scoring loci were selected using a sliding window technique to ensure uniform locus distribution. Finally, 5,311 loci were selected as the SNP loci for the 5K low-density array. These loci were designed and fabricated using Infinium iSelect HD technology.

[0134] This chip has a wide range of applications, including genotype filling, breeding value prediction, genome-wide association studies, kinship identification, and genomic background selection. Specific applications are as follows: Using genotype data from a reference population, Beagle software is used for genotype filling, and low-density chip data is filled into the original locus data with a filling accuracy exceeding 90%. Combining phenotypic data and environmental factors, genetic evaluation is performed using the dual-trait GBLUP method to predict breeding values and improve evaluation accuracy. Genome-wide association studies are used to identify gene loci associated with important economic traits and conduct early selection and gene mapping for target traits. SNP chips are used to establish kinship matrices for kinship identification, calculate population inbreeding coefficients, and detect pedigree errors. Genomic background selection is performed using SNP markers to optimize breeding strategies, achieve early selection, shorten generation intervals, and accelerate genetic progress.

[0135] In addition, the 5K SNP chip has significant advantages: low-cost preparation is suitable for large-scale genotyping testing, and it integrates population information from multiple breeds to ensure high site polymorphism and heterozygosity, is non-population-specific, and is applicable to multiple pig breeds. The use of the chip effectively reduces the cost of obtaining genotyping information and improves the accuracy of assessments. The SNP molecular markers it provides are characterized by uniform distribution and high genome-wide coverage. Test results show that they have high genotype filling accuracy. Utilizing population information and using software to fill to medium and high density, it can be used for genomic selection, thereby achieving early seed selection, shortening generation intervals, and accelerating genetic progress. SNP molecular markers can also be used for kinship testing, breed identification, and pedigree error correction.

[0136] Through these working principles and applications, this pig whole-genome low-density 5K SNP array provides a reliable and economical tool for genomic selection and breeding, accelerating the progress of genetic improvement. This array not only reduces the cost of obtaining genotype information but also improves data accuracy through efficient genotype imputation technology, thereby optimizing breeding strategies, enabling early selection, and accelerating genetic progress. It also plays a key role in identifying loci associated with important economic traits and analyzing population genetic structure through genome-wide association studies and kinship testing. In summary, the application of the 5K SNP array not only improves the accuracy and efficiency of breeding but also provides strong support for genetic improvement.

[0137] The above embodiments are only used to illustrate the technical solutions of the present invention, rather than to limit the same. Although the present invention has been described in detail with reference to the aforementioned embodiments, those skilled in the art should understand that they can still modify the technical solutions described in the aforementioned embodiments, or make equivalent replacements for some of the technical features therein. However, these modifications or replacements will not cause the essence of the corresponding technical solutions to deviate from the spirit and scope of the technical solutions of the various embodiments of the present invention.

Claims

1. A SNP molecular marker for the whole pig genome, characterized in that: The SNP molecular marker is selected from at least one of the markers shown in Table 2.

2. A molecular probe, characterized in that The molecular probe is used to specifically identify the SNP molecular marker according to claim 1.

3. A pig whole genome SNP chip, characterized in that: The SNP chip comprises probes targeting the SNP molecular markers according to claim 1.

4. The pig whole genome SNP chip according to claim 3, characterized in that The molecular marker is associated with the economic trait; Preferably, the economic traits include one or more of meat yield, meat quality, and disease resistance; More preferably, the economic traits include one or more of age corrected to 100 kg, and backfat thickness corrected to 100 kg.

5. A kit, characterized in that The kit comprises the molecular probe according to claim 2, or the SNP chip according to claim 3 or 4.

6. Use of the molecular probe according to claim 2, or the SNP chip according to claim 3 or 4, or the kit according to claim 5 in porcine genotyping detection.

7. Use of the molecular probe according to claim 2, or the SNP chip according to claim 3 or 4, or the kit according to claim 5 in pig whole genome breeding.

8. Use of the molecular probe according to claim 2, or the SNP chip according to claim 3 or 4, or the kit according to claim 5 in pig breed identification.

9. Use of the molecular probe according to claim 2, or the SNP chip according to claim 3 or 4, or the kit according to claim 5 in pig kinship identification.

10. Use of the molecular probe according to claim 2, or the SNP chip according to claim 3 or 4, or the kit according to claim 5 in analysis of genetic diversity in pig populations.

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