SNPs associated with pork quality and carcass and their application
By conducting GWAS analysis on the Selenium Black Pork and Pork Quality Resource Group, it was found that the PRKN gene was significantly related to pork quality, and specific primers were designed for PCR amplification, which solved the problem of difficult to lock in pork quality-related genes in the existing technology, and achieved rapid and low-cost pork quality detection and breeding selection.
Patent Information
- Application Number
- CN202410787853.8
- Authority / Receiving Office
- CN · China
- Patent Type
- Patents(China)
- Current Assignee / Owner
- Filing Date
- 2024-06-18
- Publication Date
- 2025-04-01
- Estimated Expiration
- 2044-06-18
AI Technical Summary
The prior art is difficult to effectively lock in candidate genes related to pork quality, resulting in a large confidence interval and making it difficult to conduct accurate pork quality detection and breeding selection.
Through GWAS analysis of the Selenium Black Pork and Pork Quality Resource Group, it was found that there are signal sites significantly related to pork quality in the PRKN gene region, and specific primers were designed for PCR amplification to quickly identify the PRKN genotype, thereby detecting the differences in pork quality and carcass.
It has achieved rapid and low-cost detection of the differences in pork quality and carcass, providing effective molecular markers for the breeding of pig breeds, and improving the accuracy of breeding selection.
Smart Images
Figure CN118531138B_ABST
Abstract
Description
Technical Field
[0001] The present application relates to the technical field of pig breeding, and in particular to SNPs associated with pork quality and carcass and their applications. Background Art
[0002] Pork is one of the most consumed meats in the world, and meat quality and carcass quality are its important economic qualities. As consumers' requirements for meat quality increase, meat quality determines consumers' acceptance and purchasing tendency. The livestock industry has changed its goal from pursuing carcass quality and yield to improving pork quality to meet new market demands.
[0003] Pork quality is jointly regulated by quantitative trait loci (QTL) in the genome. The detection methods of quantitative quality loci include QTL positioning by constructing genetic linkage maps and genome-wide association studies (GWAS). Compared with QTL positioning, GWAS provides higher resolution than traditional linkage mapping, reduces the probability of false positives, and saves time and cost. Therefore, GWAS has become an important method for studying causal variation sites and genetic structure of pork quality. Many quality-related candidate variation sites and even genes have been identified in GWAS studies, but there are still problems such as large confidence intervals and difficulty in locking candidate genes. Summary of the invention
[0004] Parkin RBR E3 ubiquitinprotein ligase, referred to as PRKN gene, encodes Parkin protein, an E3 ubiquitin ligase responsible for marking useless proteins in the body and degrading them by ubiquitination, which helps maintain the normal function and health of cells. PRKN gene mutations can lead to abnormal protein accumulation, accelerate neuronal cell death, and cause diseases such as Parkinson's disease and Alzheimer's disease. In addition, there are literature reports that Parkin participates in mediating organelle-specific autophagy such as mitochondria, affects inflammatory diseases by eliminating damaged organelles and maintaining homeostasis, and promotes cell survival and proliferation. However, there are no reports on the role of this gene in pork quality.
[0005] The present application, through GWAS analysis of the pork quality resource population of Xidu black pigs, found that there are signal sites significantly associated with pork quality in the PRKN gene region. Therefore, the present application designs specific primers based on the SNP mutation site on the eighth intron of the PRKN gene and performs amplification, and distinguishes the meat quality differences between individual pigs based on the polymorphism detection results of the amplified products. Primers are designed using the molecular marker, and the nucleotide sequence containing the SNP site is PCR amplified. Sequencing the amplified product can quickly identify the PRKN genotype, thereby detecting differences in pork quality and carcass, and providing guidance for the breeding of pig varieties. In addition, the primers provided in the present application can specifically amplify the SNP site sequence contained in the gene intron of PRKN, and the detection method has low cost. It can be detected only by PCR amplification, and the difference in meat quality between different pigs can be compared without a large amount of group-scale sampling and measurement.
[0006] To this end, the embodiments of the present application disclose at least the following technical solutions:
[0007] (1): Molecular markers associated with pork quality and carcass, including a nucleotide sequence formed by a single nucleotide mutation G>A at 6716269 bp in the eighth intron of the porcine PRKN gene.
[0008] (2): Molecular marker primers associated with pork quality and carcass, including a DNA molecule as shown in SEQ ID NO:3 and a DNA molecule as shown in SEQ ID NO:4.
[0009] (3): A nucleic acid molecule, which is amplified by PCR using the molecular marker primers described in (2), and the genotype of the nucleic acid molecule is associated with the quality of the pork.
[0010] (4): A kit comprising the molecular marker primers described in (2) and other reagents required for PCR amplification.
[0011] (5): Methods for testing pork quality and carcass, including:
[0012] Obtaining the pig genomic DNA to be tested;
[0013] Perform PCR amplification using the molecular marker primers described in (2);
[0014] The genotype of the 6716269 bp portion of the pig chromosome 1 was detected based on the nucleotide sequence of the amplified product;
[0015] The pork quality is determined based on the genotype.
[0016] (6): A pig screening method including the detection method described in (5).
[0017] (7): The use of the molecular marker described in (1), the molecular marker primer described in (2), the nucleic acid molecule described in (3), or the kit described in (4), wherein the use is selected from any one of the following:
[0018] 1) Detection and analysis of the pork quality, wherein the pork quality and carcass are selected from at least one of the number of ribs, meat color score 1, meat color score 24, muscle color value L1, muscle color value L24, drip loss 48h, intramuscular fat content and moisture;
[0019] 2) Screening and breeding of pigs. BRIEF DESCRIPTION OF THE DRAWINGS
[0020] Figure 1 It is the overall technical flow chart of this application.
[0021] Figure 2 This is the reverse sequencing result of the complementary chain of the single nucleotide mutation G>A mutation at 6716269bp in the eighth intron of the pig PRKN gene. The red box in the figure is the SNP site. From top to bottom, they are CC homozygous, CT heterozygous and TT homozygous, which correspond to GG homozygous, GA heterozygous and AA homozygous at 6716269bp in the sequence of chromosome 1 of the pig genome (NC 010443.5 (5698508.6731132)).
[0022] Figure 3 It is a visual diagram of the nucleotide sequence of the eighth intron fragment of the porcine PRKN gene (SEQ ID NO: 1 or SEQ ID NO: 2). The red frame represents the location of the mutation, and the mutation position is located at the 300th base of the sequence. The underlined sequence represents the primer position. DETAILED DESCRIPTION
[0023] In order to make the purpose, technical scheme and advantages of the present application clearer, the present application is further described in detail below in conjunction with the examples. It should be understood that the specific embodiments described herein are only used to explain the present application and are not intended to limit the present application. The reagents not described separately in detail in the present application are all conventional reagents and can be obtained from commercial channels; the methods not described in detail are all conventional experimental methods and can be obtained from the prior art.
[0024] The present application example sequenced the mutation site of a portion of the nucleotide sequence of the PRKN gene and found that the genotype at 6716269 bp of the eighth intron of the PRKN gene was associated with pork quality.
[0025] To this end, the present application discloses a molecular marker associated with pork quality, including a nucleotide sequence formed by a single nucleotide mutation G>A at 6716269bp in the eighth intron of the pig PRKN gene. Among them, the pig PRKN gene refers to GeneID: 733673 in the GeneBank database, assembly number Sscrofa11.1 (GCF 000003025.6), and position information: NC010443.5 (5698508..6731132).
[0026] In some embodiments, the pork quality and carcass are selected from at least one of the number of rib logs, meat color score 1, meat color score 24, muscle color value L1, muscle color value L24, drip loss 48h, intramuscular fat content and moisture.
[0027] In some embodiments, at 6716269 bp of the eighth intron of the porcine PRKN gene, the number of rib pairs of individuals with AA genotype is significantly higher than that of individuals with other genotypes.
[0028] In some embodiments, at 6716269 bp of the eighth intron of the pig PRKN gene, the meat color score 1 of individuals with AA genotype is significantly higher than that of individuals with other genotypes.
[0029] In some embodiments, at 6716269 bp of the eighth intron of the pig PRKN gene, the meat color score 24 of individuals with AA genotype is significantly higher than that of individuals with other genotypes.
[0030] In some embodiments, at 6716269bp of the eighth intron of the pig PRKN gene, the muscle color value L1 of individuals with the GG genotype is significantly higher than that of individuals with other genotypes.
[0031] In some embodiments, at 6716269bp of the eighth intron of the pig PRKN gene, the muscle color value L24 of individuals with the GG genotype is significantly higher than that of individuals with other genotypes.
[0032] In some embodiments, at 6716269bp of the eighth intron of the porcine PRKN gene, the drip loss of individuals with the GG genotype at 48h was significantly higher than that of individuals with other genotypes.
[0033] In some embodiments, at 6716269 bp of the eighth intron of the porcine PRKN gene, the intramuscular fat of individuals with the GG genotype is significantly higher than that of individuals with other genotypes.
[0034] In some embodiments, at 6716269bp of the eighth intron of the pig PRKN gene, the water content of individuals with AA genotype is significantly higher than that of individuals with other genotypes.
[0035] Based on this, according to the genotype at 6716269bp of the eighth intron of the pig PRKN gene, the pork quality of individual pigs can be molecularly marked to facilitate the selection of pig breeds with excellent meat quality.
[0036] Therefore, specific primers were designed with reference to the eighth intron of the porcine PRKN gene in the GeneBank database (the sequences of the primers are shown in SEQ ID NO:3 and SEQ ID NO:4 in the sequence listing), PCR amplification was performed using porcine genomic DNA as a template, the amplified products were gel-recovered and sequenced and analyzed, and gene fragments as shown in SEQ ID NO:1 and SEQ ID NO:2 in the sequence listing were obtained.
[0037] Based on this, the present application also discloses molecular marker primers associated with pork quality, including a DNA molecule as shown in SEQ ID NO: 3 and a DNA molecule as shown in SEQ ID NO: 4. The "molecular marker primers" are used to amplify molecular markers containing pork quality linkage, such as nucleotide sequences of SNPs, to analyze the genotype of the molecular marker, thereby knowing the pork quality.
[0038] On the other hand, the embodiment of the present application also discloses a nucleic acid molecule, which is amplified by PCR using the molecular marker primers, and the genotype of the nucleic acid molecule is associated with the pork quality. Further, the nucleic acid molecule is shown in SEQ ID NO: 1-2.
[0039] On the other hand, the embodiments of the present application also disclose a kit, including the molecular marker primers and other reagents required for PCR amplification.
[0040] Based on this, the present application also discloses a method for detecting pork quality, including: obtaining the genomic DNA of the pig to be tested; performing PCR amplification using the molecular marker primers; detecting the genotype at 6716269bp of the eighth intron of the pig PRKN gene according to the nucleotide sequence of the amplified product; and determining the pork quality according to the genotype. For example, the number of pig rib logs, meat color score 1, meat color score 24, muscle color value L1, muscle color value L24, drip loss 48h, intramuscular fat content and moisture are determined according to the genotype.
[0041] In some embodiments, the detection method further comprises sequencing the amplified product, and determining the genotype at 6716269 bp of the eighth intron of the pig PRKN gene according to the sequencing result.
[0042] Based on this, the embodiments of the present application also disclose a method for screening pigs, including the detection method described above, to determine the number of pig ribs, meat color score 1, meat color score 24, muscle color value L1, muscle color value L24, drip loss 48h, intramuscular fat content and moisture, and then screen pig breeds to obtain excellent pig breeds.
[0043] Based on this, the present application also discloses the application of the molecular marker, the molecular marker primer, the nucleic acid molecule or the kit, and the application is selected from any of the following:
[0044] 1) Detection and analysis of the pork quality, wherein the pork quality and carcass are selected from at least one of the number of ribs, meat color score 1, meat color score 24, muscle color value L1, muscle color value L24, drip loss 48h, intramuscular fat content and moisture;
[0045] 2) Screening and breeding of pigs.
[0046] The present application is now further described in conjunction with specific examples. The following examples are only intended to explain the present application, but do not constitute a limitation to the present application. The test samples and test processes used in the following examples include the following (if the specific experimental conditions are not specified in the examples, they are usually in accordance with conventional conditions or the conditions recommended by the reagent company; the reagents, consumables, etc. used in the following examples, if not otherwise specified, can all be obtained from commercial sources).
[0047] 1. Extraction of porcine genomic DNA
[0048] The experimental pig breed of this application is Selenium City Black Pig, and the samples come from Hubei Huajian Selenium Garden Agriculture and Animal Husbandry Technology Co., Ltd. The genomic DNA of the pig was extracted using the genomic DNA kit produced by Beijing Biotech Biotechnology Co., Ltd. The extraction was performed according to the instructions of the kit. The concentration and quality of the extracted DNA were tested and stored at -20°C for later use. The remaining muscle samples were sealed in bags and stored at 4°C, and sent to the Agricultural Pig Quality Supervision and Inspection and Testing Center of the Ministry of Agriculture of Huazhong Agricultural University (Wuhan) within 4 hours to measure the quality of pork in accordance with the Agricultural Industry Standard of the People's Republic of China "Technical Specifications for Pork Quality Determination" (Standard No.: NY / T 821-2019).
[0049] 2. Obtaining the porcine PRKN gene fragment and detecting the PRKN gene SNP site
[0050] 1. Obtaining the eighth intron fragment of the porcine PRKN gene
[0051] (1) PCR amplification
[0052] The following primer pairs were designed based on the porcine PRKN gene sequence (Gene ID: 733673 in the GeneBank database):
[0053] Forward primer PRKN-F: 5'-CACTCCCTCCATGAGCCACAGTTAA-3',
[0054] Reverse primer PRKN-R: 5′-AGCGGGTGATCTGTGCC-3′.
[0055] The above primers were used to perform PCR amplification in a mixed genomic DNA pool of 40 Sedu Black Pigs. The PCR reaction system was 50 μL, and the concentrations of each component in the system were 100 ng template DNA, 10× buffer (containing Mg 2+ )4 μL, 0.5 μM each of the upstream and downstream primers mentioned above, 2.5 μM dNTPs, and 1 U Taq DNA polymerase.
[0056] The PCR operation program was as follows: preheating at 98°C for 45s; denaturation at 98°C for 10s, annealing at 56°C for 30s, extension at 72°C for 30s, for a total of 34 cycles; extension at 72°C for 10min; storage at 4°C. PCR products were electrophoresed using 1.5% agarose gel.
[0057] (2) PCR product purification
[0058] The above PCR products were purified using the Gel Extraction Kit of Shanghai Shenggong Biotechnology Co., Ltd. (according to the instructions of the kit), and the specific steps are as follows: first, the gel containing the target fragment was cut from the agarose gel, placed in a 1.5mL centrifuge tube, 400μL of sol solution was added, and the gel was completely melted in a 50-60℃ water bath. When heating the melted gel, it was mixed every 2 minutes and cooled to room temperature; the centrifuge column was placed in a collection tube, the mixed solution was transferred to the centrifuge column, and it was placed at room temperature for 2 minutes; centrifuged at 12000r / min for 1 minute, at which time the DNA was adsorbed on the column; discarded Collect the waste liquid in the tube, put the centrifuge column into the same collection tube, add 700μL of elution buffer, and centrifuge at 12000r / min for 1min; pour out the waste liquid in the collection tube, and centrifuge at 12000r / min for 1min; put the centrifuge column into a pre-prepared sterilized 1.5mL centrifuge tube, add 40μL of elution buffer or double distilled water (Ph>7.0), and place it at room temperature or 37℃ for 2-3min; centrifuge at 12000r / min for 1min, and the liquid in the centrifuge tube is the recovered DNA fragments.
[0059] 2. Obtaining the mutation site of the eighth intron fragment of the porcine PRKN gene
[0060] The DNA fragments recovered above were sent to Wuhan Aoke Dingsheng Biotechnology Co., Ltd. for sequencing using an ABI3730XL sequencer, and a single-base mutation site was found ( Figure 2), a G>A mutation at the 6716269 bp of the PRKN genome nucleotide sequence (i.e., the full sequence) (GeneID: 733673 in the GeneBank database), and the mutation sites corresponding to the PRKN gene fragment of the present application are: a G>A base mutation (i.e., allele mutation) at 300 bp in SEQ ID NO: 1; an A>G base mutation (i.e., allele mutation) at 300 bp in SEQ ID NO: 2, such as Figure 3 shown.
[0061] 3. Molecular marker genotyping
[0062] The DNA sample of the individual to be tested was used as a template, and the eighth intron sequence fragment of the porcine PRKN gene was amplified according to the method described in step 1 above. The obtained PCR purified product was directly sent to Wuhan Aoke Dingsheng Biotechnology Co., Ltd. for sequencing, and the genotyping results were directly read from the sequencing results, such as Figure 2 shown.
[0063] 3. Genetic diversity detection and analysis of its association with quality
[0064] Using the method provided in the examples of this application, 267 Selenium City black pigs (from Hubei Huajian Selenium Garden Agriculture and Animal Husbandry Technology Co., Ltd.) were subjected to genetic diversity detection and quality association analysis. SPSS statistical software (Statistical Package for the Social Sciences, Version 26.0) general linear model GLM was used for statistical analysis. The model used was: Y ijklm =μ+G i +A j +X k +S l +e ijklm , where: Y ijklm represents the pork quality phenotypic value; μ represents the population mean; G i represents genotype effect; A j represents the year-season effect; X k represents the gender effect; S l represents the paternal effect; eijklm represents the random residual effect. The results are expressed as the least squares mean ± standard error, and P < 0.05 was considered significant.
[0065] The results of association analysis are shown in Table 1. It was found that the G>A site at 6716269bp of chromosome 1 of the pig genome significantly affected the number of pig rib logarithms, meat color score 1, meat color score 24, muscle color value L1, muscle color value L24, drip loss 48h, intramuscular fat content and water content. As shown in Table 1, the number of rib logarithms of AA genotype individuals was significantly higher than that of other genotype individuals, the meat color score 1 of AA genotype individuals was significantly higher than that of other genotype individuals, the meat color score 24 of AA genotype individuals was significantly higher than that of other genotype individuals, the muscle color value L1 of GG genotype individuals was significantly higher than that of other genotype individuals, the muscle color value L24 of GG genotype individuals was significantly higher than that of other genotype individuals, the drip loss 48h of GG genotype individuals was significantly higher than that of other genotype individuals, the intramuscular fat content of GG genotype individuals was significantly higher than that of other genotype individuals, and the water content of AA genotype individuals was significantly higher than that of other genotype individuals. Therefore, in the process of pig breeding, the G>A marker at 6716269bp of chromosome 1 of the pig genome is used for early molecular marker-assisted selection of reserve pig herds, so that individuals with suitable genotypes can be selected as high-quality pig breeds.
[0066] Table 1 Analysis of the association between the G>A mutation at bp 6716269 of chromosome 1 of the pig genome and pork quality and ketone bodies
[0067]
[0068]
[0069] Note: Shoulder marks are significant difference marks of the same quality in different genotypes
[0070] The above is only a preferred specific implementation of the present application, but the protection scope of the present application is not limited thereto. Any changes or substitutions that can be easily conceived by any technician familiar with the technical field within the technical scope disclosed in the present application should be covered within the protection scope of the present application.
Claims
1. A method for detecting the quality of Xidu black pig pork, wherein the pork quality is the number of ribs, meat color score, drip loss 48h, intramuscular fat content and moisture, and the detection method comprises: Obtaining the pig genomic DNA to be tested; Perform PCR amplification using molecular marker primers, wherein the molecular marker primers are a DNA molecule as shown in SEQ ID NO:3 and a DNA molecule as shown in SEQ ID NO:4; According to the nucleotide sequence of the amplified product, the 6716269bp position of chromosome 1 of the pig genome GCF 000003025.6 was detected; determining the pork quality based on the genotype; Among them, the number of rib logarithms of individuals with AA genotype was significantly higher than that of individuals with other genotypes, the meat color score of individuals with AA genotype was significantly higher than that of individuals with other genotypes, the drip loss of individuals with GG genotype was significantly higher than that of individuals with other genotypes, the intramuscular fat content of individuals with GG genotype was significantly higher than that of individuals with other genotypes, and the water content of individuals with AA genotype was significantly higher than that of individuals with other genotypes.
2. A method for screening Xidu black pig varieties, comprising using the detection method as described in claim 1; to determine the number of pig ribs, meat color score, drip loss 48h, intramuscular fat content and moisture, and then screen the pig varieties to obtain excellent pig varieties.