APC gene molecular marker related to intramuscular fat of pig and application of APC gene molecular marker

Abstract

The invention relates to an APC gene molecular marker related to pig intramuscular fat and application of the APC gene molecular marker, a regulatory gene corresponding to the molecular marker is a pig APC gene, and when the expression quantity of the APC gene is reduced, the adipogenic differentiation level of precursor fat cells is reduced. The molecular marker is a 116914227 basic group, a 116914249 basic group, a 116916126 basic group, a 1170344649 basic group, a 117034881 basic group, a 117034886 basic group, a 117181303 basic group and a 117207159 basic group of a chromosome 2. The APC gene and the SNP site can be used as molecular markers in genetic breeding of pork quality characters, and pig breeding work aiming at the intramuscular fat content character of pigs can be guided by regulating and controlling the expression quantity of the APC gene or the dominant genotype of each SNP marker obtained through screening.

Description

Technical Field

[0001] The present invention relates to the fields of genetic engineering and genetic breeding, and particularly relates to an APC gene molecular marker related to intramuscular fat in pigs and its application. Background Art

[0002] The content of intramuscular fat (IMF) in pigs is a key parameter for evaluating pork quality, as it significantly affects meat tenderness, water-holding capacity, shear value, flavor, and juiciness. There are intricate connections between IMF in pigs and their overall quality, flavor, nutritional components, and potential impacts on human health. The IMF content is one of the most significant meat quality traits and is closely related to other meat quality traits. Lipid accumulation in pork is initiated by fatty acid biosynthesis and is regulated by a complex gene network. The IMF content is significantly correlated with the fatty acid content in pork and the proportion of different fatty acids therein. Generally, the ideal standard for the IMF content is 2% - 3%. When the IMF is 2% - 3%, the muscle shows marbling, and the intramuscular fat is positively correlated with the meat texture and taste. When the IMF is below 2%, it will have an adverse impact on the texture and taste of the meat. However, in the process of pursuing high lean meat percentage in modern pig farming, the content of IMF has gradually decreased inadvertently. Currently, the IMF content of most commercial pigs is below 2%, which not only greatly reduces the deliciousness of pork but also has a negative impact on the economic benefits of the pork industry.

[0003] Therefore, in pig breeding, exploring the key factors affecting IMF deposition has become the key to improving pork quality. Some genes regulating IMF have also been initially discovered in the prior art, such as H-FABP, TNF-α, FAM134B, etc., but the gene regulation for IMF breeding applications is still in its primary stage.

[0004] The APC gene (APC Regulator Of WNT Signaling Pathway) is a protein-coding gene. This gene encodes a tumor suppressor protein that acts as an antagonist of the Wnt signaling pathway. It is also involved in other processes, including cell migration and adhesion, transcriptional activation, and apoptosis. Defects in this gene are known to cause familial adenomatous polyposis. There has been no report publicly stating the association between the APC gene and the intramuscular fat content in pigs. Summary of the Invention

[0005] To solve the above problems, the present invention provides an APC gene molecular marker related to intramuscular fat in pigs and its application.

[0006] The present invention discloses the application of a molecular marker related to intramuscular fat in pigs in pig breeding. The regulatory gene corresponding to the molecular marker is the porcine APC gene, and the gene number of the porcine APC gene in the ensembl database is ENSSSCG00000014207. The APC gene is involved in regulating the adipogenic differentiation of preadipocytes. When the expression level of the APC gene decreases, the adipogenic differentiation level of the preadipocytes decreases.

[0007] Furthermore, the molecular marker is located at position 116914227 on chromosome 2 of the Sscrofa11.1 version of pigs. The SNP name is rs325214531, the base mutation is T or C, and the genotypes are CC, CT, and TT. Among them, the intramuscular fat content of pigs with the TT genotype is greater than that of pigs with the CT genotype, and the intramuscular fat content of pigs with the CT genotype is greater than that of pigs with the CC genotype.

[0008] Furthermore, the molecular marker is located at position 116914249 on chromosome 2 of the Sscrofa11.1 version of pigs. The SNP name is rs336509405, the base mutation is T or C, and the genotypes are CC, CT, and TT. Among them, the intramuscular fat content of pigs with the TT genotype is greater than that of pigs with the CT genotype, and the intramuscular fat content of pigs with the CT genotype is greater than that of pigs with the CC genotype.

[0009] Furthermore, the molecular marker is located at position 116916126 on chromosome 2 of the Sscrofa11.1 version of pigs. The SNP name is rs332768788, the base mutation is T or G, and the genotypes are GG, GT, and TT. Among them, the intramuscular fat content of pigs with the TT genotype is greater than that of pigs with the CT genotype, and the intramuscular fat content of pigs with the GT genotype is greater than that of pigs with the GG genotype.

[0010] Furthermore, the molecular marker is located at position 117034649 on chromosome 2 of the Sscrofa11.1 version of pigs. The SNP name is rs343288160, the base mutation is G or A, and the genotypes are AA, GA, and GG. Among them, the intramuscular fat content of pigs with the GG genotype is greater than that of pigs with the GA genotype, and the intramuscular fat content of pigs with the GA genotype is greater than that of pigs with the AA genotype.

[0011] Furthermore, the molecular marker is located at position 117034881 on chromosome 2 of the Sscrofa11.1 version of pigs. The SNP name is rs81363174, the base mutation is C or T, and the genotypes are CC, TC, and TT. Among them, the intramuscular fat content of pigs with the CC genotype is greater than that of pigs with the TC genotype, and the intramuscular fat content of pigs with the TC genotype is greater than that of pigs with the TT genotype.

[0012] Furthermore, the molecular marker is located at position 117034886 on chromosome 2 of the pig Sscrofa11.1 version. The SNP name is rs698883832, the base mutation is C or T, and the genotypes are CC, TC, and TT. Among them, the intramuscular fat content of pigs with the TT genotype is greater than that of pigs with the TC genotype, and the intramuscular fat content of pigs with the TC genotype is greater than that of pigs with the CC genotype.

[0013] Furthermore, the molecular marker is located at position 117181303 on chromosome 2 of the pig Sscrofa11.1 version. The SNP name is rs81295606, the base mutation is G or T, and the genotypes are GG and TG. Among them, the intramuscular fat content of pigs with the TG genotype is greater than that of pigs with the GG genotype.

[0014] Furthermore, the molecular marker is located at position 117207159 on chromosome 2 of the pig Sscrofa11.1 version. The SNP name is rs81259662, the base mutation is A or G, and the genotypes are AG and GG. Among them, the intramuscular fat content of pigs with the AG genotype is greater than that of pigs with the GG genotype.

[0015] The application of the pig APC gene disclosed in the present invention is in pig breeding related to the trait of intramuscular fat content in pigs.

[0016] The application of the molecular marker disclosed in the present invention is in pig breeding related to the trait of intramuscular fat content in pigs.

[0017] The beneficial effects of the present invention are as follows:

[0018] In the preliminary experiments of the present invention, it was found that there may be an association between the APC gene and the intramuscular fat content in pigs. Through processes such as genome-wide association analysis, SNP locus analysis, differential expression gene screening, and verification of genes on cells, a molecular marker of the APC gene related to intramuscular fat in pigs and its application were successfully discovered. The screened APC gene and SNP loci can be used as molecular markers in the genetic breeding of pork quality traits for molecular marker-assisted selection (MAS), genome-wide selection (GS), etc. By regulating the expression level of the APC gene or screening for the dominant genotypes of each SNP marker, it is possible to guide pig breeding work for the trait of intramuscular fat content in pigs and obtain a commercial pig population with an intramuscular fat content higher than 2%. Description of the Drawings

[0019] Figure 1 Is the Manhattan plot of the GWAS results for the intramuscular fat trait in pigs;

[0020] Figure 2 Is the pathway diagram of the APC gene participating in the regulation of cell adipogenic differentiation;

[0021] Figure 3Interference efficiency of three different siRNAs for the APC gene;

[0022] Figure 4 Expression changes of downstream genes in the pathway involved in regulating adipogenic differentiation of cells after interfering with the APC gene;

[0023] Figure 5 Effect of interfering with the APC gene on adipogenic differentiation of cells in cell experiments;

[0024] Figure 6 Results of comparison of relative lipid droplet sizes. Specific implementation mode

[0025] The present invention will be further described below in conjunction with embodiments.

[0026] The technical solutions in the embodiments of the present invention will be clearly and completely described below in conjunction with the accompanying drawings in the embodiments of the present invention. Obviously, the described embodiments are only a part of the embodiments of the present invention, rather than all the embodiments. Based on the embodiments of the present invention, all other embodiments obtained by those of ordinary skill in the art without making creative efforts belong to the scope of protection of the present invention.

[0027] Example 1: Screening of key genes related to intramuscular fat in pigs:

[0028] 1.1 Experimental animals and phenotypic trait determination:

[0029] A total of 461 Large White pigs from a pig farm in Beijing were selected for the experiment. The carcass weight was about 70 - 80 kg, and the age was about 170 - 180 days. They were raised under the same feeding conditions and slaughtered in the same slaughterhouse according to the "Technical Specification for Determination of Carcass Traits of Lean-Type Pigs (NY / T 825 - 2004)". Referring to the "Technical Regulations for Determination of Pork Quality (NY / T 821 - 2019)", the longissimus dorsi muscle near the 12th - 13th ribs on the left side of each pig's carcass was taken to measure the meat quality traits. The intramuscular fat content of pigs was measured using a near-infrared meat quality tester (FOSS FoodScan 2, Denmark).

[0030] 1.2 Genotyping and transcriptome sequencing:

[0031] 1.2.1 Genotyping: The longissimus dorsi muscle tissues of all experimental pigs were collected, and the sample DNA was extracted using a high-throughput DNA extraction kit:

[0032] The extracted DNA samples were subjected to two kinds of tests: using 1% agarose gel electrophoresis to detect the purity and integrity of DNA; using Qubit to accurately quantify the DNA concentration. The concentration of qualified DNA samples was diluted to 50 ng / µl, and GenoBaits Porcine SNP50K Panel was used for genotyping;

[0033] PLINK software was used to perform quality control on the chip data, and the quality control criteria were as follows: SNPs on sex chromosomes were excluded; SNPs with a genotype detection rate lower than 95% were excluded; SNPs with a minor allele frequency (MAF) lower than 1% were excluded; SNPs seriously deviating from Hardy-Weinberg equilibrium (P-value < 1×10 -6 -6) were excluded; individuals with a genotype detection rate lower than 90% were excluded.

[0034] 1.2.2 Transcriptome sequencing: mRNA libraries of the above individuals were constructed and sequenced. Total RNA of muscle tissues was extracted by the Trizol method, and high-quality RNA was further sequenced after quality inspection. Using a high-quality transcriptome sequencing library, paired-end (PE) sequencing was performed through the IlluminaHiseq 2000 sequencing platform to obtain 110-bp long sequencing reads. Trimmomatic was used to screen the original reads data, and IlluQC.pl (NGS QC toolkit) was used to perform quality control on the sequencing reads to remove reads with more than 10% unknown sequences and a quality score less than 20. Subsequently, Hisat2 was used to establish fast and accurate sequence alignment metrics. Finally, Samtools and featurests were used to convert the transcriptome gene expression count file into the gene expression level of each tissue sample. Quality control and alignment were performed on the RNA sequencing data to obtain the gene expression count value counts. The count value counts were the number of aligned reads, and the TPM value of gene expression was obtained through normalization.

[0035] 1.3 Mining of key candidate genes:

[0036] 1.3.1 Genome-wide association study (GWAS): The single-trait mixed linear model (LMM) in the GEMMA software was used to test the association between each SNP and the phenotype. The statistical model is described as follows: y = Wα + xβ + u + e; where y represents the phenotype of the animal; W represents the covariates (with sample body weight as the covariate, slaughter batch effect and individual gender as fixed effects); α represents the corresponding coefficients including the intercept; x represents the marker genotype; β is the effect value of the marker; u represents the random effect; and e is the error. The Bonferroni multiple correction was used to determine the chromosomal significance threshold (1 / total number of SNPs) to screen for significant SNPs, and candidate genes related to the trait were selected from the 500 kb upstream and downstream regions around these significant SNPs. After threshold screening, a total of 22 SNP loci were found to be significantly associated with the IMF trait at the chromosomal significant level. The loci were distributed on multiple chromosomes, including positions of the 117,181,303rd base pair and the 117,207,159th base pair on chromosome 2 of the Sus scrofa 11.1 version. There were 144 candidate genes near these loci within 500 kb upstream and downstream. It was found that the region near the positions of the 117,181,303rd base pair and the 117,207,159th base pair contained the APC gene. As Figure 1 shown, the horizontal line on the figure is the significance threshold line. The points above the threshold line are the 22 significant SNP loci. The SNP locus indicated by the arrow is at the positions of the 117,181,303rd base pair and the 117,207,159th base pair on chromosome 2 of the Sus scrofa 11.1 version, and the nearby region contains the APC gene.

[0037] (2) Gene differential expression analysis: The mRNA expression count matrix was grouped according to the high and low IMF content for gene differential expression analysis. DESeq2 was used to analyze the differential expression between different subgroups based on gene expression counts, and the Wald test was used for significance testing. Genes with |Fold Change| > 1 and P-value < 0.05 were selected as differentially expressed genes (DEGs). The analysis results found that the APC gene was one of the DEGs. After quality control, a total of 21,545 genes were used for differential expression analysis, and there were 9,230 significantly different genes. Among them, 39 GWAS candidate genes overlapped with the DEGs, and the APC gene was one of the common genes.

[0038] (3)Weighted gene co-expression network analysis: The weighted gene co-expression network analysis was performed using the R package WGCNA. First, a sample gene expression matrix was constructed by combining the gene TPM values of 17 samples, and outlier samples were identified and removed. Subsequently, a co-expression network was constructed. Second, a one-step method was used to construct the network and determine gene modules. Based on an approximate independence value of 0.9, an appropriate soft threshold (β = 14) was selected for network construction. Subsequently, the network was transformed into a topological overlap matrix (TOM), which measures the direct correlation between pairwise genes and their consistency with other genes in the dataset. Then, hierarchical clustering was performed based on the differences in TOM. Finally, by analyzing the correlation between phenotypic traits and the module eigengenes (ME) of each module, the association between gene modules and phenotypic information was established. Among the numerous gene modules, the turquoise module had the highest correlation with intramuscular fat in pigs (correlation coefficient 0.91, P-value < 0.01). Analysis found that the APC gene was a gene in the turquoise module.

[0039] (4)Gene function enrichment analysis: To comprehensively understand biological interactions and integrate phenotypic, genomic, and transcriptional information, the intersection of GWAS candidate genes, DEGs, and genes in the WGCNA functional modules was used to identify key candidate genes affecting traits. First, the overlapping genes of DEGs and genes in the WGCNA functional modules highly correlated with phenotypes were annotated using Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway analysis and Gene Ontology (GO) analysis. Based on the R package clusterProfiler, the biological processes (BP), cellular components (CC), and molecular functions (MF) they participated in were explored using the GO database. The KEGG database was used to classify gene pathways or functions. Analysis found that the APC gene was involved in the Wnt (KEGG pathway: ssc04310) and PPAR (KEGG pathway: ssc03320) signaling pathways.

[0040] (5)GWAS-DEGs-WGCNA joint analysis: By combining the common genes in the GWAS, DEGs, and WGCNA joint analysis, that is, using the intersection genes among GWAS candidate genes, DEGs, and genes in the significantly modules of WGCNA, and genes significantly enriched in the key GO and KEGG pathways related to lipid metabolism (P-value < 0.05) were identified as key genes.

[0041] Based on the above five-dimensional analysis, it was found that among numerous genes, the APC gene was the intersection gene among GWAS candidate genes, DEGs, and significantly modules of WGCNA. The APC gene might affect the Wnt (KEGG pathway: ssc04310) and PPAR (KEGG pathway: ssc03320) signaling pathways, thereby affecting pig fat metabolism, such asFigure 2 As shown in Figure 2 , in the Wnt signaling pathway, the expression level of the APC gene affects the expression level of its downstream gene, the TCF7L2 gene, which in turn affects the expression of PPARβ / δ. Due to the interaction among the PPAR family members, the expression of PPARβ / δ also affects the expression of PPARα, thereby affecting lipid metabolism, adipogenesis, and cell differentiation. According to the intersection genes in the genome-wide association analysis, gene differential expression analysis, and weighted gene co-expression network analysis, after performing functional enrichment analysis on the genes, a potential gene regulatory pathway map of the APC gene affecting lipid metabolism was found. The APC gene may affect the expression levels of related genes in the Wnt (KEGG pathway: ssc04310) and PPAR (KEGG pathway: ssc03320) signaling pathways, thus affecting porcine fat metabolism.

[0042] Example 2: Verification of the association between the APC gene and intramuscular fat in pigs

[0043] On the basis of analyzing and determining in Example 1 that the key gene related to intramuscular fat in pigs is the APC gene, its function was verified at the molecular and cellular levels in mouse 3T3-L1 preadipocytes.

[0044] After comparison and retrieval in relevant biological databases, both mice and pigs are mammals with a relatively close evolutionary relationship. There is an Apc gene homologous to the porcine APC gene in mice, which has similar biological functions and similar biological pathways. Therefore, the verification in mouse cells can also be used as evidence for the biological function of the porcine APC gene.

[0045] Mouse 3T3-L1 preadipocytes were cultured in a specific medium containing growth factors and hormones required to maintain their preadipocyte characteristics, and were treated with differentiation medium for one week to induce adipogenic differentiation. 3T3-L1 preadipocytes were cultured in 12-well plates and grown to 60% - 80% confluence, and then transfected with siRNA.

[0046] According to the gene sequence of mouse Apc (ensembl database gene ID: ENSMUSG00000005871) homologous to porcine APC (ensembl database gene ID: ENSSSCG00000014207) gene, 3 pairs of siRNA (Apc-mouse-756, Apc-mouse-1780, Apc-mouse-1879) were designed to interfere with gene expression, and a non-specific fragment was used as a negative control (NC-siRNA). The siRNA sequences are shown in Table 1. The siRNA sequences are shown as SEQ ID NO.1 - SEQ ID NO.8 in sequence.

[0047] Table 1 siRNA sequences

[0048]

[0049] During cell culture, the cells were divided into 4 groups. One group had no interference (NC group), and the other 3 groups were interfered with 3 pairs of different siRNAs respectively. The efficiency of reducing the expression of APC gene after interfering with the cells by 3 pairs of different siRNAs was compared. As Figure 3 shown, the expression level of APC gene in cells was the lowest after interference with the siRNA pair Apc-mouse-1780. The siRNA with the greatest impact on interfering expression, namely Apc-mouse-1780, was selected for subsequent experiments.

[0050] After the adipogenic differentiation of 3T3-L1 preadipocytes, total RNA was extracted and reverse transcribed into cDNA for real-time fluorescence quantitative PCR. The primer sequences for RT-qPCR are shown in Table 2. The primer sequences are shown as SEQ ID NO.9 - SEQ ID NO.16 in sequence.

[0051] Table 2 RT-qPCR primer information

[0052]

[0053] The expression levels of key candidate genes and their downstream genes PPARα and TCF7L2 in lipid regulation-related pathways were detected. As Figure 4 shown, after using Apc-mouse-1780 to interfere with the cells to reduce the expression level of APC gene, the expression levels of the downstream genes Ppara and Tcf7l2 of the APC gene were both reduced compared with the non-interfered control group (NC group). The Ppara and Tcf7l2 in mice are homologous to the PPARα and TCF7L2 genes in pigs. After fixing the induced adipogenic 3T3-L1 preadipocytes, the differentiated mature cells were stained with Oil Red O to observe the intracellular lipid accumulation on the 11th day. As Figure 5 shown, after using Apc-mouse-1780 to interfere with the cells to reduce the expression level of APC gene, the adipogenic differentiation level of the cells was reduced compared with the untreated group. Using imagej software to Figure 5 perform gray-scale analysis on the Oil Red O staining pictures, and comparing the lipid droplet sizes between the experimental group after using Apc-mouse-1780 to interfere with the cells to reduce the expression level of APC gene and the treated control group. As Figure 6 shown, the lipid droplets in the experimental group after using Apc-mouse-1780 to interfere with the cells to reduce the expression level of APC gene were significantly smaller than those in the untreated control group.

[0054] After the screening in Example 1 and verification in Example 2, the APC gene was determined to be a key gene related to intramuscular fat in pigs. The gene number of the porcine APC gene in the ensembl database is ENSSSCG00000014207. The APC gene is involved in regulating the adipogenic differentiation of preadipocytes. When the expression level of the APC gene decreases, the adipogenic differentiation level of the preadipocytes decreases. In pig breeding, a commercial pig population with ideal intramuscular fat content traits can be obtained by regulating the expression level of the APC gene.

[0055] Example 3: SNP molecular marker analysis related to the APC gene:

[0056] To further determine the SNP markers that potentially regulate the expression of the above APC gene and facilitate their application in the genetic selection of pig meat quality traits, the 50K chip sites were filled to the sequencing data level to obtain more SNP markers, which is convenient for screening causal mutations or key mutation sites in the transcriptional region and promoter region of the APC gene.

[0057] 3.1 Filling 50K chip SNP sites to the sequencing level: Based on the genotyping results of the GenoBaits PorcineSNP50K Panel (liquid-phase 50K chip, containing a total of 108,923 core SNP and segment SNP sites) of the above experimental pig population, the whole-genome sequencing data of 1602 pigs of multiple breeds were used as the reference population (source: https: / / doi.org / 10.1038 / s41588-023-01585-7), and the chip data was filled to the sequencing data level. Both the sequencing data and the chip data were aligned to the pig reference genome Sus scrofa 11.1 version. The Beagle 5.1 software was used to fill the genotypes of 18 autosomes (with 105,477 SNP) of the chip data. After filling, the number of SNP sites was 42,523,218. The VCFtools 0.1.16 software was used to perform quality control on the filled genotype data according to the following principles: (1) Remove SNP sites with a minor allele frequency less than 0.01; (2) Remove SNP sites with a severe deviation from the Hardy-Weinberg equilibrium P < 1×10-6; (3) Remove SNP sites with a genotyping missing rate greater than 5%. After quality control, 16,166,580 SNP sites remained for subsequent analysis, and the average DR2 (Dosage R-squared) reported by the Beagle software was greater than 0.90.

[0058] 3.2 Association analysis of important SNPs of the APC gene with traits: Referring to the DNA sequence and annotation information of the porcine APC gene (ENSSSCG00000014207) published in the Ensembl database (https: / / www.ensembl.org / ), after imputation, a total of 1703 SNPs were obtained within the entire range of the APC gene and its promoter for association analysis. SNPs were screened in the transcriptional region of the gene (including CDS, 3'-UTR region, and 5'-UTR region) and its upstream 2000 bp (promoter) region for association analysis with traits. Loci that were significant (P-value < 0.05) after analysis of covariance (ANOVA) and Duncan's test were candidate SNP markers to search for markers potentially affecting gene transcription, expression, and intramuscular fat content in pigs. Finally, 6 SNP markers were screened, which were located at positions 116914227, 116914249, 116916126, 117034649, 117034881, and 117034886 on chromosome 2 of the Sscrofa11.1 version of the pig.

[0059] 3.3 Functions and advantages of key SNP markers of the APC gene: The information of the two SNP loci related to the APC gene disclosed in Example 1 and the 6 SNP loci obtained in this example were compared with the intramuscular fat content data of different genotypes of 461 Large White pigs in Example 1 to obtain Table 3.

[0060] Table 3 GWAS significant SNP loci related to the APC gene and markers potentially affecting gene transcription and expression

[0061]

[0062] As shown in Table 3, the molecular marker is located at position 117181303 on chromosome 2 of the Sscrofa11.1 version of the pig, the SNP name is rs81295606, the base mutation is G or T, and the genotypes are GG and TG. Among them, the intramuscular fat content of pigs with the TG genotype is greater than that of pigs with the GG genotype. Selecting the TG genotype as the dominant genotype can increase the intramuscular fat content of pigs by 5.8%.

[0063] The molecular marker is located at position 117207159 on chromosome 2 of the Sscrofa11.1 version of the pig, the SNP name is rs81259662, the base mutation is A or G, and the genotypes are AG and GG. Among them, the intramuscular fat content of pigs with the AG genotype is greater than that of pigs with the GG genotype. Selecting the AG genotype as the dominant genotype can increase the intramuscular fat content of pigs by 5.8%.

[0064] The molecular marker is located at position 116914227 on chromosome 2 of the Sus scrofa 11.1 version. The SNP name is rs325214531, the base mutation is T or C, and the genotypes are CC, CT, and TT. Among them, the intramuscular fat content of pigs with the TT genotype is greater than that of pigs with the CT genotype, and the intramuscular fat content of pigs with the CT genotype is greater than that of pigs with the CC genotype. Selecting the TT genotype as the dominant genotype can increase the intramuscular fat content of pigs by 11.8%.

[0065] The molecular marker is located at position 116914249 on chromosome 2 of the Sus scrofa 11.1 version. The SNP name is rs336509405, the base mutation is T or C, and the genotypes are CC, CT, and TT. Among them, the intramuscular fat content of pigs with the TT genotype is greater than that of pigs with the CT genotype, and the intramuscular fat content of pigs with the CT genotype is greater than that of pigs with the CC genotype. Selecting the TT genotype as the dominant genotype can increase the intramuscular fat content of pigs by 10.55%.

[0066] The molecular marker is located at position 116916126 on chromosome 2 of the Sus scrofa 11.1 version. The SNP name is rs332768788, the base mutation is T or G, and the genotypes are GG, GT, and TT. Among them, the intramuscular fat content of pigs with the TT genotype is greater than that of pigs with the CT genotype, and the intramuscular fat content of pigs with the GT genotype is greater than that of pigs with the GG genotype. Selecting the TT genotype as the dominant genotype can increase the intramuscular fat content of pigs by 11.46%.

[0067] The molecular marker is located at position 117034649 on chromosome 2 of the Sus scrofa 11.1 version. The SNP name is rs343288160, the base mutation is G or A, and the genotypes are AA, GA, and GG. Among them, the intramuscular fat content of pigs with the GG genotype is greater than that of pigs with the GA genotype, and the intramuscular fat content of pigs with the GA genotype is greater than that of pigs with the AA genotype. Selecting the GG genotype as the dominant genotype can increase the intramuscular fat content of pigs by 15.81%.

[0068] The molecular marker is located at position 117034881 on chromosome 2 of the Sus scrofa 11.1 version. The SNP name is rs81363174, the base mutation is C or T, and the genotypes are CC, TC, and TT. Among them, the intramuscular fat content of pigs with the CC genotype is greater than that of pigs with the TC genotype, and the intramuscular fat content of pigs with the TC genotype is greater than that of pigs with the TT genotype. Selecting the CC genotype as the dominant genotype can increase the intramuscular fat content of pigs by 15.79%.

[0069] Furthermore, the molecular marker is located at position 117034886 on chromosome 2 of the Sus scrofa 11.1 version, with the SNP name rs698883832. The base mutation is C or T, and the genotypes are CC, TC, and TT. Among them, the intramuscular fat content of pigs with the TT genotype is greater than that of pigs with the TC genotype, and the intramuscular fat content of pigs with the TC genotype is greater than that of pigs with the CC genotype. Selecting the TT genotype as the dominant genotype can increase the intramuscular fat content of pigs by 12.43%.

[0070] According to the SNP molecular marker information provided in Table 3, in pig breeding, it can be comprehensively considered according to the actual situation. By measuring relevant loci and selecting different genotypes for breeding, a commercial pig population with ideal intramuscular fat content traits can be obtained.

[0071] For those skilled in the art, it is obvious that the present invention is not limited to the details of the above exemplary embodiments, and without departing from the spirit or basic characteristics of the present invention, the present invention can be implemented in other specific forms. Therefore, from any point of view, the embodiments should be regarded as exemplary and non-limiting. The scope of the present invention is defined by the appended claims rather than the above description. Therefore, all changes falling within the meaning and scope of the equivalent elements of the claims are intended to be included in the present invention.

[0072] In addition, it should be understood that although this specification is described according to embodiments, not every embodiment only contains an independent technical solution. This narrative manner of the specification is only for clarity. Those skilled in the art should regard the specification as a whole, and the technical solutions in each embodiment can also be appropriately combined to form other embodiments that can be understood by those skilled in the art.

Claims

1. Application of a molecular marker related to intramuscular fat content in pigs in pig breeding, characterized in that, The regulatory gene corresponding to the molecular marker is the porcine APC gene, and the gene number of the porcine APC gene in the ensembl database is ENSSSCG00000014207. The APC gene is involved in regulating the adipogenic differentiation of preadipocytes. When the expression level of the APC gene decreases, the adipogenic differentiation level of the preadipocytes decreases.

2. Use of the molecular marker related to intramuscular fat content in pigs according to claim 1 in pig breeding, characterized in that, The molecular marker is located at position 116914227 on chromosome 2 of the porcine Sscrofa11.1 version. The SNP name is rs325214531, the base mutation is T or C, and the genotypes are CC, CT, and TT. Among them, the intramuscular fat content of pigs with the TT genotype is greater than that of pigs with the CT genotype, and the intramuscular fat content of pigs with the CT genotype is greater than that of pigs with the CC genotype.

3. Use of the molecular marker related to intramuscular fat of pigs according to claim 1 in pig breeding, characterized in that, The molecular marker is located at position 116914249 on chromosome 2 of the porcine Sscrofa11.1 version. The SNP name is rs336509405, the base mutation is T or C, and the genotypes are CC, CT, and TT. Among them, the intramuscular fat content of pigs with the TT genotype is greater than that of pigs with the CT genotype, and the intramuscular fat content of pigs with the CT genotype is greater than that of pigs with the CC genotype.

4. The application of the molecular marker related to porcine intramuscular fat according to claim 1 in pig breeding, characterized in that, The molecular marker is located at position 116916126 on chromosome 2 of the porcine Sscrofa11.1 version. The SNP name is rs332768788, the base mutation is T or G, and the genotypes are GG, GT, and TT. Among them, the intramuscular fat content of pigs with the TT genotype is greater than that of pigs with the CT genotype, and the intramuscular fat content of pigs with the GT genotype is greater than that of pigs with the GG genotype.

5. The application of the molecular marker related to intramuscular fat in pigs according to claim 1 in pig breeding, characterized in that, The molecular marker is located at position 117034649 on chromosome 2 of the porcine Sscrofa11.1 version. The SNP name is rs343288160, the base mutation is G or A, and the genotypes are AA, GA, and GG. Among them, the intramuscular fat content of pigs with the GG genotype is greater than that of pigs with the GA genotype, and the intramuscular fat content of pigs with the GA genotype is greater than that of pigs with the AA genotype.

6. Use of the molecular marker related to intramuscular fat in pigs according to claim 1 in pig breeding, characterized in that, The molecular marker is located at position 117034881 on chromosome 2 of the porcine Sscrofa11.1 version. The SNP name is rs81363174, the base mutation is C or T, and the genotypes are CC, TC, and TT. Among them, the intramuscular fat content of pigs with the CC genotype is greater than that of pigs with the TC genotype, and the intramuscular fat content of pigs with the TC genotype is greater than that of pigs with the TT genotype.

7. Use of the molecular marker related to intramuscular fat of pigs according to claim 1 in pig breeding, characterized in that, The molecular marker is located at position 117034886 on chromosome 2 of the porcine Sscrofa11.1 version. The SNP name is rs698883832, the base mutation is C or T, and the genotypes are CC, TC, and TT. Among them, the intramuscular fat content of pigs with the TT genotype is greater than that of pigs with the TC genotype, and the intramuscular fat content of pigs with the TC genotype is greater than that of pigs with the CC genotype.

8. The application of the molecular marker related to intramuscular fat of pigs according to claim 1 in pig breeding, characterized in that, The molecular marker is located at position 117181303 on chromosome 2 of the porcine Sscrofa11.1 version. The SNP name is rs81295606, the base mutation is G or T, and the genotypes are GG and TG. Among them, the intramuscular fat content of pigs with the TG genotype is greater than that of pigs with the GG genotype.

9. Use of the molecular marker related to intramuscular fat of pigs according to claim 1 in pig breeding, characterized in that, The molecular marker is located at position 117207159 on chromosome 2 of the Sus scrofa 11.1 version, the SNP name is rs81259662, the base mutation is A or G, and the genotypes are AG and GG. Among them, the intramuscular fat content of pigs with the AG genotype is greater than that of pigs with the GG genotype.

Images