SNP (Single Nucleotide Polymorphism) molecular marker on pig chromosome 1 influencing pig backfat thickness

Abstract

The invention provides an SNP (Single Nucleotide Polymorphism) molecular marker on a pig chromosome 1 influencing the back fat thickness of a pig. The SNP molecular marker is located at the 118 site from the 5'terminal on SEQ ID No.1, corresponds to the 270593210 site from the 5 'terminal on the No.1 chromosome of the international pig genome of the version 11.1, and is C or A.

Description

Technical Field

[0001] The present invention relates to the field of molecular markers, and particularly to SNP molecular markers on porcine chromosome 1 that affect porcine backfat thickness. Background Art

[0002] Porcine backfat thickness is closely related to the growth rate, feed conversion rate and meat quality of pigs, and is one of the important traits affecting pork quality and economic benefits. In modern pig farming, backfat thickness is not only related to the fat content of pork, but also closely related to many factors such as the slaughter rate of pigs, meat processing characteristics, and feed efficiency. Therefore, as a key economic trait, backfat thickness has become one of the important goals of pig breed improvement.

[0003] Therefore, exploring the marker loci that affect backfat thickness can be used to achieve precise and efficient pig breed improvement, thereby optimizing meat quality, improving production efficiency and reducing costs. Summary of the Invention

[0004] One aspect of the present invention provides a porcine SNP molecular marker, the nucleic acid sequence of the SNP molecular marker is as shown in SEQ ID No.1, the SNP molecular marker is located at the 118th position from the 5' end on SEQ ID No.1, corresponding to the 270593210th position from the 5' end on chromosome 1 of the international pig genome version 11.1, and is C or A.

[0005] Another aspect of the present invention provides an application of an SNP molecular marker in assisting in the identification of porcine backfat thickness. The SNP molecular marker is located at the 118th position from the 5' end on SEQ ID No.1, corresponding to the 270593210th position from the 5' end on chromosome 1 of the international pig genome version 11.1, and is C or A. That is, the C / A genotype or C / C genotype with thinner backfat thickness can be screened out through high-throughput SNP molecular markers first, and then the backfat thickness of the C / A genotype or C / C genotype can be quantitatively measured based on conventional methods as needed, or the quantitative measurement step can be omitted, and a selection can be made only based on the genotype of the SNP marker. For example, only individuals with the C / C genotype are selected, or individuals with the C / A genotype and C / C genotype are selected.

[0006] In a specific embodiment, based on the backfat thickness, the preferred order of the genotypes at the 118th position from the 5' end on SEQ ID No.1 is: C / C genotype, C / A genotype, and A / A genotype.

[0007] In a specific embodiment, the pig is at least one of Duroc, Large White and Landrace pigs or a hybrid chimeric pig of at least two of them.

[0008] The third aspect of the present invention provides a method for assisting pig genetic improvement, the method comprising: determining a SNP molecular marker of a breeding pig in a core breeding pig population; the SNP molecular marker is located at the 118th position from the 5' end on SEQ ID No.1, corresponding to the 270593210th position from the 5' end on chromosome 1 of the 11.1 version of the international pig genome, and is C or A; making corresponding selections according to the SNP molecular marker: selecting breeding pig individuals with C / C genotype and / or C / A genotype at the 118th position from the 5' end on SEQ ID No.1 in the core breeding pig population, and eliminating breeding pig individuals with A / A genotype, so as to gradually increase the frequency of allele C generation by generation.

[0009] In a specific embodiment, breeding pig individuals with C / C genotype at the 118th position from the 5' end on SEQ ID No.1 are selected in the core breeding pig population, and breeding pig individuals with C / A genotype and A / A genotype at the 118th position from the 5' end are eliminated, so as to gradually increase the frequency of allele C generation by generation.

[0010] In a specific embodiment, the SNP molecular marker of the breeding pig as described in one of the present invention is determined by analyzing the sequence of the nucleic acid of the breeding pig, wherein the sequence of the nucleic acid is as shown in SEQ ID No.1.

[0011] In a specific embodiment, the source of the pig is at least one of Duroc, Large White and Landrace pigs or a hybrid chimeric pig of at least two of them.

[0012] In a specific embodiment, the trait of pig genetic improvement is backfat thickness.

[0013] Advantages of the present invention:

[0014] The 1_270593210 SNP marker of the present invention is significantly correlated with pig backfat thickness. Therefore, the genotype of this locus in the pig population can be determined by the SNP marker of the present invention, and the pig backfat thickness can be assisted in identification or the pig population can be genetically improved for pig backfat thickness through this SNP marker.

[0015] By improving the 1_270593210 SNP molecular marker locus, increasing the frequency of allele C and decreasing the frequency of allele A, the backfat thickness of pigs can be reduced. By reducing the backfat thickness, the lean meat rate of pig carcasses can be increased, the meat production performance and production efficiency of pigs can be improved, the economic value and utilization value of carcasses can be enhanced, and the human needs can be met. Description of the Drawings

[0016] Figure 1Shows the Manhattan Plot of backfat thickness of Duroc, Landrace and Yorkshire pigs in GWAS analysis. Among them, the X-axis is the chromosome number of pigs, and the Y-axis is -log 10 (P-value), and the red dots are the leading SNPs (lead SNP).

[0017] Figure 2 Shows the analysis chart of backfat thickness results of pigs with different genotypes. Specific implementation mode

[0018] The present invention will be further described below in conjunction with embodiments, but the embodiments of the present invention are only exemplary descriptions, and this implementation mode does not constitute a limitation to the present invention under any circumstances.

[0019] The pig population used in the present invention is Duroc, Landrace and Yorkshire pigs of Jiangxi Jiada Group Co., Ltd., among which there are 707 Duroc pigs, 1252 Landrace pigs and 2507 Yorkshire pigs.

[0020] The pigs eat and drink, and the whole feeding method, feeding conditions, etc. are always kept consistent, all of which are conventional feeding methods.

[0021] Example 1

[0022] 1. Obtaining, quality control and genotyping of whole-genome resequencing data of pigs

[0023] Ear tissues of each individual were collected from the pig population, and genomic DNA of each individual was extracted by the standard phenol-chloroform method. The extracted genomic DNA was dissolved in TE buffer. The quality of the extracted genomic DNA was detected with a Nanodrop-ND1000 spectrophotometer, and the quality standard was reached when the A260 / 280 ratio was between 1.8 and 2.0 and the A260 / 230 ratio was around 1.7 - 1.9.

[0024] Dilute the concentration of the qualified DNA samples to 50 ng / μl, and genotype each DNA sample using the "Zhongxin No. 1" 50K chip to obtain genotype information at 57,466 loci. Use Plink1.9 to perform quality control on the obtained genotype data, and remove SNPs with a minor allele frequency (MAF) lower than 0.01, a genotype missing rate higher than 0.01, lacking chromosome position information, and located on the sex chromosome, obtaining 44,766 high-quality SNPs. Then use Shapite v5.1.1 to construct haplotypes, and subsequently use Beagle v5.4 to impute genotypes. Perform quality control on the obtained genotype data through Plink, and remove SNPs with a correlation with the actual alleles lower than 0.85, a minor allele frequency lower than 0.01, and a missing rate higher than 0.01. Finally, retain 8,206,050 molecular markers.

[0025] 2. Measurement of the backfat thickness phenotype of pigs

[0026] Use an ultrasonic detector to measure the subcutaneous fat thickness at the position of the 3rd to 4th thoracic vertebrae from the bottom of live pigs, and record the backfat thickness of each individual.

[0027] The descriptive statistical results of the backfat thickness were calculated using R language software, and the results are shown in Table 1.

[0028] Table 1. Descriptive statistical results of backfat thickness in all individuals

[0029] Trait Number of individuals Maximum value Minimum value Average value Standard deviation Coefficient of variation Backfat thickness 4466 30.53 mm 5.68 mm 12.69 mm 2.81 mm 22.12％

[0030] As can be seen from Table 1, the coefficient of variation of the backfat thickness is greater than 20%, indicating that there is a very large selection space for this trait.

[0031] 3. Genome-wide association (GWAS) analysis

[0032] Using the mixed linear model in GEMMA (Genome-wide Efficient Mixed Model Association algorithm, version number 0.98.1) software, perform GWAS analysis on the molecular marker information of the obtained pig population and the backfat thickness of the corresponding individuals respectively. The expression is as follows: y = Xa + Qb + u + e; u ~ MVNn(0, βt -1 K), e ~ MVNn(0, t -1 E). Where y represents the vector of phenotypic values of all individuals, X represents the covariate matrix, a represents the corresponding coefficient vector including the intercept, Q represents the genotype vector of molecular markers, b represents the effect of molecular markers, u represents the random effect vector, e represents the error vector, β represents the ratio of two variances, t-1 represents the variance of the residuals, K represents the kinship matrix, E represents the identity matrix, and MVNn represents the multivariate normal distribution.

[0033] The GWAS analysis results of backfat thickness in the pig population are shown in Figure 1 . From Figure 1 it can be seen that the locus most significantly affecting pig backfat thickness is located on chromosome 1.

[0034] The present invention only focuses on the case of the physical position 270593210 corresponding to the P value of 8.507284E-11 on chromosome 1. This molecular marker locus is located at the 118th site starting from the 5' end on SEQ ID No. 1. The genotype information of this locus was verified by sanger sequencing. The basic genetic parameter information of backfat thickness in the pig population at this molecular marker locus is shown in Table 2.

[0035] Table 2. Basic genetic parameter information of molecular marker loci for backfat thickness in the pig population

[0036] Trait Backfat thickness Molecular marker name 1_270593210 Chromosome 1 Physical location 270593210 Mutation information C / A Minor allele frequency 0.164 Effect value 0.499 P value 8.507284E-11

[0037] From the results in Table 2, it can be seen that the 1_270593210 molecular marker has a significant effect on backfat thickness.

[0038] Using the PLINK software, the genotypes of each individual in the pig population at the 1_270593210 molecular marker locus were extracted from the sequencing file. After counting the number of individuals with each genotype, the genotypes of these individuals were corresponded to their respective backfat thicknesses. Then, the stat_compare_means function in the ggpubr package of R language was used to statistically analyze the differences in phenotypic distributions under different genotypes. The results are shown in Figure 2 and Table 3. Among them, the P value is obtained from the variance test.

[0039] Table 3. Effect of molecular marker locus 1_270593210 on backfat thickness

[0040] Trait C / C C / A A / A P value Backfat thickness 11.90 ± 3.95 mm 11.87 ± 4.44 mm 11.42 ± 6.72 mm 2.6E-05

[0041] From Figure 2 and Table 3, it can be seen that the 1_270593210 molecular marker can significantly affect backfat thickness. When reducing backfat thickness, the lean meat rate of pig carcasses can be increased, thereby improving the meat production performance and production efficiency of pigs, and enhancing the economic value and utilization value of carcasses. Therefore, the preferred ranking of alleles at this locus for backfat thickness is all C / C > C / A > A / A.

[0042] 4. Size of phenotypic variation that the molecular marker locus can explain

[0043] Heritability is one of the most important basic genetic parameters in quantitative genetics, which can be divided into broad-sense heritability, narrow-sense heritability and realized heritability. Heritability in the breeding process generally refers to narrow-sense heritability (h 2 ), which refers to the proportion of the variance of the breeding value of quantitative traits in the phenotypic variance, and is the additive effect part after excluding the dominant effect and epistatic effect, and can be stably inherited during the process of generation transmission.

[0044] Since the present invention uses an additive effect model to perform GWAS analysis on backfat thickness, the size of the phenotypic variance explained (PVE) by the molecular marker locus is the size of h 2 explained by the marker. The PVE value of backfat thickness explained by this molecular marker locus is 0.94%. This result indicates that the phenotype that can be explained by this locus has an impact on backfat thickness.

[0045] Although the present invention has been described with reference to specific embodiments, those skilled in the art should understand that various changes can be made without departing from the true spirit and scope of the present invention. In addition, various changes can be made to the subject matter, spirit and scope of the present invention to adapt to specific situations, materials, material compositions and methods. All such changes are included within the scope of the claims of the present invention.

Claims

1. A SNP molecular marker of pigs, the nucleic acid sequence of the SNP molecular marker is as shown in SEQ ID No.1, the SNP molecular marker is located at the 118th position starting from the 5'-end on SEQ ID No.1, corresponding to the 270593210th position starting from the 5'-end on chromosome 1 of the international pig genome version 11.1, and is C or A.

2. An application of a SNP molecular marker in assisting in identifying the backfat thickness of pigs, the SNP molecular marker is located at the 118th position starting from the 5'-end on SEQ ID No.1, corresponding to the 270593210th position starting from the 5'-end on chromosome 1 of the international pig genome version 11.1, and is C or A.

3. The application according to claim 2, characterized in that, Based on the backfat thickness, the preferred order of the genotypes at the 118th position starting from the 5'-end on SEQ ID No.1 is: C / C genotype, C / A genotype, and A / A genotype in sequence.

4. The application according to claim 2, characterized in that, The pigs are at least one of Duroc, Large White, and Landrace pigs or hybrid chimeric pigs of at least two of them.

5. A method for assisting pig genetic improvement, the method comprising: A SNP molecular marker for determining breeding pigs in the core breeding pig population; The SNP molecular marker is located at the 118th position starting from the 5'-end on SEQ ID No.1, corresponding to the 270593210th position starting from the 5'-end on chromosome 1 of the international pig genome version 11.1, and is C or A; make corresponding selections according to the SNP molecular marker: select breeding pig individuals with C / C genotype and / or C / A genotype at the 118th position starting from the 5'-end on SEQ ID No.1 in the core breeding pig population, and eliminate breeding pig individuals with A / A genotype to gradually increase the frequency of allele C.

6. The method according to claim 5, wherein In the core breeding pig population, select breeding pig individuals with C / C genotype at the 118th position starting from the 5'-end on SEQ ID No.1, and eliminate breeding pig individuals with C / A genotype and A / A genotype at the 118th position starting from the 5'-end to gradually increase the frequency of allele C.

7. The method according to claim 5 or 6, characterized in that, Determine the SNP molecular marker of the breeding pigs as described in claim 1 by analyzing the nucleic acid sequence of the breeding pigs, wherein the nucleic acid sequence is as shown in SEQ ID No.

1.

8. The method according to claim 5 or 6, characterized in that, The pigs are derived from at least one of Duroc, Large White, and Landrace pigs or hybrid chimeric pigs of at least two of them.

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