SNP (Single Nucleotide Polymorphism) marker on pig chromosome 1 influencing pig head length

Abstract

The invention provides an SNP (Single Nucleotide Polymorphism) marker on a pig chromosome 1 influencing the length of a pig head. The nucleotide sequence of the SNP marker is as shown in SEQ ID No.1, and the site of the SNP marker is located at the 301st site from the 5'end on the nucleic acid as shown in SEQ ID No.1, corresponds to the 51602938th site from the 5 'end on the No.1 chromosome of the international pig genome of the version 11.1, and is T or C. The invention further discloses the application of the SNP marker.

Description

Technical Field

[0001] The present invention relates to the field of molecular markers, and in particular to a SNP marker on pig chromosome 1 that affects pig head length. Background Art

[0002] The selection and breeding of pig breeds is of great significance in the breeding industry, and higher meat production is being selected by breeders. The selection and breeding of other traits related to meat production is also of great significance in the breeding industry, such as the pig head length trait.

[0003] 1) Pig head length is positively correlated with meat production characteristics. Long-headed pigs have more muscles, so more meat can be obtained after slaughter, such as pig head meat;

[0004] 2) The pig head has a very high status in traditional Chinese culture, representing wealth, blessing and good luck. The pig head also plays an important role in people's diet. People prefer a big pig head, which indicates more good luck and blessings in the coming year.

[0005] Therefore, the selection and breeding of pig head length is of great significance in production practice and traditional cultural inheritance. Therefore, it is necessary to explore the molecular markers that affect pig head length and improve the breeding population. Summary of the invention

[0006] One of the present inventions provides a SNP marker for pigs, the nucleic acid sequence of the SNP marker is shown in SEQ ID No.1, the site of the SNP marker is located at the 301st position from the 5' end on the nucleic acid shown in SEQ ID No.1, corresponding to the 51602938th position from the 5' end on chromosome 1 of the 11.1 version of the international pig genome, and is T or C.

[0007] The second aspect of the present invention provides an application of SNP markers in assisting the identification of pig head length. That is, the T / T genotype or T / C genotype (or C / T genotype, both of which have the same meaning) with longer pig head length can be firstly screened out by SNP marker high-throughput, and then the head length of pigs with T / T genotype or T / C genotype can be quantitatively determined based on conventional methods; or the quantitative determination step can be omitted, and selection can be made based only on the genotype of the SNP marker, for example, only individuals with the T / T genotype can be selected, or individuals with the T / T genotype and the T / C genotype can be selected.

[0008] In a specific embodiment, based on the length of the pig head, the preferred order of the genotype of the 301st position from the 5' end on the SEQ ID No. 1 is: T / T genotype, T / C genotype and C / C genotype.

[0009] In a specific embodiment, the pig is a hybrid chimeric pig of Duroc, Large White, Landrace, Pietrain, Erhualian, Laiwu, Bamaxiang and Tibetan pig.

[0010] In a specific embodiment, the pig is a hybrid chimeric F6 generation of Duroc, Large White, Landrace, Pietrain, Erhualian, Laiwu, Bamaxiang and Tibetan pigs.

[0011] The third aspect of the present invention provides a method for assisting pig genetic improvement, the method comprising: determining a SNP marker of a sow in a core group of sows; the site of the SNP marker is located at the 301st position from the 5' end on the nucleic acid shown in SEQ ID No.1, corresponding to the 51602938th position from the 5' end on chromosome 1 of the 11.1 version of the international porcine genome, which is T or C; making corresponding selections based on the SNP marker: selecting sow individuals with a T / C genotype and / or a T / T genotype at the 301st position from the 5' end on the SEQ ID No.1 in the core group of sows, and eliminating sow individuals with a C / C genotype at this position, so as to increase the frequency of allele T from generation to generation.

[0012] In a specific embodiment, in the core group of sows, sow individuals with T / T genotype at the 301st position from the 5' end on the SEQ ID No. 1 are selected, and sow individuals with T / C genotype and C / C genotype at the position are eliminated to increase the frequency of allele T from generation to generation.

[0013] In a specific embodiment, the SNP marker of the sow is determined by analyzing the sequence of the nucleic acid of the sow, wherein the sequence of the nucleic acid is shown as SEQ ID No.1.

[0014] In a specific embodiment, the pig is a hybrid chimeric pig of Duroc, Large White, Landrace, Pietrain, Erhualian, Laiwu, Bamaxiang and Tibetan pig.

[0015] In a specific embodiment, the pig is derived from the hybrid chimeric F6 generation of Duroc, Large White, Landrace, Pietrain, Erhualian, Laiwu, Bamaxiang and Tibetan pigs.

[0016] In a specific embodiment, the trait for genetic improvement of pigs is pig head length.

[0017] Beneficial effects of the present invention:

[0018] The 1_51602938 SNP marker of the present invention is significantly correlated with pig head length, so the SNP marker of the present invention can be used to phenotype the site of the pig herd, and the SNP marker can be used to assist in identifying the pig's head length or to genetically improve the head length of the pig herd.

[0019] By improving the 1_51602938 SNP site, increasing the frequency of allele T at the site and reducing the frequency of allele C, the length of the pig head can be increased, thereby increasing meat production. This can not only improve production efficiency, but also enhance the competitiveness of breeding companies in the market. BRIEF DESCRIPTION OF THE DRAWINGS

[0020] Figure 1 Manhattan Plot showing the head length of chimeric F6 pigs in GWAS analysis. The X-axis is the position of the molecular marker site on the chromosome, and the Y-axis is the -log 10 (P value).

[0021] Figure 2 The box plot (Box Plot) of the head length of F6 pigs with different genotypes of the most significant locus 1_51602938 is shown. The X-axis represents the genotype of the SNP molecular marker locus, the Y-axis represents the phenotypic value of the individual head length (unit: cm), and the numbers above the box plot represent the number of individuals of each genotype in the pig herd. DETAILED DESCRIPTION

[0022] The present invention will be further described below in conjunction with examples, but the examples of the present invention are only exemplary descriptions, and the implementation manner does not constitute a limitation of the present invention under any circumstances.

[0023] The chimeric family F6 pig group used in the present invention is the offspring of four Western commercial pig breeds (Duroc, Large White, Landrace, Pietrain) and four Chinese local pig breeds (Erhualian, Laiwu, Bamaxiang, Tibetan pig) after multiple generations of hybridization.

[0024] Example 1

[0025] 1. Pig genotype detection and data quality control processing

[0026] A small muscle tissue sample was collected from each individual of the F6 population (n=795), and the genomic DNA of each individual was extracted by the standard phenol-chloroform method, and the extracted genomic DNA was dissolved in TE buffer. The quality of the extracted genomic DNA was detected by Nanodrop-ND1000 spectrophotometer, and the quality standard was reached when the A260 / 280 ratio was 1.8-2.0 and the A260 / 230 ratio was about 1.7-1.9.

[0027] The concentration of the DNA samples that met the standards was diluted to 50 ng / μl, and each DNA sample was sequenced using the HiSeqXTen sequencer platform of Illumina (the average sequencing depth was about 7.8×). All the double-end reads obtained were aligned to the 11.1 version of the International Pig Genome using BWA software, and then the genotype data of each individual was obtained using SAMTools, Platypus and Beagle software in turn. Plink1.9 was used to perform quality control on the obtained genotype data, and individuals with minor allele frequency (MAF) < 0.03 and family Mendelian error rate higher than 0.1 were eliminated. Finally, 29,441,528 molecular markers were determined in the F6 population.

[0028] 2. Determination of pig head length phenotype

[0029] After the pigs reach the same market age, they are slaughtered and measured at the same slaughterhouse. The measurement location is the cutting workshop of the slaughterhouse. The individual is slaughtered and bled according to the "Livestock and Poultry Slaughter Operation Procedures for Pigs" (GB / T 17236-2019), and the hair and internal organs are removed. The pig head is cut along the junction of the first cervical vertebra and the occipital bone. The length of the pig head is measured from the back edge of the parietal bone to the front edge of the snout with a ruler.

[0030] The descriptive statistics of pig head length were calculated by the stat.desc() function of the pastecs package in R language, and the results are shown in Table 1.

[0031] Table 1. Descriptive statistics of all individual pig head lengths

[0032]

[0033] As shown in Table 1, there are significant differences in pig head length among individuals in the F6 population, with the maximum value being 33.1 cm and the minimum being 21.3 cm. The coefficient of variation is 6.31%, indicating that this trait has a certain breeding space.

[0034] 3. Genome-wide association study (GWAS)

[0035] The mixed linear model in GEMMA (Genome-wide Efficient Mixed Model Association algorithm, version 0.98.1) software was used to perform GWAS analysis on the genotyping data of the above pigs and the corresponding head length phenotype data of F6 (n = 795) individuals. 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 phenotypic value vector of all individuals, X represents the covariate matrix, a represents the corresponding coefficient vector including the intercept, Q represents the genotype vector of the molecular marker, b represents the effect of the molecular marker, u represents the random effect vector, e represents the error vector, β represents the ratio of the two variances, t -1 represents the variance of the residual, K represents the affinity matrix, E represents the identity matrix, and MVNn represents the multivariate normal distribution.

[0036] The results of GWAS analysis of pig head length in pig populations are shown in Figure 1 .Depend on Figure 1 It can be seen that the locus that most significantly affects the length of the pig's head is on chromosome 1.

[0037] The present invention only focuses on the case where the highest point of the -log P value of chromosome 1 corresponds to the physical position 51602938, and the molecular marker site is located at the 301st site from the 5' end on SEQ ID No. 1. The basic genetic parameter information of the pig head length of the pig population at the molecular marker site is shown in Table 2.

[0038] Table 2. Basic genetic parameter information of molecular marker loci in pig population

[0039]

[0040] From the results in Table 2, it can be seen that the 1_51602938 molecular marker has a significant effect on pig head length.

[0041] The genotypes of each of the 795 pigs in the F6 population at the 1_51602938 molecular marker site were extracted from the sequencing file using PLINK software. After counting the number of individuals of each genotype, the genotypes of these individuals were matched with their corresponding pig head lengths. The multGomp package in the R language was then used to statistically analyze the differences in phenotypic distribution under different genotypes. The results are shown in Figure 2 and Table 3. Among them, the P value is obtained from the variance test.

[0042] Table 3. Effect of molecular marker locus 1_51602938 on pig head length

[0043]

[0044] Depend on Figure 2 As shown in Table 3, the 1_51602938T or C genotype has a significant effect on the pig head length. Among them, the three genotypes of this site are ranked as T / T>T / C>C / C in terms of the pig head length.

[0045] 4. The amount of phenotypic variation that can be explained by molecular marker loci

[0046] Heritability is the most important basic genetic parameter in quantitative genetics and can be divided into broad-sense heritability, narrow-sense heritability and realized heritability. In the breeding process, heritability generally refers to narrow-sense heritability (h 2 ), which refers to the ratio of the variance of the breeding value of a quantitative trait to the variance of the phenotypic trait. It is the additive effect after eliminating the dominant effect and epistatic effect, and can be stably inherited during the generation-to-generation transmission process.

[0047] Since the additive effect model is used in the present invention to perform GWAS analysis on the pig head length trait, the size of the phenotypic variance explained (PVE) by the molecular marker site is the h 2 It was calculated that the PVE explained by the pig head length in the F6 population at this molecular marker site was 2.00%.

[0048] Although the present invention has been described with reference to specific embodiments, it will be appreciated by those skilled in the art that various changes may be made without departing from the true spirit and scope of the present invention. In addition, the subject matter, spirit and scope of the present invention may be varied to accommodate specific situations, materials, material combinations and methods. All of these changes are included within the scope of the claims of the present invention.

Claims

1. A SNP marker for pigs, the nucleic acid sequence of the SNP marker is shown in SEQ ID No. 1, the site of the SNP marker is located at the 301st position from the 5' end on the nucleic acid shown in SEQ ID No. 1, corresponding to the 51602938th position from the 5' end on chromosome 1 of the 11.1 version of the international pig genome, and is T or C.

2. An application of a SNP marker in assisting the identification of pig head length, wherein the site of the SNP marker is located at the 301st position from the 5' end on the nucleic acid shown in SEQ ID No. 1, corresponding to the 51602938th position from the 5' end on chromosome 1 of the 11.1 version of the international pig genome, and is T or C.

3. The use according to claim 2, characterized in that: Based on the length of the pig head, the preferred order of the genotype of the 301st position from the 5' end on the SEQ ID No. 1 is: T / T genotype, T / C genotype and C / C genotype.

4. The use according to claim 2, characterized in that: The pigs are hybrid chimeric pigs of Duroc, Large White, Landrace, Pietrain, Erhualian, Laiwu, Bamaxiang and Tibetan pigs.

5. A method for assisting pig genetic improvement, the method comprising: Determine a SNP marker for breeding pigs in the breeding pig core group; The site of the SNP marker is located at the 301st position from the 5' end on the nucleic acid shown in SEQ ID No. 1, corresponding to the 51602938th position from the 5' end on chromosome 1 of the 11.1 version of the international porcine genome, which is T or C; make corresponding selections according to the SNP marker: In the core group of sows, sows with T / C genotype and / or T / T genotype at the 301st position from the 5' end on SEQ ID No.1 are selected, and sows with C / C genotype at this position are eliminated to increase the frequency of allele T generation by generation.

6. The method according to claim 5, characterized in that In the core group of sows, sows with T / T genotype at the 301st position from the 5' end on SEQ ID No. 1 are selected, and sows with T / C genotype and C / C genotype at the position are eliminated to increase the frequency of allele T generation by generation.

7. The method according to claim 5 or 6, characterized in that: The SNP marker of the sow is determined by analyzing the sequence of the nucleic acid of the sow, wherein the sequence of the nucleic acid is shown as SEQ ID No.

1.

8. The method according to claim 5 or 6, characterized in that: The pigs are hybrid chimeric pigs of Duroc, Large White, Landrace, Pietrain, Erhualian, Laiwu, Bamaxiang and Tibetan pigs.

9. The method according to claim 5 or 6, characterized in that: The trait of pig genetic improvement is pig head length.

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