SNP markers on pig chromosome 1 affecting pig head length

Abstract

The application provides a SNP marker on a pig chromosome 1 affecting pig head length. The nucleic acid sequence of the SNP marker is shown as SEQ ID No. 1, and the site of the SNP marker is located at position 301 from the 5' end on the nucleic acid shown as SEQ ID No. 1, corresponding to the 5' end of the 51602938 site on the chromosome 1 of the international pig genome version 11.1, being T or C.

Description

Technical Field

[0001] This invention relates to the field of molecular markers, and in particular to SNP markers on pig chromosome 1 that affect pig head length. Background Technology

[0002] The selection and breeding of pig breeds is of great significance in the livestock industry, and breeders are constantly selecting for higher meat yields. The selection and breeding of other traits related to meat yield are also of great importance in the livestock industry, such as head length.

[0003] 1) The length of a pig's head is positively correlated with its meat yield. Pigs with long heads have more muscle, so they can yield more meat after slaughter, such as pig head meat.

[0004] 2) Pig's head holds a very high position in traditional Chinese culture, representing wealth, fortune, and good luck. Pig's head also plays an important role in people's diet, with large-headed pigs being a preferred choice, signifying more good luck and fortune in the coming year.

[0005] Therefore, the selection of pig head length is of great significance in both production practice and the inheritance of traditional culture. Thus, it is essential to explore the molecular markers that influence pig head length and to improve breeding populations. Summary of the Invention

[0006] One aspect of the present invention provides a pig SNP marker, the nucleic acid sequence of which is shown in SEQ ID No. 1, and the SNP marker site is located at position 301 from the 5' end on the nucleic acid shown in SEQ ID No. 1, corresponding to position 51602938 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 this invention provides an application of SNP markers in assisting in the identification of pig head length. Specifically, high-throughput screening using SNP markers can first identify T / T or T / C genotypes (or C / T genotypes, which have the same meaning) for pigs with longer head lengths. Then, the head length of pigs with T / T or T / C genotypes can be quantitatively measured using conventional methods; alternatively, the quantitative measurement step can be omitted, and selection can be made solely based on the genotype of the SNP marker, for example, selecting only individuals with the T / T genotype, or selecting individuals with both T / T and T / C genotypes.

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

[0009] In one specific embodiment, the pig is a crossbreed of Duroc, Large White, Landrace, Pietrain, Erhualian, Laiwu, Bama Xiang, and Tibetan pigs.

[0010] In one specific embodiment, the pig is a crossbreed F6 generation of Duroc, Large White, Landrace, Pietrain, Erhualian, Laiwu, Bama Xiang, and Tibetan pigs.

[0011] The third invention provides a method for assisting in the genetic improvement of pigs. The method includes: identifying a SNP marker in a core breeding population; the SNP marker is located at position 301 from the 5' end of the nucleic acid as shown in SEQ ID No. 1, corresponding to position 51602938 from the 5' end of chromosome 1 in version 11.1 of the International Pig Genome, and is either T or C; making corresponding selections based on the SNP marker: selecting breeding pig individuals in the core breeding population with the T / C genotype and / or T / T genotype at position 301 from the 5' end of SEQ ID No. 1, and culling breeding pig individuals with the C / C genotype at that position, so as to increase the frequency of allele T generation by generation.

[0012] In one specific implementation, in the core breeding pig population, breeding pig individuals with the T / T genotype at the 301st locus from the 5' end of SEQ ID No.1 are selected, and breeding pig individuals with the T / C and C / C genotypes at that locus are culled, in order to increase the frequency of allele T generation by generation.

[0013] In one specific embodiment, the SNP marker of the breeding pig is determined by analyzing the sequence of the nucleic acid of the breeding pig, wherein the sequence of the nucleic acid is shown in SEQ ID No. 1.

[0014] In one specific embodiment, the pigs are hybrid chimeric pigs of Duroc, Large White, Landrace, Pietrain, Erhualian, Laiwu, Bama Xiang, and Tibetan pigs.

[0015] In one specific embodiment, the pigs are derived from a crossbreed F6 generation of Duroc, Large White, Landrace, Pietrain, Erhualian, Laiwu, Bama Xiang, and Tibetan pigs.

[0016] In one specific embodiment, the genetically modified trait of the pig is head length.

[0017] The beneficial effects of this invention are:

[0018] The 1_51602938 SNP marker of this invention is significantly correlated with pig head length. Therefore, the SNP marker of this invention can be used to genotype this locus in pig populations, and the SNP marker can be used to assist in the identification of pig head length or to genetically improve the head length of pig populations.

[0019] By modifying the 1_51602938 SNP locus, increasing the frequency of allele T and decreasing the frequency of allele C, it is possible to increase pig head length and thus meat yield. This not only improves production efficiency but also enhances the competitiveness of breeding enterprises in the market. Attached Figure Description

[0020] Figure 1 This displays a Manhattan plot showing the head length of chimeric F6 pigs in a GWAS analysis. The X-axis represents the location of the molecular marker sites on the chromosome, and the Y-axis represents the -log[missing value]. 10 (P-value).

[0021] Figure 2 Box plots showing the head length of pigs in F6 pigs for different genotypes of the most significant locus 1_51602938 are displayed. The X-axis represents the genotype of the SNP molecular marker locus, the Y-axis represents the phenotypic value of the pig's head length (in cm), and the numbers above the box plot represent the number of individuals with each genotype in the pig population. Detailed Implementation

[0022] The present invention will be further described below with reference to the embodiments. However, the embodiments of the present invention are merely illustrative examples and should not be construed as limiting the present invention under any circumstances.

[0023] The chimeric family F6 pig herd used in this invention is the offspring of four Western commercial pig breeds (Duroc, Large White, Landrace, and Pietrain) and four Chinese local pig breeds (Erhualian, Laiwu, Bama Xiang, and Tibetan pig) through multiple generations of crossbreeding.

[0024] Example 1

[0025] 1. Genotyping and data quality control processing of pigs

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

[0027] DNA samples meeting the standards were diluted to 50 ng / μl, and each DNA sample was sequenced using the Illumina HiSeqXTen sequencing platform (average sequencing depth approximately 7.8×). All paired-end reads were aligned to version 11.1 of the international pig genome using BWA software. Genotypic data for each individual were then obtained using SAMTools, Platypus, and Beagle software. Plink 1.9 was used for quality control of the obtained genotypic data, removing individuals with a minor allele frequency (MAF) <0.03 and a family Mendelian error rate higher than 0.1. Finally, 29,441,528 molecular markers were identified in the F6 population.

[0028] 2. Determination of pig head length phenotype

[0029] After pigs reach a uniform market age, they are slaughtered and measured at the same slaughterhouse, specifically in the slaughtering workshop. Individuals are slaughtered and bled according to the "Livestock and Poultry Slaughtering Operation Procedures for Pigs" (GB / T 17236-2019), after which hair and internal organs are removed. The pig's head is obtained by making a horizontal cut along the junction of the first cervical vertebra and the occipital bone. The length of the pig's head is measured using a ruler from the posterior edge of the parietal bone to the anterior edge of the snout.

[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 head length for all individual pigs

[0032]

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

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

[0035] GWAS analysis was performed on the genotyping data of the above pigs and the head length phenotype data of the corresponding F6 (n=795) individuals using the mixed linear model in GEMMA (Genome-wide Efficient Mixed Model Association algorithm, version 0.98.1) software. 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 effects vector, e represents the error vector, β represents the ratio of the two variances, and t -1 Let represent the variance of the residuals, K represent the kinship matrix, E represent the identity matrix, and MVNn represent the multivariate normal distribution.

[0036] The GWAS analysis results of pig head length in the pig population are shown below. Figure 1 .Depend on Figure 1 It is known that the most significant site affecting pig head length is located on chromosome 1.

[0037] This invention focuses only on the case of the highest -log P value on chromosome 1, corresponding to the physical location 51602938, which is the 301st position from the 5' end as shown in SEQ ID No. 1. Basic genetic parameters of pig head length at this molecular marker locus are shown in Table 2.

[0038] Table 2. Basic genetic parameters of molecular marker loci in pig populations

[0039]

[0040] The results in Table 2 show that the 1_51602938 molecular marker has a significant effect on pig head length.

[0041] Genotypes at the 1_51602938 molecular marker locus were extracted from the sequencing files for each of the 795 individuals in the F6 population using PLINK software. After counting the number of individuals with each genotype, the genotypes of these individuals were correlated with their corresponding pig head lengths. Then, the multGomp package in R was used to statistically analyze the differences in phenotypic distribution among different genotypes. The results are shown in […]. Figure 2 See Table 3. The p-value is obtained from the variance test.

[0042] Table 3. Effect of molecular marker site 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 impact on pig head length. The order of preference for the three genotypes at this locus in terms of pig head length is T / T > T / C > C / C.

[0045] 4. The magnitude of phenotypic variation that molecular marker sites can explain.

[0046] Heritability is one of the most important fundamental genetic parameters in quantitative genetics, and it 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 proportion of the variance of the quantitative trait breeding value to the variance of the phenotypic value, is the additive effect part after eliminating the dominant effect and epistatic effect, and can be stably inherited in the process of generation transmission.

[0047] Since this invention uses an additive effects model for GWAS analysis of the pig head length trait, the magnitude of the phenotypic variance explained (PVE) at the molecular marker site is the h explained by that marker. 2 The size of the head. Calculations showed that the PVE explained by this molecular marker site in the F6 pig population was 2.00%.

[0048] While the present invention has been described with reference to specific embodiments, those skilled in the art will understand that various changes can be made without departing from the true spirit and scope of the invention. Furthermore, numerous modifications can be made to the subject, spirit, and scope of the invention to suit specific situations, materials, material compositions, and methods. All such modifications are included within the scope of the claims of the present invention.

Claims

1. Use of a reagent for detecting a SNP marker in the auxiliary identification of the length of a pig's head, the SNP marker being located at position 301 from the 5' end on a nucleic acid as shown in SEQ ID No. 1, corresponding to position 51602938 from the 5' end on chromosome 1 of the 11.1 version of the international pig genome, being T or C; Based on the length of the pig's head, the preferred order of genotypes at position 301 from the 5' end on SEQ ID No. 1 is in turn: T / T genotype, T / C genotype and C / C genotype; The pig is a hybrid chimeric pig of Duroc, Large White, Landrace, Pietrain, Erhualian, Laiwu, Bama Xiang and Tibetan pig.

2. A method of assisting genetic improvement of pigs for the trait of head length in pigs of hybrid chimeric pigs of Duroc, Large White, Landrace, Pietrain, Erhualian, Laiwu, Bama Xiang and Zang pigs, the method comprising: A SNP marker is determined for a breeding pig in a breeding pig core group; the SNP marker is located at position 301 from the 5' end on a nucleic acid as shown in SEQ ID No. 1, corresponding to position 51602938 from the 5' end on chromosome 1 of the 11.1 version of the international pig genome, being T or C; a corresponding selection is made according to the SNP marker: In the breeding pig core group, breeding pig individuals that are T / C genotype and / or T / T genotype at position 301 from the 5' end on SEQ ID No. 1 are selected, and breeding pig individuals that are C / C genotype at this position are culled, to increase the frequency of allele T from generation to generation.

3. The method of claim 2, wherein, In the breeding pig core group, breeding pig individuals that are T / T genotype at position 301 from the 5' end on SEQ ID No. 1 are selected, and breeding pig individuals that are T / C genotype and C / C genotype at this position are culled, to increase the frequency of allele T from generation to generation.

4. The method according to claim 2 or 3, characterized in that, A SNP marker is determined for a breeding pig by analyzing the sequence of a nucleic acid of the breeding pig, wherein the sequence of the nucleic acid is as shown in SEQ ID No. 1.

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