A SNP marker for evaluating the age of pigs reaching 100 kg body weight and its application

Abstract

The present invention belongs to the field of nucleic acid detection methods, and relates to a SNP marker for evaluating the age of pigs reaching 100 kg in weight and its application. The SNP site is the 1,420,224th deoxynucleotide of the positive chain of chromosome 6 of the pig reference genome version 10.2, which is A or G. The present invention finds that the SNP site is significantly correlated with the age trait of pigs reaching 100 kg in weight, and the age of pigs reaching 100 kg in weight of individuals with the genotype of AA at the SNP site is statistically significantly lower than that of individuals with the genotype of AA at the SNP site and individuals with the genotype of AA at the SNP site.

Description

Technical Field

[0001] The invention belongs to the field of nucleic acid detection methods and relates to a SNP marker for evaluating the age of a pig reaching 100 kg in weight and an application thereof. Background Art

[0002] Pigs are the first of the six domestic animals, and pig farming occupies an important position in the world economy. The age at which pigs reach 100 kg is an important indicator for evaluating the growth rate of pigs, which can indirectly reflect the feed utilization rate. A large amount of data shows that the shorter the age at which pigs reach 100 kg, the faster the growth rate, which can reduce the production cost of the pig farm and improve the economic benefits of the pig farm. Therefore, how to effectively improve the growth rate of pigs, shorten the age at which pigs reach 100 kg, and cultivate efficient breeding pigs is the main goal of every pig farming enterprise and breeder. At present, the improvement of pork yield and quality by traditional breeding technology has reached a bottleneck period, and it is urgent to use more advanced modern molecular breeding technology for pig genetic improvement. Single nucleotide polymorphism (SNP) refers to the DNA sequence polymorphism caused by the variation of a single nucleotide at the genome level. It is the most common type of heritable variation. It has the advantages of large number, wide distribution, easy genotyping and good genetic stability. Therefore, it is widely used as a third-generation molecular marker in various genetic analysis work. Genome-wide association analysis is the main means of identifying the genetic link between phenotype and genotype, and can be used to discover SNPs that affect the age of pigs reaching 100 kg. By determining the genotype of the pigs to be tested, early selection of the growth rate of the pigs can be carried out, thereby saving production costs and accelerating genetic progress. Summary of the invention

[0003] The purpose of the present invention is to provide a SNP marker for evaluating the age of a pig reaching 100 kg in weight and its application.

[0004] The present invention claims protection for the use of a substance for detecting the polymorphism or genotype of a SNP site in identifying or assisting in identifying a pig reaching 100 kg in weight per day, wherein the SNP site is the 1,420,224th deoxynucleotide of the positive strand of chromosome 6 of the pig reference genome version 10.2 (the 100th nucleotide of sequence 1 in the sequence list), which is A or G.

[0005] Wherein, the substance is a SNP chip (such as Neogen_POR80K chip of Neogen Company).

[0006] The present invention also claims the use of a substance for detecting the polymorphism or genotype of the SNP site MARC0080181 in pig breeding, wherein the SNP site MARC0080181 is the 1,420,224th deoxynucleotide of the positive strand of chromosome 6 of the pig reference genome version 10.2 (the 100th nucleotide of sequence 1 in the sequence list), which is A or G.

[0007] The pig breeding refers to the cultivation of pigs that require fewer days of feeding to reach a weight of 100 kg.

[0008] Wherein, the substance is a SNP chip (such as Neogen_POR80K chip of Neogen Company).

[0009] The present invention provides a method for identifying or assisting in identifying a pig that reaches 100 kg in weight, the method comprising: detecting the genotype of a SNP marker in the genome of the pig to be tested, wherein the age of a pig with an AA genotype that reaches 100 kg in weight is smaller than that of a pig with a GG genotype and a pig with a GA genotype that reaches 100 kg in weight;

[0010] Wherein, the SNP marker is the 1,420,224th deoxynucleotide of the positive strand of chromosome 6 in the pig reference genome 10.2 (the 100th nucleotide of sequence 1 in the sequence list), which is A or G;

[0011] The AA genotype is the homozygous type of the SNP being A;

[0012] The GA genotype is a heterozygous type in which the SNP is G and A;

[0013] The GG genotype is the homozygous type in which the SNP is G.

[0014] The present invention also provides a pig breeding method, which comprises: detecting the genotype of the above-mentioned SNP marker in the genome of the pig to be tested, and selecting pigs with AA genotype for breeding; the purpose of the pig breeding is to cultivate pigs that require fewer days of feeding to reach a weight of 100 kg.

[0015] The above-mentioned pig to be tested is a Large White pig, specifically a Large White sow.

[0016] The beneficial effect of the present invention is that the experimental results show that the whole genome association analysis of the age at which pigs reach 100 kg in 590 large white sows found that the site MARC0080181 was significantly correlated with the age at which pigs reach 100 kg in weight, and the site was located on pig chromosome 6. Among them, the age at which AA genotype pigs reach 100 kg in weight is statistically significantly lower than that of AG and GG genotype individuals. Therefore, the site can be used as a molecular marker for the age at which pigs reach 100 kg in weight, so as to improve the growth rate of pigs and improve economic benefits. BRIEF DESCRIPTION OF THE DRAWINGS

[0017] Figure 1 The results of association analysis between different genotypes of MARC0080181 locus and the age at which pigs reach 100 kg body weight (D100);

[0018] Figure 2 The genotype frequency and allele frequency of the MARC0080181 locus in the tested pig population;

[0019] Figure 3 The difference in age at which a body weight of 100 kg is reached between individuals with different genotypes at the MARC0080181 locus. DETAILED DESCRIPTION

[0020] The present invention is further described in detail below in conjunction with specific embodiments, and the examples provided are only for illustrating the present invention, rather than for limiting the scope of the present invention. The examples provided below can be used as a guide for further improvements by those of ordinary skill in the art, and do not constitute a limitation of the present invention in any way.

[0021] The experimental methods in the following examples, unless otherwise specified, are all conventional methods, and are performed according to the techniques or conditions described in the literature in the field or according to the product instructions. The materials, reagents, etc. used in the following examples, unless otherwise specified, can all be obtained from commercial channels.

[0022] Example 1

[0023] Experimental materials: 590 Large White sows were all from Hebei Meishen original breeding pig farm.

[0024] 1. Determination and correction of pig 100kg body weight age

[0025] Select gilts weighing between 80 and 105 kg, weigh them using an electronic weighing platform (fast for 12 hours before weighing), and record the pig's ear number data, weight, actual age, etc. and convert them into the age when the weight reaches 100 kg according to the following correction formula: Corrected age = measured age - [(actual weight - 100) / CF], where: CF value for boars = (actual weight / measured age) × 1.826040, CF value for sows = (actual weight / measured age) × 1.714615.

[0026] 2. DNA Extraction and SNP Typing

[0027] 1. Genomic DNA Extraction

[0028] The ear tissue samples of the target pigs were collected, placed in PBS buffer and stored at low temperature. In this experiment, the DP1902 cell / tissue genomic DNA extraction kit of Beijing Biotech Biotechnology Co., Ltd. was used to extract DNA from the pig ear tissue, and the DNA quality was tested by UV spectrophotometer and gel electrophoresis. The qualified DNA was placed at -20℃ for long-term storage.

[0029] 2. Genotyping

[0030] The genomic DNA was obtained and the Neogen_POR80K chip and GenCall (Version 7.0.0) software of Neogen Company were used to type the genomic DNA of the pig to be tested, and the genotype of the corresponding SNP marker MARC0080181 was obtained.

[0031] III. Quality Control of Phenotypic and Genotypic Data

[0032] 1. Quality control standards for phenotypic data: remove individuals with missing phenotypic values; remove individuals with deviations from the mean greater than 3 standard deviations.

[0033] 2. Filtering criteria for SNP chip typing: eliminate SNP sites with a genotype detection rate of less than 95%; eliminate individuals with a detection rate of less than 95%; eliminate individuals with a minimum allele frequency (MAF) of less than 1%; eliminate SNP sites with a Hardy-Weinberg Equilibrium (HWE) chi-square test P value less than 1.0E-4; eliminate SNP sites on sex chromosomes.

[0034] 4. Genome-wide association analysis of pig age data and genotype data at 100 kg body weight

[0035] 1. Test methods

[0036] In this experiment, 590 large white sows were subjected to genome-wide association analysis. The present invention found that the SNP site MARC0080181 was significantly correlated with the age of pigs reaching 100 kg body weight in the large white sow population.

[0037] 2. Statistical analysis model

[0038] The GAPIT (http: / / www.zzlab.net / GAPIT / ) software package for compressed mixed linear models was used for statistical analysis. The statistical analysis model is: Y = Xβ + Z u + e, where Y is the value of the observed phenotype; β is the unknown value containing fixed effects, including genetic markers, population structure (Q matrix) and intercept; u is the unknown value of the random additive genetic effect of multiple background QTLs from individuals or lines; X and Z are known design matrices; e is the unobserved residual vector.

[0039] 3. Discovery of SNP loci associated with pigs reaching 100 kg body weight

[0040] A genome-wide association analysis of 590 large white sows was performed on the age of 100 kg body weight, and it was found that the site MARC0080181 was significantly associated with the 100 kg body weight age trait of the pig. The SNP site MARC0080181 is the 1,420,224th deoxynucleotide of the positive strand of chromosome 6 of the pig reference genome version 10.2 (the 100th nucleotide of sequence 1 in the sequence list, represented by r as A or G), which is A or G. The results are as follows Figure 1-3 As shown, Figure 1 The results of association analysis between different genotypes of MARC0080181 locus and the age at which pigs reach 100 kg body weight (D100); Figure 2 The genotype frequency and allele frequency of the MARC0080181 locus in the tested pig population; Figure 3 The difference in age at which a body weight of 100 kg is reached between individuals with different genotypes at the MARC0080181 locus.

[0041] The results showed that the age at which AA genotype pigs reach 100 kg was significantly lower than that of AG and GG genotype individuals. Therefore, this locus can be used as a molecular marker for the age at which pigs reach 100 kg in weight, to improve the growth rate of pigs and increase economic benefits.

[0042] The present invention has been described in detail above. It will be apparent to those skilled in the art that the present invention may be implemented in a wide range under equivalent parameters, concentrations and conditions without departing from the spirit and scope of the present invention and without the need for unnecessary experimentation. Although the present invention provides specific embodiments, it should be understood that further improvements may be made to the present invention. In short, according to the principles of the present invention, this application intends to include any changes, uses or improvements to the present invention, including changes made by conventional techniques known in the art that depart from the scope disclosed in this application. Applications of some of the basic features may be made within the scope of the following appended claims.

Claims

1. Use of a material for detecting the polymorphism or genotype of a SNP site in identifying the age at which a pig reaches 100 kg in weight, wherein the SNP site is the 1,420,224th deoxynucleotide of the positive strand of chromosome 6 of the pig reference genome version 10.2, which is A or G, and the pig is a Large White pig; the age at which a pig with the AA genotype reaches 100 kg in weight is younger than the age at which a pig with the GG genotype and the age at which a pig with the GA genotype reaches 100 kg in weight.

2. The use according to claim 1, characterized in that: The substance is a SNP chip.

3. Application of a material for detecting the polymorphism or genotype of the SNP site MARC0080181 in pig breeding, wherein the SNP site MARC0080181 is the 1,420,224th deoxynucleotide of the positive strand of chromosome 6 of the pig reference genome version 10.2, which is A or G, and the pig is a Large White pig; the pig breeding refers to breeding pigs that require fewer days of feeding to reach a weight of 100 kg; pigs with AA genotype reach 100 kg in weight in days of age less than pigs with GG genotype and pigs with GA genotype reach 100 kg in weight in days of age.

4. The use according to claim 3, characterized in that: The substance is a SNP chip.

5. A method for identifying the age of pigs reaching 100 kg in weight, characterized in that: The method comprises: detecting the genotype of the SNP marker in the genome of the pig to be tested, and the AA genotype pigs reaching 100 kg in weight are smaller than the GG genotype pigs and the GA genotype pigs reaching 100 kg in weight; Wherein, the SNP marker is the deoxynucleotide 1,420,224 of the positive strand of chromosome 6 in the pig reference genome 10.2, which is A or G; The AA genotype is the homozygous type of the SNP being A; The GA genotype is a heterozygous type in which the SNP is G and A; The GG genotype is the homozygous type of the SNP being G; The pig to be tested is a Large White pig.

6. A pig breeding method, characterized in that: The method comprises: detecting the genotype of the SNP marker in claim 5 in the genome of the pig to be tested, and selecting pigs with genotype AA for breeding; the purpose of pig breeding is to cultivate pigs that require fewer days of feeding to reach a body weight of 100 kg, and the pig to be tested is a Large White pig.

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