SNP molecular marker related to pig fetal distance traits

A molecular marker and spacing technology, applied in recombinant DNA technology, microbial determination/inspection, DNA/RNA fragments, etc., can solve the problems of small number of samples, difficult identification of major genes, single variety, etc., and achieve the effect of high sensitivity

Active Publication Date: 2020-04-21
HUAZHONG AGRI UNIV
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  • Summary
  • Abstract
  • Description
  • Claims
  • Application Information

AI Technical Summary

Problems solved by technology

[0004] Fetal spacing traits are complex traits controlled by multiple genes, and it is difficult to accurately identify the main effect genes using conventional genetic methods. Genome-wide association analysis based on high-density SNP chips or sequencing provides a basis for the positioning of candidate genes for complex diseases or quantitative traits. Effective technical means (Yin Jianliang et al. 2017)
At present, most of the research on fetal spacing traits stays in the statistical analysis of phenotypes, but for the related genome-wide association analysis research, there are reasons such as small number of samples and single breed, so it is necessary to expand the breed or number of pigs studied (Yuan Wang et al., 2017)

Method used

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  • SNP molecular marker related to pig fetal distance traits
  • SNP molecular marker related to pig fetal distance traits
  • SNP molecular marker related to pig fetal distance traits

Examples

Experimental program
Comparison scheme
Effect test

Embodiment 1

[0034] Embodiment 1: Genotyping and detection

[0035](1) Genomic DNA was extracted and tested for quality by collecting Danish pig ear samples from a pig farm in southern China, and genotyping with GeneSeek Porcine 50K SNP high-density chip to obtain SNP typing data.

[0036] Use Plink1.9 software to convert the original data into VCF format, and then use this software to perform quality control on VCF format files: Specifically:

[0037] 1) maf 0.01: remove the SNP sites whose minimum allele frequency is less than 1%;

[0038] 2) geno 0.1: SNP sites whose genotype detection rate is less than 90% are eliminated;

[0039] 3) mind 0.1: Eliminate individuals whose genotype deletion rate is greater than 10%;

[0040] 4) hwe le-6: remove the SNP sites with Hardy-Weinberg balance test P value less than 10-6,

[0041] 5) Use beagle 4.1 software to fill in missing genotypes on the chip data after quality control, the command is as follows:

[0042] java-jar-Xmx8g beagle.jar gt=qc...

Embodiment 2

[0044] Embodiment 2: The method in the genome-wide association analysis of pig-fetal spacing traits

[0045] The phenotypes of Danish pigs' fetal spacing used in the association analysis with genotypes were from a certain pig farm in southern China, with a total of 964 individuals. Genome-wide association analysis (GWAS) was performed using the FarmCPU model in the MVP package under the R language. The specific model formula is as follows: y i = M i1 b 1 +M i2 b 2 +...+M it b t +S ij d j +e i (1) where y i is the trait observation value of the i-th individual; M i1 , M i2 ,...,M it is the genotype of t possible associated sites added to the model, and this part is empty during the first iteration; b 1 , b 2 ,...,b t is the corresponding effect value of the possible association sites added to the model; S ij is the genotype of the jth genetic marker of the i individual; d j is S ij The corresponding effect value of e i is the residual vector; y i = u i +e ...

Embodiment 3

[0051] Example 3: Application of rs328285068 molecular marker typing method in correlation analysis of pig-fetal spacing traits / correlation analysis between rs328285068 molecular marker (SWQ ID NO: 1 in the sequence table) and pig-fetal spacing traits:

[0052] Association analysis of the rs328285068 molecular marker and pig fetal spacing traits using a mixed linear model (MLM). The specific model is as follows:

[0053] the y ijklmn =μ+G i +HYS j +Breed+ID m +ε ijklmn

[0054] Among them, y ijklmn is the phenotypic value of the mth individual inter-fetal distance trait; μ is the group mean; G i is the genotype effect, HYS k is the joint effect of place of birth, year of birth and season of birth (fixed effect); Breed is the breed effect (fixed effect); ID m is the individual additive effect (random effect), ε ijklmno is the residual effect of the model, and the F test was used to analyze the significance of the inter-internal spacing traits among the three genotype ...

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Abstract

The invention belongs to the technical field of pig molecular marker screening, and particularly relates to an SNP molecular marker related to pig fetal distance traits. An accession number is rs328285068; the method comprises the following steps: collecting a Dan-series boar ear sample from a certain pig farm in south of China, extracting genome DNA, carrying out quality detection, performing genotyping by using a GeneSeek Porcine 50K SNP high-density chip to obtain SNP typing data, screening the SNP molecular marker related to the pig fetal distance traits, wherein the nucleotide sequence ofthe SNP molecular marker is shown in the formula of SEQ ID NO: 1, allelic mutation (substitution) of G / A exists at the 51st basic group of the sequence, and the mutation (substitution) causes the nucleotide of the sequence to generate polymorphism. When the 51st nucleotide of the sequence shown in the formula of SEQ ID NO: 1 is A, it is judged that the boar has a shorter fetal distance.

Description

technical field [0001] The invention relates to the technical field of porcine molecular marker screening, in particular to a SNP molecular marker related to pig-fetal spacing traits and its application. The molecular markers described in the invention can be used for auxiliary prediction and selection of pig-fetal spacing traits. Background technique [0002] In the pig industry, the number of weaned pigs per year (The number of weaned pigsper Sow per Year, PSY) provided by each sow is not only an important productivity trait of sows, but also reflects the comprehensive pig raising level of an enterprise or a country. Indicators (Yuan Senquan 1993). The farrowing interval (FI) is a common indicator used to characterize the production efficiency of pig farms. It is defined as the number of days between sows' two farrowings. It is directly related to the number of sows' annual litters. It will directly affect the size of PSY. In order to improve the economic benefits of pig...

Claims

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Application Information

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Patent Type & Authority Applications(China)
IPC IPC(8): C12Q1/6888C12N15/11
CPCC12Q1/6888C12Q2600/124C12Q2600/156
Inventor 余梅王宏涛赵书红刘向东李新云刘小磊郭猛李小平
Owner HUAZHONG AGRI UNIV
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