SNP (single nucleotide polymorphism) molecular marker related to primary mating day-age characters of sow

A technology of molecular markers and traits, applied in the direction of recombinant DNA technology, microbial measurement/inspection, DNA/RNA fragments, etc., can solve the problems of cost increase and achieve the effect of fast sensitivity

Active Publication Date: 2020-04-03
北京嘉华种猪育种有限公司 +1
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  • Summary
  • Abstract
  • Description
  • Claims
  • Application Information

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Problems solved by technology

Moreover, Zhang Wenbo et al. (2001) reported that the cost per piglet of sows eliminate...

Method used

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  • SNP (single nucleotide polymorphism) molecular marker related to primary mating day-age characters of sow
  • SNP (single nucleotide polymorphism) molecular marker related to primary mating day-age characters of sow
  • SNP (single nucleotide polymorphism) molecular marker related to primary mating day-age characters of sow

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Experimental program
Comparison scheme
Effect test

Embodiment 1

[0032] Embodiment 1: Genotyping and detection

[0033] (1) Genomic DNA was extracted by collecting ear samples of Danish large white pigs from a certain pig farm in southern China (commercially purchased kits were used according to conventional methods) and tested for quality, and gene analysis was performed by GeneSeek Porcine 50K SNP high-density chip Type to get SNP typing data.

[0034] 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:

[0035]1) maf 0.01: remove the SNP sites whose minimum allele frequency is less than 1%;

[0036] 2) geno 0.1: SNP sites whose genotype detection rate is less than 90% are eliminated;

[0037] 3) mind 0.1: Eliminate individuals whose genotype deletion rate is greater than 10%;

[0038] 4) hwe le-6: remove the SNP sites with Hardy-Weinberg balance test P value less than 10-6,

[0039] 5) Use beagle 4.1 software to fill in the missin...

Embodiment 2

[0042] Example 2: The method in the genome-wide association analysis of pig first mating age traits

[0043] The phenotype data of age at first mating of Dan-line Large White pigs used for association analysis with genotypes came from a pig farm in southern China, with a total of 786 individuals. Genome-wide association analysis (GWAS) was performed using the FarmCPU model in the MVP package under the R language. The specific model 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 association sites added to the model, and this part is empty in 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...

Embodiment 3

[0049] Example 3: The application of the molecular marker typing method of the accession number rs81253440 fragment in the correlation analysis of pig first mating age traits

[0050] / rs81253440 Molecular marker (Sequence Listing SWQ ID NO: 1) and correlation analysis of age at first mating of pigs:

[0051] The association analysis of rs81253440 molecular marker and age at first mating traits of pigs was carried out using mixed linear model (MLM). The specific model is as follows:

[0052] the y ijklmn =μ+G i +HYS j +ID m +ε ijklmn

[0053] Among them, y ijklmn is the phenotypic value of the m-th individual's first mating age 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); 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 differences in the age at first...

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Abstract

The invention belongs to the technical field of pig molecular marker screening, and particularly relates to a SNP (single nucleotide polymorphism) molecular marker related to the primary mating day age of a sow. The accession number of the SNP molecular marker is rs81253440, a Danish landrace sow ear sample from a certain piggery in the South China is collected, genome DNA is extracted, quality detection is carried out, and a GeneSeek Porcine50K SNP superchip is used for carrying out genetic typing to obtain SNP typing data so as to obtain the SNP molecular marker related to the primary matingday-age characters of the sow. The nucleotide sequence of the SNP molecular marker is disclosed in SEQ ID NO:1, the allele mutation of a G/T is in the presence in the 51st basic group of the sequence, and the mutation causes the nucleotide of the disclosed sequence to generate polymorphism; and when the 51st nucleotide on the nucleotide sequence is T, the primary mating day age of the sow is judged to be increased.

Description

technical field [0001] The invention belongs to the technical field of porcine molecular marker screening, and in particular relates to a SNP molecular marker related to pig first mating age traits and an application thereof. The molecular marker of the invention can be used for auxiliary prediction and selection of pig first mating age traits. Background technique [0002] Reproductive traits are one of the important economic traits of pig farms, which directly affect the economic benefits of large-scale pig farms, and the age of sows at first mating is an important factor affecting reproductive traits (Jian Yunhua et al. 2017). Studies have shown that if mating is too early, the body maturity and sexual maturity of the back sow are not high, which not only affects its own development, but also leads to small litter size, weak piglets, and increased chances of dystocia in sows; It will cause restlessness in gilts and affect their normal physiological activities (Shu Dengqu...

Claims

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Application Information

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IPC IPC(8): C12Q1/6888C12N15/11
CPCC12Q1/6888C12Q2600/124C12Q2600/156C12Q2600/172
Inventor 余梅王宏涛李新云刘向东赵书红刘小磊郭猛李小平
Owner 北京嘉华种猪育种有限公司
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