Method for dividing breeding swine blood linkage based on whole genome SNP information

A whole-genome and genome-wide technology, applied in the field of breeding pig pedigree based on whole-genome SNP information, can solve the problems of only considering the pedigree information from the father and the unreliable division method, and achieve a clear and concise interface, accurate division, and kinship Predict accurate results

Active Publication Date: 2019-08-27
WENS FOOD GRP CO LTD +1
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Problems solved by technology

[0004] The purpose of the present invention is to establish a kind of breeding pig lineage division method based on the whole genome SNP i

Method used

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  • Method for dividing breeding swine blood linkage based on whole genome SNP information
  • Method for dividing breeding swine blood linkage based on whole genome SNP information
  • Method for dividing breeding swine blood linkage based on whole genome SNP information

Examples

Experimental program
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Effect test

Embodiment 1

[0037] Example 1 Lineage division based on genomic SNP data

[0038] Experimental materials: The experimental materials are 60 breeding boars (the initial letter is represented by V) in the original breeding pig farm of Qingyuan No. 2 District, a subsidiary of Wen's Food Group Co., Ltd. All 60 breeding boars have been subjected to genomic SNP genotype mining by GBS (genotyping-by-sequencing) technology.

[0039] The flow chart of this embodiment is shown in figure 1 ,Specific steps are as follows:

[0040]DNA was extracted from ear tissues of all boars, and genomic libraries were constructed for all boars using the simplified genome (GBS) technology based on two restriction enzymes EcoRI and MspI, and sequenced on the Illumina HiSeq X Ten high-throughput sequencing platform. The obtained raw data were quality-controlled by Fastqc software, and the processed fragments were compared to the reference genome by BWA 0.7.15 software. After base quality correction, SNP typing was p...

Embodiment 2

[0042] Embodiment 2 new lineage division method compares with traditional division method

[0043] Experimental materials: All the ancestor information from the parents to the great-grandfather of the above 60 breeding boars was retrieved from the pedigree (except for the 60 boars, the initials of the boars are represented by S, and the sows are represented by D), all ancestors are not Genome SNP mining, as the material of traditional ancestry classification, is used to compare with the results of ancestry classification in the present invention.

[0044] Call out the pedigree of all 60 boars to the great-grandfather in the field, and draw the pedigree through Pedigraph software. After all the parents of the 60 boars are taken into account, the following is generated: image 3 From the results shown, it can be seen that the pedigree structure is extremely complex, and it is difficult to divide individuals into a certain lineage. Therefore, considering only absorbing informati...

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Abstract

The invention discloses a method for dividing breeding swine blood linkage based on whole genome SNP information. The method comprises the steps of acquiring a body tissue of a dividing object, extracting the DNA, typing the genome SNP of each individual through a certain gene typing technique, and screening a qualified SNP site through quality control. calculating an additive heredity correlationvalue between individuals through the genome SNP genotype, then subtracting the additive heredity correlation value from one and using the obtained value as the distance between two individuals, thenperforming cluster analysis on the two individuals through an R-language hclust function, and using 0.9844 as a threshold for dividing the blood linkage. Compared with a traditional blood linkage dividing method, the method according to the invention has advantages of realizing a clear and concise obtained result, sufficiently reserving allele information which is transmitted from the parents, and realizing high reliability in blood linkage dividing.

Description

technical field [0001] The invention relates to the field of animal breeding, in particular to a method for dividing breeding pig bloodlines based on whole genome SNP information. Background technique [0002] In breeding science, it is generally considered that the distance between the mating parents and the common ancestor is within 6 generations (that is, the inbreeding coefficient of the offspring is greater than 0.78%), which is inbreeding, referred to as inbreeding. Because inbreeding can increase the probability of recessive deleterious homozygosity, it may lead to inbreeding depression. Therefore, the purpose of kin selection in core breeding farms is usually to avoid inbreeding, and sufficient bloodlines in the field are a necessary condition for preventing inbreeding depression. In order to ensure that there are enough bloodlines, it is necessary to carry out accurate bloodline division of the breeding pigs to be selected in the field, and fully guarantee the numb...

Claims

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Application Information

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IPC IPC(8): G16B20/20G16B20/30C12Q1/6888
CPCG16B20/20G16B20/30C12Q1/6888C12Q2600/156
Inventor 蔡更元董林松吴珍芳
Owner WENS FOOD GRP CO LTD
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