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Method for tracing blood lineage sources of buffaloes and carrying out genome matching based on whole-genome SNP information

A whole-genome and genome-wide technology, applied in the field of animal breeding, can solve problems such as the lack of detailed buffalo genetic relationships, unreliable division methods, and lack of pedigree information, and achieve the effects of reducing the probability of inbreeding, improving the production performance of offspring, and accurately tracing

Active Publication Date: 2020-07-03
FOSHAN UNIVERSITY
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  • Abstract
  • Description
  • Claims
  • Application Information

AI Technical Summary

Problems solved by technology

[0004] In order to solve the problems of unreliable division methods in the prior art, lack of pedigree information, and lack of detailed genetic relationship between buffaloes, the present invention provides a method for tracing the origin of buffalo bloodlines based on the whole genome SNP information and performing genome matching based on this

Method used

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  • Method for tracing blood lineage sources of buffaloes and carrying out genome matching based on whole-genome SNP information
  • Method for tracing blood lineage sources of buffaloes and carrying out genome matching based on whole-genome SNP information
  • Method for tracing blood lineage sources of buffaloes and carrying out genome matching based on whole-genome SNP information

Examples

Experimental program
Comparison scheme
Effect test

Embodiment 1

[0045] Example 1 Lineage traceability analysis and genome selection based on genomic SNP data

[0046] Experimental material: Blood samples from 4 test hybrid buffaloes. All buffaloes have been subjected to genome SNP genotype mining through Illumina next-generation data sequencing technology.

[0047] Specific steps are as follows:

[0048] (1) Extract blood sample DNA from all buffaloes and sequence them on the IlluminaHiSeq high-throughput sequencing platform; download the second-generation sequencing data of the world's major buffalo breeds from the BIG Sub database (BIG Sub: CRA001463), and obtain the genome SNP genes type information.

[0049] (2) SNP quality control: The raw data obtained in step (1) were quality controlled by Fastqc and Trimmomatic software, and the processed fragments were compared to the reference genomes of swamp buffalo and river buffalo (GWHAAJZ00000000 and GWHAAKA00000000) by BWA software , after base quality correction, SNP typing was perform...

Embodiment 2

[0054] Example 2 The comparison between the new lineage tracing method and the pedigree results

[0055] Experimental material: Test hybrid buffalo map

[0056] Based on the ancestral component analysis of the Bayesian method and the buffalo SNP information collected in Example 1, use ADMIXTURE to analyze the genetic structure of the buffalo population. The preset subgroup number (K ​​value) is 2-8, and the SNP of each individual is carried out. Bayesian inference subgroups, and finally calculate the proportion of different components of all SNPs for each individual.

[0057] When the number of subgroups (K value) is 2, the structure at this time is the composition of swamp buffalo and river buffalo. ADMIXTURE will calculate the proportion of these two parts of all individuals, and preliminarily deduce it based on the proportion of the two parts in the hybrid buffalo For the number of hybrid generations, when the proportion of ingredients is 40-60%, it is the first generation...

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Abstract

The invention provides a method for tracing blood lineage sources of buffaloes and carrying out genome matching based on whole-genome SNP information. The method comprises the following steps: extracting DNA from buffalo individuals to undergo blood lineage test, carrying out sequencing, and downloading second-generation sequencing data of main buffalo varieties in the world from a database to obtain genotype information of genomic SNP; performing quality control screening on genome SNP sites, and selecting SNP sites; combining obtained SNP information, converting SNP data into a ped format ofPLINK, performing STUCTURE analysis, presetting different K values, and speculating subgroup types; and calculating an inbreeding coefficient between the buffaloes to be tested so as to provide a basis for subsequent genome selection and matching. According to the invention, the blood lineage of buffaloes can be traced more accurately; various components are displayed in proportion by the novel tracing method, and buffaloes can be subjected selective breeding on such a basis, so the production performance of offspring is improved; and by calculating the genetic relationship between individuals, the probability of intimate mating is reduced.

Description

technical field [0001] The invention belongs to the technical field of animal breeding, and specifically relates to a method for tracing the source of buffalo bloodlines based on the SNP information of the whole genome and performing genome matching according to the bloodlines. Background technique [0002] Domesticated buffaloes are divided into two main types—swamp buffaloes and river buffaloes. All buffaloes in my country are swamp buffaloes. Long-term service selection makes their production traits low. River buffaloes are widely distributed in South Asia and Central Asia. There are many excellent varieties for milk and meat in China and Europe. Therefore, the current buffalo breeding is to use foreign high-quality river buffaloes and local buffaloes for breeding. However, the crossbreeding work cannot be completed by only one generation of crossbreeding. Repeated crossbreeding of multiple breeds in generations requires farms or farmers to carry out accurate pedigree rec...

Claims

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Application Information

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Patent Type & Authority Applications(China)
IPC IPC(8): G16B20/30G16B20/20G16B5/20G06K9/62C12Q1/6888
CPCG16B20/30G16B20/20G16B5/20C12Q1/6888C12Q2600/156G06F18/295
Inventor 刘庆友罗西尔阮珏石德顺周宇崔奎青李志鹏李辉冯彤王晓波
Owner FOSHAN UNIVERSITY
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