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Obtaining method and application of SNP related to milk buffalo milk production traits

A technology of milk buffaloes and traits, applied in the direction of biochemical equipment and methods, recombinant DNA technology, microbial determination/inspection, etc.

Active Publication Date: 2020-11-27
GUANGXI ZHUANG AUTONOMOUS REGION BUFFALO INST
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  • Summary
  • Abstract
  • Description
  • Claims
  • Application Information

AI Technical Summary

Problems solved by technology

At the same time, there are few reports on the SNP typing of milk buffalo based on simplified genome sequencing technology, and the GWAS research report on milk buffalo based on this has not yet been reported.

Method used

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  • Obtaining method and application of SNP related to milk buffalo milk production traits
  • Obtaining method and application of SNP related to milk buffalo milk production traits
  • Obtaining method and application of SNP related to milk buffalo milk production traits

Examples

Experimental program
Comparison scheme
Effect test

Embodiment 1

[0045] Example 1: Buffalo Genotyping

[0046] A total of 309 Mediterranean buffalo individuals were used for simplified genome sequencing analysis. The GATK4 software package was used for SNP typing, and the reference genome was the Mediterranean buffalo genome ((UOA_WB_1). The plink software was used for SNP quality control, and the standard was: SNP detection rate -6 . In addition, chromosomally unknown or duplicated SNPs were also removed. After quality control, a total of 274 individuals and 142326 SNPs were used for subsequent analysis.

[0047] Result analysis:

[0048] Table 1 SNP distribution statistics of buffalo based on simplified genome sequencing

[0049]

[0050]

[0051] It can be seen from Table 1 that a total of 142,326 SNPs were detected based on the simplified genome sequencing technology, covering the size of the buffalo genome of about 2.62Gb. The number of SNPs per chromosome ranged from 2661 to 10976. The average density of SNPs is one SNP per ...

Embodiment 2

[0052] Example 2: Calculation of regression breeding values ​​for milk production traits

[0053] 1) Calculate the estimated breeding value (EBV) formula of each individual milk production trait according to the animal model with the Asreml-R4 software package as follows:

[0054] the y ijklmn =u+Herd i +Year j +Season k +Parity l +Age m +a n +e ijklmn

[0055] Among them, y ijklmn is the observed value of phenotype; u is the overall mean; Herd i is the field fixed effect (4 levels); Year j Year fixed effect (≤2007 and 2008-2016); Season k is the seasonal fixed effect (2 levels); Parity l Parity effect (1 to 7 and≥8); Age m is the fixed effect of calving age; a n is the individual additive effect; e ijklmn is a random error;

[0056] 2) For the calculation of DEBV for each individual milk production trait, first use R language to calculate the weighted value. The formula is (Garrick et al.2009) where c is assumed to be 0.4 (Saatchi et al.2014); h 2 is the he...

Embodiment 3

[0057] Example 3: Genome-wide association (GWAS) analysis of milk production traits

[0058] The association analysis between SNPs and milk production traits was carried out using the FarmCPU method in the rMVP R package. The threshold for significant SNP screening is P-4 . The results are shown in the table below:

[0059] Table 2 GWAS analysis results of buffalo milk production traits

[0060]

[0061]

[0062]

[0063]

[0064] Remarks: Significant marker level is P value-4 .

[0065] It can be seen from Table 2 that a total of 128 SNPs passed the selection threshold and can be regarded as SNPs significantly related to milk production traits. Among them, there are 24 SNPs related to milk production, and 11, 42, 22 and 29 SNPs related to milk fat amount, milk fat percentage, milk protein amount and milk protein percentage, respectively. The important ones are snp16586372 (p-value 5.39E-06 this locus is on chromosome 22), snp6752954 (p-value 7.16E-06 this locu...

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Abstract

The invention relates to the field of animal molecular markers, in particular to an obtaining method and application of SNP related to milk buffalo milk production traits. The application of five SNPloci of a buffalo in buffalo milk production traits or molecular breeding analysis is provided. Nucleotide sequences of the five SNP molecular markers are shown in SEQ ID NO.1-5. The invention furtherdiscloses a buffalo milk production trait or molecular breeding analysis method. The five SNP loci can provide support for upstream and downstream processes of breeding, and have the advantages of high determination accuracy and the like; the milk production performance of a milk buffalo can be improved, and technical support is provided and a theoretical basis is laid for breeding of the milk buffalo with excellent milk production performance.

Description

【Technical field】 [0001] The invention relates to the field of animal molecular markers. It specifically relates to the method and application of SNPs related to milk production traits of milk buffalo cattle. 【Background technique】 [0002] Buffalo is a unique breeding stock resource in southern my country, but its low milk yield and reproductive performance have become two major scientific problems affecting its industrial development. Obviously, the use of advanced molecular marker technology in the selection of high-quality milk buffalo germplasm resources will effectively improve the efficiency of selection. [0003] Genome-wide association analysis (GWAS), that is, on a genome-wide scale. Look for single nucleotide polymorphisms (SNPs) on the mutation site, and screen out SNPs associated with phenotypic traits. With the completion of genome sequencing of various organisms and the continuous development of high-throughput chips, GWAS has been widely used in the resear...

Claims

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Application Information

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IPC IPC(8): C12Q1/6888C12N15/11G16B30/00
CPCC12Q1/6888G16B30/00C12Q2600/156C12Q2600/124
Inventor 邓廷贤陆杏蓉梁莎莎段安琴马小娅梁贤威庞春英
Owner GUANGXI ZHUANG AUTONOMOUS REGION BUFFALO INST
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