CN112210613A - SNP molecular marker related to serum insulin concentration of Chinese Holstein cow - Google Patents

SNP molecular marker related to serum insulin concentration of Chinese Holstein cow Download PDF

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CN112210613A
CN112210613A CN202011289913.1A CN202011289913A CN112210613A CN 112210613 A CN112210613 A CN 112210613A CN 202011289913 A CN202011289913 A CN 202011289913A CN 112210613 A CN112210613 A CN 112210613A
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甘乾福
李毅冉
梁学武
刘庆华
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Fujian Agriculture and Forestry University
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Abstract

The invention provides an SNP molecular marker related to the serum insulin concentration of Chinese Holstein cows, belonging to the technical field of molecular breeding. After the Chinese Holstein cow is scanned in the whole genome, an unpublished SP locus is found in the obviously associated SNP loci and is positioned on the No. 20 chromosome of the cowDOCK2In the gene, the A/G mutation occurred at 14406bp of its sequence. By utilizing genome-wide association analysis (GWAS) and a high-throughput sequencing technology, the genetic mechanism of the insulin secretion of the dairy cows can be disclosed more efficiently.

Description

SNP molecular marker related to serum insulin concentration of Chinese Holstein cow
Technical Field
The invention belongs to the technical field of molecular breeding, and particularly relates to an SNP molecular marker related to the serum insulin concentration of Chinese Holstein cows.
Background
The Holstein cow is the cow variety with the highest milk yield and the most feeding amount in the world at present. The variety originates from the northern Netherlands province and the Sifleilan province, and is also called black and white cow because the appearance fur is color blocks distributed in black and white alternately. After the last 50 th century, the Chinese cattle are hybridized with Chinese local yellow cattle and introduced into partial areas of China, and are gradually distributed all over the country in continuous domestication and breeding to become a dairy cow variety which is bred in large scale in China, and the Chinese Holstein cow is formally named as the Chinese Holstein cow in 1992 by the Chinese black and white cow. The bred Chinese Holstein cows have strong and uniform physique, clear color and good development of a lactation system. Due to the difference of the introduced bull varieties and the difference of the feeding environment, the Chinese Holstein cows are roughly divided into three body types: the blood system of the American Holstein cow is mostly introduced into large Holstein cows, the height of an adult cow is about 1.35m, and the weight of the adult cow can reach 600 Kg; the father blood system of the medium-sized cow is mainly the medium-sized Holstein bull in European countries, and the height of the adult cow is more than 1.33 m; the small-sized cow is bred by hybridization of introduced Holstein bull and local small-sized cow, and the height of adult cow is about 1.30 m.
China Holstein cows are dairy in most areas, and are biased to meat and milk dual-purpose in parts of south China. The average annual milk yield of the whole group of the specially bred cows can reach over 9000Kg, the milk yield in a lactation period can reach over 1 ten thousand Kg, and the cow milk is rich in nutritional ingredients such as protein, lipid and the like. However, the occupied amount of the milk in per capita in China is small, and the milk quality is low, which is still a problem to be solved urgently in the whole industry. Only by improving the overall genetic level of the dairy cow population in China, the health condition and the production level of the dairy cows can be fundamentally improved.
Research shows that the function of insulin can reduce blood sugar and influence the secretion of other hormones and the proliferation of cells, and in vivo experiments of cows, the insulin can actually improve the synthesis efficiency of milk protein and the milk yield. By utilizing genome-wide association analysis (GWAS) and a high-throughput sequencing technology, the genetic mechanism of the insulin secretion of the dairy cows can be disclosed more efficiently.
Disclosure of Invention
The invention aims to provide an SNP marker related to the concentration of insulin in serum of Chinese Holstein cows and application thereof.
In order to realize the purpose, the following technical scheme is adopted:
the SNP locus related to the serum insulin concentration of the Chinese Holstein cow is positioned in the Chinese Holstein cowDOCK2The A/G mutation occurred at 14406bp of the sequence of the Gene (as indicated by Bos taurus UMD 3.1.1, Gene ID: 510083).
The invention adopts a whole genome high-throughput chip sequencing technology to carry out whole genome scanning on the Chinese Holstein cows.
The total amount of the research sample of the invention is 1217 Chinese Holstein cows, which comprises 48 half-sib-series, and a combined detection method of 50K chips (BovineSNP; Illumina, San Diego, CA, USA) and 26K chips (GeneSeek, Neogen Corporation, Lincoln, NE, USA) is adopted.
The invention detects the mononucleotide mutation site related to the concentration of insulin in the serum of Chinese Holstein cow.
The whole genome scanning result in the invention adopts R software, and utilizes a farmCPU (fixed and random model cloning Probability unification) algorithm to carry out linear regression analysis, thereby determining the single nucleotide mutation site which is obviously related to the target character.
The invention has the advantages that:
the whole gene scanning scheme adopted by the invention for Chinese Holstein cows is more economic and effective, the detection speed is high, and the cost is low. The detection of the SNP locus having relevance to the insulin concentration character in the serum can provide scientific basis for the marker assistance of biochemical components in blood of Chinese Holstein cows.
Drawings
FIG. 1 is a genome-wide analytical Manhattan chart of Chinese Holstein cows with respect to the serum insulin concentration profile.
FIG. 2 is a Q-Q diagram of genome wide analysis of Chinese Holstein cows on the character of insulin concentration in serum.
Detailed Description
The following embodiments further illustrate the present invention, but should not be construed as limiting the invention, and modifications or substitutions to the method and steps of the present invention may be made without departing from the spirit and substance of the invention.
Unless otherwise specified, the technical means used in the examples are conventional means well known to those skilled in the art.
Example 1
1. Test animal
1226 cows are the total number in a large Holstein cow breeding base in Fujian, China. The father lines of the cows are all from high-yielding breeding bulls, and the number of the father lines is 48, and each half-sib line comprises 5-50 individuals.
2. Phenotypic data
And (3) collecting blood of tail bone blood vessels of all dairy cows to be detected by 5ml, putting the blood into an anticoagulation test tube containing 20% EDTA, storing all samples in an environment at 4 ℃, and sending the samples to a hospital in the city of Fuzhou within 24 hours for routine detection of ion and hormone content and blood. And (5) sorting and summarizing the data by using Excel software and storing the data for later use.
3. Genotype data
After all cows were bled, 5ml of blood from each cow was placed in an anticoagulation tube containing 20% EDTA and frozen at-80 ℃ for 24 hours. After all blood samples are collected, the blood samples are sent to a biological detection company for genotyping detection.
4. Statistical analysis
In the invention, a more economic and effective method is adopted for carrying out the scanning scheme of the genotype data. Two cows were randomly selected from each half-sib and genotyped using a 50K chip (BovineSNP; Illumina, San Diego, Calif., USA), with the remaining cows all being genotyped using a 26K chip (GeneSeek, Neogen Corporation, Lincoln, NE, USA). The versions of Beagle3.3.1[75] were used to determine the agile error rates that occurred when 26K chips and 50K chips caused allele errors when genotyping was performed. Screening of data was performed using quality control of genotype data using PLINK1.07[76], removing SNP sites with detection rate <95%, removing sites with Minor Allele Frequency (MAF) below 0.05, and removing individuals with SNP site detection deletion rate >10%, P <10-6 at Hardy-Weinberg test. Finally, we obtained a total of 1216 effective individuals, and 47396 SNP sites.
In the invention, a loose FDR correction multiple test is adopted to determine the significance threshold, and firstly, the P-value corresponding to the SNP locus is determined according to P1≤≤P2≤P3≤P4≤....≤.PkWherein K is the number of effective SNPs, finding a sequence satisfying the condition
Figure DEST_PATH_IMAGE001
Where i is the ith sample number of the comparison, and the finally obtained maximum P-value is the significance threshold after FDR correction.
5. Analytical model
The invention adopts the farm CPU to carry out the correlation analysis of the SNP sites, 2016, Liu XiaoLei et al combine a plurality of algorithms to provide a new model, a Fixed Effect Model (FEM) and a Random Effect Model (REM) are used in an iteration way, the model is called as farm CPU (fixed and random model cloning Probability university) and the correlation sites with possibility are added into the fixed effect model as covariates, the model is as follows,
Figure 551444DEST_PATH_IMAGE002
…………… (1)
in the model, the model is divided into a plurality of models,
Figure DEST_PATH_IMAGE003
representing an observed value for an ith individual;
Figure 908607DEST_PATH_IMAGE004
，
Figure DEST_PATH_IMAGE005
……
Figure 197637DEST_PATH_IMAGE006
genotypes of possible association sites as t added models, and zero in the initial part of iterative operation;
Figure DEST_PATH_IMAGE007
，
Figure 455181DEST_PATH_IMAGE008
……
Figure DEST_PATH_IMAGE009
adding corresponding effect values representing possible relevance sites into the model;
Figure 945199DEST_PATH_IMAGE010
representing the genotype of the jth genetic marker in the ith individual;
Figure DEST_PATH_IMAGE011
is that
Figure 757035DEST_PATH_IMAGE012
(ii) an effect value corresponding to the locus genotype;
Figure DEST_PATH_IMAGE013
is a residual vector and obeys
Figure 318598DEST_PATH_IMAGE013
~N(0,
Figure 227385DEST_PATH_IMAGE014
) Is normally distributed.
And after one-time statistical detection is carried out on all the mark points by using a fixed effect model, all the covariate sites are removed, and all the remaining points to be observed can obtain a P value. And if the P value as the covariate is null, the highest statistical power is selected for replacement through simulation test. After the whole process is finished. All genetic markers will have a corresponding P value.
The random effect model predicts the associated sites by the SUPER algorithm and optimizes different combination results by using the P values and the position information of all genetic markers. The model of the random effect is as follows,
Figure DEST_PATH_IMAGE015
………………… (2)
in the model of the random effect,
Figure 747360DEST_PATH_IMAGE016
and
Figure DEST_PATH_IMAGE017
the meaning of (c) is the same in the fixed effect model;
Figure 46492DEST_PATH_IMAGE018
is the total genetic effect of the ith individual; when the total genetic effect of an individual is 0, the variance-covariance matrix
Figure DEST_PATH_IMAGE019
，
Figure 146166DEST_PATH_IMAGE020
As the genetic variance of an unknown locus, K is used as the affinity matrix. The random matrix will produce the possible association sites that are added as covariates to the fixed effect model. The fixed effect and the random effect are operated in an iteration mode, and when the position point generated by the random effect is the same as the result in the previous iteration, the iteration is stopped.
6. Analysis of results
After statistical analysis, 308 effective SNP sites related to the serum insulin concentration of Chinese Holstein cows are obtained, wherein 15 SNP sites reach the FDR significant level, nearby genes are positioned through an Ensemble website (http:// asia. ensemblel.org/index. html) according to the positions of the sites, and an SNP site which is not related to public publication is preliminarily determined through annotation of the genes in the Ensemble website and the NCBI websitePoint, located on chromosome 20DOCK2At 14405bp in the gene, rs109881742 is coded.
TABLE 1
Figure DEST_PATH_IMAGE021
There is a literature that shows that,DOCK2the gene participates in the physiological activities of mouse pancreatic cells and fat cells, has certain influence on Insulin Resistance (IR), and can be preliminarily guessed to be positioned inDOCK2SNP loci in the genes have relevance to the concentration of insulin in the serum of the dairy cows.
The molecular genetic marker provided by the invention is not limited by the age and sex of the Chinese Holstein cow, and can be applied to various age stages and early breeding activities of the Chinese Holstein cow to accelerate variety breeding and early disease diagnosis.
The whole gene scanning scheme adopted by the invention for Chinese Holstein cows is more economic and effective, the detection speed is high, and the cost is low.
In the invention, the detection of the SNP locus having relevance to the concentration character of the insulin in the serum can provide scientific basis for the marking assistance of biochemical components in blood of Chinese Holstein cows.
The above description of the embodiments and results of the present invention is provided for the purpose of improving the corresponding conditions of the present invention without departing from the technical principle of the present invention, and the modifications should be construed as the scope of the present invention.

Claims (2)

1. An SNP molecular marker related to the serum insulin concentration of Chinese Holstein cows is characterized in that: the molecular marker is from Chinese Holstein cowDOCK2At 14406bp of the gene sequence, A/G mutation occurred.
2. The use of the SNP molecular marker of claim 1, for breeding cows.
CN202011289913.1A 2020-11-18 2020-11-18 SNP molecular marker related to serum insulin concentration of Chinese Holstein cow Pending CN112210613A (en)

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Citations (3)

* Cited by examiner, † Cited by third party
Publication number Priority date Publication date Assignee Title
WO2003056913A1 (en) * 2002-01-07 2003-07-17 Japan Science And Technology Agency Nonhuman model animal lacking the ability to control lymphocyte migration
CN105392491A (en) * 2013-03-12 2016-03-09 Hmi医疗创新有限公司 Plant extracts with anti-diabetic and other useful activities
CN107267605A (en) * 2017-06-13 2017-10-20 甘肃民族师范学院 The SNP marker related to china holstein cowses reproductive trait and its application

Patent Citations (3)

* Cited by examiner, † Cited by third party
Publication number Priority date Publication date Assignee Title
WO2003056913A1 (en) * 2002-01-07 2003-07-17 Japan Science And Technology Agency Nonhuman model animal lacking the ability to control lymphocyte migration
CN105392491A (en) * 2013-03-12 2016-03-09 Hmi医疗创新有限公司 Plant extracts with anti-diabetic and other useful activities
CN107267605A (en) * 2017-06-13 2017-10-20 甘肃民族师范学院 The SNP marker related to china holstein cowses reproductive trait and its application

Non-Patent Citations (3)

* Cited by examiner, † Cited by third party
Title
QIANFU GAN等: "Genome-wide association studies for the concentrations of insulin, triiodothyronine, and thyroxine in Chinese Holstein cattle", 《TROPICAL ANIMAL HEALTH AND PRODUCTION》 *
宋军营 等: "DOCK2介导神经炎症与阿尔茨海默病", 《现代免疫学》 *
杨建等: "SHIP2基因与2型糖尿病", 《国际内科学杂志》 *

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Application publication date: 20210112