CN112280872A - SNP molecular marker related to magnesium ion concentration of serum of Chinese Holstein cow - Google Patents
SNP molecular marker related to magnesium ion concentration of serum of Chinese Holstein cow Download PDFInfo
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- JLVVSXFLKOJNIY-UHFFFAOYSA-N Magnesium ion Chemical compound [Mg+2] JLVVSXFLKOJNIY-UHFFFAOYSA-N 0.000 title claims abstract description 20
- 229910001425 magnesium ion Inorganic materials 0.000 title claims abstract description 20
- 210000002966 serum Anatomy 0.000 title claims abstract description 17
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- 241000283690 Bos taurus Species 0.000 claims abstract description 56
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- 238000009395 breeding Methods 0.000 abstract description 6
- 150000002500 ions Chemical class 0.000 abstract description 4
- 230000008859 change Effects 0.000 abstract description 3
- 238000005516 engineering process Methods 0.000 abstract description 3
- 238000012098 association analyses Methods 0.000 abstract description 2
- 210000000349 chromosome Anatomy 0.000 abstract description 2
- 230000008303 genetic mechanism Effects 0.000 abstract description 2
- 238000012165 high-throughput sequencing Methods 0.000 abstract description 2
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- 210000004369 blood Anatomy 0.000 description 11
- 239000008280 blood Substances 0.000 description 11
- 238000001514 detection method Methods 0.000 description 11
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- 241001465754 Metazoa Species 0.000 description 2
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Abstract
The invention provides an SNP molecular marker related to the serum magnesium ion 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 After the Chinese Holstein cow is scanned in the whole genome, an unpublished SNP locus is found in SNP loci which are obviously associated in the genome and are positioned on the No. 3 chromosome of the cowKCNA2The T/C mutation occurred near the gene at a distance of 28874 bp. By utilizing genome-wide association analysis (GWAS) and a high-throughput sequencing technology, the genetic mechanism of the ion concentration change in the serum of the dairy cow can be disclosed more efficiently.
Description
Technical Field
The invention belongs to the technical field of molecular breeding, and particularly relates to an SNP molecular marker related to the concentration of magnesium ions in serum 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.
The ion concentration in blood relates to various biochemical processes such as acid-base balance in organisms, cell homeostasis maintenance, tissue protein synthesis, cell membrane potential, normal proceeding of enzymatic reaction, osmotic pressure maintenance and the like. It is clear that electrolyte minerals play an important role in a series of metabolic activities of the body, and an imbalance in the concentration of electrolyte minerals leads to an uncomfortable state of the body. Magnesium ions have important significance in animal bodies, and the functions of the magnesium ions comprise maintaining the health of bones and teeth and supporting the activities of nerves and muscles; the activation of enzyme, energy, protein and fat metabolism activities, etc. are all independent of magnesium ions. By utilizing genome-wide association analysis (GWAS) and a high-throughput sequencing technology, the genetic mechanism of the ion concentration change in the serum of the dairy cow can be disclosed more efficiently.
Disclosure of Invention
The invention aims to provide an SNP marker related to the concentration of magnesium ions in serum of Chinese Holstein cows and application thereof.
In order to realize the purpose, the following technical scheme is adopted:
SNP molecular marker related to serum magnesium ion concentration of Chinese Holstein cow, and SNP locus of SNP molecular marker is far away from Chinese Holstein cowKCNA2At 28874bp of the sequence of the Gene (Bos taurus UMD 3.1.1, Gene ID: 539608), a T/C mutation occurred.
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 magnesium ion concentration 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 SNP sites with relevance to magnesium ion concentration characters in 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 character of magnesium ion concentration in serum.
FIG. 2 is a Q-Q diagram of the whole genome analysis of Chinese Holstein cows on the character of magnesium ion 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
A more economical and effective method is adopted to carry 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 version of beagle3.3.1 was used to determine the agile error rate that occurred when 26K and 50K chips caused allele estimates to be erroneous when genotyping was performed. Data screening was performed using quality control of genotype data using PLINK1.07 to remove SNP sites with detection rate <95%, remove sites with Minor Allele Frequency (MAF) below 0.05, and remove individuals with SNP site detection deletion rate >10% with P <10-6 on the 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
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
In 2016, Liu Xiao Lei et al combine various algorithms to provide a model, and a Fixed Effect Model (FEM) and a Random Effect Model (REM) are iteratively used, wherein the model is called as FarmCPU (fixed and random model cloning usability Unit). The association sites with the possibility are added into the fixed effect model as covariates, and the model is as follows:
in the model, the model is divided into a plurality of models,
representing an observed value for an ith individual;
，
……
genotypes of possible association sites as t added models, and zero in the initial part of iterative operation;
，
……
adding corresponding effect values representing possible relevance sites into the model;
representing the genotype of the jth genetic marker in the ith individual;
is that
(ii) an effect value corresponding to the locus genotype;
is a residual vector and obeys
~N(0,
) 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,
in the model of the random effect,
and
the meaning of (c) is the same in the fixed effect model;
is the total genetic effect of the ith individual; when the total genetic effect of an individual is 0, the variance-covariance matrix
，
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, 676 effective SNP sites related to the serum magnesium ion concentration of Chinese Holstein cows, wherein 5 SNP sites reach the FDR significant level, and the adjacent genes are located by comparing the positions of the sites through an Ensemble website (http:// asia. ensemblel. org/index. html), and through Ensemble and EnsembleThe annotation of each gene in NCBI website preliminarily determines a SNP locus which is not published and associated and is positioned at the distance of No. 3 chromosomeKCNA2The gene is 288746bp, and rs136416571 is coded.
TABLE 1
There is a literature that shows that,KCNA2the gene encodes a potassium channel protein, the function of which has been verified in Drosophila. The gene controls the propagation between potassium ion channels and chemical synapses, thereby controlling ion channel activity. The vicinity of the SNP site mentioned in the present invention also includesKCNA10AndKCNA3genes, otherwise indicated in the literatureKCNA2With the two groups in the family, act synergistically. In dairy cows, researches show that the concentration of potassium ions is an important factor influencing the content of magnesium ions, and the lower the content of potassium ions in serum is, the lower the concentration of magnesium ions is. It can be preliminarily presumed that the mutation at the site of SNP (rs 136416571) located on chromosome 3 indirectly causes the change in the concentration of magnesium ions.
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 magnesium ion concentration character 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 concentration of magnesium ions in serum of Chinese Holstein cows is characterized in that: the molecular marker is from Chinese Holstein cowKCNA2At 28874bp of the gene sequence, T/C mutation occurred.
2. The use of the SNP molecular marker of claim 1, wherein the SNP molecular marker is related to the concentration of magnesium ions in serum of Chinese Holstein cows.
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Citations (3)
| Publication number | Priority date | Publication date | Assignee | Title |
|---|---|---|---|---|
| CN101906480A (en) * | 2010-09-10 | 2010-12-08 | 西北农林科技大学 | Molecular marking method of using neuroendocrine factor genes to select kidding characters |
| US20150368652A1 (en) * | 2014-06-23 | 2015-12-24 | The Johns Hopkins University | Treatment of neuropathic pain |
| 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 |
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- 2020-11-18 CN CN202011289914.6A patent/CN112280872A/en active Pending
Patent Citations (3)
| Publication number | Priority date | Publication date | Assignee | Title |
|---|---|---|---|---|
| CN101906480A (en) * | 2010-09-10 | 2010-12-08 | 西北农林科技大学 | Molecular marking method of using neuroendocrine factor genes to select kidding characters |
| US20150368652A1 (en) * | 2014-06-23 | 2015-12-24 | The Johns Hopkins University | Treatment of neuropathic pain |
| 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 (2)
| Title |
|---|
| Q. F. GAN 等: "Genome-wide association study identifies loci linked to serum electrolyte traits in Chinese Holstein cattle", 《ANIMAL GENETICS》 * |
| 王娟等: "利用酿酒酵母转座子文库筛选线粒体镁代谢相关基因", 《生物化学与生物物理进展》 * |
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