CN113493843A - SNP genetic marker influencing egg yolk weight of chicken and application thereof - Google Patents
SNP genetic marker influencing egg yolk weight of chicken and application thereof Download PDFInfo
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Abstract
The invention provides an SNP genetic marker influencing the egg yolk weight of chickens, belonging to the field of genetic breeding and biotechnology of chickens, wherein the SNP number of the SNP genetic marker is rs316497033, which corresponds to the 24015134 th site of the chromosome sense strand of the chicken reference genome Ga l us _ Ga l us-GRCg6 version sequence information No. 3 published in NCBI, and the basic group is A or G. The SNP genetic marker is beneficial to genetically improving the egg yolk weight of the laying hens and can be used for genome selection or molecular marker-assisted selection. The invention also provides application of the SNP genetic marker influencing the egg yolk weight of the chicken in chicken genetic breeding.
Description
Technical Field
The invention belongs to the field of chicken genetic breeding and biotechnology, and particularly relates to an SNP genetic marker influencing the egg yolk weight of chickens and application thereof.
Background
The consumption market puts new requirements on the breeding of laying hens, and more consumers prefer eggs with high yolk proportion because the yolk stores most of nutrient substances and flavor substances of the eggs. In order to meet the requirements of the market on the variety of laying hens, the research on the genetic structure of the yolk weight needs to be developed urgently to obtain candidate genes related to the yolk weight, improve the selection accuracy and accelerate the breeding progress.
Disclosure of Invention
In order to solve the breeding problem of laying hens with high egg laying yolk proportion, the invention provides an SNP genetic marker influencing the egg yolk weight of the laying hens, which is beneficial to genetically improving the egg yolk weight of the laying hens and can be used for genome selection or molecular marker-assisted selection.
The invention also provides application of the SNP genetic marker influencing the egg yolk weight of the chicken in chicken genetic breeding.
The invention is realized by the following technical scheme:
the application provides an SNP genetic marker influencing the yolk weight of chickens, the SNP number of the SNP genetic marker is rs316497033, which corresponds to the 24015134 th position (named as YW _ tag3) of the positive chain of chromosome 3 of sequence information of the chicken reference genome Gallus _ Gallus-GRCg6 published in NCBI, and the base is A or G.
Based on the same invention concept, the application provides the application of the SNP genetic marker influencing the egg yolk weight of the chicken in chicken genetic breeding.
Based on the same invention concept, the application provides an early selection method of the chicken vitellosis character, and the chicken vitellosis character is selected early based on the genotype of the SNP genetic marker.
Optionally, the method includes:
detecting the 24015134 th genotype of the sense chain of the No. 3 chromosome of the chicken to be detected;
early selection is carried out on the yolk weight traits of the chickens to be detected based on the genotype at 24015134 th site of the sense chain of the No. 3 chromosome, wherein the yolk weight of the AA genotype individuals is larger than that of the AG genotype individuals, and the yolk weight of the AG genotype individuals is larger than that of the GG genotype individuals.
Optionally, the detecting the genotype of the 24015134 th site of the sense strand of the chicken chromosome 3 to be detected specifically comprises:
carrying out PCR amplification on the genome DNA of the chicken to be detected by taking YW _ tag3f and YW _ tag3r as primers;
sequencing the PCR amplification product to obtain the 24015134 th genotype of the sense strand of the No. 3 chromosome of the chicken to be detected;
wherein the base sequence of the YW _ tag3f is shown in SEQ ID NO.1, and the base sequence of the YW _ tag3r is shown in SEQ ID NO. 2.
Based on the same inventive concept, the present application provides primers for detecting the SNP genetic marker, including two single-stranded DNAs: YW _ tag3f and YW _ tag3r, wherein the base sequence of the YW _ tag3f is shown as SEQ ID NO.1, and the base sequence of the YW _ tag3r is shown as SEQ ID NO. 2.
Based on the same inventive concept, the application provides an application of a primer for detecting the SNP genetic marker in chicken genetic breeding.
Based on the same inventive concept, the present application provides a kit comprising primers YW _ tag3f and YW _ tag3 r.
Based on the same inventive concept, the application provides the application of the kit in chicken genetic breeding.
One or more technical schemes in the invention at least have the following technical effects or advantages:
1. the SNP genetic marker provided by the invention can be used for genetically improving the egg yolk weight of laying hens by 0.55g through homozygous favorable alleles, can be used for genome selection or molecular marker-assisted selection, improves the genome selection accuracy and quickly obtains genetic progress.
2. The invention provides a primer for detecting the SNP genetic marker, the primer designed according to the SNP genetic marker is used for amplifying and identifying the genetic locus of a chicken to be detected, the specificity is strong, the accuracy rate is high, and a solid foundation is provided for the breeding of laying hens.
The foregoing description is only an overview of the technical solutions of the present invention, and the embodiments of the present invention are described below in order to make the technical means of the present invention more clearly understood and to make the above and other objects, features, and advantages of the present invention more clearly understandable.
Drawings
In order to more clearly illustrate the technical solutions in the present application, the drawings needed to be used in the description of the embodiments will be briefly introduced below, and it is obvious that the drawings in the following description are some embodiments of the present invention, and it is obvious for those skilled in the art to obtain other drawings without creative efforts.
FIG. 1 is a graph of yolk weight genetic characteristics analyzed using a stochastic regression model.
FIG. 2 is a Manhattan diagram of genetic markers associated with egg yolk weight in chickens.
FIG. 3 is a diagram of chicken yolk weight associated genetic marker QQ.
Detailed Description
The present invention will be described in detail below with reference to specific embodiments and examples, and the advantages and various effects of the present invention will be more clearly apparent therefrom. It will be understood by those skilled in the art that these specific embodiments and examples are for the purpose of illustrating the invention and are not to be construed as limiting the invention.
Throughout the specification, unless otherwise specifically noted, terms used herein should be understood as having meanings as commonly used in the art. Accordingly, unless defined otherwise, all technical and scientific terms used herein have the same meaning as commonly understood by one of ordinary skill in the art to which this invention belongs. If there is a conflict, the present specification will control.
Unless otherwise specifically stated, various raw materials, reagents, instruments, equipment and the like used in the present invention are commercially available or can be prepared by existing methods.
It should be further noted that the terms "comprises," "comprising," or any other variation thereof, are intended to cover a non-exclusive inclusion, such that a process, method, article, or apparatus that comprises a list of elements does not include only those elements but may include other elements not expressly listed or inherent to such process, method, article, or apparatus.
It is noted that, in this document, relational terms such as "first" and "second," and the like, may be used solely to distinguish one entity or action from another entity or action without necessarily requiring or implying any actual such relationship or order between such entities or actions.
In order to solve the technical problems, the general idea is as follows:
the yolk weight belongs to the function value character, can be measured for multiple times and can be expressed by a function equation, and the function value character is the current popular trend by applying a random regression model to analyze. In recent years, genetic evaluation work is carried out on egg yolk weight of laying hens by a random regression model by a team to obtain appropriate model parameters and genetic parameters (Guojun et al, analysis of egg yolk quality genetic parameters [ J ] by using the random regression model, 2016,39(1): 145-149.).
On the basis of the existing research, by means of phenotype data and genotype data of Dongxiang green-shell layer chicken-white legging resource population, random regression analysis and GWAS (global genome association research) analysis are integrated, and a laying chicken yolk weight genetic marker is explored. The GWAS method is used for researching the association between the base variation and the phenotypic value, can identify the genetic marker influencing the economic traits, and is particularly suitable for the traits which are difficult to measure, the late-stage traits of life bodies, the restrictive traits and the slaughtering traits. If the chicken yolk genetic marker can be screened by whole genome association analysis, the molecular marker-assisted breeding or whole genome selection can be used for rapidly acquiring genetic progress.
Based on the SNP genetic marker, the invention provides the SNP genetic marker influencing the egg yolk weight of the chicken and the application thereof.
The following examples are provided to illustrate the SNP genetic markers affecting the yolk weight of chicken.
Example 1
Random regression analysis yielded pseudophenotypic data:
the experimental chicken is from the resource group of laying hens of the poultry institute of Jiangsu, and the information about the group construction is detailed in the literature (Guomilitary et al, application of a stochastic regression model to analyze the genetic parameters of egg yolk quality of laying hens [ J ]]The Nanjing university of agriculture, 2016,39(1): 145-149.). Namely: using Dongxiang green-shell laying hens and white leghorns as parents, and obtaining F through positive and negative crossing1Generation, F2And (4) generation. The experimental chicken is raised in a single cage, mechanically fed and cleared of dung. Yolk weight data were measured at 40-60 weeks of age, every 4 weeks.
And preliminarily screening the pedigree records and the production data, removing obvious error and repeated data, removing outliers, removing less than 3 record individuals, and sorting into an Excel format. After data washing, 11759 records remain in the resource population yolk duplicate dataset. And determining that the batch and the production day age are listed as fixed effects through one-factor variance analysis. The yolk weight (covariance) components were then analyzed with the WOMBAT software along with genetic parameters. The genetic model formula is as follows:
wherein, yiklThe yolk weight of the Kth chicken of the ith week age in the ith batch; HYiIs a batch fixing effect; bmIs the mth fixed regression coefficient; a iskmIs the mth random regression coefficient of additive effect; p is a radical ofkmIs the mth random regression coefficient of the permanent environmental effect; z is a radical ofklmIs an embedded legendre polynomial covariate; e.g. of the typeiklIs the residual effect; n is1、n2、n3Are the embedding fixed effect, additive inheritance and permanent environmental effect legendre polynomial orders.
The invention adopts AIC criterion and BIC criterion to select the statistical model most suitable for describing the yolk weight and compares the statistical models so as to improve the accuracy of data analysis. Through model comparison and analysis, the additive genetic effect in the egg yolk weight random regression model is preferably embedded into a Legendre polynomial of 3 th order, the permanent environmental effect is preferably embedded into a Legendre polynomial of 4 th order, and the fixed regression term is preferably embedded into a Legendre polynomial of 2 th order. The residual error is treated by heterogenization and divided into 5 levels.
And the eigenvalue and eigenvector of the additive genetic matrix are obtained by R calculation. In order to obtain the characteristic equation, calculating lambdae, wherein E is a characteristic vector and lambada is a Legendre polynomial coefficient matrix. The characteristic curve corresponding to the egg yolk additive genetic effect of the layer resource population is shown in figure 1, the additive genetic 1 st characteristic curve is nearly linear, and the whole process is positive. The 2 nd characteristic curve shows a descending trend with increasing week age and a negative value after 50 weeks of age. The No. 3 characteristic curve shows cosine wave trend, 45-56 weeks old is a negative value, and the rest is a positive value. The 1 st characteristic coefficient of the additive genetic coefficient matrix is equivalent to the intercept of a yolk weight curve, and the biological meaning is the average yolk weight; the 2 nd characteristic coefficient is equivalent to the slope of the vitelline weight curve and is used for changing the trend of the vitelline weight curve. The invention lists the 1 st characteristic value as pseudo-phenotype data of GWAS analysis.
Example 2
Yolk-weight genome-wide association analysis
A disposable syringe is used for collecting about 2ml of blood sample from the vein of a test chicken wing, and the blood sample is placed into a BD anticoagulation tube (Bydi medical equipment Co., Ltd. Suzhou) and stored at 70 ℃. Extracting genome DNA from blood sample, detecting by 0.8% agarose electrophoresis and ultraviolet spectrophotometry, diluting DNA sample to 50 + -5 ng/μ l after qualified, and using for gene chip typing.
Chicken high-density gene chip using Onfei corporation
600K Chicken Genotyping Array, reference chipThe manual carries out the quality control of data, mainly include: performing quality control before parting by using APT software; quality control is carried out by PLINK, and SNP markers with detection rate lower than 0.97 and deviating from Hardy Weinberg balance are removed; analyzing information of metrics.R, SNP _ filter.R, SNP CR and FLD, and screening SNP; genotype filling was performed with BEAGLE. 435867 SNPs and 1512 samples remained after quality control for subsequent analysis.
Before the whole genome association analysis, multi-dimensional principal component analysis is carried out to eliminate false positive, and the former 5 principal components are used as covariate parameters to be added into the fixed effect of the genetic model. The independent test estimation of each SNPs locus is calculated by using an R script "simpleM" method, and 59308 independent markers are obtained. Correction was performed using Bonferroni to obtain a significant genome threshold of 8.43 × 10-7The genome proposal threshold is 1.69X 10-5. The yolk reprint phenotype values obtained in example 1 were analyzed by a mixed linear model to obtain the P-value for the significance test of each SNPs marker. The matrix expression of the linear model is as follows,
y＝Wα+xβ+u+ε
wherein y represents a sample phenotype value vector; w represents a covariance matrix; alpha is an intercept vector; x-tagged genotype vector; u is a random effect vector; ε is the residual error.
The genome-wide association analysis was performed on the first characteristic coefficient of the additive genetic effect of the yolk of 1512 chickens, and the results are shown in fig. 2 and 3. From the manhattan chart, the chicken chromosome 3 has a genome significant level marker, and chromosomes 1, 2, 15 and 22 have genome suggested markers. The QQ diagram further verifies that the GWAS result is reliable. Summarizing the screened genetic markers of yolk weight:
TABLE 1 genomic significance level of genetic markers
Note that: the marker chromosomal physical location is referenced to the chicken whole genome (Gallus galllus GRCg 6).
Example 3
Verification of genetic markers
The SNP genetic marker is applied to carry out association analysis on resource groups of Dongxiang green-shell laying hens, white leghorns. The specific operation steps are as follows:
1) PCR primers: DNA template sequence information was downloaded from the NCBI website and PCR amplification primers were designed using primer premier software, with primer information as shown in Table 2. PCR primers were synthesized by Biotechnology engineering (Shanghai) Ltd.
TABLE 2 amplification primers for detection of the yolk weight genetic marker
2) Extracting genome DNA: 1478 parts of genome DNA of the blood sample is extracted by a CTAB method, and PCR amplification is carried out after the genome DNA is detected by an ultraviolet spectrophotometer and detected by agarose electrophoresis.
3) And (3) PCR amplification process:
reaction system: the 10. mu.l system included 50ng of the identification material DNA template, 0ng of each of the forward and reverse primers, 5. mu.L of 2 XPower Taq MasterMix, and the remaining volume was made up with ultrapure water.
Reaction procedure: firstly, denaturation at 94 ℃ for 30s, annealing at 51-54 ℃ for 30s, and extension at 72 ℃ for 30s for 5 cycles; then denaturation at 94 ℃ for 30s, annealing at 51-54 ℃ for 30s, and extension at 72 ℃ for 30s for 30 cycles; extending for 5min at 72 ℃, and storing at 4 ℃.
4) The amplified product is sent to a sequencing company for sequence polymorphism detection.
5) Correlation analysis: the individuals tested all had genotypes and average yolk weights at 40-60 weeks of age, and correlation analysis was performed. The analysis results are shown in table 3, and GG is the dominant genotype of the genetic marker YW _ tag 3.
TABLE 3 genetic markers associated with mean yolk weight analysis results
And screening to obtain the SNP yolk weight related genetic marker through random regression analysis and whole genome association analysis. Verification experiments show that the selection of dominant allele type (GG) can improve the egg yolk weight of laying hens.
The primer combination can be used for breeding to improve the yolk weight and can also be used for preparing a kit.
One or more technical solutions in the present application at least have the following technical effects or advantages:
(1) the SNP genetic marker influencing the egg yolk weight of the chicken is beneficial to genetically improving the egg yolk weight of the laying hens, can improve the average egg yolk weight by 0.55g through homozygous favorable alleles, can be used for genome selection or molecular marker-assisted selection, improves the accuracy of genome selection and quickly obtains genetic progress.
(2) The primer for detecting the SNP genetic marker is designed according to the SNP genetic marker, is used for amplifying and identifying the genetic locus of a chicken to be detected, has strong specificity and high accuracy, and provides a solid foundation for the breeding of laying hens.
Finally, it should also be noted that the terms "comprises," "comprising," or any other variation thereof, are intended to cover a non-exclusive inclusion, such that a process, method, article, or apparatus that comprises a list of elements does not include only those elements but may include other elements not expressly listed or inherent to such process, method, article, or apparatus.
While preferred embodiments of the present invention have been described, additional variations and modifications in those embodiments may occur to those skilled in the art once they learn of the basic inventive concepts. Therefore, it is intended that the appended claims be interpreted as including preferred embodiments and all such alterations and modifications as fall within the scope of the invention.
It will be apparent to those skilled in the art that various changes and modifications may be made in the present invention without departing from the spirit and scope of the invention. Thus, if such modifications and variations of the present invention fall within the scope of the claims of the present invention and their equivalents, the present invention is also intended to include such modifications and variations.
Sequence listing
<110> scientific research institute for poultry in Jiangsu province
Xueyi Technology (Chengdu) Co., Ltd.
<120> SNP genetic marker influencing egg yolk weight of chicken and application thereof
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<213> 1 (Artificial sequence)
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Claims (9)
1. An SNP genetic marker affecting the egg yolk weight of a chicken, which has the SNP number rs316497033 corresponding to the 24015134 th position of the chromosome sense strand of the chicken reference genome Gallus _ gal lus lu-GRCg 6 version sequence information 3 published in NCBI, wherein the base is A or G.
2. Use of a SNP genetic marker affecting the egg yolk weight of a chicken according to claim 1 in genetic breeding of chicken.
3. A method for early selection of a chicken vitellogenin, which comprises early selection of a chicken vitellogenin based on the genotype of the SNP genetic marker of claim 1.
4. The method for early selection of the egg yolk weight trait of the chicken according to claim 3, wherein the method comprises the following steps:
detecting the 24015134 th genotype of the sense chain of the No. 3 chromosome of the chicken to be detected;
early selection is carried out on the yolk weight traits of the chickens to be detected based on the genotype at 24015134 th site of the sense chain of the No. 3 chromosome, wherein the yolk weight of the AA genotype individuals is larger than that of the AG genotype individuals, and the yolk weight of the AG genotype individuals is larger than that of the GG genotype individuals.
5. The method for early selection of the yolk weight trait of the chicken as claimed in claim 4, wherein the detecting the genotype of the 24015134 th site of the sense chain of chromosome 3 of the chicken to be detected specifically comprises:
carrying out PCR amplification on the genome DNA of the chicken to be detected by taking YW _ tag3f and YW _ tag3r as primers;
sequencing the PCR amplification product to obtain the 24015134 th genotype of the sense strand of the No. 3 chromosome of the chicken to be detected;
wherein the base sequence of the YW _ tag3f is shown in SEQ ID NO.1, and the base sequence of the YW _ tag3r is shown in SEQ ID NO. 2.
6. The primer for detecting the SNP genetic marker according to claim 1, comprising two single-stranded DNAs: YW _ tag3f and YW _ tag3r, wherein the base sequence of the YW _ tag3f is shown as SEQ ID NO.1, and the base sequence of the YW _ tag3r is shown as SEQ ID NO. 2.
7. Use of the primer of claim 6 in genetic breeding of chicken.
8. A kit comprising the primer of claim 6.
9. Use of the kit of claim 8 in genetic breeding of chicken.
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Cited By (3)
| Publication number | Priority date | Publication date | Assignee | Title |
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| CN115927647A (en) * | 2022-07-13 | 2023-04-07 | 江苏省家禽科学研究所 | SNP genetic marker related to egg weight curve slope and application thereof |
| CN117070639A (en) * | 2023-08-08 | 2023-11-17 | 江苏省家禽科学研究所 | Application of SNP genetic marker related to total chicken egg laying weight in chicken genetic breeding |
| CN117210570A (en) * | 2023-08-08 | 2023-12-12 | 江苏省家禽科学研究所 | Application of SNP genetic marker related to eggshell strength in genetic breeding of chickens |
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| CN106701919A (en) * | 2016-11-25 | 2017-05-24 | 浙江省农业科学院 | Molecular genetic maker for egg quality of laying hen and application of molecular genetic marker |
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Cited By (6)
| Publication number | Priority date | Publication date | Assignee | Title |
|---|---|---|---|---|
| CN115927647A (en) * | 2022-07-13 | 2023-04-07 | 江苏省家禽科学研究所 | SNP genetic marker related to egg weight curve slope and application thereof |
| CN115927647B (en) * | 2022-07-13 | 2023-08-01 | 江苏省家禽科学研究所 | SNP genetic marker related to egg heavy curve slope and application thereof |
| CN117070639A (en) * | 2023-08-08 | 2023-11-17 | 江苏省家禽科学研究所 | Application of SNP genetic marker related to total chicken egg laying weight in chicken genetic breeding |
| CN117210570A (en) * | 2023-08-08 | 2023-12-12 | 江苏省家禽科学研究所 | Application of SNP genetic marker related to eggshell strength in genetic breeding of chickens |
| CN117070639B (en) * | 2023-08-08 | 2024-02-02 | 江苏省家禽科学研究所 | Application of SNP genetic marker related to total chicken egg laying weight in chicken genetic breeding |
| CN117210570B (en) * | 2023-08-08 | 2024-02-23 | 江苏省家禽科学研究所 | Application of SNP genetic marker related to eggshell strength in genetic breeding of chickens |
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