CN115992248B - Molecular marker related to muscovy duck propagation traits and application thereof - Google Patents
Molecular marker related to muscovy duck propagation traits and application thereof Download PDFInfo
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- Y—GENERAL TAGGING OF NEW TECHNOLOGICAL DEVELOPMENTS; GENERAL TAGGING OF CROSS-SECTIONAL TECHNOLOGIES SPANNING OVER SEVERAL SECTIONS OF THE IPC; TECHNICAL SUBJECTS COVERED BY FORMER USPC CROSS-REFERENCE ART COLLECTIONS [XRACs] AND DIGESTS
- Y02—TECHNOLOGIES OR APPLICATIONS FOR MITIGATION OR ADAPTATION AGAINST CLIMATE CHANGE
- Y02P—CLIMATE CHANGE MITIGATION TECHNOLOGIES IN THE PRODUCTION OR PROCESSING OF GOODS
- Y02P60/00—Technologies relating to agriculture, livestock or agroalimentary industries
- Y02P60/80—Food processing, e.g. use of renewable energies or variable speed drives in handling, conveying or stacking
- Y02P60/87—Re-use of by-products of food processing for fodder production
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Abstract
The application discloses a molecular marker related to a muscovy duck propagation trait and application thereof, and belongs to the technical field of biology. The molecular marker comprises SNP3 and SNP4, wherein the SNP3 is positioned in a sequence shown as SEQ ID NO:1, wherein g.254G > A site of the nucleotide sequence shown in the formula 1 is mutated into G or A; the SNP4 is located as set forth in SEQ ID NO:1, wherein g.270C > T site of the nucleotide sequence shown in 1, and the base is mutated into C or T. According to the application, through analyzing the TAT gene, the exon region of the gene is found to have a plurality of SNP loci which are obviously related to the reproductive performance of the muscovy ducks, a novel SNP molecular marker is provided for MAS, and the molecular marker can accurately identify the reproductive traits of the muscovy ducks at different ages so as to provide scientific data for the breeding of the muscovy ducks.
Description
Technical Field
The application relates to the technical field of biology, in particular to a molecular marker related to the reproduction traits of Muscovy ducks and application thereof.
Background
The muscovy ducks are called as tumor head ducks, foreign ducks, american ducks, fragrant ducks, wild gooses, musk ducks and the like. The Muscovy duck is of Duck genus of Duck family, and Duck species of Duck genus of Duck family. The feather color of the Muscovy ducks in China at present mainly comprises black and white. In addition, there are small amounts of black and white mixed plumes. The introduced muscovy ducks in China have a history of over 200 years, and are cultivated in a plurality of places in China at present. In the breeding season, male muscovy ducks can emit musk odor, so the muscovy ducks are also called musk ducks. Female muscovy ducks have nest-like properties, the utilization period of the female ducks is generally two years, and the utilization period of the male ducks is generally 1-1.5 years. The muscovy duck is one of excellent lean-type duck varieties, and has the characteristics of thin skin, tenderness, high growth speed, coarse feeding resistance, good liver production performance and the like. The characteristics of the qualified number of eggs, the egg yield of 300 days old and the like are key indexes for identifying the reproductive performance of the muscovy ducks. The single nucleotide polymorphism (Single Nucleotide Polymorphism, SNP) refers to a genomic DNA polymorphism caused by single base changes such as insertion, deletion, transversion and transition of a genomic DNA sequence, and has the characteristics of stable inheritance, easy detection and the like. SNP can be used for Molecular Mark-assistt Selection (MAS) to improve seed Selection accuracy and breeding effect.
Tyrosine aminotransferase (tyrosine aminotransferase, TAT) is the rate limiting enzyme in the first stage of the tyrosine degradation process and converts tyrosine ammonia to hydroxyphenylacetone. Previous studies have shown that TAT is a specifically expressed enzyme in the liver, with the highest activity. However, in recent years, results show that TAT is also expressed in reproductive organs such as oviducts, testes, ovaries and the like. TAT has also been studied as a gene induced by estrogen during oviduct development and differentiation in chicks. Multiple SNP loci of TAT gene are obviously related to the reproductive performance of Muscovy ducks. Therefore, a novel SNP molecular marker can be provided by combining with the reproductive performance index of the Muscovy ducks.
Disclosure of Invention
The application aims to provide a molecular marker related to the reproduction traits of muscovy ducks and application thereof, so as to solve the problems in the prior art, and the molecular marker can accurately identify the reproduction traits of muscovy ducks of different ages so as to provide scientific data for breeding the muscovy ducks.
In order to achieve the above object, the present application provides the following solutions:
the application provides a molecular marker related to a muscovy duck propagation trait, which comprises SNP3 and SNP4, wherein the SNP3 is positioned in a sequence shown as SEQ ID NO:1, wherein g.254G > A site of the nucleotide sequence shown in the formula 1 is mutated into G or A; the SNP4 is located as set forth in SEQ ID NO:1, wherein g.270C > T site of the nucleotide sequence shown in 1, and the base is mutated into C or T.
The application also provides application of the molecular marker detection reagent in identifying the reproduction traits of the Muscovy ducks.
The application also provides a primer group for detecting the molecular marker, and the nucleotide sequence of the primer group is shown as SEQ ID NO: 2-3.
The application also provides application of the primer group in identifying the reproduction traits of the muscovy ducks or preparing products for identifying the reproduction traits of the muscovy ducks.
The application also provides a kit for identifying the reproduction traits of the muscovy ducks, which comprises the primer set.
The application also provides a method for identifying the reproduction traits of the muscovy ducks, which comprises the following steps:
(1) Extracting the genomic DNA of the muscovy duck to be detected, and amplifying by using the primer group to obtain an amplified product;
(2) Sequencing the amplified product, and detecting the genotype of the molecular marker;
(3) And judging the reproductive character of the muscovy ducks to be detected according to the genotyping result.
Further, in the step (3), the propagation property is optimal if the genotype of the SNP3 molecular marker is AA and/or the genotype of the SNP4 molecular marker is CT.
Further, in step (1), the amplification system for amplifying is: template DNA 2. Mu. L, mix 26. Mu.L and 2. Mu.L of each of the upstream and downstream primers.
Further, in step (1), the amplification reaction procedure is: pre-denaturation at 98 ℃ for 3min, denaturation at 98 ℃ for 10s, annealing at 60 ℃ for 10s, extension at 72 ℃ for 15s,15 cycles, each cycle annealing temperature being reduced by 1 ℃; denaturation at 98℃for 10s, annealing at 50℃for 10s, extension at 72℃for 15s,25 cycles; finally, the extension is carried out for 3min at 72 ℃.
The application also provides application of the molecular marker or the primer group or the kit in breeding of the muscovy duck reproductive traits.
The application discloses the following technical effects:
according to the application, through analyzing a TAT gene, a plurality of SNP loci which are obviously related to the reproductive performance of the Muscovy ducks are found in an exon region of the gene, a novel SNP molecular marker is provided for MAS, and experiments prove that SNP3 (g.254G > A locus) is obviously related to the egg yield of 28, 29, 30, 34, 35, 36, 37, 38, 39 and 40 weeks old (p < 0.05), and is extremely obviously related to the egg yield of 31, 32 and 33 weeks old (p < 0.01); SNP4 (g.270C > T site) was significantly correlated with the presence of 35, 36, 37, 38, 39, 40 week old egg yield (p < 0.05). The association of other SNP sites with reproductive traits did not reach significant levels (p > 0.05). Therefore, the molecular marker provided by the application can accurately identify the propagation characters of the muscovy ducks at different ages so as to provide scientific data for the breeding of the muscovy ducks.
Drawings
In order to more clearly illustrate the embodiments of the present application or the technical solutions in the prior art, the drawings that are needed in the embodiments will be briefly described below, and it is obvious that the drawings in the following description are only some embodiments of the present application, and other drawings may be obtained according to these drawings without inventive effort for a person skilled in the art.
FIG. 1 is a diagram showing different genotypes of SNP1-SNP6 in the 5' UTR region of TAT gene.
Detailed Description
Various exemplary embodiments of the application will now be described in detail, which should not be considered as limiting the application, but rather as more detailed descriptions of certain aspects, features and embodiments of the application.
It is to be understood that the terminology used herein is for the purpose of describing particular embodiments only and is not intended to be limiting of the application. In addition, for numerical ranges in this disclosure, it is understood that each intermediate value between the upper and lower limits of the ranges is also specifically disclosed. Every smaller range between any stated value or stated range, and any other stated value or intermediate value within the stated range, is also encompassed within the application. The upper and lower limits of these smaller ranges may independently be included or excluded in the range.
Unless otherwise defined, 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 application belongs. Although only preferred methods and materials are described herein, any methods and materials similar or equivalent to those described herein can be used in the practice or testing of the present application. All documents mentioned in this specification are incorporated by reference for the purpose of disclosing and describing the methods and/or materials associated with the documents. In case of conflict with any incorporated document, the present specification will control.
It will be apparent to those skilled in the art that various modifications and variations can be made in the specific embodiments of the application described herein without departing from the scope or spirit of the application. Other embodiments will be apparent to those skilled in the art from consideration of the specification of the present application. The specification and examples of the present application are exemplary only.
As used herein, the terms "comprising," "including," "having," "containing," and the like are intended to be inclusive and mean an inclusion, but not limited to.
Examples
1. Materials and methods
1.1 animal sample
652 female white ducks (Shandong's Shandong Mars duck farm, south China, guangdong) were selected at 60 weeks of age. Subcutaneous venous blood 2mL was collected and stored at-80 ℃ and used as a DNA extraction sample. And recording family information and reproduction characters such as open date (AFE), daily egg yield, total egg yield, qualified egg yield and the like of the selected population.
1.2 major reagents
Blood sample DNA extraction kit (brand: OMEGA; product number: D3392; guangzhou Hi-Bo Biotechnology Co., ltd.), gold plate Mix (green) (brand: optimaceae; product number: TSE101; beijing Optimaceae Biotechnology Co., ltd.), DNA marker (brand: novezan; product number: MD101; jiangsu Norvazan Biotechnology Co., ltd.), high purity low electroosmotic agarose (brand: optimaceae; product number: TSJ001; beijing Optimaceae Biotechnology Co., ltd.).
1.3 Experimental methods
1.3.1 primer design
Primers were designed based on the sequence of the green head wild duck (Mallard) TAT gene (ENSAPLG 00000009051) published by Ensemble using NCBI (National Center for Biotechnology Information Search database) Primer-BLAST tool, offered by the prime synthesis service by the department of biotechnology, inc. The primer sequence-related information is shown in Table 1.
TABLE 1 PCR amplification primer sequences
1.3.2 DNA extraction of blood samples
Blood sample DNA is extracted by reference to a blood sample DNA extraction kit operating manual.
1.3.3 PCR amplification of the TAT Gene exon sequences
Blood sample genomic DNA of 652 half-sibling white muscovy ducks (same male parent) above was used as a template, and the following reaction system was followed: template DNA 2. Mu.L, gold medal Mix 26. Mu.L, upstream primer 2. Mu.L, downstream primer 2. Mu.L.
The reaction procedure: pre-denaturation at 98℃for 3min, denaturation at 98℃for 10s, annealing at 60℃for 10s, extension at 72℃for 15s (15 cycles of annealing temperature minus 1℃for each cycle), denaturation at 98℃for 10s, annealing at 50℃for 10s, extension at 72℃for 15s (25 cycles of annealing), final extension at 72℃for 3min, and preservation at 4 ℃. PCR products were submitted to Sanger sequencing by the prime biotechnology company, inc.
1.3.4 SNPs determination and genotyping
Analysis of sequence peak patterns was performed on Sanger sequencing results of PCR products using Snapgene software to determine potential SNP sites. Genotyping was performed by comparing sequencing data for each sample by the SeqMan tool of DNAstar 11 software.
1.3.5 genotype and reproductive trait association analysis
Analyzing a plurality of SNP loci of the TAT gene by utilizing Haploview 4.2 software to obtain loci in haplotype blocks, and analyzing distribution of loci in haplotype blocks in 652 white ducks individuals by utilizing PHASE 2.1 software to obtain haplotype data.
And carrying out association analysis on the SNPs loci and propagation trait data of individuals corresponding to genotypes by adopting a SAS 9.4GLM program package.
2. Results
2.1 PCR amplification of TAT gene exon sequence and SNP screening
Selecting 652 white Muscovy ducks, performing PCR amplification by taking blood sample DNA of each individual as a template, performing Sanger sequencing on the obtained PCR product (the nucleotide sequence is shown as SEQ ID NO: 1), and performing comparison analysis on the sequenced peak diagram, wherein 6 SNP loci are detected in total, and the PCR product comprises the following steps: g.120G > T (SNP 1), g.122G > A (SNP 2), g.254G > A (SNP 3), g.270C > T (SNP 4), g.312G > A (SNP 5) and g.3412 > A (SNP 6), as shown in FIG. 1.
SEQ ID NO:1:
TGGCTAGATCTTGTGTGAGGCAGCAGGCAGAGCTGTGTCCAGCCAGCCCCACAACCCCCTGCCTGTAGGCAGCTGCTGTCCTGCTGCTTCGCTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTCTTCACAGACCCCCTAAGCTCATGGAAAGAAGCAGACACTTCTCTCTTTTCCACTGCAGCTCCCACACTCTCTGGTATCTGGTGTCTGTGGTCTCCATATACTCAGTATCTTCACCCCACAGTGGTCTGTGCTGCCCATGAACAAGCTGCAGGCAGGGGCACATGGCTGATTCTGCACCAGGACCCGCAGCCTACGGCCCTGTGTGGCCAGTAGCTCCCGTGCTGCCTGCACTCCCCCTCTGGGGCAGGAGATGGTCGTGGTCTCAGAGGACAAGAGACACTCACCCACCTCTCACCTGTCTTAACTTAGGAGGTCAGAGCTCTTTATACCAAGCCCTTTGTGCAACAAAGGGAGTAAGTTATTGTGAC。
2.2 analysis of association of SNP loci with exon sequences of TAT Gene and propagation Properties
The 6 SNP loci were analyzed for association with reproductive traits (total number of eggs, number of pass of eggs, 300-day-old egg yield, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57-week-old egg yield, AFE and 50-day-open egg yield).
As shown in table 2, the results show that g.254g > a locus is significantly correlated with the presence of 28, 29, 30, 34, 35, 36, 37, 38, 39, 40 weeks old and AFE (p < 0.05), is significantly correlated with the presence of 31, 32, 33 weeks old egg yield (p < 0.01), and most of the traits of AA genotype are better than AG/GG genotype; the g.270C > T locus is significantly correlated with egg production at 35, 36, 37, 38, 39, 40 weeks of age (p < 0.05), and each trait of CT genotype is superior to CC/TT genotype. The association of other SNP sites with reproductive traits did not reach significant levels (p > 0.05).
TABLE 2 association of SNP loci with reproductive status
The above embodiments are only illustrative of the preferred embodiments of the present application and are not intended to limit the scope of the present application, and various modifications and improvements made by those skilled in the art to the technical solutions of the present application should fall within the protection scope defined by the claims of the present application without departing from the design spirit of the present application.
Claims (6)
1. The application of a molecular marker related to the reproduction traits of the muscovy ducks in identifying the egg yield traits of the muscovy ducks is characterized in that the molecular marker is positioned in the TAT gene of the muscovy ducks and corresponds to the eighth position in the CCTGCAGCTTGTTCA sequence, and the base mutation is C or T; the molecular markers are obviously related to the egg yield of 35, 36, 37, 38, 39 and 40 weeks old, and each character of the CT genotype is superior to that of the CC and TT genotypes.
2. The use according to claim 1, wherein the genotyping detection product is a primer set having a nucleotide sequence set forth in SEQ ID NO: 2-3.
3. The use according to claim 1, wherein the genotyping detection product is a kit comprising the primer set of claim 2.
4. The method for identifying the egg yield traits of the muscovy ducks is characterized by comprising the following steps of:
(1) Extracting the genomic DNA of the muscovy duck to be detected, and amplifying by using the primer set in the claim 2 to obtain an amplified product;
(2) Sequencing the amplified product, detecting the genotype of the molecular marker of claim 1;
(3) Judging the egg yield characteristics of the muscovy ducks to be detected according to the genotyping result; the molecular markers are obviously related to the egg yield of 35, 36, 37, 38, 39 and 40 weeks old, and each character of the CT genotype is superior to that of the CC and TT genotypes.
5. The method of claim 4, wherein in step (1), the amplified amplification system is: template DNA 2. Mu. L, mix 26. Mu.L and 2. Mu.L of each of the upstream and downstream primers.
6. The method of claim 4, wherein in step (1), the amplified reaction procedure is: pre-denaturation at 98 ℃ for 3min, denaturation at 98 ℃ for 10s, annealing at 60 ℃ for 10s, extension at 72 ℃ for 15s,15 cycles, each cycle annealing temperature being reduced by 1 ℃; denaturation at 98℃for 10s, annealing at 50℃for 10s, extension at 72℃for 15s,25 cycles; finally, the extension is carried out for 3min at 72 ℃.
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CN114350818A (en) * | 2022-01-11 | 2022-04-15 | 华南农业大学 | Prolactin gene SNP molecular marker related to egg laying traits of Muscovy ducks and application thereof |
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Title |
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