CN117587133A - SNP locus combination for identifying goose variety and identification method thereof - Google Patents

SNP locus combination for identifying goose variety and identification method thereof Download PDF

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CN117587133A
CN117587133A CN202311551426.1A CN202311551426A CN117587133A CN 117587133 A CN117587133 A CN 117587133A CN 202311551426 A CN202311551426 A CN 202311551426A CN 117587133 A CN117587133 A CN 117587133A
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goose
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朱春红
章双杰
李慧芳
陶志云
刘宏祥
刘向萍
王志成
宋卫涛
徐文娟
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Jiangsu Institute Poultry Sciences
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Abstract

The invention discloses SNP locus combination for identifying a goose variety and an identification method thereof, and belongs to the technical field of biology. The invention screens out DA1P to DA15P 15 SNP loci, utilizes primer combinations for amplifying the SNP loci to determine genotypes of all loci, and judges the probability that the individual belongs to a goose according to the Bayesian theorem. Through experimental verification, the combined use of 15 SNP loci is proved to judge whether an individual to be detected belongs to a goose, and when the probability is greater than 0.95, the goose is judged to be a goose, and the accuracy rate can reach 100%. The method for identifying the goose variety is simple and convenient to operate and high in accuracy, and can effectively strike the degree of flooding of the counterfeit goose in the market.

Description

SNP locus combination for identifying goose variety and identification method thereof
Technical Field
The invention relates to the technical field of biology, in particular to SNP locus combinations for identifying a goose variety and an identification method thereof.
Background
The goose is a local variety in Hainan province, belongs to medium-sized goose species, has the characteristics of coarse feeding resistance, strong disease resistance, egg production in four seasons, delicious meat quality and the like, and has a large development and utilization prospect. At present, more false geese and hybrid individuals of the geese and other varieties are sold in the market in a masquerading way, so that certain impact is caused to the pure-bred individual market of the geese, and the brand of the geese is seriously influenced. Therefore, it is necessary to provide a product and a method for effectively and accurately identifying the variety of the swan.
The existing method for identifying the goose in the market mainly depends on appearance observation. The observation subjectivity is strong, the identification error rate is high, and incorrect classification and identification are easy to cause particularly when the hybrid offspring of the swan and other varieties of swans are identified. And the local variety geese are similar when just hatching, and the identification error rate is higher.
The single nucleotide polymorphism (Single nucleotide polymorphism, SNP) mainly refers to DNA sequence polymorphism caused by single nucleotide variation at genome level, and has the characteristics of rich sites, wide distribution, high genetic stability, representativeness, convenience and rapidness in detection and the like. SNP markers, which utilize specific SNP loci with large variety variability in the genomic DNA of individuals to carry out variety identification through genotypes of different locus combinations, and the identification result is more objective and accurate. In view of the above, development of a product and a method for effectively and accurately identifying a variety of a goose in scientific research and practice are urgently needed, and the method is applied to the variety identification work of the goose.
Disclosure of Invention
The invention aims to provide an SNP locus combination for identifying a goose variety and an identification method thereof, so as to solve the problems in the prior art, and the genotype of 15 SNP loci of the goose is detected to jointly judge whether an individual to be detected belongs to the goose, and the method is simple and convenient to operate, high in accuracy and capable of effectively striking the flooding degree of the fake goose in the market.
In order to achieve the above object, the present invention provides the following solutions:
the invention provides a primer combination for identifying a goose variety, wherein the primer combination is used for amplifying SNP locus combination shown in DA1P-DA15P, and the SNP locus combination shown in DA1P-DA15P is as follows:
DA1P is located at 8129687 on NW_025927668.1 chromosome and has polymorphism A or C;
DA2P is located at 926886 on NW_025927673.1 chromosome and has polymorphism C or G;
DA3P is located at 936602 on NW_025927673.1 chromosome and has G or C polymorphism;
DA4P is located at 945751 on NW_025927673.1 chromosome and has polymorphism C or A;
DA5P is located at 946693 on NW_025927673.1 chromosome and has a polymorphism of T or C;
DA6P is located at 951840 on NW_025927673.1 chromosome and has polymorphism A or G; DA7P is located at 963963 on NW_025927673.1 chromosome and has G or C polymorphism; DA8P is located at 970250 on NW_025927673.1 chromosome and has a polymorphism of G or A; DA9P is located at 971259 on NW_025927673.1 chromosome and has a polymorphism of T or A; DA10P is located at 983590 on NW_025927673.1 chromosome and has polymorphism T or A; DA11P is located at 985387 on NW_025927673.1 chromosome and has polymorphism C or T; DA12P is located at 4763516 on NW_025927679.1 chromosome and has a polymorphism of T or C; DA13P is located at 1202481 on NW_025927866.1 chromosome, and its polymorphism is A or C; DA14P is located at 469618 on NW_025927879.1 chromosome and has a polymorphism of T or C; DA15P is located at position 471621 on the NW_025927879.1 chromosome and has a polymorphism of C or T. Preferably, the amplification primer combination of the SNP locus combination shown in DA1P-DA15P is as follows: DA1F:5'-TTAATTGCGTGCATCGAGCC-3' (SEQ ID NO: 1);
DA1R：5’-GTGATGGAAAAGGCCAGTGC-3’(SEQ ID NO：2)；DA2F：5’-CAGTTGGCTAAGCTGAGGGTG-3’(SEQ ID NO：3)；
DA2R：5’-GTTTGGATTCTGGGTCTCCCC-3’(SEQ ID NO：4)；
DA3F：5’-CTGACCTATCTGCACAGGGC-3’(SEQ ID NO：5)；
DA3R：5’-TCTGGGGCAGACAAGTGAAC-3’(SEQ ID NO：6)；
DA4F：5’-TACTTCGTTGTTGGTGACCCT-3’(SEQ ID NO：7)；DA4R：5’-TTGGCCCAACCCATAAAACAC-3’(SEQ ID NO：8)；DA5F：5’-GCATGAGCCATGCAGAGTTTC-3’(SEQ ID NO：9)；DA5R：5’-AAAGTGCCAGAAGAGTATAGCCAA-3’(SEQ ID NO：10)；
DA6F：5’-TGCCTGTGTCCCATTGAAGT-3’(SEQ ID NO：11)；DA6R：5’-AGCAAGCGCAGAGCAAAATC-3’(SEQ ID NO：12)；
DA7F：5’-CTCTGCCCCATGAGCGTTAC-3’(SEQ ID NO：13)；DA7R：5’-TGGAGCTATGAGTGCCAAAGAA-3’(SEQ ID NO：14)；
DA8F：5’-GGTGTCAGGGGCTCTTTTCA-3’(SEQ ID NO：15)；
DA8R：5’-CATCAGTACCCAGCTCTGCC-3’(SEQ ID NO：16)；DA9F：5’-AATTTGGACGGCACCTCACA-3’(SEQ ID NO：17)；DA9R：5’-ATGGGCTCCCAGAAAGGGAA-3’(SEQ ID NO：18)；DA10F：5’-AACCATAGCTCAGGTTTGCAC-3’(SEQ ID NO：19)；
DA10R：5’-GAGCCATCAGAGCTAAAAGCAAG-3’(SEQ ID NO：20)；
DA11F：5’-TGCCTCTTGCAGTTCCATCAG-3’(SEQ ID NO：21)；
DA11R：5’-ACAAGGCAAAAAGTGGACATGC-3’(SEQ ID NO：22)；
DA12F：5’-CGGTATTATTGCAGTGCGGG-3’(SEQ ID NO：23)；
DA12R：5’-TCTTACACGGTGGCACGAAT-3’(SEQ ID NO：24)；
DA13F：5’-GAGTAAGAGCACCTGGCTGG-3’(SEQ ID NO：25)；
DA13R：5’-ATCTGGAGGCTCAGGAGAGG-3’(SEQ ID NO：26)；
DA14F：5’-TCTGCAGAGCTGTCACTTCA-3’(SEQ ID NO：27)；
DA14R：5’-CTCCCCGGCTTCATTGACTT-3’(SEQ ID NO：28)；
DA15F：5’-CAGGGGACTGTGCTATGGTG-3’(SEQ ID NO：29)；
DA15R：5’-GTTCTCACACATGCCAGGGA-3’(SEQ ID NO：30)。
the invention also provides a method for identifying the variety of the swan, which comprises the following steps:
extracting total DNA of a goose genome to be detected;
taking the total DNA as a template, and carrying out PCR amplification by using the primer combination to obtain an amplification product;
sequencing the amplification product, and judging genotypes of sites shown by DA1P to DA 15P;
and judging whether the goose to be detected belongs to a goose in the goose mounting state according to the genotype determination result.
Preferably, the probability that the goose to be detected belongs to the goose mounting is judged according to the Bayesian theorem, and the calculation formula is as follows:
the probability that the individual belongs to non-goose is
Wherein p is i Representing the frequency of the corresponding genotype of the goose variety aiming at the ith SNP in the SNP locus; q i The i-th SNP in the SNP locus is indicated, and the average frequencies of genotypes corresponding to other varieties are indicated.
Preferably, in order to ensure accuracy according to the calculation result, 0.95 is taken as a threshold value, and the probability of belonging to the goose is greater than or equal to 0.95, and the goose is judged to be the goose; judging that the non-goose is not mounted if the probability of the non-goose is more than or equal to 0.95; if less than 0.95, only one possibility can be determined, for example, the probability of belonging to a goose is 0.85, and only 85% of the possibility is considered to belong to the goose.
Preferably, the genotypes of the sites shown by DA1P to DA15P in the geese and other varieties, and the average frequency of genotypes are as follows:
DA1P site: when the genotype is AA, the genotype frequency of the goose is 0.72, and the genotype frequency of other varieties is 0.02; when the genotype is AC, the genotype frequency of the goose is 0.26, and the genotype frequency of other varieties is 0.21; when the genotype is CC, the genotype frequency of the goose is 0.02, and the genotype frequency of other varieties is 0.77;
DA2P site: when the genotype is CC, the genotype frequency of the goose is 0.49, and the genotype frequency of other varieties is 0.00; when the genotype is CG, the genotype frequency of the goose is 0.42, and the genotype frequency of other varieties is 0.06; when the genotype is GG, the genotype frequency of the goose is 0.09, and the genotype frequency of other varieties is 0.94;
DA3P site: when the genotype is GG, the genotype frequency of the goose is 0.56, and the genotype frequency of other varieties is 0.00; when the genotype is GC, the genotype frequency of the goose is 0.38, and the genotype frequency of other varieties is 0.07; when the genotype is CC, the genotype frequency of the goose is 0.06, and the genotype frequency of other varieties is 0.93;
DA4P site: when the genotype is CC, the genotype frequency of the goose is 0.49, and the genotype frequency of other varieties is 0.00; when the genotype is CA, the genotype frequency of the goose is 0.42, and the genotype frequency of other varieties is 0.08; when the genotype is AA, the genotype frequency of the goose is 0.09, and the genotype frequency of other varieties is 0.92;
DA5P site: when the genotype is TT, the genotype frequency of the goose is 0.56, and the genotype frequency of other varieties is 0.00; when the genotype is TC, the genotype frequency of the goose is 0.38, and the genotype frequency of other varieties is 0.06; when the genotype is CC, the genotype frequency of the goose is 0.06, and the genotype frequency of other varieties is 0.94;
DA6P site: when the genotype is AA, the genotype frequency of the goose is 0.45, and the genotype frequency of other varieties is 0.00; when the genotype is AG, the genotype frequency of the goose is 0.44, and the genotype frequency of other varieties is 0.07; when the genotype is GG, the genotype frequency of the goose is 0.11, and the genotype frequency of other varieties is 0.93;
DA7P site: when the genotype is GG, the genotype frequency of the goose is 0.52, and the genotype frequency of other varieties is 0.00; when the genotype is GC, the genotype frequency of the goose is 0.40, and the genotype frequency of other varieties is 0.08; when the genotype is CC, the genotype frequency of the goose is 0.08, and the genotype frequency of other varieties is 0.92;
DA8P site: when the genotype is GG, the genotype frequency of the goose is 0.56, and the genotype frequency of other varieties is 0.00; when the genotype is GA, the genotype frequency of the goose is 0.38, and the genotype frequency of other varieties is 0.10; when the genotype is AA, the genotype frequency of the goose is 0.06, and the genotype frequency of other varieties is 0.90;
DA9P site: when the genotype is TT, the genotype frequency of the goose is 0.52, and the genotype frequency of other varieties is 0.00; when the genotype is TA, the genotype frequency of the goose is 0.40, and the genotype frequency of other varieties is 0.09; when the genotype is AA, the genotype frequency of the goose is 0.08, and the genotype frequency of other varieties is 0.91;
DA10P site: when the genotype is TT, the genotype frequency of the goose is 0.56, and the genotype frequency of other varieties is 0.00; when the genotype is TA, the genotype frequency of the goose is 0.38, and the genotype frequency of other varieties is 0.07; when the genotype is AA, the genotype frequency of the goose is 0.06, and the genotype frequency of other varieties is 0.93;
DA11P site: when the genotype is CC, the genotype frequency of the goose is 0.52, and the genotype frequency of other varieties is 0.00; when the genotype is CT, the genotype frequency of the goose is 0.40, and the genotype frequency of other varieties is 0.07; when the genotype is TT, the genotype frequency of the goose is 0.08, and the genotype frequency of other varieties is 0.93;
DA12P site: when the genotype is TT, the genotype frequency of the goose is 0.81, and the genotype frequency of other varieties is 0.01; when the genotype is TC, the genotype frequency of the goose is 0.18, and the genotype frequency of other varieties is 0.20; when the genotype is CC, the genotype frequency of the goose is 0.01, and the genotype frequency of other varieties is 0.79;
DA13P site: when the genotype is AA, the genotype frequency of the goose is 0.60, and the genotype frequency of other varieties is 0.00; when the genotype is AC, the genotype frequency of the goose is 0.35, and the genotype frequency of other varieties is 0.15; when the genotype is CC, the genotype frequency of the goose is 0.05, and the genotype frequency of other varieties is 0.85;
DA14P site: when the genotype is TT, the genotype frequency of the goose is 0.72, and the genotype frequency of other varieties is 0.02; when the genotype is TC, the genotype frequency of the goose is 0.26, and the genotype frequency of other varieties is 0.25; when the genotype is CC, the genotype frequency of the goose is 0.02, and the genotype frequency of other varieties is 0.73;
DA15P site: when the genotype is CC, the genotype frequency of the goose is 0.77, and the genotype frequency of other varieties is 0.02; when the genotype is CT, the genotype frequency of the goose is 0.22, and the genotype frequency of other varieties is 0.25; when the genotype is TT, the genotype frequency of the goose is 0.01, and the genotype frequency of other varieties is 0.73.
Preferably, the other varieties include a long-music goose, an open-eye goose, a daozhou gray goose, a steel goose, a Lin county white goose, a lion head goose, a black-hair goose, a Yongkang gray goose and a seed goose.
The invention also provides a kit for identifying the variety of the swan, which comprises the primer combination.
The invention also provides application of the primer combination or the kit in identifying varieties of swans.
The invention discloses the following technical effects:
the invention discloses 15 SNP loci, and according to the Bayesian theorem, the probability that the individual belongs to a goose can be judged through the joint genotype of the 15 SNP loci. The probability of judging the goose by combining 15 SNP loci can reach 100%, and the method is simple and convenient to operate and high in accuracy, and can effectively hit the degree of flooding of the fake goose in the market.
Detailed Description
Various exemplary embodiments of the invention will now be described in detail, which should not be considered as limiting the invention, but rather as more detailed descriptions of certain aspects, features and embodiments of the invention.
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 invention. 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 invention. 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 invention 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 invention. 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 invention described herein without departing from the scope or spirit of the invention. Other embodiments will be apparent to those skilled in the art from consideration of the specification of the present invention. The specification and examples of the present invention 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.
The invention provides a primer combination for identifying a goose variety, which is used for amplifying SNP locus combinations shown in DA1P to DA15P (see table 1):
TABLE 1
Sequence number Chromosome of the human body Site(s) Major allele Minor allele
DA1P NW_025927668.1 8129687 A C
DA2P NW_025927673.1 926886 C G
DA3P NW_025927673.1 936602 G C
DA4P NW_025927673.1 945751 C A
DA5P NW_025927673.1 946693 T C
DA6P NW_025927673.1 951840 A G
DA7P NW_025927673.1 963963 G C
DA8P NW_025927673.1 970250 G A
DA9P NW_025927673.1 971259 T A
DA10P NW_025927673.1 983590 T A
DA11P NW_025927673.1 985387 C T
DA12P NW_025927679.1 4763516 T C
DA13P NW_025927866.1 1202481 A C
DA14P NW_025927879.1 469618 T C
DA15P NW_025927879.1 471621 C T
The screening method of the SNP locus combination shown in DA1P to DA15P comprises the following steps: firstly, determining the average value of different allele frequencies of each site of domestic representative varieties such as a long-music goose, an eye-open goose, a state gray goose, a steel goose, a white goose in a county, a lion head goose, a black-mand goose, a Yongkang gray goose, a seed goose and the like, then comparing the average value with different allele frequencies of each site of a mounted goose, screening SNP sites with larger allele frequency difference, and preferentially selecting a site with allele frequency of 0 or 1 of one site of the mounted goose, wherein the allele frequency of other groups is a site close to 1 or close to 0.
Primer combinations for amplification of the DA1P to DA15P sites are shown below in Table 2:
TABLE 2
The invention provides a method for identifying a goose variety, which comprises the following steps:
extracting total DNA of a goose genome to be detected;
using the total DNA as a template, and carrying out PCR amplification by using the primer combination to obtain an amplification product;
sequencing the amplified product, and judging the genotype;
and judging whether the goose to be detected belongs to a goose in the goose mounting state according to the genotype determination result.
In the identification method of the present invention, it is preferable to collect the genomic DNA from the fin vein of the goose to be tested, the extraction method of the genomic DNA is not particularly limited, and the genomic DNA is extracted by a conventional extraction method in the art, and in the embodiment of the present invention, a phenol-chloroform method is preferable.
In the invention, the identification of goose variety is carried out by adopting the site combination in DA1P-DA15P, and the PCR amplification is carried out by adopting the corresponding upstream and downstream primers. The PCR amplification method is not particularly limited, and conventional PCR amplification methods in the art can be adopted.
According to the invention, after sequencing the PCR amplification product of the goose to be detected, judging the genotype, comparing the genotype corresponding to the selected SNP combination, judging the probability that the goose to be detected belongs to the goose with the following calculation formula according to the Bayesian theorem:
the probability that the goose to be detected belongs to non-mounted goose is
Wherein p is i Representing the frequency of the genotype corresponding to the goose variety in the ith SNP in the SNP combination; q i Mean frequencies of genotypes corresponding to other varieties in the ith SNP in the SNP combination are shown. Considering the extreme cases of genotyping error rate and the product of frequency multiplication being 0 when the genotyping frequency is 0, the genotyping frequency smaller than 0.05 is uniformly adjusted to be 0.05, and meanwhile, the maximum genotyping frequency is adjusted to ensure that the sum of the three genotyping frequencies is 1.
According to the calculation result, in order to ensure the accuracy, 0.95 is taken as a threshold value, and the probability of belonging to the goose is greater than or equal to 0.95, and the goose is judged to be the goose; judging that the non-goose is not mounted if the probability of the non-goose is more than or equal to 0.95; if less than 0.95, only one possibility can be determined, for example, the probability of belonging to a goose is 0.85, and only 85% of the possibility is considered to belong to the goose.
The genotypes and genotype frequencies of the SNP loci in the swan and other varieties are shown in the following table 3:
TABLE 3 Table 3
For example, the 15 SNP sites DA1P to DA15P were selected, and if the combined genotype was AA CC CC CA TC AA GG GG TT TT CC TC AA TC CT, the probability that the individual belongs to a goose is:
the probability that the individual belongs to non-goose is
The genotype frequencies of other varieties refer to the genotype frequency average value of each site obtained by combining and calculating the different varieties, wherein the genotype frequencies of other varieties are domestic representative varieties such as Changle geese, opening geese, daozhou gray geese, steel geese, linxian white geese, lion head geese, black-mand geese, yongkang gray geese, and seed geese. The goose calculates the genotype frequency of each locus individually.
In practical application, the invention can also be prepared into a kit for identifying the variety of the swan, and the kit comprises the primer combination and other conventional reagents for detection.
The invention also provides application of the primer combination or the kit in identifying varieties of swans.
The present invention will be described in detail below with reference to specific embodiments for the purpose of making the objects, technical solutions and advantages of the present invention more apparent, but they should not be construed as limiting the scope of the present invention.
Example 1
10 geese were randomly selected from 10 geese of other varieties (Changle geese, onychium geese, taozhou gray geese, steel geese, ling county white geese, lion head geese, black-bristle geese, yongkang gray geese and seed geese), and the fin vein was sampled, genomic DNA was extracted by phenol-chloroform method, and PCR amplification was performed according to primers of 15 SNP loci in Table 2.
The PCR system (20. Mu.L) was: 2. Mu.L of DNA template, 1.5. Mu.L (10 ng/. Mu.L) of forward and reverse primers, 10. Mu.L of 2 XPCR reagent in the day root PCR kit, and the balance of the kit were made up with ultrapure water.
The PCR procedure was: firstly, denaturation at 94 ℃ for 1min, then annealing at 94 ℃ for 30s, annealing at 55 ℃ for 30s and extension at 72 ℃ for 30s, which are 35 cycles, finally extension at 72 ℃ for 5min and preservation at 4 ℃. The PCR instrument was a Burley T100 gradient PCR instrument.
The amplified product was sent to the division of biological engineering (Shanghai) for sequence polymorphism detection and genotyping. Judging whether the goose belongs to the goose with the probability of 0.95 as a threshold value according to the sequencing result by combining the genotypes of the 15 SNP loci, judging that the goose belongs to the goose, and judging that the goose is right by 10 goose-mounting results; the probability of the non-mounted geese is larger than 0.95, the non-mounted geese are judged, and all 10 non-mounted geese are judged to be correct. The results are shown in Table 4 below.
TABLE 4 Table 4
The above embodiments are only illustrative of the preferred embodiments of the present invention and are not intended to limit the scope of the present invention, and various modifications and improvements made by those skilled in the art to the technical solutions of the present invention should fall within the protection scope defined by the claims of the present invention without departing from the design spirit of the present invention.

Claims (9)

1. A primer combination for identifying a goose variety, which is characterized in that the primer combination is a primer combination for amplifying SNP locus combination shown by DA1P-DA15P, and the SNP locus combination shown by DA1P-DA15P is as follows:
DA1P is located at 8129687 on NW_025927668.1 chromosome and has polymorphism A or C;
DA2P is located at 926886 on NW_025927673.1 chromosome and has polymorphism C or G;
DA3P is located at 936602 on NW_025927673.1 chromosome and has G or C polymorphism;
DA4P is located at 945751 on NW_025927673.1 chromosome and has polymorphism C or A;
DA5P is located at 946693 on NW_025927673.1 chromosome and has a polymorphism of T or C;
DA6P is located at 951840 on NW_025927673.1 chromosome and has polymorphism A or G;
DA7P is located at 963963 on NW_025927673.1 chromosome and has G or C polymorphism;
DA8P is located at 970250 on NW_025927673.1 chromosome and has a polymorphism of G or A;
DA9P is located at 971259 on NW_025927673.1 chromosome and has a polymorphism of T or A;
DA10P is located at 983590 on NW_025927673.1 chromosome and has polymorphism T or A;
DA11P is located at 985387 on NW_025927673.1 chromosome and has polymorphism C or T;
DA12P is located at 4763516 on NW_025927679.1 chromosome and has a polymorphism of T or C;
DA13P is located at 1202481 on NW_025927866.1 chromosome, and its polymorphism is A or C;
DA14P is located at 469618 on NW_025927879.1 chromosome and has a polymorphism of T or C;
DA15P is located at position 471621 on the NW_025927879.1 chromosome and has a polymorphism of C or T.
2. The primer combination according to claim 1, wherein the amplification primer combination of the SNP site combination shown in DA1P-DA15P is:
DA1F：5’-TTAATTGCGTGCATCGAGCC-3’；
DA1R：5’-GTGATGGAAAAGGCCAGTGC-3’；
DA2F：5’-CAGTTGGCTAAGCTGAGGGTG-3’；
DA2R：5’-GTTTGGATTCTGGGTCTCCCC-3’；
DA3F：5’-CTGACCTATCTGCACAGGGC-3’；
DA3R：5’-TCTGGGGCAGACAAGTGAAC-3’；
DA4F：5’-TACTTCGTTGTTGGTGACCCT-3’；
DA4R：5’-TTGGCCCAACCCATAAAACAC-3’；
DA5F：5’-GCATGAGCCATGCAGAGTTTC-3’；
DA5R：5’-AAAGTGCCAGAAGAGTATAGCCAA-3’；
DA6F：5’-TGCCTGTGTCCCATTGAAGT-3’；
DA6R：5’-AGCAAGCGCAGAGCAAAATC-3’；
DA7F：5’-CTCTGCCCCATGAGCGTTAC-3’；
DA7R：5’-TGGAGCTATGAGTGCCAAAGAA-3’；
DA8F：5’-GGTGTCAGGGGCTCTTTTCA-3’；
DA8R：5’-CATCAGTACCCAGCTCTGCC-3’；
DA9F：5’-AATTTGGACGGCACCTCACA-3’；
DA9R：5’-ATGGGCTCCCAGAAAGGGAA-3’；
DA10F：5’-AACCATAGCTCAGGTTTGCAC-3’；
DA10R：5’-GAGCCATCAGAGCTAAAAGCAAG-3’；
DA11F：5’-TGCCTCTTGCAGTTCCATCAG-3’；
DA11R：5’-ACAAGGCAAAAAGTGGACATGC-3’；
DA12F：5’-CGGTATTATTGCAGTGCGGG-3’；
DA12R：5’-TCTTACACGGTGGCACGAAT-3’；
DA13F：5’-GAGTAAGAGCACCTGGCTGG-3’；
DA13R：5’-ATCTGGAGGCTCAGGAGAGG-3’；
DA14F：5’-TCTGCAGAGCTGTCACTTCA-3’；
DA14R：5’-CTCCCCGGCTTCATTGACTT-3’；
DA15F：5’-CAGGGGACTGTGCTATGGTG-3’；
DA15R：5’-GTTCTCACACATGCCAGGGA-3’。
3. a method for identifying a goose variety, comprising the steps of:
extracting total DNA of a goose genome to be detected;
performing PCR amplification by using the primer combination according to claim 1 or 2 with the total DNA as a template to obtain an amplification product;
sequencing the amplification product, and judging genotypes of sites shown by DA1P to DA 15P;
and judging whether the goose to be detected belongs to a goose in the goose mounting state according to the genotype determination result.
4. A method according to claim 3, characterized in that the probability that the goose to be tested belongs to a goose with a mounted goose is determined according to the bayesian theorem, and the calculation formula is as follows:
the probability that the goose to be detected belongs to the non-mounted goose is calculated as follows:
wherein p is i Representing the frequency of the genotype corresponding to the goose variety in the ith SNP in the SNP locus combination; q i The average frequency of genotypes corresponding to other varieties in the ith SNP in the SNP locus combination is shown.
5. The method of claim 4, wherein, according to the calculation result, in order to ensure accuracy, 0.95 is taken as a threshold value, and the probability of belonging to the goose is greater than or equal to 0.95, and the goose is determined to be the goose; and judging that the goose is not mounted if the probability of the goose being not mounted is more than or equal to 0.95.
6. The method of claim 3, wherein the genotypes at the sites shown by DA1P to DA15P in geese and other varieties, and the average frequencies of genotypes are as follows:
DA1P site: when the genotype is AA, the genotype frequency of the goose is 0.72, and the genotype frequency of other varieties is 0.02; when the genotype is AC, the genotype frequency of the goose is 0.26, and the genotype frequency of other varieties is 0.21; when the genotype is CC, the genotype frequency of the goose is 0.02, and the genotype frequency of other varieties is 0.77;
DA2P site: when the genotype is CC, the genotype frequency of the goose is 0.49, and the genotype frequency of other varieties is 0.00; when the genotype is CG, the genotype frequency of the goose is 0.42, and the genotype frequency of other varieties is 0.06; when the genotype is GG, the genotype frequency of the goose is 0.09, and the genotype frequency of other varieties is 0.94;
DA3P site: when the genotype is GG, the genotype frequency of the goose is 0.56, and the genotype frequency of other varieties is 0.00; when the genotype is GC, the genotype frequency of the goose is 0.38, and the genotype frequency of other varieties is 0.07; when the genotype is CC, the genotype frequency of the goose is 0.06, and the genotype frequency of other varieties is 0.93;
DA4P site: when the genotype is CC, the genotype frequency of the goose is 0.49, and the genotype frequency of other varieties is 0.00; when the genotype is CA, the genotype frequency of the goose is 0.42, and the genotype frequency of other varieties is 0.08; when the genotype is AA, the genotype frequency of the goose is 0.09, and the genotype frequency of other varieties is 0.92;
DA5P site: when the genotype is TT, the genotype frequency of the goose is 0.56, and the genotype frequency of other varieties is 0.00; when the genotype is TC, the genotype frequency of the goose is 0.38, and the genotype frequency of other varieties is 0.06; when the genotype is CC, the genotype frequency of the goose is 0.06, and the genotype frequency of other varieties is 0.94;
DA6P site: when the genotype is AA, the genotype frequency of the goose is 0.45, and the genotype frequency of other varieties is 0.00; when the genotype is AG, the genotype frequency of the goose is 0.44, and the genotype frequency of other varieties is 0.07; when the genotype is GG, the genotype frequency of the goose is 0.11, and the genotype frequency of other varieties is 0.93;
DA7P site: when the genotype is GG, the genotype frequency of the goose is 0.52, and the genotype frequency of other varieties is 0.00; when the genotype is GC, the genotype frequency of the goose is 0.40, and the genotype frequency of other varieties is 0.08; when the genotype is CC, the genotype frequency of the goose is 0.08, and the genotype frequency of other varieties is 0.92;
DA8P site: when the genotype is GG, the genotype frequency of the goose is 0.56, and the genotype frequency of other varieties is 0.00; when the genotype is GA, the genotype frequency of the goose is 0.38, and the genotype frequency of other varieties is 0.10; when the genotype is AA, the genotype frequency of the goose is 0.06, and the genotype frequency of other varieties is 0.90;
DA9P site: when the genotype is TT, the genotype frequency of the goose is 0.52, and the genotype frequency of other varieties is 0.00; when the genotype is TA, the genotype frequency of the goose is 0.40, and the genotype frequency of other varieties is 0.09; when the genotype is AA, the genotype frequency of the goose is 0.08, and the genotype frequency of other varieties is 0.91;
DA10P site: when the genotype is TT, the genotype frequency of the goose is 0.56, and the genotype frequency of other varieties is 0.00; when the genotype is TA, the genotype frequency of the goose is 0.38, and the genotype frequency of other varieties is 0.07; when the genotype is AA, the genotype frequency of the goose is 0.06, and the genotype frequency of other varieties is 0.93;
DA11P site: when the genotype is CC, the genotype frequency of the goose is 0.52, and the genotype frequency of other varieties is 0.00; when the genotype is CT, the genotype frequency of the goose is 0.40, and the genotype frequency of other varieties is 0.07; when the genotype is TT, the genotype frequency of the goose is 0.08, and the genotype frequency of other varieties is 0.93;
DA12P site: when the genotype is TT, the genotype frequency of the goose is 0.81, and the genotype frequency of other varieties is 0.01; when the genotype is TC, the genotype frequency of the goose is 0.18, and the genotype frequency of other varieties is 0.20; when the genotype is CC, the genotype frequency of the goose is 0.01, and the genotype frequency of other varieties is 0.79;
DA13P site: when the genotype is AA, the genotype frequency of the goose is 0.60, and the genotype frequency of other varieties is 0.00; when the genotype is AC, the genotype frequency of the goose is 0.35, and the genotype frequency of other varieties is 0.15; when the genotype is CC, the genotype frequency of the goose is 0.05, and the genotype frequency of other varieties is 0.85;
DA14P site: when the genotype is TT, the genotype frequency of the goose is 0.72, and the genotype frequency of other varieties is 0.02; when the genotype is TC, the genotype frequency of the goose is 0.26, and the genotype frequency of other varieties is 0.25; when the genotype is CC, the genotype frequency of the goose is 0.02, and the genotype frequency of other varieties is 0.73;
DA15P site: when the genotype is CC, the genotype frequency of the goose is 0.77, and the genotype frequency of other varieties is 0.02; when the genotype is CT, the genotype frequency of the goose is 0.22, and the genotype frequency of other varieties is 0.25; when the genotype is TT, the genotype frequency of the goose is 0.01, and the genotype frequency of other varieties is 0.73.
7. The method of claim 4 or 6, wherein the other varieties comprise geese, geese in the open eye, geese in the state of the road, geese in the steel, geese in the county, geese in the lion head, geese in the black, geese in the Yongkang, and geese in the seed.
8. A kit for identifying a goose variety, comprising the primer combination of claim 1 or 2.
9. Use of a primer combination according to any one of claims 1-2 or a kit according to claim 8 for identifying a goose variety.
CN202311551426.1A 2023-11-21 2023-11-21 SNP locus combination for identifying goose variety and identification method thereof Pending CN117587133A (en)

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Cited By (1)

* Cited by examiner, † Cited by third party
Publication number Priority date Publication date Assignee Title
CN117802248A (en) * 2024-02-29 2024-04-02 江西科技师范大学 Primer combination and method for identifying Xingguo gray goose variety

Cited By (2)

* Cited by examiner, † Cited by third party
Publication number Priority date Publication date Assignee Title
CN117802248A (en) * 2024-02-29 2024-04-02 江西科技师范大学 Primer combination and method for identifying Xingguo gray goose variety
CN117802248B (en) * 2024-02-29 2024-04-30 江西科技师范大学 Primer combination and method for identifying Xingguo gray goose variety

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