SNP molecular marker combinations and their applications and identification methods for Huaxi cattle kinship identification

Abstract

The present invention discloses a SNP molecular marker combination for identifying the kinship of Huaxi cattle, as well as its application and identification method, and belongs to the technical field of genotyping. The present invention provides a SNP molecular marker combination for identifying the kinship of Huaxi cattle, which can complete the identification of the kinship of Huaxi cattle using at least 70 of the 1,000 sites. The 1,000 sites provided by the present invention are SNP markers distributed on 29 autosomes, and the average distance between adjacent SNP markers on the same chromosome is 2M. The average values ​​of MAF, HExp, and PIC of the marker combination are 0.4846, 0.4983, and 0.3741, respectively; when the maternal genotype is unknown, the cumulative exclusion probability is 0.9999999999999. The SNP marker combination of the present invention can be used for complete and accurate pedigree identification of Huaxi cattle, thereby improving the accuracy of Huaxi cattle breeding.

Description

Technical Field

[0001] The present invention belongs to the technical field of genotyping, and in particular relates to a SNP molecular marker combination and application and an identification method for Huaxi cattle kinship identification. Background Art

[0002] The accuracy of pedigree is crucial for cattle breeding. Incorrect pedigree will greatly reduce the accuracy of genetic assessment, affect the effect of selection, and hinder the genetic improvement of the herd, thus causing huge economic impact on the breeding industry. However, in actual breeding production, pedigree records are often recorded incorrectly due to various factors, such as breeding records, calving records, and human errors. Especially in extensive free-range pastures, it is difficult to determine the father or even the parents of the calf, which may lead to pedigree errors. The average pedigree error rate of cattle herds in countries around the world can reach 11%. [1] Due to different feeding methods and production management conditions in different countries, there are certain differences in pedigree error rates, but pedigree errors are difficult to completely avoid in actual production management. Guo Gang et al. [2] Studies have shown that the average pedigree error rate for Holstein cows in the Beijing area is 20.9%. If the world average pedigree error rate of 11% were to occur in actual production, it would lead to underestimated estimates of inbreeding coefficients, sire variance, and cross-national genetic correlations. Israel and Weller et al. [3] A simulation study showed that if the pedigree error rate reaches 10%, assuming a heritability of 0.25, the genetic progress of the Israeli beef cattle population will be lost by 4.3% over 20 years. In the genetic evaluation process of dairy cows, if the error rate of the cow's sire record is 11%, the genetic progress of the population will be reduced by 11% to 15%. Weller et al. [4] It is proposed that in order to ensure that the genetic progress of cattle herds is above 1% each year, the pedigree error rate should be controlled below 8%. Therefore, complete and accurate pedigrees are essential for the production and development of the entire cattle industry.

[0003] The Huaxi cattle, a new breed of beef cattle developed over 40 years by the Beijing Institute of Animal Husbandry and Veterinary Medicine, Chinese Academy of Agricultural Sciences, passed approval in 2021 from the National Committee for Animal Genetic Resources and received the National New Animal Breed Certificate. They are characterized by rapid growth, high feed conversion rate, high net meat percentage, excellent meat production and reproductive performance, and strong stress tolerance. Compared to similar international beef cattle breeds, Huaxi cattle achieve advanced daily weight gain, dressing rate, and net meat percentage. Huaxi cattle are well-adapted to my country's pastoral and agricultural areas, the agricultural-pastoral transition zone in northern China, and the grassy hills and slopes of southern China. Because pastoral farming practices are predominantly extensive, breeding involves both natural crosses between bulls and artificial insemination. This, coupled with human error during artificial insemination, results in a high rate of pedigree errors. Therefore, confirming kinship is crucial to accurately estimate individual breeding values ​​of Huaxi cattle and accelerate genetic research.

[0004] Currently, commonly used molecular methods for paternity testing primarily include DNA fingerprinting, microsatellites, and single nucleotide polymorphism (SNP) molecular markers. Although over the past few decades, the molecular markers used have gradually evolved from allelase and microsatellites (STR) to SNPs, the theoretical basis of paternity analysis has not deviated from the requirement to adhere to Mendel's laws of inheritance. SNP markers, or single nucleotide polymorphisms (SNPs), refer to DNA sequence polymorphisms caused by variations in a single base at the genomic level. These are usually caused by a single base transition or transversion, but can also be caused by insertions or deletions. However, the probability of the former is twice that of the latter. Generally speaking, the minimum allele frequency of a SNP marker in a population is no less than 1%, but cases with a frequency less than 1% are not ruled out (e.g., in cDNA).

[0005] Currently, there are no reports on the use of SNP markers to identify the kinship of Huaxi cattle. The lack of pedigree records significantly hinders the development of a quality traceability system for Huaxi cattle. Furthermore, pedigree information is crucial for cattle genetic research. Therefore, a complete and accurate pedigree is essential for the development and promotion of the Huaxi cattle industry. When accurate records cannot be guaranteed, kinship identification becomes a crucial step in genetic breeding and improvement of Huaxi cattle.

[0006] References:

[0007] [1]Banos G,Wiggans GR,Powell R L.Impact of paternity errors in cowidentification on genetic evaluations and international comparisons[J].Journal of dairy science,2001,84(11):2523-2529.

[0008] [2] Guo Gang, Zhou Lei, Liu Lin, Li Dong, Zhang Shengli, Liu Jianfeng, Ding Xiangdong, Zhang Yi, Wang Yachun, Zhang Qin, Zhang Yuan. Study on parentage inference of Chinese Holstein cattle in Beijing using SNP markers [J]. Acta Animal Husbandry and Veterinary Sinica, 2012, 43(01): 44-49.

[0009] [3]Israel C,Weller J I.Effect of misidentification on genetic gain and estimation of breeding value in dairy cattle populations[J].Journal ofDairy Science,2000,83(1):181-187.

[0010] [4]Weller JI, Feldmesser E, Golik M, et al.Factors affecting incorrect paternity assignment in the Israeli Holstein population[J].Journal of DairyScience,2004,87(8):2627-2640. Summary of the Invention

[0011] The purpose of the present invention is to provide a SNP molecular marker combination, application and identification method for Huaxi cattle kinship identification. The SNP marker combination can be used for complete and accurate pedigree identification of Huaxi cattle, thereby improving the accuracy of Huaxi cattle breeding.

[0012] The present invention provides a SNP molecular marker combination for identifying the kinship of Huaxi cattle, comprising at least 70 of the SNP molecular markers shown in Table 1.

[0013] Preferably, the sites of each SNP molecular marker use Bos_taurus_UMD_3.1 as the reference genome.

[0014] The present invention also provides a probe for identifying the above SNP molecular marker combination.

[0015] The present invention also provides a gene chip prepared based on the above SNP molecular marker combination.

[0016] Preferably, the type of the gene chip includes a liquid phase chip.

[0017] The present invention also provides the use of the above-mentioned SNP molecular marker combination, the above-mentioned probe or the above-mentioned gene chip in identifying the kinship of Huaxi cattle.

[0018] The present invention also provides the use of the above-mentioned SNP molecular marker combination, the above-mentioned probe or the above-mentioned gene chip in the genetic improvement and breeding of Huaxi cattle.

[0019] The present invention also provides a method for identifying the kinship of Huaxi cattle, comprising the following steps: using the genomic DNA of the cattle to be tested as a template, identifying the genotype of the above-mentioned SNP molecular marker combination, calculating the LOD value of the parent-offspring index according to the genotype of the individual cattle to be tested, and identifying the kinship of the cattle to be tested according to the LOD value.

[0020] Preferably, when the LOD value is greater than 0, the candidate parent is likely to be the true parent, and the individual with the highest LOD value is the most similar parent; when the LOD value is less than 0, the candidate parent is unlikely to be the true parent.

[0021] Beneficial effects: The present invention provides a SNP molecular marker combination for identifying the kinship of Huaxi cattle. By analyzing the sequencing results of 1,252 Huaxi cattle, multiple SNP sites on 29 autosomes were screened out, and the identification of the kinship of Huaxi cattle can be completed by at least 70 of the 1,000 sites. The present invention provides 1,000 SNP markers distributed on 29 autosomes, and the average distance between adjacent SNP markers on the same chromosome is 2M. The average values ​​of the minimum allele frequency (MAF), expected heterozygosity (HExp), and polymorphic information content (PIC) of the marker combination are 0.4846, 0.4983, and 0.3741, respectively; when the maternal genotype is unknown, the cumulative exclusion probability is 0.9999999999999. The SNP marker combination of the present invention can be used for complete and accurate pedigree identification of Huaxi cattle, can improve the accuracy of Huaxi cattle breeding, accelerate its genetic progress, and has good application prospects and economic benefits. BRIEF DESCRIPTION OF THE DRAWINGS

[0022] Figure 1 The specific operational steps for identifying the kinship of Huaxi cattle. DETAILED DESCRIPTION

[0023] The present invention provides a SNP molecular marker combination for identifying the kinship of Huaxi cattle, comprising at least 70 of the SNP molecular markers shown in Table 1.

[0024] The present invention screened out 1,000 SNP sites on 29 autosomes by analyzing the sequencing results of 1,252 Huaxi cattle, which can be used for SNP marker combinations for identifying the kinship of the Huaxi cattle herd. The 1,000 SNP marker combinations provided by the present invention are distributed on 29 autosomes, and the average distance between adjacent SNPs on the same chromosome is 2M. In the SNP molecular marker information in Table 1 of the present invention, the sites use Bos_taurus_UMD_3.1 as the reference genome. The SNP molecular marker combination described in the present invention is 1,000 SNP sites, and the average values ​​of the minimum allele frequency (MAF), expected heterozygosity (HExp), and polymorphic information content (PIC) of this marker combination are 0.4846, 0.4983, and 0.3741, respectively; the cumulative exclusion probability of this 1,000 SNP marker combination is 0.9999999999999, and the paternity test efficiency is extremely high.

[0025] Table 11000 SNP molecular marker information

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[0063] The present invention also provides a probe for identifying the above SNP molecular marker combination.

[0064] The present invention does not particularly limit the design method of the probe, and the probe can be designed using conventional methods in the art, as long as it can specifically recognize and bind to the corresponding SNP site.

[0065] The present invention also provides a gene chip prepared based on the above SNP molecular marker combination.

[0066] The type of gene chip of the present invention preferably includes a liquid phase chip, which can be used to visually determine the genotype of the corresponding SNP molecular marker site, thereby facilitating the determination of kinship.

[0067] The present invention also provides the use of the above-mentioned SNP molecular marker combination, the above-mentioned probe or the above-mentioned gene chip in identifying the kinship of Huaxi cattle.

[0068] When identifying the kinship of Huaxi cattle, the present invention first uses the genomic DNA of the cattle to be tested as a template, utilizes conventional methods in the art, such as sequencing and gene chips, to determine the genotype of the aforementioned SNP molecular marker sites, and then performs paternity testing based on the likelihood method. The present invention preferably calculates the LOD value of the paternity index based on the genotype of the individual cattle to be tested, establishes a likelihood function, and applies hypothesis testing to find the most similar father. The process and calculation method are as follows:

[0069] According to the calculation formula proposed by Kalinowski et al. (2007): Kalinowski ST, Taper ML, Marshall TC. Revising how the computer program CERVUS accommodates genotyping error increases success in paternity assignment [J]. Molecular Ecology, 2007, 16(5): 1099-1106.

[0070] (1) When the maternal genotype is unknown, the probability that the father is the true father

[0071] L(H1)=P(g a ){(1-ε) 2 T(g o |g a )+ε(1-ε) 2 P(g o )+ε 2 P(g o )}

[0072] L(H2)=P(g a ){(1-ε) 2 P(g o )+ε(1-ε) 2 P(g o )+ε 2 P(g o )}

[0073] (2) When the maternal genotype is known, the probability that the father is the true father

[0074] L(H1)=P(g m )P(g a ){(1-ε) 3 T(g o |g m , g a )+ε(1-ε) 2 [T(g o |g m )+T(g o |g a )+P(g o )]+ε 2 (1-ε) 3 P(g o )+ε 3 P(g o )}

[0075] L(H2)=P(g m )P(g a ){(1-ε) 3 T(g o |g m )+ε(1-ε) 2 [T(g o |g m )+P(g o )]+ε 2 (1-ε) 3 P(g o )+ε 3 P(g o )}.

[0076] (3) The probability that the hypothetical maternal parent and the hypothetical paternal parent will be the parents of the offspring

[0077] L(H1)=P(g m )P(g a ){(1-ε) 3 T(g o |g am , g a )+ε(1-ε) 2 [T(g o |g am )+T(g o |g a )+P(g o )]+ε 2 (1-ε) 3 P(g o )+ε 3 P(g o )}

[0078] L(H2)=P(g am )P(g a ){(1-ε) 3 P(g o )+ε(1-ε) 2 P(g o )+ε 2 (1-ε) 3 P(g o )+ε 3 P(g o )}.

[0079] (4) The expression of likelihood ratio is: L(H1) / L(H2), then

[0080] LOD=ln[L(H1) / L(H2)]

[0081] In the above formula, H1: assumes that the father is the real father, H2: assumes that the father is an unrelated individual. L(H1) and L(H2) are the likelihood functions under the assumption H. o is the offspring genotype, g a is the genotype of the hypothetical father, g m is the known maternal genotype, g am is the assumed maternal genotype, T is the standard Mendelian transmission probability, P is the genotype probability, and ε is the genotype discrimination error rate.

[0082] According to the above calculation formula, the LOD value of the likelihood ratio of each candidate parent at all detection sites can be obtained, and the possibility of the candidate parent being the true parent of the offspring can be known, so as to make a judgment on the kinship between the parent-offspring pairs.

[0083] Based on the definition of LOD value, Marshall et al. pointed out that an LOD value equal to 0 indicates that the hypothetical father and a random male individual in the population have the same probability of being the real father of the offspring; when the LOD value is less than 0, it indicates that the hypothetical father cannot be the real father of the offspring, which usually means that there is a genotype mismatch between the hypothetical father and the offspring at one or more loci; and when the LOD value is greater than 0, it indicates that the hypothetical father is very likely to be the real father of the offspring. When the LOD value is large enough, the kinship between the offspring and the candidate father can be determined.

[0084] When the LOD values ​​calculated for multiple candidate parents are all greater than 0, then they are all likely to be the real father of the offspring, but there is only one real father. At this time, the candidate parents can be arranged in order according to the size of the LOD value. The one with a larger LOD value has a greater chance of becoming the real father. However, sometimes some positive LOD values ​​are approximately equal, making it difficult to distinguish. In view of this situation, Marshall et al. (Marshall TC, Slate J, Kruuk LEB, et al. Statistical confidence for likelihood-based paternity inference in natural populations [J]. Molecular ecology, 1998, 7 (5): 639-655.) defined a statistic Δ for paternity testing:

[0085] Δ=LOD max -LOD sec

[0086] Δ is a statistic used to evaluate the reliability of the identification results. max Indicates the LOD value that is most similar to the parent, LOD sec Indicates the LOD value of the second most likely parent. The larger the Δ value, the higher the confidence that the most likely parent is the true parent. Using Δ for paternity testing can ensure the accuracy of the test. The confidence level assigned to the most likely parent is also displayed: * indicates an extremely significant paternity relationship, with a confidence level exceeding 95%; + indicates a moderately significant paternity relationship, with a confidence level exceeding 80%; - indicates a nonsignificant paternity relationship, with a confidence level between 0 and 80%.

[0087] Therefore, the method provided by the present invention for identifying the kinship of Huaxi cattle is to calculate the LOD value of the parentage index based on the genotype of the individual cattle to be tested, and to identify the kinship of the Huaxi cattle to be tested based on the LOD value. When the LOD value is greater than 0, the candidate parent is likely to be the true parent, and the individual with the highest LOD value is the most likely parent; when the LOD value is less than 0, the candidate parent is unlikely to be the true parent.

[0088] The present invention also provides the use of the above-mentioned SNP molecular marker combination, the above-mentioned probe or the above-mentioned gene chip in the genetic improvement and breeding of Huaxi cattle.

[0089] The SNP molecular marker combination and corresponding products described in the present invention can be used for complete and accurate pedigree identification of Huaxi cattle, improve the accuracy of Huaxi cattle breeding, accelerate its genetic progress, and have good application prospects and economic benefits.

[0090] The present invention also provides a method for identifying the kinship of Huaxi cattle, comprising the following steps: using the genomic DNA of the cattle to be tested as a template, identifying the genotype of the above-mentioned SNP molecular marker combination, calculating the LOD value of the parent-offspring index according to the genotype of the individual cattle to be tested, and identifying the kinship of the cattle to be tested according to the LOD value.

[0091] The specific LOD calculation method of the present invention is the same as described above and will not be repeated here. In the present invention, when the LOD value is greater than 0, the candidate parent is likely to be the true parent, and the individual with the highest LOD value is the most similar parent; when the LOD value is less than 0, the candidate parent is unlikely to be the true parent.

[0092] To further illustrate the present invention, the SNP molecular marker combination, application and identification method for Huaxi cattle kinship identification provided by the present invention are described in detail below in conjunction with the examples, but they should not be understood as limiting the scope of protection of the present invention.

[0093] Unless otherwise specified, the technical means used in the examples are conventional means well known to those skilled in the art, and the chemical reagents used in the examples are all commercially available.

[0094] Example 1

[0095] Screening of 1,000 SNP molecular markers related to kinship identification in Huaxi cattle

[0096] 1. Screening of SNP markers related to Huaxi cattle kinship identification

[0097] Next-generation sequencing of 1,252 Huaxi cattle from the Ulagai Management Area in Inner Mongolia was performed using the Illumina platform, yielding a total of 12,468,401 single-nucleotide polymorphism (SNP) markers. SNPs were screened using the following quality control criteria: ① location on an autosome; ② a minimum allele frequency greater than 0.35; ③ a call rate greater than 0.95 for each SNP marker; ④ spacing between adjacent SNPs on the same chromosome greater than 1 Mb; To avoid linkage disequilibrium between the selected SNP markers, screening was performed on separate chromosomes. ⑤ Hardy-Weinberg equilibrium (HW) test P > 1 × 10 6 . After preliminary screening, 17,023 polymorphic SNP sites were obtained.

[0098] CERVUS3.0.7 software was used to calculate the genetic polymorphism parameters of 17,023 SNPs, including allele frequency, expected heterozygosity, polymorphic information content, Hardy-Weinberg equilibrium, average probability of excluding a suspected parent (PE), cumulative probability of exclusion (CPE) of site combinations, and null allele frequency.

[0099] Based on the statistical results of each parameter, the markers were screened again by chromosome. First, the loci were re-ranked by PE value. Then, based on PIC and MAF values, the loci with the highest values ​​for each parameter were retained, ensuring that the distance between adjacent SNPs on the same chromosome was greater than 2M. The final number of markers screened was 1,000. The distribution of SNPs on each chromosome is shown in Table 2.

[0100] Table 2 Number of SNPs on each chromosome and distances between adjacent SNPs

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[0103] The final SNP molecular marker combination is the 1,000 SNP sites shown in Table 1. The average distance between adjacent sites on the same chromosome is 2M. The average MAF, HExp, and PIC of this marker combination are 0.4846, 0.4983, and 0.3741, respectively. The cumulative exclusion probability of this 1,000 SNP marker combination is 0.99999999999999, and the paternity test efficiency is extremely high.

[0104] 2. Establishment of a SNP-marked Huaxi cattle kinship identification system

[0105] The more SNP markers there are, the higher the accuracy of kinship identification. The number of SNP markers varies, and the detection cost also varies. Since the operational difficulty and detection cost vary greatly in different actual production, in order to meet the needs of various situations, the highest paternity testing accuracy is achieved at the most reasonable cost. This example, through simulation studies and verification in the Huaxi cattle population, ultimately determined the minimum number of SNP combinations required to achieve ideal identification efficacy under different circumstances.

[0106] The 1,000 SNP markers were randomly divided into subsets containing 500, 300, 200, 100, 80, 70, 60, 50, 40, 30, and 20 SNPs to determine the minimum number of SNP markers required for different situations. Simulation experiments for paternity testing were performed using CERVUS 3.0.7 software to determine the most suitable SNP combination.

[0107] The simulation parameters were set as follows: a locus typing success rate of 1, an analytical error rate of 0.01, confidence thresholds of 80% and 95%, 10,000 simulated progeny, and a candidate parent detection rate of 100%. Statistical analysis of the simulation results (Table 3) revealed that CPE1 increased from 0.93051929 (20 SNPs) to 1 (200 SNPs), CPE2 increased from 0.98424600 (20 SNPs) to 1 (100 SNPs minus 200 SNPs), and CPE3 increased from 0.998644213 (20 SNPs) to 1 (60 SNPs minus 200 SNPs). When the number of loci increased to a certain level, the exclusion rate remained constant, reaching a maximum of 1. As shown in Table 3, when the number of SNP markers reaches 70, CPE1 and CPE2 both exceed 99.99%, and CPE3 even reaches 1. In addition, the paternity test allocation rate (80% and 95% confidence levels) of the combination of more than 70 SNP markers can reach 100%, and at the level of 95% parentage confidence, the proportion of parentage inference can reach 100%.

[0108] Therefore, simulation studies indicate that, to achieve optimal identification efficacy, a marker combination of at least 70 loci is required in practical applications. This study ultimately screened 1,000 SNP markers as a SNP marker combination for kinship identification in the Huaxi cattle population (Table 1).

[0109] Table 3 Exclusion probability, allocation rate and inference rate of different gradient combinations

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[0111] Note: CPE1 is the cumulative probability of excluding a suspected parent, CPE2 is the cumulative probability of excluding a suspected parent when the genotype of the other parent is known, and CPE3 is the cumulative probability of excluding a pair of suspected parents. The assignment rate is the percentage of simulated offspring to which the parent is assigned at this confidence level, and the inference rate is the probability that the assigned parent is the true parent at this confidence level.

[0112] Example 2

[0113] The application of 1,000 SNP molecular markers shown in Table 1 in identifying the genetic relationship of Huaxi cattle, such as Figure 1 As shown:

[0114] To verify the feasibility and accuracy of the 1,000 SNP marker combinations screened for parentage inference in Huaxi cattle in an actual population, this example selected 10 pairs of clear paternity relationships from the Huaxi cattle population in the Ulagai Management District of Inner Mongolia, which was sequenced using the Illumina platform for next-generation sequencing, for paternity verification testing. The candidate sires of these 10 offspring cattle (numbered A1-A10) were set as 14 sires (numbered P1-P14) that had been used for breeding with the test population. To ensure the reliability of the test results, three replicates were performed, each time randomly selecting 70 sites from the 1,000 SNP markers to form the identification combination.

[0115] Phylogenetic inference was performed using CERVUS 3.0.7 software, with the results shown in Tables 4–13. Specifically, for the first test results of individual A1, the LOD values ​​of the 14 candidate paternal parents were ranked from highest to lowest. P1 had the highest LOD value of 15.27655587, with a Δ value of 15.27655587 and a confidence level exceeding 95%. Therefore, P1 is the most likely parent of A1. The LOD values ​​of the other candidate paternal parents were all negative, indicating that P2–P14 cannot be the true parent of A1.

[0116] The most likely father was found using the combination of 1,000 SNP molecular markers of the present invention. The results of three experimental verifications were consistent with the pedigree records, with a confidence level of 95%, verifying the accuracy and feasibility of the SNP combination provided by the present invention in paternity testing of Huaxi cattle.

[0117] Table 4 Paternity verification test

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[0120] Note: * indicates that the parent-child relationship is extremely significant, with a confidence level of more than 95%; + indicates that the parent-child relationship is relatively significant, with a confidence level of 80% to 95%; - indicates that the parent-child relationship does not meet the significance requirement, with a confidence level of 0 to 80%; the same below.

[0121] Table 5 Paternity verification test

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[0124] Table 6 Parentage verification test

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[0127] Table 7 Paternity verification test

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[0130] Table 8 Paternity verification test

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[0133] Table 9 Paternity verification test

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[0136] Table 10 Parentage verification test

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[0139] Table 11 Paternity verification test

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[0142] Table 12 Paternity verification test

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[0145] Table 13 Paternity verification test

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[0148] Although the above embodiment provides a detailed description of the present invention, it is only a part of the embodiments of the present invention, not all of the embodiments. People can also obtain other embodiments based on this embodiment without creativity, and these embodiments all fall within the scope of protection of the present invention.

Claims

1. A gene chip prepared based on a combination of SNP molecular markers for identification of kinship of Huaxi cattle, characterized in that: The SNP molecular marker combination is as follows: the loci of each SNP molecular marker use Bos_taurus_UMD_3.1 as the reference genome, 2. The gene chip according to claim 1, characterized in that The types of the gene chip include liquid phase chip.

3. Use of the gene chip according to claim 1 or 2 in identifying the kinship of Huaxi cattle.

4. Use of the gene chip according to claim 1 or 2 in genetic improvement and breeding of Huaxi cattle.

5. A method for identifying the kinship of Huaxi cattle, characterized in that: The following steps are involved: The genomic DNA of the tested cattle is used as a template, and the gene chip described in claim 1 or 2 is used to detect the genotype corresponding to the SNP molecular marker combination therein, and the LOD value of the parentage index is calculated according to the genotype of the individual cattle to be tested, and the kinship of the tested cattle is identified according to the LOD value.

6. The method according to claim 5, characterized in that When the LOD value is greater than 0, the candidate parent is likely to be the true parent, and the individual with the highest LOD value is the most similar parent; when the LOD value is less than 0, the candidate parent cannot be the true parent.

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