Pig parent-child relationship identification, pedigree identification and pedigree reconstruction method and application
By performing DNA sampling and genomic SNP typing on individual pigs, calculating the kinship and gene delivery error rate, the problem of unclear parent-child relationship caused by errors in genealogy records in pig breeding is solved, and efficient and accurate genealogy identification and reconstruction are achieved to ensure the normal development of breeding work.
Patent Information
- Application Number
- CN202510272269.3
- Authority / Receiving Office
- CN · China
- Patent Type
- Applications(China)
- Current Assignee / Owner
- Filing Date
- 2025-03-07
- Publication Date
- 2025-06-27
AI Technical Summary
During the pig breeding process, the pedigree record errors caused by employees' work mistakes, resulting in unclear parent-child relationships, which affects the normal development of breeding work.
By sampling DNA tissues of two pig individuals who were diagnosed with parent-child relationships, genomic SNP typing, calculating kinship and gene delivery error rates, determining whether the parent-child relationship is correct, so as to identify whether the genealogy is incorrect, and performing genealogy reconstruction when errors are found.
It has achieved efficient and accurate identification and reconstruction of pig parent-child relationships and genealogy, ensuring the accuracy and reliability of breeding work, and avoiding breeding problems caused by pedigree errors.
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Figure CN120220799A_ABST
Abstract
Description
Technical Field
[0001] The present invention relates to the field of animal genetic breeding, and particularly to a method and application for identifying parent-offspring relationships, pedigree identification, and pedigree reconstruction of pigs. Background Art
[0002] The pedigree of pigs refers to the systematic information recording the blood relationship and genetic background of pig individuals. It is usually used for breeding management, genetic improvement, and breed protection. The core purpose of the pedigree is to trace the family history of pigs, clarify the parent-offspring relationships of their ancestors and descendants, so as to provide a basis for scientific breeding, avoid inbreeding, and optimize genetic characteristics.
[0003] Therefore, the pedigree plays an important role in breeding of breeding pigs. It can be used to establish bloodlines and families, and can also be used for genetic evaluation of breeding pigs and on-site selection and mating, etc. However, in actual breeding, errors in pedigree records often occur due to work mistakes of employees. For example, mis-matching semen will lead to incorrect fathers, and the situation where both parents are incorrect due to artificial fostering of newborn piglets before registration in the file, etc. The above situations will seriously affect the normal progress of breeding work. Therefore, a method for identifying parent-offspring relationships, pedigree identification, and pedigree reconstruction of pigs needs to be established. The key to pedigree reconstruction is to perform paternity testing well. Only when all parent-offspring relationships are ensured to be correct, can the pedigree be guaranteed to be accurate. Summary of the Invention
[0004] The purpose of the present invention is to provide a method and application for identifying parent-offspring relationships, pedigree identification, and pedigree reconstruction of pigs, so as to identify the parent-offspring relationships of pigs or further identify whether the pedigree of pigs is incorrect, and when it is found that the pedigree is incorrect, the pedigree can be reconstructed efficiently and accurately.
[0005] According to the first aspect of the present invention, a method for identifying parent-offspring relationships of pigs is provided. The method includes the following steps:
[0006] S1: Perform DNA tissue sampling between two pig individuals whose parent-offspring relationships are to be identified;
[0007] S2: Perform genome SNP genotyping on the sampled individuals;
[0008] S3: Identify whether there are errors in the pedigree by calculating the kinship and the gene transmission error rate. Among them, the kinship is calculated by using the genome SNP genotypes between individuals, and the following calculation formula is adopted:
[0009]
[0010] Wherein: I ij represents the kinship between individual i and individual j, B ik is the genotype of the kth SNP locus of individual i, B jkis the genotype of the k-th SNP locus of individual j. The genotypes AA, Aa, and aa are represented by 0, 1, and 2 respectively, and p k is the allele frequency of allele a at the k-th SNP locus, and m is the total number of SNP loci;
[0011] The gene transmission error rate is calculated as follows:
[0012]
[0013] where E ij is the proportion of loci with genotype mismatch between individual i and individual j, and e k is the gene matching degree at the k-th SNP locus, represented by 0 or 1, and m is the total number of SNP loci;
[0014] S4: According to the I ij value and the E ij value to determine whether the parent-child relationship is correct: I ij The value is between 0.3 - 0.8, and when E ij is less than 0.01, the parent-child relationship can be determined, otherwise it is a non-parent-child relationship.
[0015] Thus, through this parent-child relationship identification method, the parent-child relationship can be identified efficiently and accurately, and then used to identify whether the pedigree is incorrect, facilitating the subsequent breeding work.
[0016] In some embodiments, the e k as the gene matching degree at the k-th SNP locus means that when the genotypes of individual i and individual j at the k-th locus are contradictory, e k is recorded as 1, otherwise it is recorded as 0.
[0017] In some embodiments, the genotypes of individual i and individual j at the k-th locus being contradictory means that at the k-th locus, the genotype of individual i is AA and the genotype of individual j is aa, or the genotype of individual i is aa and the genotype of individual j is AA.
[0018] In some embodiments, the pig is a Duroc breeding pig.
[0019] According to the second aspect of the present invention, there is provided an application of a pig parent-child relationship identification method in pig parent-child relationship identification. Thus, this method can quickly and accurately identify the pig parent-child relationship, facilitating the subsequent breeding work.
[0020] According to the third aspect of the present invention, a method for identifying a pig pedigree is provided. This method identifies the parent-child relationships of all pigs in the pedigree by using the above-mentioned method for identifying pig parent-child relationships. When the parent-child relationships of all pigs are correct, the pedigree is error-free; if the parent-child relationships of one or more pigs are incorrect, the pedigree is incorrect. Thus, this method can quickly and accurately identify the pedigree, facilitating the subsequent breeding work.
[0021] According to the fourth aspect of the present invention, an application of a method for identifying a pig pedigree in pig pedigree identification is provided. Thus, this method can quickly and accurately identify the pedigree, facilitating the subsequent breeding work.
[0022] According to the fifth aspect of the present invention, a method for reconstructing a pig pedigree is provided. This method includes the following steps:
[0023] S1: When the pedigree is incorrect, perform DNA tissue sampling on the piglets in the pedigree error and all pigs that have served as fathers or mothers.
[0024] S2: Perform genomic SNP genotyping on the sampled individuals.
[0025] S3: Calculate the genetic relationship and gene transmission error rate between each pair of the sampled individuals. Among them, the genetic relationship is calculated by using the genomic SNP genotypes between individuals, and the following calculation formula is adopted:
[0026]
[0027] In the formula: I ij represents the genetic relationship between individual i and individual j, B ik is the genotype of individual i at the kth SNP locus, B jk is the genotype of individual j at the kth SNP locus. The genotypes AA, Aa, and aa are represented by 0, 1, and 2 respectively, p k is the allele frequency of allele a at the kth SNP locus, and m is the total number of SNP loci;
[0028] The gene transmission error rate is calculated in the following way:
[0029]
[0030] Among them, E ij is the proportion of loci with genotype mismatch between individual i and individual j, e k is the gene matching degree at the kth SNP locus, represented by 0 or 1, and m is the total number of SNP loci;
[0031] S4: When the calculated I ij value between the piglet and... is between 0.3 - 0.8 and E ijWhen it is less than 0.01, the individual is the father / mother of the piglet;
[0032] S5: After finding the correct father / mother, the pedigree of the piglet can be reconstructed.
[0033] Therefore, through this pedigree reconstruction method, the pedigree can be reconstructed efficiently and accurately, which is conducive to the subsequent breeding work, such as bloodline division, genetic evaluation, seed selection and matching, and plays an important auxiliary role.
[0034] In certain embodiments, the pig pedigree reconstruction method further includes identifying the original pedigree. Pedigree reconstruction is required only if the original pedigree is wrong. The identification of the original pedigree is performed using the above-mentioned pig pedigree identification method.
[0035] According to a sixth aspect of the present invention, a method for reconstructing a pig pedigree is provided for use in pig pedigree reconstruction. Thus, the pedigree can be reconstructed efficiently and accurately through the application, which is beneficial to subsequent breeding work, such as bloodline division, genetic evaluation, and selection and matching.
[0036] Beneficial effects of the present invention:
[0037] 1. A method and application for identifying pig parent-offspring relationships and pedigrees is disclosed. By calculating kinship and gene transmission error rates, parent-offspring relationships can be identified efficiently and accurately, and then the pedigree can be further identified to facilitate the subsequent breeding work.
[0038] 2. A pig pedigree reconstruction method and application is disclosed, which finds I by calculating the relationship and gene transmission error rate. ij The value is between 0.3-0.8 and E ij If the correlation coefficient between two individuals is less than 0.01, it can be determined that the two individuals have a parent-child relationship, and then the pedigree can be reconstructed. The reconstruction of the pedigree is conducive to the subsequent breeding work, such as bloodline division, genetic evaluation, and seed selection and matching, which plays an important auxiliary role. BRIEF DESCRIPTION OF THE DRAWINGS
[0039] Figure 1 This is a flow chart of the pig pedigree identification method;
[0040] Figure 2 Flowchart of the porcine pedigree reconstruction method. DETAILED DESCRIPTION
[0041] The invention is further described in detail below.
[0042] Example 1 Method for identifying pig parentage and pedigree and verification of the method
[0043] A total of 234 Duroc breeding pigs born from September to November 2024 in a certain pig farm under Qingyuan Wenshi Swine Technology Co., Ltd. were selected for this experiment. All these pigs have pedigree records. Among them, the parents of 189 pigs are clearly and accurately recorded (denoted as the "correct pedigree group"), the semen was deliberately taken wrongly during the mother's insemination for 18 pigs, resulting in an incorrect father (denoted as the "father error group"), and for another 27 pigs, the ear tag of the mother was deliberately misremembered, resulting in an incorrect mother (denoted as the "mother error group").
[0044] The following method was used to identify the correctness of the above-mentioned pig pedigrees. The identification process is as Figure 1 shown. Specifically: DNA tissue samples were taken from the piglets recorded in the pedigrees of the three groups (correct pedigree group, father error group, mother error group) and their fathers / mothers, and genomic SNP genotyping was performed. Through the calculation methods of kinship and gene transmission error rate, the piglets were matched with the parental individuals to be tested to verify / identify the parent-offspring relationship, and the correctness of the pedigree was identified by verifying all the parent-offspring relationships in the pedigree.
[0045] Among them, the kinship was calculated by using the genomic SNP genotypes of an individual and the parental individual to be tested (or between two pig individuals), and the following calculation formula was used:
[0046]
[0047] In the formula: I ij represents the kinship between individual i and individual j, B ik is the genotype of the k-th SNP locus of individual i, B jk is the genotype of the k-th SNP locus of individual j. The genotypes AA, Aa, and aa are represented by 0, 1, and 2 respectively, p k is the allele frequency of allele a at the k-th SNP locus, and m is the total number of SNP loci. Theoretically, if i and j are in a parent-offspring relationship, the value of I ij should be around 0.5. When it is lower than 0.3, it usually indicates that the two are not in a parent-offspring relationship. The genotypes AA, Aa, and aa represent dominant homozygotes, heterozygotes, and recessive homozygotes. Here, only A / a is taken as an example, and other letters can also be used, such as BB, Bb, bb, etc. (the same below).
[0048] The gene transmission error rate was calculated using the following method:
[0049]
[0050] Among them, E ij is the proportion of loci with genotype mismatches between individual i and individual j, and e kis the gene matching degree of the k-th SNP locus, represented by 0 or 1, and m is the total number of SNP loci. Theoretically, if individuals i and j are parent-child relationships, then for any SNP locus, when individual i has the AA genotype, individual j cannot have the aa genotype; similarly, when individual i has the aa genotype, individual j cannot have the AA genotype. When there is a contradiction in the genotypes of individuals i and j at the k-th locus (that is, at this locus, the genotype of individual i is AA and the genotype of individual j is aa, or the genotype of individual i is aa and the genotype of individual j is AA), e k is recorded as 1, otherwise it is recorded as 0. However, due to partial genotyping errors during the genotyping process, even if individuals i and j are parent-child relationships, there will be a relatively small value of E ij . Usually, when individuals i and j are parent-child relationships, E ij is less than 0.01; otherwise, E ij will be greater than 0.01.
[0051] Because there are full-sib or identical twin pigs, the kinship and the gene transmission error rate need to be combined with each other to verify / identify parent-child relationships. Only when the I ij value is between 0.3 and 0.8 and E ij is less than 0.01 can it be determined as a parent-child relationship, otherwise it is a non-parent-child relationship.
[0052] When identifying the parent-child relationships of all pigs in the pedigree, when the parent-child relationships of all pigs are correct, the pedigree is correct; if the parent-child relationship of one or more pigs is incorrect, the pedigree is incorrect.
[0053] Using the above method to calculate the kinship and gene transmission error rate for 234 Duroc pigs (i.e., 189 pigs in the correct pedigree group, 18 pigs in the father error group, and 27 pigs in the mother error group) to verify / identify parent-child relationships (or pedigree relationships), the results are shown in Table 1 below:
[0054] Table 1 Results of parent-child relationship / pedigree identification / verification
[0055]
[0056] As can be seen from the results in Table 1:
[0057] 1. After verification, all 189 pigs in the correct pedigree group are parent-child relationships: the calculated kinship coefficients I ij are all within the range of 0.3741 - 0.6067, meeting the range of 0.3 - 0.8; the maximum gene transmission error rate E ij is only 0.0032, meeting E ijLess than 0.01, thus meeting all the conditions for judging parent - child relationship. The verification result is consistent with the actual situation, indicating that this paternity testing method is correct. Since all the tested samples are determined to be parent - child relationships after identification, the pedigree of this group is also correct.
[0058] 2. After verification of the 18 pigs in the wrong - father group, the coefficient of relationship I ij The maximum value is only 0.1519 and the minimum value is - 0.0827, not within the range of 0.3 - 0.8; and the gene transmission error E ij The minimum value is 0.0425 and the maximum value is 0.0816, which also does not meet the condition that E ij is less than 0.01. Therefore, neither of the two data can be determined as a parent - child relationship. The verification result is consistent with the actual situation, indicating that this paternity testing method is correct. Since there are samples that cannot be determined as parent - child relationships (i.e., there are non - parent - child relationships), it shows that there is an error in this pedigree and it needs to be reconstructed.
[0059] 3. After verification of the 27 pigs in the wrong - mother group, the coefficient of relationship I ij The maximum value is only 0.2901 and the minimum value is - 0.0740, not within the range of 0.3 - 0.8; and the gene transmission error rate E ij The minimum value is 0.0315 and the maximum value is 0.0922, which also does not meet the condition that E ij is less than 0.01. Therefore, neither of the two data can be determined as a parent - child relationship. The verification result is consistent with the actual situation, indicating that this paternity testing method is correct. Since there are samples that cannot be determined as parent - child relationships (i.e., there are non - parent - child relationships), it shows that there is an error in this pedigree and it needs to be reconstructed.
[0060] In summary, by sampling the DNA tissues of the piglets recorded in the pedigree and their parents, then performing genomic SNP genotyping on all sampled individuals, and finally calculating the coefficient of relationship and the gene transmission error rate to verify the correctness of the parent - child relationship in the pedigree, the method can effectively identify whether the parent - child relationship between the piglets and their parents is established, and further determine whether the pedigree is correct, and the accuracy rate of the identification is 100%.
[0061] Example 2 Reconstruction method of the breeding pig pedigree
[0062] For the samples with determined pedigree errors, calculate the coefficient of relationship and the gene transmission error rate pairwise between the piglets with pedigree errors and other individuals in the pig farm (all pigs that have served as fathers or mothers) (first sample the DNA tissues of the piglets with pedigree errors and other individuals in the pig farm, then perform genomic SNP genotyping on the sampled individuals, and finally calculate the coefficient of relationship and the gene transmission error rate. The calculation formulas for the coefficient of relationship and the gene transmission error rate are as shown in Example 1). It is required that both the coefficient of relationship I ij value is within the range of 0.3 - 0.8 and the gene transmission error rate E ijIt can be determined as a parent - offspring relationship only when it is less than 0.01. (If the individual meeting the requirements is a sow, it is the mother of the piglet; if the individual meeting the requirements is a boar, it is the father of the piglet). In this way, the correct father or mother can be retrieved, and pedigree reconstruction can be carried out. The reconstruction method is as Figure 2 shown in
[0063] For example, for the piglets in the father - error group and mother - error group in Example 1, by using the pedigree reconstruction method to calculate the kinship and gene - transfer error rate pairwise among the individuals in the pig farm, all the parents of the piglets in the father - error group and mother - error group were successfully retrieved. Taking the 18 individuals in the "father - error group" as an example, the retrieved information is shown in Table 2 below:
[0064] Table 2 Pedigree Reconstruction Result Table
[0065]
[0066]
[0067] From the results in Table 2, it can be seen that when the father is incorrect, the maximum value of the kinship coefficient I ij is only 0.1519, and the minimum value is - 0.0827, neither of which belongs to the range of 0.3 - 0.8; and for the gene - transfer error E ij the minimum value is 0.0425 and the maximum value is 0.0816, which also does not meet the condition that E ij is less than 0.01. Therefore, none of them can be determined as a parent - offspring relationship. When calculating the kinship and gene - transfer error rate with other boars, only when both the kinship coefficient I ij is in the range of 0.3 - 0.8 and the gene - transfer error rate E ij is less than 0.01 for pairwise pigs are they considered to have a parent - offspring relationship, and the correct father can be retrieved. Moreover, when the father is correct, the maximum value of the kinship coefficient I ij is only 0.5397, and the minimum value is 0.4043, both of which belong to the range of 0.3 - 0.8; and for the gene - transfer error E ij the minimum value is 0.00083 and the maximum value is 0.00171, which also meets the condition that E ij is less than 0.01. So, it is judged that there is a parent - offspring relationship between pairwise. And the selected correct sire also coincides with the actual situation (because the individuals in the "father - error group" had the semen taken wrongly deliberately, so their true fathers are known and are exactly the same as the "retrieved father individual number" in Table 2).
[0068] In addition to Duroc pigs, in other pig breeds such as Large White, Landrace or other local pig breeds and commercial pigs, the above - mentioned parent - offspring relationship, pedigree identification and reconstruction methods are applicable, and the verified accuracy is 100%.
[0069] Therefore, the above results all indicate that by using the method in the present invention for parentage, pedigree identification and reconstruction, the accuracy of parentage, pedigree identification and reconstruction is 100%, which plays an important auxiliary role in the subsequent breeding work.
Claims
1. A method for identifying the parentage relationship of pigs, wherein: The method comprises the following steps: S1: DNA tissue sampling between two pig individuals whose parentage is to be identified; S2: Perform genomic SNP typing on sampled individuals; S3: Identify whether there are errors in the pedigree by calculating the kinship and gene transmission error rate, wherein the kinship is calculated by using the genomic SNP genotypes between individuals, using the following calculation formula: Where: I ij represents the kinship relationship between individual i and individual j, B ik is the genotype of the kth SNP site of individual i, B jk is the genotype of the kth SNP site of individual j. The genotypes AA, Aa, and aa are represented by 0, 1, and 2, respectively. k is the allele frequency of the kth SNP site a, and m is the total number of SNP sites; The gene transmission error rate is calculated as follows: Where E ij is the proportion of sites with genotype mismatch between individuals i and j, e k is the gene matching degree of the kth SNP site, represented by 0 or 1, and m is the total number of SNP sites; S4: According to I ij Value and E ij Value to determine whether the parent-child relationship is correct: I ij The value is between 0.3-0.8, and E ij When it is less than 0.01, it can be determined as a parent-child relationship, otherwise it is not a parent-child relationship.
2. The method for identifying pig parentage according to claim 1, wherein: In step S3 of the method, k The gene matching degree of the kth SNP site refers to the genotype of individual i and individual j when the genotypes at the kth site are contradictory. k It is recorded as 1, otherwise it is recorded as 0.
3. The method for identifying pig parentage according to claim 2, wherein: The conflicting genotypes of individual i and individual j at the kth site means that the genotypes of individual i at the kth site are AA and that of individual j are aa, or that of individual i is aa and that of individual j is AA.
4. The method for identifying pig parentage according to any one of claims 1 to 3, wherein: The pigs are Duroc breeders.
5. Application of the pig parentage identification method described in any one of claims 1 to 3 in pig parentage identification.
6. A method for identifying pig pedigree, wherein: The method identifies the parentage of all pigs in the pedigree by using the method described in any one of claims 1 to 3, and when the parentage of all pigs is correct, the pedigree is correct; If the parentage of one or more pigs is incorrect, the pedigree is incorrect.
7. Use of the pig pedigree identification method described in claim 6 in pig pedigree identification.
8. A method for reconstructing a pig pedigree, wherein: The method comprises the following steps: S1: When there is a pedigree error, DNA tissue sampling is performed on the piglets in the pedigree error and all pigs that have been fathers or mothers; S2: Perform genomic SNP typing on sampled individuals; S3: For the sampled individuals, the kinship and gene transmission error rate are calculated between each other, wherein the kinship is calculated by using the genomic SNP genotypes between individuals, using the following calculation formula: Where: I ij represents the kinship relationship between individual i and individual j, B ik is the genotype of the kth SNP site of individual i, B jk is the genotype of the kth SNP site of individual j. The genotypes AA, Aa, and aa are represented by 0, 1, and 2, respectively. k is the allele frequency of the kth SNP site a, and m is the total number of SNP sites; The gene transmission error rate is calculated as follows: Where E ij is the proportion of sites with genotype mismatch between individuals i and j, e k is the gene matching degree of the kth SNP site, represented by 0 or 1, and m is the total number of SNP sites; S4: When the I calculated between the piglets ij The value is between 0.3-0.8 and E ij When it is less than 0.01, the individual is the father / mother of the piglet; S5: After finding the correct father / mother, the pedigree of the piglet can be reconstructed.
9. The pig pedigree reconstruction method according to claim 8, wherein: The method further comprises identifying the original pedigree. Pedigree reconstruction is required only if the original pedigree is wrong. The original pedigree is identified by adopting the method described in any one of claims 1-3.
10. Use of the porcine pedigree reconstruction method according to claim 8 or 9 in porcine pedigree reconstruction.