A genomic mating method for a boar

Abstract

The application discloses a genomic mating method for a breeding pig, and discloses a method for further scoring genomic genetic mating results, genomic performance mating results, single gene mating results and the number of mating litters of a boar core group, and calculating the average of each score value, so as to quantize the effect of each combination of a male and a female through the score value. A field staff can select a mating order according to the score value from high to low according to the average score value of each group, so as to realize accurate mating and eliminate the influence of a subjective factor, and the method is more scientific and accurate.

Description

TECHNICAL FIELD

[0001] The present application relates to the field of animal genetics and breeding, in particular to a genomic mating method for breeding pigs. BACKGROUND

[0002] Genomic mating is an important part of breeding pigs. In the published patent "A genomic breeding method for breeding pigs" (Patent No. ZL202210578814.8, Publication No. CN 114931127A), a genomic mating method has been developed, but this method only provides the calculation method of genomic kinship mating, performance mating, and single gene mating for breeding pigs (see the patent specification for details). However, it does not provide how to obtain the final mating scheme based on these calculation results. Field staff often only rely on their own feelings to determine the final mating combination based on the above results, which has a large subjective nature, making the mating effect greatly discounted, and the accuracy and efficiency are very low.

[0003] Therefore, there is an urgent need for a mating method that can quantify the mating results in the above-mentioned patent. The mating results of each public-private combination to be mated are quantified by scores, thereby providing more explicit references for field mating personnel to achieve precise mating. SUMMARY

[0004] The purpose of the present application is to provide a genomic mating method for breeding pigs, which assigns scores to the mating results and calculates the average score of each score, and selects the mating order according to the score from high to low, thereby providing more explicit references for field mating personnel to achieve precise mating.

[0005] According to a first aspect of the present application, a genomic mating method for breeding pigs is provided, comprising:

[0006] 1) Organizing sampling of the public and private pigs to be mated;

[0007] 2) Genomic SNP typing of the public and private pigs to be mated;

[0008] 3) Genomic kinship mating, genomic performance mating, and single gene mating;

[0009] The genomic kinship mating is calculated by using the genomic information of the individual to calculate the inbreeding coefficient of the expected offspring of all public and private pigs to be mated, using the following calculation formula:

[0010]

[0011] In the formula, Iij is the expected inbreeding coefficient of the offspring of the ith boar and the jth sow, Bik is the genotype of the ith boar at the kth SNP site, Bjk is the genotype of the jth sow at the kth SNP site, the genotypes AA, Aa and aa are represented by 0, 1 and 2 respectively, pk is the allele frequency of the kth SNP site a, and m is the total number of SNP sites;

[0012] In the formula, E() represents mathematical expectation, GVo is the genetic value of the offspring, ai represents the additive effect value of the ith site, and di represents the dominant effect value of the ith site. Before the calculation result, the probability of each genotype of each site of the offspring is predicted according to the genotypes of the boar and the sow, and the additive effect and the dominant effect value are calculated, and then the expected genetic value of the offspring is obtained by accumulating all the sites.

[0013]

[0014] In the formula, E() represents mathematical expectation, GVo is the genetic value of the offspring, ai represents the additive effect value of the ith site, and di represents the dominant effect value of the ith site. Before the calculation result, the probability of each genotype of each site of the offspring is predicted according to the genotypes of the boar and the sow, and the additive effect and the dominant effect value are calculated, and then the expected genetic value of the offspring is obtained by accumulating all the sites.

[0015] In the formula, E() represents mathematical expectation, GVo is the genetic value of the offspring, ai represents the additive effect value of the ith site, and di represents the dominant effect value of the ith site. Before the calculation result, the probability of each genotype of each site of the offspring is predicted according to the genotypes of the boar and the sow, and the additive effect and the dominant effect value are calculated, and then the expected genetic value of the offspring is obtained by accumulating all the sites.

[0016] The method further comprises calculating and scoring the selection result in step 3), and selecting the optimal combination for mating according to the score. The method for calculating and scoring comprises:

[0017] S1: Scoring the result of genomic inbreeding selection: first set an upper limit value A and a lower limit value B for the inbreeding coefficient. When the inbreeding coefficient is lower than the lower limit value B, the full score is 100. When the inbreeding coefficient is between A and B, the score is calculated as follows: score = 100-200×inbreeding coefficient value%. When the inbreeding coefficient is greater than the upper limit value A, the score is 0.

[0018] S2: Scoring the result of genomic performance selection: taking the average selection index value calculated from the selected on-farm core group of sows and the core group of boars as the reference value X, and taking the calculated selection index value as S, the score is calculated as follows: score = 100+2.0×(S-X), the upper limit is 110 points, and there is no lower limit.

[0019] S3: Scoring the result of single gene selection: if there is no letter in the selection result, the score is 100 points; each time a capital letter appears, deduct 4 points, and each time a lowercase letter appears, deduct 2 points; if there is no genotype combination, deduct 4 points.

[0020] S4: calculating the average score of the scores in S1-S3, and selecting the mating priority combination order according to the scores from high to low.

[0021] Therefore, by further scoring the genomic genetic mating result, the genomic performance mating result and the single gene mating result, and calculating the average of the scores, the on-site staff can select the mating order according to the scores from high to low according to the average scores of each group, so as to achieve accurate selection and eliminate the influence of subjective factors, and the method is more scientific and accurate.

[0022] In some embodiments, the upper limit value A in S1 is 6.25, and the lower limit value B is 2.

[0023] In some embodiments, the reference value X in S2 is the average of the selection indexes calculated for each sow and boar in the selected field, that is, the reference value X.

[0024] In some embodiments, the above method is suitable for the selection of breeding group sows.

[0025] In some embodiments, when the core group sows need to be selected, the number of mating litters of the boar core group is also scored, and the scoring method comprises: setting an upper limit value Y of the number of mating litters of the boar core group, when the number of mating litters is more than 80% but not more than Y, deducting 1 point for each additional litter, when the number of mating litters is more than Y, deducting 2 points for each additional litter, and not setting a lower limit, and when the number of mating litters is less than 80% of Y, the score is 100 points.

[0026] In some embodiments, the upper limit value Y is set as Y=0.11K, and K is the number of core group sows.

[0027] In some embodiments, the calculation method of Y=0.11K is as follows: the ratio of sows to boars in the core field is 1:30, the annual replacement rate of boars is controlled at 100%, each core group sow has 2.5 litters per year, and the number of core group sows in the field is K, then the average number of mating litters of each boar in the core group sows is 2.5x100% / 30xK=0.083K; when the boar is excellent, the number of mating litters is allowed to be 30% higher than the average number, so the upper limit value Y should be set as 0.083Kx130%=0.11K.

[0028] In some embodiments, when the core group sows are selected, the total score is = (genomic genetic mating result score + genomic performance mating result score + single gene mating result score + boar core group mating litter score) / 4.

[0029] According to a second aspect of the present application, the above method is applied to the selection of breeding pigs.

[0030] According to a third aspect of the present application, a computer application method for boar genomic mating is provided, which is based on the above-mentioned boar genomic mating method and the calculation results thereof. Thus, the software designed by the computer application method can directly calculate the scores of each male-female combination, or directly sort and output the order of mating a certain female with a male boar (according to the scores from high to low), which is more convenient for on-site staff to mate and improves the mating efficiency.

[0031] Advantages of the present application:

[0032] 1. By the method of the present application, the genomic kinship mating results, genomic performance mating results, single gene mating results, and the number of litters of a core group of male boars are further scored, and the average of each score is calculated. The mating results of each male-female combination are quantified by scores. On-site staff can select the mating order according to the average scores of each group from high to low, achieve accurate mating, eliminate the influence of human subjective factors, and be more scientific and accurate.

[0033] 2. The final mating results of each male-female combination are summarized into a score, and the score is used to determine which semen of a male boar is used for mating a female boar. This method is simple, efficient, and convenient, and can maximize the elimination of the influence of human subjective factors, and be more scientific and accurate.

[0034] 3. The scoring method of the present application can be designed into the software function to directly calculate the scores of each male-female combination, or directly sort and output the order of mating a certain female with a male boar (according to the scores from high to low), which is more convenient for on-site staff to mate and improves the mating efficiency. BRIEF DESCRIPTION OF DRAWINGS

[0035] Figure 1 The flowchart of the present application;

[0036] Figure 2 The mating software interface diagram of one embodiment of the present application. DETAILED DESCRIPTION

[0037] The present application is further described in detail below.

[0038] In the published patent "A genomic breeding method for breeding sows" (Patent No.: ZL202210578814.8, Publication No. CN 114931127 A), a genomic breeding method is disclosed, but this method only provides the calculation method of genomic kinship selection, genomic performance selection, single gene selection, and core group boar mating litter number selection methods for sows (see the patent specification for details), but does not provide how to obtain the final selection scheme based on these calculation results. On-site staff often only rely on their own feelings to determine the final mating combination based on the above results, which has a large subjective nature, making the selection effect greatly discounted.

[0039] Therefore, according to the genomic kinship selection results, genomic performance selection results, single gene selection results, and boar mating litter number results in the core group, this application assigns scores, and different scoring methods are given according to the different nature of the sow population (core group and expansion group). Each item is calculated separately, and finally a total score is obtained, with a higher total score indicating a better mating combination (selection process as shown in Figure 1

[0040] As disclosed in CN 114931127 A, first, select the combination of boars and sows to be mated according to the estrus condition of sows and boar information, then sample DNA from all boars and sows to be mated, then extract DNA through biotechnology, and perform genomic SNP typing. For each site, the SNP genotype is composed of AA, Aa, and aa, which are first converted to 0, 1, and 2, respectively.

[0041] After obtaining the typing results, the additive effect value and dominant effect value of each SNP site are estimated by the genomic selection algorithm (the calculation of additive effect value and dominant effect value is described in the reference Wang C, Prakapenka D, Wang S, et al. GVCBLUP: A Computer Package for Genomic Prediction and Variance Component Estimation of Additive and Dominance Effects. BMC Bioinformatics, 2014, 15(1): 1-9).

[0042] 1. Scoring according to genomic kinship selection results

[0043] Inbreeding in sows can easily lead to population decline, so the inbreeding coefficient needs to be controlled within a certain range. Each male-female combination may have a genomic inbreeding coefficient and a pedigree inbreeding coefficient. First, refer to the genomic inbreeding coefficient, and if not, refer to the pedigree inbreeding coefficient.

[0044] ​Genomic inbreeding selection is to calculate the inbreeding coefficient of all the expected offspring of two individuals by using the genomic information of the individuals, and the following formula is used:

[0045]

[0046] In the formula, Iij is the expected inbreeding coefficient of the offspring of the ith boar and the jth sow, Bik is the genotype of the ith boar at the kth SNP site, Bjk is the genotype of the jth sow at the kth SNP site, the genotypes AA, Aa and aa are represented by 0, 1 and 2 respectively, pk is the allele frequency of the kth SNP site a, and m is the total number of SNP sites.

[0047] When the inbreeding coefficient is calculated, a upper limit value A and a lower limit value B need to be set. The setting standards of the upper limit value A and the lower limit value B are as follows: there is more or less inbreeding in the breeding process of the pig population, and generally an inbreeding coefficient within 2% will not have a great impact on the pig population. However, the inbreeding coefficient cannot be too high, and generally, when the distance between two individuals and the common ancestor is within three generations, it is considered to be high inbreeding (inbreeding coefficient greater than 6.25%). Therefore, if the inbreeding coefficient of the offspring of two individuals exceeds 6.25%, the two individuals are not allowed to mate. Therefore, the upper limit value A can be set to 6.25, and the lower limit value B can be set to 2. When the inbreeding coefficient is between 2 and 6.25, mating is allowed but the inbreeding coefficient is as low as possible. When the inbreeding coefficient exceeds the upper limit value 6.25, the score of the combination is 0. When the inbreeding coefficient is lower than 2, the score is 100. When the inbreeding coefficient is between 2 and 6.25, the following strategy is used to calculate the score: score = 100-200 x inbreeding coefficient value %. The inbreeding selection score of the sows in the core population and the multiplication population is calculated according to the above principles.

[0048] 2. Scoring according to the results of genomic performance selection

[0049] Genomic performance selection is to calculate the additive effect and dominant effect values of each SNP site first, and then use the following formula for genomic performance selection:

[0050]

[0051] In the formula, E() represents mathematical expectation, GVo is the genetic value of the offspring, ai represents the additive effect value of the ith site, and di represents the dominant effect value of the ith site. Before calculating the results, the probability of each genotype appearing at each site of the offspring and the additive effect value and dominant effect value are predicted according to the genotypes of the boars and sows, and then all the sites are added to obtain the expected genetic value of the offspring.

[0052] The score of the selection of the core group sows is calculated as follows: according to the average selection index value (the selection index is the maternal index in the Large White and the Long White, and the paternal index in the Duroc) of the selected core group sows and the core group boars, the average index value is taken as the reference value X. A selection index value S can be calculated for each boar-sow combination (calculated by formula (2)), and the score is calculated by the following formula: score = 100 + 2.0 x (S-X), with an upper limit of 110 points and no lower limit.

[0053] The score of the selection of the core group sows is calculated as follows: according to the average selection index value (the selection index is the maternal index in the Large White and the Long White, and the paternal index in the Duroc) of the selected core group sows and the core group boars, the average index value is taken as the reference value X. A selection index value S can be calculated for each boar-sow combination (calculated by formula (2)), and the score is calculated by the following formula: score = 100 + 2.0 x (S-X), with an upper limit of 110 points and no lower limit.

[0054] 3. Scoring according to the results of single gene selection

[0055] Single gene selection is to calculate the probability of the occurrence of harmful genotypes in offspring by Mendelian inheritance law, and when the probability is ≥25% and <50%, a lowercase letter is used as a prompt, and when the probability is ≥50%, an uppercase letter is used as a prompt. A unique letter is used for each locus, and if there are multiple loci to be selected by single gene selection, each locus is calculated separately, and then the letters are combined for evaluation.

[0056] The results of single gene selection are prompted by letters, and when there is a letter prompt, it means that an unfavorable genotype has occurred, and an uppercase letter indicates the occurrence of an unfavorable homozygous genotype, and a lowercase letter indicates the occurrence of an unfavorable heterozygous genotype. When there are multiple unfavorable genotypes, there will be multiple letter prompts. The scoring logic is as follows: the full score is 100 points, 4 points are deducted for each uppercase letter, and 2 points are deducted for each lowercase letter. For combinations without genotyping, 4 points are deducted uniformly, and no letter appears, which is recorded as 100 points.

[0057] 4. Scoring according to the number of boar core group mating litters

[0058] The selection score of the core group sows is calculated as follows: each core group boar has an upper limit of the number of mating litters (the upper limit is set as Y), and the Y setting standard is: the core farm male to female ratio is usually 1:30, the annual replacement rate of boars is controlled at 100%, each core group sow mates 2.5 litters per year, assuming that the number of core group sows in the farm is K, then the average number of mating litters of each boar in the core group sows is 2.5x100% / 30xK=0.083K. When the boar is more excellent, the mating litter number is allowed to be 30% higher than the average litter number, so the upper limit Y should be set as 0.083Kx130%=0.11K. When the mating number exceeds 80% of Y but does not exceed Y, the combination is deducted 1 point for each additional litter. When it exceeds Y, the combination is deducted 2 points for each additional litter, and there is no lower limit. When the mating number is less than 80% of Y, it is full score 100 points. The selection of the multiplication group sows does not consider the mating litter number limit of the core group boars, so there is no need to calculate this item score.

[0059] The core group sows take the scores of the above 1-4 items (genomic kinship selection result, genomic performance selection result, single gene selection result, and boar core group mating litter result), and the multiplication group sows take the scores of 1-3 items (genomic kinship selection result, genomic performance selection result, and single gene selection result). After calculating the average value, the final score of each male-female combination is obtained, and the higher the score, the better the selection effect of the combination. Because the calculation logic of the core group and the multiplication group sows is not completely consistent, the final selection priority is also ranked separately.

[0060] 5. Application case of the selection method

[0061] Ten core group sows and five core group boars in a certain farm under Wens Food Group were selected, and the selection software developed according to the selection method disclosed in CN 114931127A patent was used for calculation, and the selection interface as shown in Figure 2 was obtained, and the selection interface as shown in Figure 2In the breeding software interface shown, the leftmost header (light green) represents the performance of the sows to be bred. Taking the first sow in the header as an example, its individual number is BX23-B02403, core level 1, maternal index 151.07, reproductive index 125.43, and paternal index 189.54. The top header (light green) represents the performance of the boars to be bred. Taking the first boar as an example, its individual number is BX23-B00598, core level 1, number of litters bred 71, maternal index 157.08, reproductive index 127.51, and paternal index 201.44. Each row (white) in the table represents the bred results of a single sow with all the boars to be bred, and each column represents the bred results of a single boar with all the sows to be bred. Taking the first row and first column of the table (white) as an example: This represents the mating calculation results of sow BX23-B02403 and boar BX23-B00598. "**" indicates that either the pedigree inbreeding coefficient or the genomic inbreeding coefficient exceeds 6.25. From left to right in the top row: 11.43 represents the genomic inbreeding coefficient, 13.15 represents the pedigree inbreeding coefficient, and blank spaces represent single-gene mating results. From left to right in the bottom row: 154.08 represents the maternal index, 126.47 represents the reproductive index, and 195.49 represents the paternal index. In this example, only the "ranking trait" is scored in the genomic performance mating results. Figure 2 In this study, ranking is based on the "maternal index," therefore, the genomic performance selection results are scored solely based on the "maternal index." Each category of each combination is scored according to the scoring method described in this application (Note: This farm allows each core herd boar to breed with a maximum of 90 litters among core herd sows; the average index value of the core herd boars and sows in this farm is...). ( (That is, the average maternal index) is 143.28). Figure 2 Taking the results of boar BX23-B00598 and sow BX23-B02403 as an example, their genomic inbreeding coefficient is 11.43, and their pedigree inbreeding coefficient is 13.15, exceeding the upper limit of 6.25, thus scoring 0. In genomic performance selection, the maternal index is 154.08, and the calculated score is 100 + 2.0 × (154.08 - 143.28) = 121.6, which is greater than 110, so the upper limit of 110 is used. In single-gene selection, there are no letter prompts, so a full score of 100 is awarded. Regarding the number of matings in the core group, the boar's litter count of 71 is lower than 80% of the upper limit (90 litters), so a full score of 100 is awarded. Following the above method, the scores of boar BX23-B00598 and all sows in various categories are obtained, as shown in Table 1.

[0062] Table 1. Mating scores of boar BX23-B00598 with all sows in various categories.

[0063]

[0064]

[0065] According to the method in Table 1, boars and sows are paired, scoring is performed in each item (pedigree selection, performance selection, single gene selection, core group mating number), and finally the average value is taken on each score, for example, boar BX23-B00598 and sow BX23-B02403, according to the data in Table 1, the score score = (0 + 110 + 100 + 100) / 4 = 77.5, and so on, the total score (average score) of all boar and sow pairings is calculated, and the results are shown in Table 2:

[0066] Table 2 Total score results of boar and sow pairings

[0067]

[0068] According to the score results in Table 2, it can be determined which boar should be used first for each sow, for example, the first sow BX23-B02403, the priority order of boars used is BX23-B00189, BX22-B05042, BX22-B05089, BX23-B00598, BX22-B03037. The score results are also consistent with the selection principle, although boar BX23-B00598 is relatively good, but it has inbreeding with sow BX23-B02403, so it is ranked last; boar BX22-B03037 not only has inbreeding with the sow, but also seriously exceeds the upper limit of core group mating litter number, so it should not be used as a core group boar, and therefore it is ranked last; the other three boars do not have serious inbreeding with the sow, although the maternal index of boar BX22-B05042 is slightly higher than that of the other two boars, but it has already mated 80 litters in the core group, which is close to the upper limit. Therefore, considering comprehensively, boar BX23-B00189 is ranked first, although its performance is slightly worse than the top three boars, but mating with high index sows can quickly improve the performance of offspring. Therefore, the above-mentioned scoring logic is generally reasonable and feasible, and because each combination has only one score, it greatly simplifies the operation difficulty of on-site personnel to determine the best mating combination.

Claims

1. A genomic mating method for breeding swine, comprising: 1) sampling the tissues of the male and female pigs to be mated; 2) genotyping the genomes of the male and female pigs to be mated; 3) performing genomic inbreeding selection, genomic performance selection, and single gene selection; the genomic inbreeding selection is performed by calculating the expected inbreeding coefficient of the offspring of the mating between any two individuals using the genomic information of the individuals, using the following formula: , wherein Iij is the expected inbreeding coefficient of the offspring of the mating between the ith male pig and the jth female pig, Bik is the genotype of the ith male pig at the kth SNP site, Bjk is the genotype of the jth female pig at the kth SNP site, the genotypes AA, Aa, and aa are represented by 0, 1, and 2, respectively, pk is the allele frequency of a at the kth SNP site, and m is the total number of SNP sites; the genomic performance selection is performed by first calculating the additive effect and the dominant effect values of each SNP site, and then using the following formula to perform the genomic performance selection: , wherein E() represents mathematical expectation, GVo is the genetic value of the offspring, ai represents the additive effect value of the ith site, and di represents the dominant effect value of the ith site; before the calculation, the probability of each genotype at each site of the offspring is predicted according to the genotypes of the male and female pigs, and the additive effect and the dominant effect values are calculated, and then the expected genetic value of the offspring is obtained by accumulating all the sites; the single gene selection is performed by predicting the probability of the occurrence of harmful genotypes in the offspring according to Mendelian inheritance law, and when the probability is ≥ 25% and < 50%, a lowercase letter is used as a prompt, and when the probability is ≥ 50%, an uppercase letter is used as a prompt, a unique letter is used for each site, and if there are multiple sites to be selected by single gene selection, each site is calculated separately, and then the letters are combined together for evaluation; characterized in that the method further comprises calculating scores for the mating results in step 3), and selecting the optimal combination for mating according to the scores, and the method for calculating the scores comprises: S1: scoring the results of the genomic inbreeding selection: first, set an upper limit value A and a lower limit value B for the inbreeding coefficient, when the inbreeding coefficient is lower than the lower limit value B, the score is 100; when the inbreeding coefficient is between A and B, the score is calculated as follows: score = 100-200 × inbreeding coefficient value%; when the inbreeding coefficient is greater than the upper limit value A, the score is 0, the upper limit value A is 6.25, and the lower limit value B is 2; S2: scoring the results of the genomic performance selection: the average selection index value calculated for the selected female pigs and male pigs is used as the reference value X, the calculated selection index value is denoted as S, and the score is calculated as follows: score = 100+2.0 × (S-X), and no lower limit is set; S3: scoring the results of the single gene selection: if no letter appears in the selection results, the score is 100; for each uppercase letter, deduct 4 points, and for each lowercase letter, deduct 2 points; and for each genotype combination, deduct 4 points. S4: When the selected group of sows needs to be mated, the reference value X in step S2 is calculated by taking the average selection index value of the selected group of sows and all boars as the reference value X, and then calculating the average score of the scores in S1-S3, and selecting the mating priority combination order from high to low according to the scores; S5: When the core group of sows needs to be mated, the reference value X in step S2 is calculated by taking the average selection index value of the selected group of sows and the core group of boars as the reference value X, the upper limit of the score of the genomic performance mating result in step S2 is 110 points, and the method further comprises assigning scores to the number of mating litters of the boar core group, the scoring method comprising: setting an upper limit value Y for the number of mating litters of the boar core group, when the mating frequency exceeds 80% but does not exceed Y, each additional litter deducts 1 point from the combination; when it exceeds Y, each additional litter deducts 2 points from the combination, and there is no lower limit; when the mating frequency is less than 80% of Y, it is full score 100 points, the upper limit value Y is set as Y=0.11K, K is the number of core group sows, and the total score is = (genomic kinship mating result score + genomic performance mating result score + single gene mating result score + boar core group mating litter number score) / 4, the mating priority combination order is selected from high to low according to the scores.

2. The method of claim 1, wherein, The calculation method of Y=0.11K is: the core farm has a ratio of 1:30 of boars to sows, the annual replacement rate of boars is controlled at 100%, each core group sow is mated 2.5 times a year, and the number of core group sows in the farm is K, then the average mating litter number of each boar in the core group sows is 2.5x100% / 30xK=0.083K; when the boar is relatively excellent, the mating litter number is allowed to be 30% higher than the average litter number, therefore the upper limit value Y should be set as 0.083Kx130%=0.11K.

3. The method of any one of claims 1 or 2 for use in breeding pig mating.

4. A computer application method useful for genomic selection of breeding swine, characterized in that, The computer application method is realized based on the method of any one of claims 1 or 2 and the calculation results thereof.

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