A method for assessing heterosis based on progeny pedigree records and individual phenotypic data
By establishing a hybrid linear model based on offspring pedigree records and individual phenotypic data, the problem of hybrid vigor calculation error when the first generation of hybrids and pure lines of parents cannot be in the same environment was solved, and the effect of accurately assessing hybrid vigor was achieved.
Patent Information
- Authority / Receiving Office
- CN · China
- Patent Type
- Applications(China)
- Current Assignee / Owner
- NORTHEAST AGRICULTURAL UNIVERSITY
- Filing Date
- 2026-03-10
- Publication Date
- 2026-06-09
AI Technical Summary
In animal breeding, the first generation of hybrids and the pure lines of the parents cannot be raised in the same environment, which leads to errors in traditional methods of calculating heterosis and makes it impossible to accurately assess heterosis.
By establishing a mixed linear model based on offspring pedigree records and individual phenotypic data, and using commercial tools such as ASReml software, the heterosis of the first generation of hybrids and pure lines of parents under different environments was calculated, eliminating the influence of environmental effects and calculating heterosis.
Heterosis, including both positive and negative heterosis, was accurately assessed, the influence of environmental effects was eliminated, and the accuracy of the calculation was improved.
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Figure CN122177204A_ABST
Abstract
Description
Technical Field
[0001] This invention belongs to the field of animal breeding, specifically relating to a method for evaluating heterosis based on offspring pedigree records and individual phenotypic data. Background Technology
[0002] Hybridization is one of the main methods of animal breeding. Through hybridization, heterosis can be fully utilized to cultivate breeds (crossbreeding lines) with good performance in different production traits. Most livestock and poultry breeds, including pigs and chickens, originate from hybrids. Heterosis refers to the F1 generation (offspring generation) produced by crossing different populations exhibiting superior viability, body weight, and other traits compared to the average level of the two parent populations. With further research, cases where the F1 generation's traits are superior to the average level of the two parent populations are defined as "positive heterosis," while cases where the F1 generation's traits are inferior to the average level of the two parent populations are defined as "negative heterosis." Accurately calculating heterosis helps assess the specific combining ability between different pure lines and provides a reference for developing hybridization programs. The traditional method for calculating heterosis is as follows: ,in, Indicates heterosis, This represents the average phenotypic value of the first generation of hybrids. This represents the average phenotypic value of the parents. Traditional methods for calculating heterosis require that the F1 generation of hybrids be raised simultaneously with pure male and female lines as controls to eliminate the influence of the rearing environment on phenotypic values.
[0003] In actual animal breeding work, when this invention needs to evaluate the heterosis between two strains, the F1 hybrids and the parent pure lines are often unable to be raised in the same building due to limitations such as biosecurity and space. Therefore, there are various environmental effects between the F1 hybrids and the parent pure lines phenotypic data. Common environmental effects include the rearing batch effect, and may also include the rearing building and hatching batch.
[0004] When F1 hybrids and parental purelines are raised in different environments, the environmental effects on phenotypic traits can introduce errors into traditional heterosis calculation methods. Therefore, there is an urgent need for a method to assess heterosis in practical animal breeding work, addressing the inapplicability of traditional heterosis calculation methods when F1 hybrids and parental purelines are not raised in the same environment. This method can calculate heterosis by raising F1 hybrids and parental purelines separately, utilizing offspring pedigree records and individual phenotypic data. Summary of the Invention
[0005] This invention provides a method for assessing heterosis based on offspring pedigree records and individual phenotypic data, addressing the problem that traditional heterosis calculation methods are inapplicable when the first-generation hybrids and the parental purelines are not raised in the same environment. This method can calculate heterosis using offspring pedigree records and individual phenotypic data by raising the first-generation hybrids and the parental purelines separately.
[0006] This invention is achieved through the following technical solution: A method for assessing heterosis based on offspring pedigree records and individual phenotypic data, the method comprising the following steps: Step 1: Select purebred male A, purebred female A, purebred male B, and purebred female B for evaluating heterosis, and record the individual numbers of purebred A and purebred B respectively. Each individual number must be a unique number. Step 2: Conduct pureline hybridization experiments and pureline closed-loop breeding experiments. The two experiments are not in any particular order. Step 3: Using the data collected in Step 2, calculate heterosis using a mathematical model when the F1 hybrids and purebred parents are raised in different environments. .
[0007] Furthermore, step 2, conducting the purebred hybridization experiment, specifically involves raising purebred hybrid offspring individuals and recording the individual ID, father ID, mother ID, individual phenotypic data, and environmental fixation effect data of the first generation of hybrids.
[0008] Furthermore, step 2, conducting a purebred closed breeding experiment, specifically involves raising purebred offspring individuals and recording the individual ID, father ID, mother ID, individual phenotypic data, and environmental fixation effect data of the purebred offspring.
[0009] Furthermore, the mathematical model for step 3 is as follows:
[0010] Where y represents the individual phenotypic value. This indicates multiple environmental fixed effects that influence phenotype; mating refers to mating mode. This indicates the random genetic effects inherited from the father in individuals. denoted by , e represents the random genetic effect of an individual from the mother, and e represents the random residual.
[0011] Furthermore, the individual phenotypic values include phenotypic data of the first generation of hybrids and phenotypic data of pure-line offspring; The mating methods include A_A, B_B, A_B, and B_A, where A_A represents a purebred A individual, B_B represents a purebred B individual, A_B represents a purebred A♂ × purebred B♀ hybrid individual, and B_A represents a purebred B♂ × purebred A♀ hybrid individual.
[0012] Furthermore, and The variance is set as Let the variance of e be denoted as Using commercially available mixed linear modeling tools, the mathematical model was solved using existing REML and BLUP algorithms to obtain the effect values of each level in mating patterns.
[0013] Furthermore, average heterosis:
[0014] Hybrid vigor of purebred A♂ × purebred B♀:
[0015] Hybrid vigor of purebred B♂ × purebred A♀:
[0016] Where mating represents the effect value of each level in mating mode.
[0017] A system for assessing heterosis based on offspring pedigree records and individual phenotypic data, the system employing the method described above for assessing heterosis based on offspring pedigree records and individual phenotypic data, the system comprising: Selection module: Select purebred males A, purebred females A, purebred males B, and purebred females B for evaluating heterosis, and record the individual numbers of purebred A and purebred B respectively. Each individual number must be a unique number. Experimental module: Conduct pure line hybridization experiments and pure line closed breeding experiments. There is no specific order between the two experiments. Computational Module: Using data collected in the experimental module, the mathematical model is solved using the commercially available mixed linear modeling tool ASReml. This yields the effect values at each level of the mating mode fixed effect, allowing for the calculation of heterosis in the F1 generation of hybrids and purebred parents raised in different environments. .
[0018] A method for assessing heterosis based on offspring pedigree records and individual phenotypic data, as described above, is applied to assessing heterosis when the first generation of hybrids and the parent purelines are not raised in the same environment.
[0019] The beneficial effects of this invention are: This invention treats the genetic effects of parental individuals as random effects. By solving the mixed linear model equations and eliminating the influence of environmental effects, heterosis, including both positive and negative heterosis, can be calculated. Attached Figure Description
[0020] Figure 1 This is a flowchart of the method of the present invention. Detailed Implementation
[0021] In the following description, specific details such as particular system architectures and techniques are set forth for illustrative purposes and not for limitation, in order to provide a thorough understanding of the embodiments of this application. However, those skilled in the art will understand that this application may also be implemented in other embodiments without these specific details. In other instances, detailed descriptions of well-known systems, apparatuses, circuits, and methods are omitted so as not to obscure the description of this application with unnecessary detail.
[0022] It should be understood that, when used in this specification and the appended claims, the term "comprising" indicates the presence of the described features, integrals, steps, operations, elements and / or components, but does not exclude the presence or addition of one or more other features, integrals, steps, operations, elements, components and / or collections thereof.
[0023] It should also be understood that the terminology used in this application specification is for the purpose of describing particular embodiments only and is not intended to limit the application. As used in this application specification and the appended claims, the singular forms “a,” “an,” and “the” are intended to include the plural forms unless the context clearly indicates otherwise.
[0024] The technical solutions in the embodiments of this application will be clearly and completely described below with reference to the accompanying drawings. Obviously, the described embodiments are only a part of the embodiments of this application, and not all of the embodiments. Based on the embodiments of this application, all other embodiments obtained by those of ordinary skill in the art without creative effort are within the scope of protection of this application.
[0025] Many specific details are set forth in the following description in order to provide a full understanding of this application. However, this application may also be implemented in other ways different from those described herein. Those skilled in the art can make similar extensions without departing from the spirit of this application. Therefore, this application is not limited to the specific embodiments disclosed below.
[0026] Implementation Method 1 This embodiment provides a method for assessing heterosis based on offspring pedigree records and individual phenotypic data. Since it is almost impossible to raise the F1 generation and parents in the same environment in actual breeding work, but calculating heterosis is an important part of breeding work, it is necessary to establish a method that can eliminate environmental errors and calculate heterosis. In actual breeding, it is not possible to raise the F1 generation and parents in the same environment, but phenotypic data and pedigree data are usually recorded. In actual data, the F1 generation and parents (or their offspring individuals) have a pedigree relationship, commonly known as a sibling relationship. This sibling relationship can be used to solve for the environmental effect values affecting the F1 generation and the offspring individuals of the parents, thereby eliminating environmental effects and solving for heterosis.
[0027] Based on actual breeding data, a mixed linear model with heterosis as a fixed effect is established, which also includes other environmental fixed effects.
[0028] To improve the accuracy of heterosis estimation in the model, this invention treats the genetic effects of parental individuals as random effects. By solving the mixed linear model equations and eliminating the influence of environmental effects, heterosis, including both positive and negative heterosis, can be calculated.
[0029] The specific method includes the following steps: Step 1: Select purebred male A, purebred female A, purebred male B, and purebred female B for evaluating heterosis, and record the individual numbers of purebred A and purebred B respectively. Each individual number must be a unique number. Step 2: Conduct pureline hybridization experiments and pureline closed-loop breeding experiments. The two experiments are not in any particular order. Step 3: Using the data collected in Step 2, calculate heterosis using a mathematical model when the F1 hybrids and purebred parents are raised in different environments. .
[0030] Furthermore, step 2, conducting the purebred hybridization experiment, specifically involves raising purebred hybrid offspring individuals and recording the individual ID, father ID, mother ID, individual phenotypic data, and environmental fixation effect data of the first generation of hybrids.
[0031] Furthermore, step 2, conducting a purebred closed breeding experiment, specifically involves raising purebred offspring individuals and recording the individual ID, father ID, mother ID, individual phenotypic data, and environmental fixation effect data of the purebred offspring.
[0032] Furthermore, the mathematical model in step 3 is a mixed linear model with heterosis as a fixed effect:
[0033] Where y represents the individual phenotypic value. This indicates multiple environmental fixed effects that influence phenotype; mating refers to mating mode. This indicates the random genetic effects inherited from the father in individuals. denoted by , e represents the random genetic effect of an individual from the mother, and e represents the random residual.
[0034] Furthermore, the individual phenotypic values include phenotypic data of the first generation of hybrids and phenotypic data of pure-line offspring; The mating methods include A_A, B_B, A_B, and B_A, where A_A represents a purebred A individual, B_B represents a purebred B individual, A_B represents a purebred A♂ × purebred B♀ hybrid individual, and B_A represents a purebred B♂ × purebred A♀ hybrid individual.
[0035] Furthermore, and The variance is set as Let the variance of e be denoted as Using commercially available mixed linear modeling tools, the mathematical model was solved using existing REML and BLUP algorithms to obtain the effect values of each level in mating patterns.
[0036] Furthermore, average heterosis:
[0037] Hybrid vigor of purebred A♂ × purebred B♀:
[0038] Hybrid vigor of purebred B♂ × purebred A♀:
[0039] Where mating represents the effect value of each level in mating mode. Specific implementation examples: This method is applicable to different livestock and poultry species. Using a subset of individuals from the 26th generation of the high- and low-abdominal-fat bidirectional selection strain of broilers from Northeast Agricultural University as the research subjects, this study evaluated the heterosis in body weight, abdominal fat weight, and abdominal fat percentage when crossing high-fat and low-fat lines. The 26th generation of the high- and low-abdominal-fat bidirectional selection strain of broilers from Northeast Agricultural University included 44 low-fat roosters, 156 low-fat hens, 45 high-fat roosters, and 148 high-fat hens. Low-fat strain was designated as pure line A, and high-fat strain as pure line B. A total of 16 chickens were selected to evaluate heterosis. Among them, there were 4 males of pure line A (individual numbers 10134109, 10118107, 10109309, and 10121106), 4 females of pure line A (individual numbers 20109323, 20121119, 20134120, and 20118126), 4 males of pure line B (individual numbers 10231411, 10210308, 10224206, and 10205307), and 4 females of pure line B (individual numbers 20224221, 20205326, 20231423, and 20210325).
[0041] First, purebred closed-loop breeding was conducted. All individuals of the 26th generation were pedigreed at a male-to-female ratio of approximately 1:4. Targeted insemination was performed, and hatching eggs were collected. After hatching, healthy chicks were selected, wing tags were attached, and chicks were raised to 7 weeks of age. Those with normal weight were slaughtered, and individual weight, abdominal fat weight, and abdominal fat percentage were recorded. A total of 861 valid data records were collected from the purebred offspring, including 440 records for purebred A and 421 records for purebred B.
[0042] Next, a purebred hybridization experiment was conducted. The hybridization experiment was carried out 15 days after the last insemination in the purebred closed-breeding program to ensure effective insemination. Sixteen chickens selected for assessing heterosis were chosen and pedigrees were established using a 1:1 male-to-female ratio. Targeted insemination was performed, and hatching eggs were collected. After hatching, healthy chicks were selected, wing tags were attached, and the chicks were raised to 7 weeks of age. Chickens with normal weight were slaughtered, and individual weight, abdominal fat weight, and abdominal fat percentage were recorded. A total of 61 valid data records were collected in the purebred hybridization experiment, including 33 data points from the purebred A♂ × purebred B♀ hybrid group and 28 data points from the purebred B♂ × purebred A♀ hybrid group.
[0043] Traditional methods for calculating heterosis require that the F1 generation of hybrids be raised simultaneously with purebred male and female lines as controls to eliminate the influence of the rearing environment on phenotypic values. However, in practice, this invention first conducted closed-loop breeding of purebreds to ensure the smooth progress of breeding work, followed by hybridization experiments to obtain phenotypic data of hybrid individuals. Because the purebred offspring and the F1 generation of hybrids were not raised in the same environment, there were batch-to-batch differences between the flocks, making it impossible to accurately assess heterosis using traditional methods. Example 2 establishes a mathematical model that includes environmental effects and mating methods. By eliminating environmental effects from the model, the mating method effect is calculated to assess heterosis.
[0044] The data records of purebred offspring and hybrid offspring obtained in Example 1 were merged and organized into 9 columns: "Individual Number, Father Number, Mother Number, Individual Sex, Feeding Batch, Parental Mating Method, Weight, Abdominal Fat Weight, and Abdominal Fat Percentage". Among them, the individual sex is represented by 1 and 2 to indicate roosters and hens, respectively; the feeding batch is represented by 1 and 2 to indicate the first batch of feeding and the second batch of feeding, respectively; and the parental mating method is represented by A_A, B_B, A_B, and B_A to indicate purebred A individuals, purebred B individuals, purebred A♂ × purebred B♀ hybrid individuals, and purebred B♂ × purebred A♀ hybrid individuals, respectively.
[0045] The mathematical model is established as follows: , where y represents the individual phenotypic value (including phenotypic data of pure-line offspring and phenotypic data of first-generation hybrids). This indicates multiple environmental fixed effects affecting the phenotype (including hatching and rearing batches, sex), and mating indicates the mating method. This indicates the random genetic effects inherited from the father in individuals. Let represent the random genetic effect inherited from the mother, and e represent the random residual. and The variance is set as Let the variance of e be denoted as .
[0046] The mathematical model was solved using the commercially available mixed linear modeling tool ASReml to obtain the effect values for each level in the fixed effect of mating mode. This mathematical model is a mixed linear model. ASReml is an internationally recognized tool for solving mixed linear models; SPSS, JMP, and other software can also be used. The calculated effect values are the relative averages of the levels within the effect. First, an assumption is made regarding the first level of the effect. Given an average of 0, calculate the relative average of the remaining levels with respect to the first level.
[0047] Calculate heterosis for the body weight trait at seven weeks of age. For the body weight trait, solve for... The value is 0g. The value is 72.08184g. The value is 59.63587g. The value is 126.92226g. The average hybridization effect value is (72.08184g + 59.63587g) / 2 = 65.85886g, and the average effect value of the parental pure lines is (0g + 126.92226g) / 2 = 63.46113g. Since the average hybridization effect value is greater than the average effect value of the parental pure lines, it is a positive heterosis (H = 2.39773g).
[0048] Calculate heterosis for the abdominal fat weight trait. For abdominal fat weight, solve for... The value is 0g. The value is 21.306662g. The value is 23.381640g. The value is 94.770100g. The average hybridization effect value is (21.306662g + 23.381640g) / 2 = 22.34415g, and the average effect value of the parental pure lines is (0g + 94.770100g) / 2 = 47.38505g. Since the average hybridization effect value is less than the average effect value of the parental pure lines, it is a negative heterosis (H = -25.0409g).
[0049] Calculate heterosis for the abdominal fat percentage trait. For abdominal fat percentage, solve for... The value is 0g. The value is 1.5272799%. The value is 1.4994472%. The value is 5.9189072%. The average hybridization effect value is (1.5272799% + 1.4994472%) / 2 = 1.513364%, and the average effect value of the parental pure lines is (0g + 5.9189072%) / 2 = 2.959454%. Since the average hybridization effect value is less than the average effect value of the parental pure lines, it is a negative heterosis (H = -1.44609%).
[0050] Implementation Method 2 This embodiment provides a system for assessing heterosis based on offspring pedigree records and individual phenotypic data. The system uses a method for assessing heterosis based on offspring pedigree records and individual phenotypic data as described in Embodiment 1. The system includes: Selection module: Select purebred males A, purebred females A, purebred males B, and purebred females B for evaluating heterosis, and record the individual numbers of purebred A and purebred B respectively. Each individual number must be a unique number. Experimental module: Conduct pure line hybridization experiments and pure line closed breeding experiments. There is no specific order between the two experiments. Computational Module: Using data collected in the experimental module, the mathematical model is solved using the commercially available mixed linear modeling tool ASReml. This yields the effect values at each level of the mating mode fixed effect, allowing for the calculation of heterosis in the F1 generation of hybrids and purebred parents raised in different environments. .
[0051] In practical breeding work, it is almost impossible to raise the F1 generation and the parents in the same environment. The F1 generation of hybrids and the pure lines of the parents often cannot be raised in the same building due to limitations such as biosecurity and space. However, calculating heterosis is an important part of breeding work. Therefore, traditional methods for calculating heterosis are not applicable to this situation, and differences in the rearing environment will introduce errors into the calculation results.
[0052] Implementation Method 3 This embodiment provides a method for assessing heterosis using offspring pedigree records and individual phenotypic data as described in Embodiment 1, which is applied to the problem of assessing heterosis when the first generation of hybrids and the parent purelines are not raised in the same environment.
Claims
1. A method for assessing heterosis based on offspring pedigree records and individual phenotypic data, characterized in that, The method includes the following steps: Step 1: Select purebred male A, purebred female A, purebred male B, and purebred female B for evaluating heterosis, and record the individual numbers of purebred A and purebred B respectively. Each individual number must be a unique number. Step 2: Conduct pureline hybridization experiments and pureline closed-loop breeding experiments. The two experiments are not in any particular order. Step 3: Using the data collected in Step 2, calculate heterosis using a mathematical model when the F1 hybrids and purebred parents are raised in different environments. .
2. The method according to claim 1, characterized in that, Step 2, conducting the purebred hybridization experiment, specifically involves raising purebred hybrid offspring individuals and recording the individual ID, father ID, mother ID, individual phenotypic data, and environmental fixation effect data of the first generation of hybrids.
3. The method according to claim 1, characterized in that, Step 2, conducting a purebred closed breeding experiment, specifically involves raising purebred offspring individuals and recording the individual ID, father ID, mother ID, individual phenotypic data, and environmental fixation effect data of the purebred offspring.
4. The method according to claim 2 or 3, characterized in that, The mathematical model for step 3 is as follows: Where y represents the individual phenotypic value. This indicates multiple environmental fixed effects that influence phenotype; mating refers to mating mode. This indicates the random genetic effects inherited from the father in individuals. denoted by , e represents the random genetic effect of an individual from the mother, and e represents the random residual.
5. The method according to claim 4, characterized in that, The individual phenotypic values include phenotypic data of the first generation of hybrids and phenotypic data of pure-line offspring; The mating methods include A_A, B_B, A_B, and B_A, where A_A represents a purebred A individual, B_B represents a purebred B individual, A_B represents a purebred A♂ × purebred B♀ hybrid individual, and B_A represents a purebred B♂ × purebred A♀ hybrid individual.
6. The method according to claim 4, characterized in that, and The variance is set as Let the variance of e be denoted as Using commercially available mixed linear modeling tools, the mathematical model was solved using existing REML and BLUP algorithms to obtain the effect values of each level in mating patterns.
7. The method according to claim 4, characterized in that, Average heterosis: Hybrid vigor of purebred A♂ × purebred B♀: Hybrid vigor of purebred B♂ × purebred A♀: Where mating represents the effect value of each level in mating mode.
8. A system for assessing heterosis based on offspring pedigree records and individual phenotypic data, characterized in that, The system uses a method for assessing heterosis based on offspring pedigree records and individual phenotypic data as described in any one of claims 1-7, the system comprising: Selection module: Select purebred males A, purebred females A, purebred males B, and purebred females B for evaluating heterosis, and record the individual numbers of purebred A and purebred B respectively. Each individual number must be a unique number. Experimental module: Conduct pure line hybridization experiments and pure line closed breeding experiments. There is no specific order between the two experiments. Computational Module: Using data collected in the experimental module, the mathematical model is solved using the commercially available mixed linear modeling tool ASReml. This yields the effect values at each level of the mating mode fixed effect, allowing for the calculation of heterosis in the F1 generation of hybrids and purebred parents raised in different environments. .
9. A computer program product comprising a computer program / instructions, characterized in that, When the computer program instructions are executed by the processor, they implement steps 1 and 3 of the method of claim 1.
10. A method for assessing heterosis using pedigree records and individual phenotypic data of offspring as described in any one of claims 1-7, applied to the problem of assessing heterosis when the first generation of hybrids and the parent purelines are not raised in the same environment.