Method for breeding optimization of aquatic animals

Abstract

The application discloses an aquaculture animal breeding optimization method, and solves the problems of the existing technology in formulating a selection index, which is not conducive to formulating a mating scheme and affects the accuracy and reliability of selection breeding. The aquaculture animal selection index formulation comprises the following steps: acquiring the measured values of all breeding target traits of all individuals or families and the inbreeding coefficients of all individuals or families; acquiring the breeding values of each trait, the average breeding values of each trait and the standard deviations of the breeding values according to the measured values; determining the average inbreeding coefficients and the standard deviations of the inbreeding coefficients of all individuals or families according to the inbreeding coefficients; calculating trait standardized breeding values; calculating standardized inbreeding coefficients; calculating comprehensive breeding values according to the trait standardized breeding values and the standardized inbreeding coefficients; and determining a selection index according to the comprehensive breeding values.

Description

[0001] This application is a divisional application. The original application was entitled "Method for Determining Selection Index of Aquatic Animals and Method for Selection Breeding", with application number 202310272856.3 and application date of March 20, 2023. Technical Field

[0002] This invention belongs to the field of aquatic genetic breeding technology, specifically, it relates to a method for determining selection indices for aquatic animals and a method for selective breeding of aquatic animals. Background Technology

[0003] In selective breeding of aquatic animals, simultaneous selection of multiple traits can improve the overall genetic progress and economic benefits of breeding objectives. Current multi-trait selection breeding research typically uses selection indices for families or individuals to achieve selection or elimination.

[0004] In existing technologies, when developing selection indices for families or individuals, the trait standardization is first calculated according to the following standardized formula.

[0005] Breeding value: Then, calculate the selection index according to the following formula: p , = [p1p2…pn], vi, = [vi1vi2…vin]. Where i represents the individual or family number, j represents the trait number, n represents the number of traits, vij represents the standardized breeding value of the j-th trait of the i-th individual or family, and aij represents the breeding value of the j-th trait of the i-th individual or family. Let σj represent the average breeding value of the j-th trait, σj represent the standard deviation of the breeding value of the j-th trait, Ii represent the selection index of the i-th individual or family, r is a variable controlling the magnitude of variation among selection indices, and pj represent the weighted value of the j-th trait. , Let represent the vector composed of the weighted values ​​of n traits, and let vi represent the standardized breeding value vector of the breeding target trait of the i-th individual or family.

[0006] The selection index is formulated using the above method, standardizing the breeding value of each trait into a set of data with a mean of 0 and a standard deviation of 1. The resulting range of standardized breeding values ​​for each trait is not fixed, and the range of standardized breeding values ​​from multiple traits combined into a selection index is also not fixed. This leads to the need for multiple iterations to converge when using optimization algorithms to formulate mating schemes, making the process of finding the optimal solution relatively complex and difficult to converge correctly. Furthermore, the selection index formulation process only considers the breeding value of the trait and does not reflect the inbreeding situation of individuals or families, failing to fully represent the breeding value of individuals or families and affecting the accuracy and reliability of genetic selection breeding. Summary of the Invention

[0007] One of the objectives of this invention is to provide a method for determining selection indices for aquatic animals, thereby addressing the problems of existing methods for determining selection indices, such as hindering the development of mating plans and affecting the accuracy and reliability of selection breeding.

[0008] To achieve the above-mentioned objectives, the present invention employs the following technical solution:

[0009] A method for determining an aquatic animal selection index, the method comprising:

[0010] Obtain the measured values ​​of all breeding target traits for all individuals or families, as well as the inbreeding coefficient Fi for all individuals or families;

[0011] Based on the measured values, the breeding value aij for each trait and the average breeding value for each trait are obtained. And the breeding value standard deviation σj; based on the inbreeding coefficient Fi, determine the average inbreeding coefficient F and the inbreeding coefficient standard deviation σ′ for all individuals or families;

[0012] Calculate the standardized breeding value of the trait a′ij:

[0013] Calculate the standardized inbreeding coefficient Fi′:

[0014] Calculate the comprehensive breeding value Yi based on the standardized breeding value a′ij and the standardized inbreeding coefficient Fi′:

[0015] The selection index Ii is determined based on the comprehensive breeding value Yi:

[0016] Where a′ij represents the standardized breeding value of the j-th trait of the i-th individual or family; aij represents the breeding value of the j-th trait of the i-th individual or family; σj represents the average breeding value of the j-th trait; σj represents the standard deviation of the breeding value of the j-th trait; Tanh represents the hyperbolic function; F i Represents the inbreeding coefficient of the i-th individual or family; F represents the average concordance coefficient; σ′ represents the standard deviation of the concordance coefficient, σ′≠0; i ' represents the standardized inbreeding coefficient of the i-th individual or family; m1, k1, q1, m2, k2, and q2 are all constants greater than 0; Yi represents the composite breeding value of the i-th individual or family; n represents the total number of traits; p jrepresents the weighted value of the j-th trait, which is a known value; wi represents the weighted value of the inbreeding coefficient of the i-th individual or family, which is a known value; Ii represents the selection index of the i-th individual or family; N represents the total number of individuals or families; respectively represent the minimum value and the maximum value among the N comprehensive breeding values.

[0017] In some embodiments of the present application, the value range of m1 is: 0<m1<1; the value range of m2 is: 0<m2<1; the value range of k1 is: 0<k1≤0.02; the value range of k2 is: 0<k2≤0.02.

[0018] In some embodiments of the present application, m1, k1, m2, and k2 satisfy: m1=m2=0.5, k1=k2=0.01.

[0019] In some embodiments of the present application, q1 and q2 satisfy: q1=q2=1.

[0020] In some embodiments of the present application, the weighted value wi of the inbreeding coefficient satisfies: -1≤wi≤0.

[0021] In some embodiments of the present application, the weighted value wi of the inbreeding coefficient satisfies: wi=-0.1.

[0022] The second objective of the present invention is to provide a selective breeding method for aquatic animals, which improves the accuracy, reliability and efficiency of selective breeding.

[0023] To achieve the above purpose of the invention, the method of the present invention adopts the following technical solutions:

[0024] A selective breeding method for aquatic animals, the method comprising:

[0025] acquiring the individual selection index of a test individual and the family selection index of a test family;

[0026] selecting reserved breeding families and reserved breeding individuals in the reserved breeding families according to the reserved breeding scheme, the individual selection index and the family selection index;

[0027] performing selective breeding based on the reserved breeding families and the reserved breeding individuals;

[0028] The individual selection index and the family selection index are formulated by the method for formulating an aquatic animal selection index according to any one of claims 1 to 6.

[0029] Compared with the prior art, the advantages and positive effects of the present invention are:

[0030] The method for determining selection indices for aquatic animals provided by this invention employs hyperbolic functions to process trait breeding values, average breeding values, and breeding value standard deviations to obtain standardized breeding values ​​for each trait. This ensures that the data distribution of the standardized breeding values ​​remains unchanged, and the range of selection indices determined based on the standardized breeding values ​​is fixed. When subsequently using optimization algorithms to formulate mating schemes, this allows for rapid convergence to obtain the optimal solution, improving the efficiency of selection breeding based on selection indices. Furthermore, this method introduces an inbreeding coefficient reflecting the inbreeding status of individuals or families, standardizes the inbreeding coefficient, determines a comprehensive breeding value based on the standardized inbreeding coefficient and standardized breeding values, and finally formulates a selection index based on the comprehensive breeding value. This allows the selection index to more comprehensively reflect the breeding value of individuals or families, thereby improving the accuracy and reliability of selection breeding based on selection indices.

[0031] Other features and advantages of the present invention will become clearer after reading the detailed embodiments of the invention in conjunction with the accompanying drawings. Attached Figure Description

[0032] To more clearly illustrate the technical solutions in the embodiments of the present invention, the accompanying drawings used in the embodiments will be briefly introduced below. Obviously, the accompanying drawings described below are some embodiments of the present invention. For those skilled in the art, other drawings can be obtained based on these drawings without creative effort.

[0033] Figure 1 A flowchart of an embodiment of the aquatic animal selection index determination method provided by the present invention;

[0034] Figure 2 A flowchart illustrating one embodiment of the aquatic animal selective breeding method provided by the present invention. Detailed Implementation

[0035] To make the objectives, technical solutions, and advantages of this invention clearer, the invention will be further described in detail below with reference to the accompanying drawings and embodiments.

[0036] It should be noted that the technical solutions of the various embodiments of the present invention can be combined with each other, but only if they can be implemented by those skilled in the art. When the combination of technical solutions is contradictory or cannot be implemented, it should be considered that such combination of technical solutions does not exist and is not within the scope of protection claimed by the present invention.

[0037] Figure 1 A flowchart of an embodiment of the aquatic animal selection index determination method provided by the present invention is shown.

[0038] like Figure 1As shown, this embodiment uses the following process to develop a selection index for aquatic animals.

[0039] S11: Obtain the measured values ​​of all breeding target traits for all individuals or families, as well as the inbreeding coefficients for all individuals or families.

[0040] For aquatic animals, the target traits for breeding include, but are not limited to, weight traits, survival rate traits, and disease resistance traits.

[0041] For weight traits, records can be traced back to each individual; therefore, weight trait measurements can be obtained for each individual. Based on the weight trait measurements of all individuals within a family, family weight trait measurements can be obtained. For survival traits, measurements need to be taken on a family basis; therefore, family survival trait measurements can be obtained. The survival trait measurements for each individual within a family are also derived from family survival trait measurements.

[0042] For disease resistance traits, since most individuals die during disease resistance testing, even if a few survive, they cannot be used as breeding individuals because they carry the virus. Therefore, it is necessary to conduct the test on a family basis, so that the family disease resistance trait test value can be obtained. The disease resistance trait test value of each individual in the family is also the family disease resistance trait test value.

[0043] The methods for obtaining weight trait values, survival rate trait values, disease resistance trait values, etc., are implemented using existing technologies.

[0044] The inbreeding coefficient of an individual or family can be obtained using existing pedigree analysis methods.

[0045] S12: Obtain the trait breeding value, average breeding value, and standard deviation of breeding value based on the measured values; determine the average inbreeding coefficient and standard deviation of inbreeding coefficient based on the inbreeding coefficient.

[0046] Based on the measured values ​​of the breeding target traits obtained from S11, the breeding values ​​for each trait were obtained using methods such as pBLUP (pedigree-based best linear unbiased prediction), GBLUP (genomic best linear unbiased prediction), and ssGBLUP (single-step genomic best linear unbiased prediction). The average breeding value and the standard deviation of the breeding value were then obtained. Based on the inbreeding coefficient of each individual or family, the average inbreeding coefficient and the standard deviation of the inbreeding coefficient were obtained using mathematical methods.

[0047] S13: Calculate the standardized breeding value and standardized inbreeding coefficient of the trait.

[0048] Specifically, the standardized breeding value a′ij of the trait is calculated according to the following formula:

[0049]

[0050] Calculate the standardized inbreeding coefficient Fi′ using the following formula:

[0051] In the above formula, a′ij represents the standardized breeding value of the j-th trait of the i-th individual or family; aij represents the breeding value of the j-th trait of the i-th individual or family. σj represents the average breeding value of the j-th trait; σj represents the standard deviation of the breeding value of the j-th trait; Tanh represents the hyperbolic function; Fi represents the proximal coefficient of the i-th individual or family. σ' represents the average inbreeding coefficient; σ′ represents the standard deviation of the inbreeding coefficient, σ′≠0; Fi′ represents the standardized inbreeding coefficient of the i-th individual or family; m1, k1, q1, m2, k2, and q2 are all constants greater than 0.

[0052] The standardized breeding values ​​of traits obtained using the above formula are adjusted using a coefficient k1 to determine the ratio of the difference between each breeding value and the average breeding value to the standard deviation of the breeding values. By appropriately setting the value of coefficient k1, the range of the adjusted value can be compressed to around "0". After applying the hyperbolic Tanh transform, the original data distribution can be kept unchanged within the limited range (-1, 1), and the value range is fixed near the value determined by m1 and q1.

[0053] Inbreeding coefficient is an important indicator in aquatic animal breeding. Incorporating the inbreeding coefficient into the formulation of comprehensive breeding values ​​and selection indices can more comprehensively reflect the breeding value of candidate individuals and families. Moreover, standardizing the inbreeding coefficient to the same order of magnitude as the standardized breeding values ​​of traits facilitates the comprehensive evaluation of breeding values.

[0054] In some embodiments, the value range of m1 is: 0 < m1 < 1; the value range of m2 is: 0 < m2 < 1; the value range of k1 is: 0 < k1 ≤ 0.02; and the value range of k2 is: 0 < k2 ≤ 0.02.

[0055] In other embodiments, m1, k1, m2, and k2 satisfy the following conditions: m1 = m2 = 0.5, k1 = k2 = 0.01. Meanwhile, q1 and q2 satisfy the following condition: q1 = q2 = 1. When k1 = 0.01, m1 = 0.5, and q1 = 1, the standardized breeding value of the trait ranges around 0.5.

[0056] S14: Calculate the comprehensive breeding value based on the trait-standardized breeding value a′ij and the standardized inbreeding coefficient Fi′.

[0057] Specifically, the comprehensive breeding value Yi is calculated according to the following formula:

[0058] In the formula, Yi represents the comprehensive breeding value of the i-th individual or family; n represents the total number of traits; p j represents the weighted value of the j-th trait, which is a known value; wi represents the weighted value of the inbreeding coefficient of the i-th individual or family, which is a known value.

[0059] The comprehensive breeding value obtained using the above formula, which also incorporates the standardized breeding value and standardized inbreeding coefficient, can more comprehensively evaluate the breeding value of an individual or family.

[0060] The weighted value p for each trait j The range of values ​​is: 0 ≤ p j The weighted values ​​are ≤1, and the sum of the weighted values ​​of all traits is 1. The weighted values ​​are determined using existing techniques. In some embodiments, the weighted value of each trait may be determined based on the desired selection intensity and heritability of the target breeding trait.

[0061] In aquatic animal breeding, the inbreeding coefficient weighting value wi ranges from -1 to 0. In some other embodiments, wi = -0.1.

[0062] S15: Determine the selection index based on the comprehensive breeding value.

[0063] After determining the overall breeding value in S14, the selection index Ii is determined using the following formula:

[0064]

[0065] In the formula, Ii represents the selection index of the i-th individual or family; N represents the total number of individuals or families. These represent the minimum and maximum values ​​among the N comprehensive breeding values, respectively.

[0066] The above embodiments employ hyperbolic functions to process trait breeding values, average breeding values, and breeding value standard deviations to obtain standardized breeding values ​​for each trait. This ensures that the data distribution of the standardized breeding values ​​remains unchanged, and the range of the selection index determined based on the standardized breeding values ​​is fixed. This allows for rapid convergence to the optimal solution when using optimization algorithms to formulate mating schemes, improving the efficiency of selection breeding based on selection indices. Furthermore, an inbreeding coefficient reflecting the inbreeding status of individuals or families is introduced and standardized. A comprehensive breeding value is then determined based on the standardized inbreeding coefficient and standardized breeding values. Finally, a selection index is formulated based on the comprehensive breeding value, enabling the selection index to more comprehensively reflect the breeding value of individuals or families.

[0067] The selection index developed using the methods described in the above embodiments, when applied to aquatic animal selection breeding methods, can improve the accuracy and reliability of selection breeding.

[0068] Figure 2The diagram shows a flowchart of an embodiment of the aquatic animal selective breeding method provided by the present invention.

[0069] like Figure 2 As shown, this embodiment employs the following process for selective breeding of aquatic animals.

[0070] S21: Obtain the individual selection index of the test individual and the pedigree selection index of the test family.

[0071] Individual selection index and family selection index adopt Figure 1 The selection index determination method is formulated in the embodiments and other embodiments.

[0072] S22: Select the seed-keeping lineage and the individuals within the seed-keeping lineage based on the seed-keeping plan, individual selection index, and family selection index.

[0073] Breeding plans can be determined based on the genetic characteristics of different breeding target traits in aquatic animals. Breeding plans include, but are not limited to, the number of breeding families, the number of breeding individuals, and the sex ratio of breeding individuals.

[0074] The general principle for selecting breeding families is as follows: select the number of families specified in the breeding program as breeding families in descending order of the family selection index. The average co-fertility coefficient among all breeding families should not be greater than the co-fertility coefficient value of the current generation calculated with an inbreeding rate of 1%, and the average family selection index of all breeding families should be the highest.

[0075] The general principle for selecting individuals for breeding is as follows: within the breeding family, select the specified number of male and female individuals as breeding individuals according to the individual selection index from high to low.

[0076] S23: Selective breeding based on the lineage and individuals selected for breeding.

[0077] The following example further illustrates the process of developing an aquatic animal selection index.

[0078] Taking the core breeding population of giant freshwater prawns as an example, harvest weight and culture survival rate were identified as the target traits based on the actual breeding needs of giant freshwater prawns.

[0079] Broodstock mating: Mature broodstock were used in a nest-like design to establish full-sib families through natural mating. The male-to-female ratio was 3-5:1, with all females coming from different families. A total of 235 full-sib families (202 half-sib families) were established, using 98 males and 235 females.

[0080] Standardized seedling rearing: Based on mating status, berried shrimp are periodically transferred to 200L white barrels in the family rearing workshop, one shrimp per barrel for individual rearing. Before stocking, brackish water with a salinity of 7‰ is pre-added to the barrels. 2000 newly hatched larvae are randomly removed and placed in white barrels pre-added with 50L of brackish water with a salinity of 14‰ for further rearing. When more than 80% of the larvae have matured into juvenile shrimp, the seawater salinity is reduced to below 3‰ in two stages, and approximately 500 shrimp are counted and transferred to a 3m deep-sea temporary rearing workshop for family shrimp larvae. 2 Intermediate rearing was carried out in temporary holding tanks. On the second day after the juvenile shrimp were acclimated to freshwater, 300 vigorous juvenile shrimp from each family were randomly and accurately counted and placed into 3m... 2 They are raised in cement ponds, and after about 60 days of rearing, the juvenile shrimp can grow to a body length of 2.5cm, reaching the mark size.

[0081] Family marking: Visual embedded rubber markers (VIEs) were used for family marking. VIEs were injected into the 6th abdominal segment of the larvae, and each family was marked with a different color combination. Sixty individuals were randomly selected from each family, and their average weight was measured before they were cultured together in three test tanks. After 60 days of testing, the marking colors and weights of all surviving individuals from 235 families were read, and a total of 16,507 test individuals were harvested.

[0082] Individual tagging: After the mixed-species test, each high-quality individual is placed in a cage made of net cage (referred to as a cage), and an individual tag with a code is hung above the cage to distinguish different individuals.

[0083] Genetic parameter and breeding value prediction: Based on measured individual body weight, family survival rate, and pedigree information of the test individuals and parents, a mixed model equation is established. Genetic parameters (genetic variance, residuals, heritability, etc.) for each trait are estimated using REML (constrained maximum likelihood method). Breeding values ​​for individual growth traits and family survival rate are calculated using methods such as pBLUP, GBLUP, or ssGBLUP. Family body weight breeding value is the average of the individual breeding values ​​within the family.

[0084] Using the trait-standardized breeding value formula Calculate the standardized breeding values ​​for body weight and survival rate. In the formula, m1 = 0.5, k1 = 0.01, and q1 = 1.

[0085] Using the standardized inbreeding coefficient formula Calculate the pedigree-standardized inbreeding coefficient. In the formula, m² = 0.5, k² = 0.01, and q² = 1.

[0086] Calculate the comprehensive breeding value Yi based on the trait-standardized breeding value a′ij and the standardized inbreeding coefficient Fi′: In the formula, n = 2. Moreover, the weighting value for the body weight trait is 0.7, the weighting value for the survival rate trait is 0.3, and the weighting value for the inbreeding coefficient is -0.1.

[0087] Finally, the selection index Ii is determined based on the comprehensive breeding value Yi:

[0088] Table 1 shows the pedigree numbers, breeding weight values, breeding survival rates, standardized breeding weight values, standardized breeding survival rates, pedigree inbreeding coefficients, standardized inbreeding coefficients, overall breeding values, selection indices, and the average breeding weight value, average breeding survival rate value, standard deviation of breeding weight value, and standard deviation of breeding survival rate value for all pedigrees for all pedigrees. The average inbreeding coefficient of the pedigrees shown in Table 1 is 0.0145, and the standard deviation of the inbreeding coefficient is 0.0205.

[0089] Table 1

[0090]

[0091] Table 2 shows the individual's identification number, breeding weight value, survival rate breeding value (equal to family survival rate breeding value), standardized breeding weight value, standardized survival rate breeding value (equal to family survival rate standardized breeding value), individual inbreeding coefficient, individual standardized inbreeding coefficient, overall breeding value, selection index, and the average breeding weight value, average survival rate breeding value, standard deviation of the breeding weight value, and standard deviation of the breeding rate value for all surviving individuals. The average inbreeding coefficient for individuals shown in Table 2 is 0.0144, and the standard deviation of the family inbreeding coefficient is 0.0204. The methods for determining the standardized breeding value, overall breeding value, and selection index are the same as those for determining the family.

[0092] Table 2

[0093]

[0094]

[0095] The above embodiments are only used to illustrate the technical solutions of the present invention, and are not intended to limit them. Although the present invention has been described in detail with reference to the foregoing embodiments, those skilled in the art can still modify the technical solutions described in the foregoing embodiments or make equivalent substitutions for some of the technical features. Such modifications or substitutions do not cause the essence of the corresponding technical solutions to deviate from the spirit and scope of the technical solutions claimed by the present invention.

Claims

1. A method for optimizing aquatic animal breeding, characterized in that, include: S1: Obtain the measured values ​​of all breeding target traits for all individuals or families, as well as the inbreeding coefficient Fi for all individuals or families; S2: Based on the measured trait values, the breeding value aij for each trait and the average breeding value for each trait are obtained using the optimal linear unbiased prediction method. And the standard deviation of the breeding value σj; S3: Determine the average inbreeding coefficient for all individuals or families based on the inbreeding coefficient Fi. and the standard deviation of the nearest intersection coefficient σ′; S4: The breeding value and the inbreeding coefficient are standardized using a nonlinear transformation function to obtain a standardized breeding value a′ij with a fixed range and a standardized inbreeding coefficient Fi′ with a fixed range. Standardized breeding value a′ ij The calculation process is as follows: Calculate the standardized inbreeding coefficient F i The calculation process for ′ is as follows: In the formula, a ij represents the breeding value of the j-th trait of the i-th individual or family; represents the average breeding value of the j-th trait; σ j represents the standard deviation of the breeding value of the j-th trait; Tanh represents the hyperbolic function; F i represents the inbreeding coefficient of the i-th individual or family; represents the average inbreeding coefficient; σ' represents the standard deviation of the inbreeding coefficient, and σ'≠0; m1, k1, q1, m2, k2, q2 are all constants greater than 0; the value range of m1 is: 0<m1<1; the value range of m2 is: 0<m2<1; the value range of k1 is: 0<k1≤0.02; the value range of k2 is: 0<k2≤0.02; q1=q2=1; S5: Calculate the comprehensive breeding value Yi based on the standardized breeding value a′ij and the standardized inbreeding coefficient Fi′. The selection index Ii is determined based on the comprehensive breeding value Yi: In the formula, n represents the total number of traits; pj represents the weighted value of the j-th trait, which is a known value; wi represents the inbreeding coefficient weighted value of the ith individual or family, wi = -0.1; Ii represents the selection index of the ith individual or family; N represents the total number of individuals or families; These represent the minimum and maximum values ​​among N comprehensive breeding values, respectively; S6: Select the breeding lineage and the individuals to be retained in the breeding lineage based on the selection index of each individual, the selection index of each family, and the seed retention plan; S7: Selective breeding is carried out based on the said breeding pedigree and the said breeding individuals.

2. The method for optimizing aquatic animal breeding according to claim 1, characterized in that, The selection process for the breeding families in step S6 is as follows: Select the specified number of families in the breeding plan as breeding families in order of the family selection index from high to low. The average co-fertility coefficient among all breeding families is not greater than the co-fertility coefficient value of the current generation calculated with an inbreeding rate of 1%, and the average family selection index of all breeding families is the highest.

3. The method for optimizing aquatic animal breeding according to claim 1, characterized in that, The selection process for individuals to be retained in step S6 is as follows: within the family lineage, a specified number of male and female individuals are selected as individuals to be retained in the retention plan, based on the individual selection index from high to low.

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