Pseudosciaena crocea fine breeding method

Abstract

The invention relates to the technical field of breeding, and particularly discloses a large yellow croaker fine breeding method which comprises the following steps: screening parents carrying a plurality of excellent character genotype markers by using an NGS technology and a bioinformatics tool, and performing genetic diversity evaluation; designing a multi-generation hybridization scheme according to the parent genotype marker, and carrying out hybridization by adopting an artificial insemination means; a non-destructive biological imaging technology and a molecular marker-assisted selection technology are adopted to comprehensively evaluate and screen out juvenile fishes which most accord with a breeding target; carrying out breeding environment adaptability evaluation on the screened juvenile fish; recording and analyzing data in the breeding process, and establishing a breeding database; according to the method, parent screening and genetic diversity evaluation are carried out by using an NGS technology and a bioinformatics tool, genome information of a large yellow croaker population can be rapidly and accurately obtained, a scientific basis is provided for subsequent multi-generation hybridization scheme design, and thus the breeding efficiency is greatly improved.

Description

Technical Field

[0001] The invention belongs to the technical field of breeding, and in particular relates to a method for fine breeding of large yellow croaker. Background Art

[0002] In the large yellow croaker breeding industry, traditional breeding methods often rely on empirical observation and phenotypic selection, which is not only time-consuming and labor-intensive, but also inefficient and difficult to accurately screen large yellow croaker varieties with excellent traits. With the rapid development of genomics and bioinformatics, molecular marker-assisted selection using high-throughput sequencing technology and bioinformatics tools has become an important means of modern breeding. However, in the field of large yellow croaker breeding, there is no systematic and sophisticated breeding method that can combine modern scientific and technological means with traditional breeding experience to achieve efficient and accurate breeding goals.

[0003] Traditional breeding methods have certain limitations in improving large yellow croaker varieties. On the one hand, phenotypic selection is easily affected by environmental factors, resulting in unstable performance of the selected varieties in different environments; on the other hand, the lack of precise molecular marker-assisted selection methods makes the breeding process lack scientific basis, making it difficult to quickly and accurately screen large yellow croaker varieties with multiple excellent traits. Summary of the invention

[0004] The object of the present invention is to provide a method for fine breeding of large yellow croaker to solve the problems raised in the above background technology.

[0005] To achieve the above object, the present invention provides the following technical solutions:

[0006] A method for fine breeding of large yellow croaker comprises the following steps:

[0007] S1. Use NGS technology and bioinformatics tools to screen parents carrying multiple genotype markers of excellent traits and conduct genetic diversity assessment;

[0008] S2. Design a multi-generation breeding plan based on the parental genotype markers and use artificial insemination to carry out breeding;

[0009] S3, using non-destructive bio-imaging technology and molecular marker-assisted selection technology to comprehensively evaluate and select the fry that best meets the breeding goals;

[0010] S4. Evaluate the adaptability of the selected fry to the breeding environment;

[0011] S5. Record and analyze data from the breeding process and establish a breeding database.

[0012] Preferably, the step S1 specifically includes:

[0013] S11. Deeply sequence the genome of the large yellow croaker population using next generation sequencing (NGS) technology to obtain genome sequence data;

[0014] S12. Analyze the sequencing data using bioinformatics tools to screen out multiple excellent genotype markers associated with the target trait;

[0015] S13. Evaluate the genetic diversity of the selected parents, including calculation of genotype frequency, heterozygosity, and genetic distance.

[0016] Preferably, the step S2 specifically includes:

[0017] S21, formulating a multi-generation breeding plan based on the parental genotype markers screened in step S1;

[0018] S22. Use artificial insemination technology, control the breeding process according to the breeding plan, and record the breeding date and parent information.

[0019] Preferably, the step S3 specifically includes:

[0020] S31. At the juvenile stage, non-destructive bio-imaging techniques are used to non-invasively detect and analyze the morphological and physiological characteristics of juvenile fish;

[0021] S32. Combined with molecular marker-assisted selection technology, the genotype of the young fish is identified to determine whether it carries the target excellent trait gene;

[0022] S33. Comprehensively evaluate the morphological, physiological and genotypic characteristics to select the young fish individuals that best meet the breeding goals.

[0023] Preferably, the step S4 specifically includes:

[0024] S41. Place the selected fry in a breeding environment and monitor key indicators;

[0025] S42. Based on the monitoring results, evaluate the adaptability of young fish to the breeding environment.

[0026] Preferably, the step S5 specifically includes:

[0027] S51. During the entire breeding process, detailed records shall be kept of data on parent selection, breeding plan, fry screening, and assessment of adaptability to the breeding environment;

[0028] S52. Use data analysis tools to organize, analyze and mine the collected data, extract useful information, and provide scientific basis and data support for subsequent breeding work;

[0029] S53. Establish a breeding database to realize the long-term preservation, sharing and query of breeding data.

[0030] Compared with the prior art, the present invention has the following beneficial effects:

[0031] (1) By using NGS technology and bioinformatics tools to screen parents and assess genetic diversity, the genome information of large yellow croaker populations can be obtained quickly and accurately, providing a scientific basis for the design of subsequent multi-generation breeding programs, thereby greatly improving breeding efficiency. Combined with non-destructive bioimaging technology and molecular marker-assisted selection technology, a comprehensive assessment of the morphology, physiological characteristics and genotype of juvenile fish can be carried out at the juvenile stage, thereby accurately selecting juvenile individuals that best meet the breeding goals and enhancing the accuracy of breeding.

[0032] (2) By evaluating the adaptability of the selected fry to the aquaculture environment, we can ensure that they have good growth performance and disease resistance in the actual aquaculture environment, reduce aquaculture risks, improve aquaculture benefits, establish a breeding database, and achieve long-term preservation, sharing and query of breeding data, providing valuable data resources for subsequent breeding research and helping to promote continuous innovation and progress in large yellow croaker breeding technology. BRIEF DESCRIPTION OF THE DRAWINGS

[0033] Figure 1 It is a work flow chart of the present invention; DETAILED DESCRIPTION

[0034] The following will be combined with the drawings in the embodiments of the present invention to clearly and completely describe the technical solutions in the embodiments of the present invention. Obviously, the described embodiments are only part of the embodiments of the present invention, not all of the embodiments. Based on the embodiments of the present invention, all other embodiments obtained by ordinary technicians in this field without creative work are within the scope of protection of the present invention.

[0035] Embodiment 1:

[0036] See also Figure 1 As shown, a method for fine breeding of large yellow croaker comprises the following steps:

[0037] S1. Use NGS technology and bioinformatics tools to screen parents carrying multiple genotype markers of excellent traits and conduct genetic diversity assessment;

[0038] NGS technology is a high-throughput sequencing method that can quickly and accurately obtain genome sequence data of large yellow croaker populations. By performing deep sequencing on large yellow croaker populations, a large amount of genome information can be obtained, providing basic data for subsequent parent screening and genetic diversity assessment.

[0039] S2. Design a multi-generation breeding plan based on the parental genotype markers and use artificial insemination to carry out breeding;

[0040] Bioinformatics tools can efficiently analyze and process sequencing data. Through alignment, assembly, annotation and other steps, excellent genotype markers associated with target traits (such as growth rate, disease resistance, meat quality, etc.) can be screened out from sequencing data. These markers will serve as the basis for subsequent parent screening and breeding program design;

[0041] S3, using non-destructive bio-imaging technology and molecular marker-assisted selection technology to comprehensively evaluate and select the fry that best meets the breeding goals;

[0042] Genetic diversity is an important indicator of population adaptability and evolutionary potential. By calculating the genotype frequency, heterozygosity, genetic distance, etc. of the selected parents, its genetic diversity level can be evaluated, providing a scientific basis for the subsequent breeding program design;

[0043] S4. Evaluate the adaptability of the selected fry to the breeding environment;

[0044] S5. Record and analyze data from the breeding process and establish a breeding database.

[0045] In one embodiment of the present invention, step S1 specifically includes:

[0046] S11. Deeply sequence the genome of the large yellow croaker population using next generation sequencing (NGS) technology to obtain genome sequence data;

[0047] S12. Analyze the sequencing data using bioinformatics tools to screen out multiple excellent genotype markers associated with the target trait;

[0048] S13. Evaluate the genetic diversity of the selected parents, including calculation of genotype frequency, heterozygosity, and genetic distance.

[0049] In one embodiment of the present invention, step S2 specifically includes:

[0050] S21, formulating a multi-generation breeding plan based on the parental genotype markers screened in step S1;

[0051] S22. Use artificial insemination technology, control the breeding process according to the breeding plan, and record the breeding date and parent information.

[0052] In one embodiment of the present invention, step S3 specifically includes:

[0053] S31. At the juvenile stage, non-destructive bio-imaging technology is used to non-invasively detect and analyze the morphological and physiological characteristics of juvenile fish;

[0054] S32. Combined with molecular marker-assisted selection technology, the genotype of the young fish is identified to determine whether it carries the target excellent trait gene;

[0055] S33. Comprehensively evaluate the morphological, physiological and genotypic characteristics to select the juvenile individuals that best meet the breeding goals, including:

[0056] M(y i ) represents the morphological evaluation score of the juvenile fish yi, which includes the evaluation of multiple morphological characteristics. The specific algorithm is as follows;

[0057]

[0058] Among them, w j is the weight of the jth feature, μ j and σ j are the mean and standard deviation of the jth feature, n is the number of morphological features, and the measured value of each feature is recorded as x ij (where i represents the i-th fry and j represents the j-th feature);

[0059] P(y i ) indicates juvenile fish y i The physiological characteristic evaluation score is a summation function that includes physiological indicators (such as heart rate, respiratory rate, etc.). The specific algorithm is:

[0060]

[0061] Among them, m is the number of physiological indicators, and the measured value of each indicator is recorded as p ik , v k is the weight of the kth indicator, norm(p ik ) indicates that p ik Standardize the process;

[0062] G(y i ) represents the genotype evaluation score of the juvenile fish yi, which is a function based on molecular marker-assisted selection technology, including the identification of target excellent trait genes. The specific algorithm is:

[0063]

[0064] Among them, there are l target genes, and the identification result of each gene is recorded as g il (1 indicates the presence of the excellent gene, 0 indicates the absence), ul is the weight of the lth gene;

[0065] F(y i ) represents the comprehensive evaluation score of juvenile fish yi, which is the integration of the evaluation results of morphology, physiological characteristics and genotype;

[0066] N represents the total number of juveniles;

[0067] Based on the above definition, the following formula is designed:

[0068]

[0069] Among them, α, β, γ are weight coefficients, and α+β+γ=1;

[0070] In order to eliminate the dimensional differences between different evaluation scores, the above formula is normalized to obtain:

[0071]

[0072] Among them, min(M), min(P), min(G) represent the minimum values ​​of morphological, physiological characteristics and genotype evaluation scores, respectively, and max(M), max(P), max(G) represent the corresponding maximum values, respectively;

[0073] In order to further improve the accuracy of the evaluation, the information filtering function H(x) is introduced, which can filter out the noise and redundant information in the evaluation score. The specific algorithm is:

[0074]

[0075] Where N(i) is the neighborhood of the i-th score, w j is the weight of the j-th score K(i,j) is a kernel function used to measure the similarity or distance between the i-th score and the j-th score (such as Gaussian kernel, linear kernel, etc.), and the evaluation score vector S = [S 1 ,S 2 ,breeding,S n ];

[0076] Therefore, the above formula can be modified as:

[0077]

[0078] Among them, F”(y i ) has a value range of [0,1], indicating that the juvenile fish y i The relative position of the comprehensive evaluation score among all fry, the closer the value is to 1, the better the fry y i The better the overall performance, the more it meets the breeding goals.

[0079] In one embodiment of the present invention, step S4 specifically includes:

[0080] S41. Place the selected fry in a breeding environment and monitor key indicators;

[0081] Place the selected young fish in the actual breeding environment and evaluate their adaptability to the breeding environment by monitoring key indicators such as their growth rate, survival rate, and disease resistance;

[0082] S42. Evaluate the adaptability of young fish to the breeding environment based on the monitoring results;

[0083] Based on the monitoring results, the adaptability of young fish to the breeding environment can be objectively evaluated. For young fish with strong adaptability, they can be considered as subsequent breeding materials; for young fish with weak adaptability, the reasons can be further analyzed.

[0084] In one embodiment of the present invention, step S5 specifically includes:

[0085] S51. During the entire breeding process, detailed records shall be kept of data on parent selection, breeding plan, fry screening, and assessment of adaptability to the breeding environment;

[0086] S52. Use data analysis tools to organize, analyze and mine the collected data, extract useful information, and provide scientific basis and data support for subsequent breeding work;

[0087] S53. Establish a breeding database to realize the long-term preservation, sharing and query of breeding data.

[0088] Although embodiments of the present invention have been shown and described, it will be appreciated by those skilled in the art that various changes, modifications, substitutions and variations may be made to the embodiments without departing from the principles and spirit of the present invention, and that the scope of the present invention is defined by the appended claims and their equivalents.

Claims

1. A method for fine breeding of large yellow croaker, characterized in that: The following steps are involved: S1. Use NGS technology and bioinformatics tools to screen parents carrying multiple genotype markers of excellent traits and conduct genetic diversity assessment; S2. Design a multi-generation breeding plan based on the parental genotype markers and use artificial insemination to carry out breeding; S3, using non-destructive bio-imaging technology and molecular marker-assisted selection technology to comprehensively evaluate and select the fry that best meets the breeding goals; S4. Evaluate the adaptability of the selected fry to the breeding environment; S5. Record and analyze data from the breeding process and establish a breeding database.

2. The method for fine breeding of large yellow croaker according to claim 1, characterized in that: The step S1 specifically includes: S11. Deeply sequence the genome of the large yellow croaker population using next generation sequencing (NGS) technology to obtain genome sequence data; S12. Analyze the sequencing data using bioinformatics tools to screen out multiple excellent genotype markers associated with the target trait; S13. Evaluate the genetic diversity of the selected parents, including calculation of genotype frequency, heterozygosity, and genetic distance.

3. The method for fine breeding of large yellow croaker according to claim 1, characterized in that: The step S2 specifically includes: S21, formulating a multi-generation breeding plan based on the parental genotype markers screened in step S1; S22. Use artificial insemination technology, control the breeding process according to the breeding plan, and record the breeding date and parent information.

4. The method for fine breeding of large yellow croaker according to claim 1, characterized in that: The step S3 specifically includes: S31. At the juvenile stage, non-destructive bio-imaging technology is used to non-invasively detect and analyze the morphological and physiological characteristics of juvenile fish; S32. Combined with molecular marker-assisted selection technology, the genotype of the young fish is identified to determine whether it carries the target excellent trait gene; S33. Comprehensively evaluate the morphological, physiological and genotypic characteristics to select the young fish individuals that best meet the breeding goals.

5. The method for fine breeding of large yellow croaker according to claim 1, characterized in that: The step S4 specifically includes: S41. Place the selected fry in a breeding environment and monitor key indicators; S42. Based on the monitoring results, evaluate the adaptability of young fish to the breeding environment.

6. The method for fine breeding of large yellow croaker according to claim 1, characterized in that: The step S5 specifically includes: S51. During the entire breeding process, detailed records shall be kept of data on parent selection, breeding plan, fry screening, and assessment of adaptability to the breeding environment; S52. Use data analysis tools to organize, analyze and mine the collected data, extract useful information, and provide scientific basis and data support for subsequent breeding work; S53. Establish a breeding database to realize the long-term preservation, sharing and query of breeding data.

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