CN113854202B - Molecular marker assisted breeding method for rapid-growing new variety of egg-shaped pompano - Google Patents
Molecular marker assisted breeding method for rapid-growing new variety of egg-shaped pompano Download PDFInfo
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Abstract
The invention discloses a molecular marker assisted breeding method for a rapid-growing new variety of trachinotus ovatus, which can effectively solve the problems of slow growth, low survival rate, poor stress resistance and disease resistance of offspring seeds, poor seed quality degradation and the like caused by genetic evaluation and optimization difficulty of candidate parents, unclear relationship and sex and blind close-up breeding of the trachinotus ovatus in the genetic breeding work of the existing trachinotus ovatus by efficiently integrating technologies such as individual phenotypic value selection, microsatellite molecular marker, additive genetic correlation matrix, linear mixed model, quantitative genetics, individual breeding value selection, sex specific molecular marker, inter-individual genetic distance analysis, group mating scheme and the like.
Description
Technical Field
The invention belongs to the technical field of aquatic animal breeding, and particularly relates to a molecular marker assisted breeding method for a new rapidly-growing variety of trachinotus ovatus.
Background
Oval pompano (Trachinotusovatus) is commonly called golden pompano and is mainly distributed in sea areas such as Indian ocean, indonesia, australia, japan, tropical and temperate Atlantic ocean, mediterranean and offshore islands, african west coast and south sea of China, east sea, yellow sea, bohai sea and the like. The trachinotus ovatus is bright in body color, free of fish meat thorns, tender in meat quality, delicious in taste, rich in nutrition, and suitable for people of all ages, and is more and more popular with consumers. The estimated culture yield of the trachinotus ovatus in 2020 China breaks through 15 million tons, the whole industrial output value is nearly 100 hundred million yuan, and the trachinotus ovatus culture fish becomes one of important mariculture fishes in coastal areas of south China.
In recent years, the culture scale of the trachinotus ovatus is continuously enlarged, the demand of seeds is gradually increased, the parent updating and breeding are not emphasized by the enterprises related to parent fish culture and seed breeding, the phenomena of parent fish aging, close-relative breeding and germplasm decline are caused, after multi-generation breeding, the trachinotus ovatus grows slowly, the survival rate is low, the feed utilization efficiency is low, and the development of the genetic breeding of the growth character of the trachinotus ovatus is particularly urgent.
At present, the colony breeding work of the trachinotus ovatus is carried out, but the colony breeding can not utilize parent fish pedigree information, so that inbreeding depression is difficult to effectively avoid, and meanwhile, the screened parents only take individual character phenotype values as evaluation indexes, so that genetic effect and environmental effect parts in the character phenotype values can not be distinguished. The family breeding technology based on the quantitative genetics can fully utilize pedigree information, eliminate the deviation of fixed environment and genetic effect, calculate individual breeding value, screen excellent individuals, and effectively control inbreeding depression, and becomes the mainstream technology of the genetic breeding of the aquatic animals at present. However, the sex of the trachinotus ovatus is difficult to identify even in a breeding season because the male and female parent fishes of the trachinotus ovatus have no obvious secondary characteristics and have similar body sizes with reproductive pores, and the trachinotus ovatus is thick and hard in abdominal wall and is difficult to extrude semen or ovum by squeezing the abdominal wall, thereby often causing damage to the parent fishes. Therefore, the large-scale construction of the trachinotus ovatus family cannot be realized at present, genetic evaluation is difficult due to unclear genetic relationship, and the important economic character genetic improvement work of the trachinotus ovatus is severely restricted by blind parent pairing with unclear sex and sex.
Disclosure of Invention
The invention aims to provide a molecular marker assisted breeding method for a new rapid-growing variety of trachinotus ovatus, which can effectively solve the problems of slow growth, low survival rate, poor adverse and disease resistance capability, seed quality degradation and the like of seeds caused by genetic evaluation and optimization difficulty of candidate parents, unclear relationship and sex and close-up propagation in the conventional genetic breeding work of trachinotus ovatus.
The method disclosed by the invention is mainly used for realizing the molecular marker-assisted breeding of the rapid-growing new species of the trachinotus ovatus by efficiently integrating technologies such as individual phenotype value selection, microsatellite molecular markers, additive genetic correlation matrixes, linear mixed models, quantitative genetics, individual breeding value selection, sex-specific molecular markers, inter-individual genetic distance analysis, group mating schemes and the like.
The above object of the present invention can be achieved by the following technical solutions: a molecular marker assisted breeding method for a new fast-growing variety of egg-shaped pompano comprises the following steps:
S 1 : measuring the adult fish body quality data of the trachinotus ovatus breeding population, selecting individual physique phenotype values, and screening individuals with excellent characters as primary selection reserved individuals;
S 2 : constructing an additive genetic correlation matrix based on microsatellite genotype data and a molecular correlation coefficient method, calculating individual body quality breeding values by using a linear mixed model, selecting the individual body quality breeding values, screening again, and obtaining candidate seed reserving individuals;
S 3 : and identifying the sex of the candidate seed reserving individuals based on the sex specific molecular marker, calculating the genetic distance between the candidate seed reserving individuals by utilizing microsatellite genotype data, and selecting and determining the final seed reserving individuals according to the design standard of a group mating scheme.
Preferably, in the present invention, step S 1 The trachinotus ovatus breeding population is obtained by the following steps: carrying out nutrition strengthening and ripening induced spawning on F3 generation individuals bred by the trachinotus ovatus, and then carrying out ecological breeding of fry in high pond and short-shore-mark and deep-water anti-wind wave cage culture.
Preferably, in the present invention, step S 1 The adult fishes of the trachinotus ovatus breeding group are fish bodies with the body mass of more than 400g and the commodity specification after 6 months of culture in a sea area, and the number of the fish bodies is measured to be 50000 tails.
Preferably, in the present invention, step S 1 The individual physique form value selection in the method is to sort the physique form values of 50000 individuals from large to small, select the first 2000 individuals as the initial selection seed reserving individuals, and the seed reserving rate is 4 percent.
Preferably, in the present invention, step S 2 The construction process of the additive genetic correlation matrix comprises the following steps: (S) 21 ) Extracting DNA of a primary seed selection individual sample and carrying out PCR amplification; (S) 22 ) Inter-individual acquisition method by using microsatellite genotype data and molecular correlation coefficientA genetic relationship matrix; (S) 23 ) And carrying out format conversion and positive definition processing on the genetic relationship matrix, and generating an additive genetic correlation matrix file.
Preferably, in the present invention, step (S) 21 ) Extracting DNA of a preliminary-selected reservationindividual sample and carrying out PCR amplification, wherein specific primer information and amplification conditions refer to the invention patent SSR fluorescent labeled primer for identifying the parent of the trachinotus ovatus and application thereof (the patent number is ZL201811417973. X).
Preferably, in the present invention, step (S) 22 ) The method for the number of the medium molecular phase relations is based on a TrioML likelihood estimation algorithm, uses an R language related software package coanda function to calculate the genetic relation coefficient between every two individuals, and constructs a genetic relation matrix.
Preferably, in the present invention, step (S) 23 ) The format conversion and positive definition processing of the intermediate genetic relationship matrix respectively adopt an R language corrcor software package vec2sm function and a matrix software package nerPD function, and utilize a synchronous software package write.
Step S of the present invention 2 Estimating individual body quality breeding value based on the adult fish body quality and genetic information (genetic relationship) of the trachinotus ovatus breeding group, and performing individual screening again by using the individual body quality breeding value to obtain better candidate seed reserving individuals.
Step S of the invention 2 The technical means adopted in the method comprises the steps of constructing an additive genetic correlation matrix by utilizing microsatellite genotype data and a molecular correlation coefficient method, estimating additive genetic variance, residual variance and individual physique breeding values by utilizing ASReml4.0 software based on a linear mixed model, selecting individual physique breeding values, screening again,
preferably, in the present invention, step S 2 Wherein the individual body mass breeding value is estimated by the following linear mixed model, and the specific model is y i ＝μ+a i +e i In the formula, y i Is the constitution quantity scale type value of the ith fish body, mu is the average value of the constitution quantities of all the fish bodies, a i Additive genetic effect (individual body mass breeding value) for the ith fish body, which obeys the expected mean value of0 and variance of
Wherein A is an additive genetic correlation matrix passing through S 23 The method comprises the following steps of calculating and obtaining,
for additive genetic variance, ei is the random residual effect of the ith fish body, subject to an expected mean of 0 and variance of
Wherein I is an identity matrix,
is the residual variance. Obtained from a model
And
numerical value, calculating individual body quality breeding value by using BLUP method.
Specifically, step S of the present invention 2 First, the statistical analysis of the linear mixture model is performed by providing individual quality values (y) i ) And an additive genetic correlation matrix (A), then when the ASReml4.0 software is used for linear mixed model operation, the quality mean value (mu) and the unit matrix (I) can be automatically calculated and generated, and the additive genetic variance is obtained
Sum residual variance
Results, finally based on
And
calculating individual body quality breeding value (a) by BLUP method i ). In step S of the present invention 2 Additive genetic variance
Residual variance
And individual physical mass breeding value (a) i ) Are obtained by calculation based on a linear mixed model and by using ASReml4.0 software,
preferably, in the present invention, step S 2 The selection of the quality breeding value of the middle individual body is to sort the quality breeding values of the 2000 initial selection seed reserving individual bodies from large to small, select the top 1000 individuals as candidate seed reserving individuals, and the seed reserving rate is 50 percent.
Preferably, in the present invention, step S 3 In the method, the sex of candidate reserved individuals is identified based on sex-specific molecular markers, the sex of 1000 candidate reserved individuals can be identified by using three sex-specific molecular markers P1, P2 and P18-1 of Trachinotus ovatus developed by the subject group, and when the sex identification results of two or more molecular markers are consistent, the sex of the individuals is determined, and the specific primer information and amplification conditions can refer to the invention patents ZL Trachinotus ovatus sex-specific molecular marker primer, kit and application thereof (patent No. 202010099694.4), trachinotus ovatus sex-specific molecular marker primer and application thereof (patent No. ZL202010099453. X) and Trachinotus ovatus sex rapid identification primer, kit and application thereof (application No. 202011134234.7).
Preferably, in the present invention, step S 3 The genetic distance between candidate species reserving individuals is calculated by utilizing microsatellite genotype data, and the genetic distance between individuals is calculated by adopting a PopGenRepor software package gd.
Preferably, in the present invention, the present invention is most preferably performed by identifying the sex of candidate seed-reserving individuals based on sex-specific molecular markers and calculating the genetic distance between candidate seed-reserving individuals using microsatellite genotype dataStep S of Final acquisition 3 The medium group mating scheme design criteria are: (S) 31 ) Designing 4-6 mating groups, and 80-130 individuals in each group; (S) 32 ) The ratio range of the male fish to the female fish in each group is 1: 3-1: 2; (S) 33 ) The genetic distance between the male fish and the female fish in each group is more than 0.2.
Preferably, in the present invention, step S 3 The medium group mating program finally selects and determines 500 individuals as final seed reserving individuals, and the seed reserving rate is 50%.
In the invention, the selection and determination of the final reseeding individuals are that 500 candidate reseeding individuals are screened as the final reseeding individuals according to the design standard of the group mating scheme, the reseeding rate is 50%, and the group mating scheme of the reseeding individuals is established.
Therefore, preferably, the present invention passes through step S 1 Step S 3 The method comprises the steps of collecting 50000 adult fish body quality data, implementing a seed selection and combination scheme and selecting and reserving excellent candidate individuals, finally screening 500 excellent seed reserving individuals, wherein the seed reserving rate is 1%, and establishing a mating scheme of the seed reserving individuals.
According to the method, through acquisition of 50000 adult fish body quality data, implementation of a seed selection and combination scheme and selection of excellent candidate individuals, 500 excellent seed reserving individuals are finally screened, the seed reserving rate is 1%, and a mating scheme of the excellent seed reserving individuals is formulated. In addition, the rest 1500 marked individuals can be used as parent fishes of propagation groups for propagating large-batch high-quality fertilized eggs.
Further, the present invention further includes a step S 4 : and (5) evaluating the breeding effect, verifying the molecular marker assisted breeding technical route of the rapidly-growing new variety of the trachinotus ovatus, and carrying out successive breeding.
Therefore, the molecular marker assisted breeding method for the rapid growth new variety of the trachinotus ovatus comprises the steps of measuring the adult fish body quality data of the bred colony of the trachinotus ovatus, firstly, selecting individual physique phenotype value, screening individuals with excellent properties as initial selection reserved individuals, secondly, constructing an additive genetic correlation matrix based on microsatellite genotype data and a molecular correlation coefficient method, calculating individual physique breeding value by using a linear mixed model, and selecting individual physique breeding value for secondary screening to obtain candidate reserved individuals; then identifying the sex of the candidate seed reserving individuals based on the sex specific molecular marker, calculating the genetic distance between the candidate seed reserving individuals by utilizing microsatellite genotype data, and selecting and determining the final seed reserving individuals according to the design standard of a group mating scheme; and finally, evaluating the breeding effect, verifying the molecular marker assisted breeding technical route of the fast-growing new species of the trachinotus ovatus, and carrying out subculture breeding. The method can effectively solve the problems of slow growth, low survival rate, poor stress and disease resistance, poor germplasm degradation and the like of offspring seeds caused by difficult genetic evaluation and optimization of candidate parents, unclear relativity and sex and blind close breeding in the genetic breeding work of the trachinotus ovatus.
Compared with the prior art, the invention has the following beneficial effects:
(1) According to the method, a genetic relationship matrix among individuals is constructed by using microsatellite genotype data and a molecular correlation coefficient method, an additive genetic correlation matrix required by a linear hybrid model is obtained by carrying out format conversion and positive definition processing on the genetic relationship matrix, genetic effects and environmental effects in characters are subdivided, individual physique breeding values are obtained, genetic analysis and individual breeding potential evaluation of the quality characters of the trachinotus ovatus are realized, the problem of difficulty in genetic evaluation caused by unclear genetic relationship is effectively solved, and the physique genetic breeding work of the trachinotus ovatus is promoted;
(2) The sex identification of candidate breed reserving individuals is carried out by using the sex specific molecular markers of the three trachinotus ovatus, the number and the proportion of the male and female parent fishes in the group mating scheme are determined, and the phenomenon that the fertility rate of roes is low due to the fact that the number of the parent fishes of a certain sex is too large can be effectively prevented;
(3) The genetic distance between individuals is calculated based on the microsatellite genotype data, the numerical value of the genetic distance between male fish and female fish individuals in each group mating is ensured to be more than 0.2, and the situations of slow seedling growth, low survival rate and the like caused by inbreeding between parents can be avoided;
(4) According to the invention, through technologies such as individual phenotype value selection, microsatellite molecular markers, additive genetic correlation matrixes, linear mixed models, quantitative genetics, individual breeding value selection, sex specific molecular markers, inter-individual genetic distance analysis and group mating schemes, the molecular marker assisted breeding method for the fast-growing new variety of the trachinotus ovatus is established, individuals with high breeding potential can be efficiently screened out, the group mating scheme can be formulated, the breeding process of the fast-growing new variety of the trachinotus ovatus can be accelerated, inbreeding is avoided, and the genetic breeding efficiency and the character improvement progress are improved.
Drawings
FIG. 1 is a heat map of a partial inter-individual affinity coefficient matrix in example 1.
Detailed Description
The present invention is further described below in conjunction with specific examples to better understand and implement the technical solutions of the present invention for those skilled in the art. Unless otherwise specified, the reagent raw materials used in the following examples are biochemical reagent raw materials which are conventionally commercially available or commercially available, and the laboratory instruments used are laboratory conventional instruments, and unless otherwise specified, the methods and apparatuses used in the following examples are those conventionally used in the art.
Example 1
The molecular marker assisted breeding method for the rapid-growing new variety of trachinotus ovatus provided by the embodiment comprises the following steps of:
(1) The method comprises the following steps of parent ripening and spawning promotion and seedling cultivation, and specifically comprises the following steps:
and (5) carrying out parent reproduction control on the trachinotus ovatus breeding population 2 months before the breeding season. The method is characterized in that a nutrition strengthening method for feeding parent fish bait (prepared by mixing iced fresh squid, trash fish, bonito, compound vitamins and the like, and conventional bait) is adopted to promote the gonadal development degree of the parent fish, chorionic gonadotropin (HCG), ovulation-promoting hormone No. 2 (LRH-A2), ovulation-promoting hormone No. 3 (LRH-A3) and 0.9% sodium chloride solution are used for preparing an oxytocic reagent according to a proportion, and the using dosages of the 3 oxytocic hormones based on the weight of the fish body are 1000IU/kg, 10mg/kg and 10mg/kg respectively. After the oxytocic reagent is injected into the back muscles of the parent fishes, the parent fishes are placed into an oviposition net cage, fertilized eggs are collected by utilizing an egg collecting net bag, and floating high-quality fertilized eggs are screened and placed into an incubation net cage of a high pond for incubation.
Opening the hatching net cage when the fry is 3 days old after the fry is released from the film, putting the fry into a fry raising pond, and performing ecological breeding work of fry in an elevated pond, wherein the main work comprises utilizing chlorella concentrated solution, organic fertilizer aquatic products and trace elements to directionally breed beneficial algae in the fry raising pond, efficiently breeding rotifers, copepods, cladocera and other biological baits based on fermentation nutrient solutions such as unicellular algae, amino acid, glucose and the like in the fry raising pond, and performing fry breeding and management (the technical key points comprise fry stocking density, fine biological bait feeding, water quality monitoring and control, daily pond patrol management and the like). After 40 days of fry cultivation, the fries are transported to a net cage in the offshore area for rough cultivation, in the rough cultivation stage, fries of different specifications are sorted by using a fish sieve regularly to obtain large-specification fries, and the large-specification fries are transported to a deepwater storm-resistant net cage for adult fish cultivation.
(2) Implementing a seed selection assembly scheme and selecting and reserving excellent candidate parents, and the specific steps are as follows:
the first step is to select individual physique phenotype values
When the quality of the fry cultured in the sea area reaches a commodity specification of more than 400g, acquiring 50000 tail adult fish body quality data, taking the individual physique scale type value as an evaluation index, screening 2000 individuals with the maximum tail body quality phenotype value by using a group breeding method as initial selection seed reserving individuals, wherein the seed reserving rate in the step is 4%.
Second, selecting individual body quality breeding value
Firstly, the eugenol is utilized to narcotize the reserved individuals for the primary selection of 2000 fish, PIT electronic marking is adopted to mark the individuals, part of decapterus maruadsi of each fish body is cut, and the decapterus maruadsi is placed into a single plastic bottle with 95 percent of alcohol for sample preservation. Secondly, extracting genome DNA of a sample by using a paramagnetic particle method, performing PCR amplification on individual DNA by using a multiplex PCR amplification system (13 microsatellite loci in total) developed by a subject group of the inventor of the application, wherein specific primer information and amplification conditions refer to the invention patent SSR fluorescence labeling primer for identifying the paternity of trachinotus ovatus and application (the patent number is ZL201811417973. X), and based on fluorescence labeling colors and microsatellite fragment sizes, reading genotype data of 13 microsatellite loci of each fish by using Gene Marker software;
then, based on a TrioML likelihood method, calculating a genetic relationship coefficient between every two individuals by using an R language related software package coannetry function, and constructing a genetic relationship coefficient matrix, wherein the color depth in a heat map of the genetic relationship coefficient matrix between some individuals (500 fish bodies) is shown in FIG. 1, the numerical value of the genetic relationship coefficient between the individuals is represented by the color depth in the heat map, the larger the color depth is, the smaller the color is, the genetic relationship coefficient is, carrying out genetic relationship matrix format conversion and positive definition processing by using a corrpcor software package vec2sm function and a matrix software package nerPD function respectively, and generating an additive genetic correlation matrix file by using a synchronized software package write.
Finally, calculating additive genetic variance, residual variance and individual physique breeding value by using ASReml software based on a linear mixed model with the specific model form of y i ＝μ+a i +e i In the formula, y i Is the body constitution of the ith fish body, mu is the mean body constitution of all fish bodies, a i Additive genetic effect (i.e., individual physique breeding value) for the ith fish subject to an expected mean of 0 and variance of
Wherein A is an additive genetic correlation matrix,
for additive genetic variance, ei is the random residual effect of the ith fish body, subject to an expected mean of 0 and variance of
Wherein I is an identity matrix,
is the residual variance.
Estimation of linear mixture model by using ASRem14.0 software
And
the number value is calculated by adopting a BLUP method, and the individual body quality breeding value is calculated, and the body quality phenotype value and the breeding value of part of candidate breed-preserved individuals (100 fish bodies) are shown in a table 1. The individual quality breeding values are sorted from large to small, the top 1000 individuals are selected as candidate seed reserving individuals, and the seed reserving rate in the step is 50%.
TABLE 1 type values and breeding values of constitution scale of candidate reseeder (100 fish body)
The third step is to select group mating scheme
Firstly, carrying out sex identification on 1000 candidate seed reserving individuals by utilizing 3 trachinotus ovatus sex-specific molecular markers P1, P2 and P18-1 developed by the subject group (wherein the 1000 candidate seed reserving individuals are determined after individual body quality breeding value selection), determining the individual sex if the sex identification results of two or more molecular markers are consistent, the specific primer information and amplification conditions refer to the invention patents of an egg-shaped pompano sex specific molecular marker primer, a kit and application thereof (the patent number is ZL 202010099694.4), an egg-shaped pompano sex specific molecular marker primer and application thereof (the patent number is ZL202010099453. X) and an egg-shaped pompano sex rapid identification primer, a kit and application thereof (the application number is 202011134234.7), the sex molecular marker identification results of partial candidate breed-reserved individuals (100 tail fish bodies) are shown in a table 2, wherein 1 in the table represents male, and 2 represents female. And then calculating the genetic distance between individuals by utilizing microsatellite genotype data of 1000 candidate seed reserving individuals and adopting a PopGenRepor software package gd.
Table 2 partial identification results of candidate seed reserving individual sex molecular markers
500 individuals are selected and determined as final seed reserving individuals in the step, the seed reserving rate is 50%, and a group mating scheme of the seed reserving individuals is formulated.
And finally, selecting and determining a final reseeded individual according to a population mating scheme design standard, wherein the standard is as follows: (1) Designing 4-6 mating groups, wherein 80-130 individuals in each group are designed; (2) The ratio range of the male fish to the female fish in each group is 1: 3-1: 2; (3) The genetic distance between the male fish and the female fish in each group is more than 0.2.
In conclusion, by collecting 50000 adult fish body quality data, implementing a seed selection and combination scheme and selecting and reserving excellent candidate individuals, 500 excellent seed reserving individuals are finally screened, the seed reserving rate is 1%, and a mating scheme of the seed reserving individuals is formulated. In addition, the remaining 1500 marked individuals can be used as parent fishes of a propagation group for propagating large-batch high-quality fertilized eggs.
Example 2
The method comprises the following specific steps of evaluating the breeding effect and implementing successive transfer breeding:
and (3) carrying out refined parent fish culture on 500 reserved species, and carrying out gonad ripening and spawning promotion and seed culture after the parent fish grows to a certain specification to obtain breeding seeds. Meanwhile, non-bred commercial seedlings with similar specifications at similar ages in days are collected as a control group, and a sea area productivity comparison test is carried out. After 6 months of sea area culture, 30 fish bodies are randomly selected from a breeding group and a control group respectively to measure the body masses, the body mass data of the two groups of fish bodies are shown in a table 3, the comparison test result shows that the body mass mean value of the fish bodies of the breeding group is 554g, the body mass mean value of the control group is 464g, the body mass of breeding seeds is improved by 19.4 percent compared with that of the control group, and the molecular marker assisted breeding technical route of the new fast-growing species of the trachinotus ovatus is reasonable and effective, and the character breeding effect is obvious.
TABLE 3 individual body quality of trachinotus ovatus breeding group and control group
In addition, the individual physique phenotype value selection, the breeding value selection, the group mating scheme selection and the like of the offspring seeds are carried out again, and the subculture breeding is carried out to accelerate the culture of the fast-growing new species of the trachinotus ovatus.
The above embodiments are described in detail for different implementations of the present invention, but the implementation manner of the present invention is not limited thereto, and those skilled in the art can achieve the object of the present invention based on the disclosure of the present invention, and any modifications and variations based on the concept of the present invention fall within the protection scope of the present invention, and the specific protection scope is subject to the claims.
Claims (3)
1. A molecular marker assisted breeding method for a new rapid-growth species of Trachinotus ovatus is characterized by comprising the following steps:
S 1 : measuring the adult fish body quality data of the trachinotus ovatus breeding population, selecting individual physique scale type value, and screening individuals with excellent characters as primary selection reserved individuals;
S 2 : constructing additive genetic correlation matrix based on microsatellite genotype data and molecular correlation coefficient method, and calculating individual body quality breeding value by using linear mixed modelSelecting and screening the individual quality breeding value again to obtain a candidate seed reserving individual;
S 3 : identifying the sex of candidate seed reserving individuals based on sex-specific molecular markers, calculating genetic distance between the candidate seed reserving individuals by utilizing microsatellite genotype data, and selecting and determining final seed reserving individuals according to a design standard of a group mating scheme;
step S 1 The selection of somatotype values for the individuals comprises: sorting the physique scale model values of 50000 individuals cultured in the sea area for 6 months from large to small, and selecting the first 2000 individuals as initial selection seed reserving individuals, wherein the seed reserving rate is 4%;
step S 2 The construction process of the additive genetic correlation matrix comprises the following steps: (S) 21 ) Extracting DNA of a primary selection seed reserving individual sample and carrying out PCR amplification; (S) 22 ) Obtaining an affinity relationship matrix between individuals by using microsatellite genotype data and a molecular correlation coefficient method; (S) 23 ) Carrying out format conversion and positive definition processing on the genetic relationship matrix and generating an additive genetic correlation matrix file; step (S) 22 ) The method for calculating the number of the intermediate molecular correlation coefficients is based on a TrioML likelihood estimation algorithm, uses an R language related software package coanda function to calculate the genetic relationship coefficients between every two individuals, and constructs a genetic relationship matrix; step (S) 23 ) The format conversion and positive definition processing of the intermediate genetic relationship matrix respectively adopt a vec2sm function and a nerPD function of a matrix software package of R language corrcor, and an additive genetic correlation matrix is generated by utilizing a write of a relationship shift pMatrix function of a synthesized software package;
step S 2 In the method, an additive genetic correlation matrix is constructed by utilizing microsatellite genotype data and a molecular correlation coefficient method, and additive genetic variance is estimated by utilizing ASReml4.0 software based on a linear mixed model
Variance of residual error
And the individual physique breeding value, and screening again by selecting the individual physique breeding value;
step S 2 The selection of the body quality breeding value of the middle individual is that the body quality breeding values of the 2000 initial selection seed reserving individuals are sorted from large to small, the top 1000 individuals are selected as candidate seed reserving individuals, and the seed reserving rate is 50 percent;
step S 3 The method for calculating the genetic distance between candidate species reserving individuals by utilizing microsatellite genotype data is characterized in that the genetic distance between individuals is calculated by adopting a PopGenRepor software package gd.kosman function based on a shared allele difference method;
step S 3 The medium group mating scheme design criteria are: (S) 31 ) Designing 4 to 6 mating groups, wherein 80 to 130 individuals are in each group; (S) 32 ) The ratio range of male fish to female fish in each group is 1 to 3 to 1; (S) 33 ) The genetic distance between the male fish and the female fish in each group is more than 0.2;
step S 3 Selecting and determining 500 individuals as final seed reserving individuals according to the middle group mating scheme, wherein the seed reserving rate is 50%, and S 1 Step S 3 The method comprises the steps of collecting 50000 adult fish body quality data, implementing a seed selection and combination scheme and selecting and reserving excellent candidate individuals, finally screening 500 excellent seed reserving individuals, wherein the seed reserving rate is 1%, and establishing a mating scheme of the seed reserving individuals.
2. The molecular marker assisted breeding method of a rapidly growing new variety of trachinotus ovatus as claimed in claim 1, wherein the method comprises the following steps: step S 2 Wherein the individual body mass breeding value is obtained by estimating the following linear mixed model, and the specific model is
In the formula (I), wherein,
is the body constitution of the ith fish,
is the average value of the physique and the mass of all fish bodies,
is additive genetic effect of ith fish body, which is subject to the expected mean value of 0 and variance of
Wherein A is an additive genetic correlation matrix,
in the form of an additive genetic variance,
is the random residual effect of the ith fish body, which is subject to the expected mean of 0 and variance of
Wherein I is an identity matrix,
estimation of linear mixture model for residual variance using ASReml4.0 software
And
and calculating the individual body quality breeding value by using a BLUP method.
3. The molecular marker assisted breeding method of a rapid-growing new variety of trachinotus ovatus as claimed in claim 1 or 2, further comprising S 4 : and (4) evaluating the breeding effect, verifying the molecular marker assisted breeding technical route of the fast-growing new species of the trachinotus ovatus, and carrying out subculture breeding.
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