CN112735519B - Method, device and storage medium for positioning segregation character - Google Patents

Abstract

The present invention provides a method, a device and a storage medium for locating biased segregation traits. The method includes: importing genetic population phenotype data to be located, genotype variation information and genome reference information of parents and offspring of the genetic population, and analyzing the reference information. The data window is divided, and the variation information is subjected to partial separation degree analysis and processing in multiple data windows to obtain the partial separation degree information to be compared, and the partial separation effect of the relative trait is extracted from the variation information to remove the variation file and the partial separation effect to increase the variation file. Perform partial separation degree analysis processing on it to obtain first and second partial separation degree information, compare the first and second partial separation degree information with the partial separation degree information to be compared, and obtain the partial separation trait location segment according to the comparison result . The invention can quickly and accurately obtain the locating section of the deviated-separated characters, and solves the problem that the deviated-separated characters cannot be located.

Description

A kind of method, device and storage medium of positioning deviation separation character

technical field

The invention mainly relates to the technical field of gene data processing, and in particular relates to a method, a device and a storage medium for locating biased segregation traits.

Background technique

One of the main methods of forward genetics is based on cross-breeding populations to locate relevant segments that control a trait. For quality traits controlled by a single gene, BC1 tester segregating populations and F2 selfing segregating populations are often constructed. If the segregation ratio of dominant traits and recessive traits is 1:1 segregated in BC1 population progeny after chi-square test, However, in the F2 population progeny, there is a 1:2:1 separation. Usually, the mapping methods for simple quality traits include QTL mapping and BSA mapping. These methods can show good results. However, locating some traits that may affect the survival rate of offspring may not have significant effect, because these traits will affect the segregation of sub-representative types, that is, the phenomenon of segregation of the phenotype of the segregated population. There is no corresponding solution.

SUMMARY OF THE INVENTION

The technical problem to be solved by the present invention is to provide a method, a device and a storage medium for positioning deviation and separation characteristics in view of the deficiencies of the prior art.

The technical solution of the present invention to solve the above-mentioned technical problems is as follows: a data processing method for positioning partial separation characteristics, comprising the following steps:

Import the phenotype data to be located in the genetic group, the genotype variation information and genome reference information of the parents and offspring of the genetic group;

Divide the genome reference information based on the data window division method to obtain multiple data windows;

Performing partial separation degree analysis processing on the genotype variation information in multiple data windows to obtain partial separation degree information to be compared;

Divide the genetic population progeny in the phenotype data to be located in the genetic population into subgroups with different traits, and extract the partial segregation effect of relative traits from the genotype variation information using the subgroup obtained by division as a standard to remove the variation file. and partial segregation effects increase the variance file;

The partial separation effect removal variation file is subjected to partial separation degree analysis processing through a plurality of the data windows to obtain first partial separation degree information, and the partial separation effect increase variation file is subjected to partial separation processing through the multiple data windows. Separation degree analysis and processing to obtain second partial separation degree information;

The first partial separation degree information and the second partial separation degree information are compared with the partial partial separation degree information to be compared, and the partial separation trait location segment is obtained according to the comparison result.

Another technical solution of the present invention to solve the above-mentioned technical problems is as follows: a device for positioning deviation and separation characteristics, comprising:

The import module is used to import the phenotype data to be located in the genetic group, the genotype variation information and genome reference information of the parents and offspring of the genetic group;

a window division module, configured to divide the genome reference information based on the data window division method to obtain a plurality of data windows;

a processing module, configured to perform partial separation degree analysis processing on the genotype variation information B in multiple data windows to obtain partial separation degree information;

The genetic population progeny in the phenotype data to be located in the genetic population is divided into at least two subgroups with different traits, and the partial segregation of relative traits is extracted from the genotype variation information B with the obtained subgroups as a standard Effect removal variation file and partial separation effect increase variation file;

Perform partial separation degree analysis processing on the partial separation effect removal variation file through a plurality of the data windows to obtain the first partial separation degree information to be compared, and add a variation file for the partial separation effect through the multiple data windows Performing partial separation degree analysis and processing to obtain the second to-be-compared partial separation degree information;

A comparison module, configured to compare the first and second partial separation degree information to be compared with the partial separation degree information to obtain a first comparison result and a second comparison result, The first comparison result and the second comparison result are intersected to obtain a partial separation trait location segment.

Another technical solution of the present invention to solve the above technical problem is as follows: a computer-readable storage medium, the computer-readable storage medium stores a computer program, and when the computer program is executed by a processor, the above positioning is realized Methods for partial segregation of traits.

Another technical solution of the present invention to solve the above technical problem is as follows: a computer-readable storage medium, the computer-readable storage medium stores a computer program, and when the computer program is executed by a processor, the above positioning is realized Methods for partial segregation of traits.

The beneficial effects of the present invention are as follows: the genome reference information is divided into windows to obtain a plurality of data windows for performing partial separation degree analysis and processing on the initial genotype variation information and the genotype variation information after the trait division, and the corresponding pending genotype variation information is obtained. The partial segregation degree information is compared with the first partial segregation degree information and the second partial segregation degree information, and they are compared and analyzed, thereby determining the partial segregation trait location segment.

Description of drawings

FIG. 1 is a schematic flowchart of a data processing method for a positioning deviation separation trait provided by an embodiment of the present invention;

FIG. 2 is a schematic diagram of functional modules of an apparatus for locating a deviated separation trait according to an embodiment of the present invention.

Detailed ways

The principles and features of the present invention will be described below with reference to the accompanying drawings. The examples are only used to explain the present invention, but not to limit the scope of the present invention.

FIG. 1 is a schematic flowchart of a data processing method for a localization biased segregation trait according to an embodiment of the present invention.

Embodiment 1: As shown in Figure 1, a data processing method for positioning partial segregation traits, comprising the following steps:

Import the phenotype data to be located in the genetic group, the genotype variation information and genome reference information of the parents and offspring of the genetic group;

Divide the genome reference information based on the data window division method to obtain multiple data windows;

Performing partial separation degree analysis processing on the genotype variation information in a plurality of the data windows to obtain the partial separation degree information to be compared;

Divide the genetic population progeny in the phenotype data to be located in the genetic population into subgroups with different traits, and extract the partial segregation effect of relative traits from the genotype variation information using the subgroup obtained by division as a standard to remove the variation file. and partial segregation effects increase the variance file;

The partial separation effect removal variation file is subjected to partial separation degree analysis processing through a plurality of the data windows to obtain first partial separation degree information, and the partial separation effect increase variation file is subjected to partial separation processing through the multiple data windows. Separation degree analysis and processing to obtain second partial separation degree information;

The first partial separation degree information and the second partial separation degree information are compared with the partial partial separation degree information to be compared, and the partial separation trait location segment is obtained according to the comparison result.

It should be understood that the "genotype variation information" in the "genotype variation information of parents and offspring of a genetic population" refers to the common information of parents and offspring of a genetic population.

In the above embodiment, the genome reference information is divided into windows to obtain a plurality of data windows for performing partial separation degree analysis and processing on the initial genotype variation information and the genotype variation information after the trait division, and the corresponding biases to be compared are obtained. The separation degree information, the first partial separation degree information and the second partial separation degree information are compared and analyzed, thereby determining the partial separation trait positioning segment.

On the basis of Example 1, Example 2: the process of dividing the genome reference information into windows to obtain multiple data windows includes:

The genome reference information is divided into windows according to a preset step value to obtain a plurality of data windows, wherein the preset step value is a length of 100 kb.

In the above embodiment, due to the long length of the genome reference information, it needs to be divided into equal lengths, which facilitates information indexing and partial separation degree analysis processing for the initial genotype variation information and the genotype variation information after trait division.

On the basis of Example 1, Example 3: before performing partial separation degree analysis and processing on the genotype variation information in multiple data windows, further includes the step of optimizing the genotype variation information, and the process includes: :

filtering out false positive sites of progeny genotypes in the genotype variation information;

According to the preset Mendelian genetic theory model, the filtered genotype variation information B is screened for variation type, and the Mendelian segregation ratio is obtained.

Specifically, the possible marker types of the offspring are inferred according to the parental marker types. When the number of individuals that do not conform to the theoretical genotype of offspring accounts for more than 5% of the total population, it can be regarded as a false positive locus and can be eliminated.

Specifically, the variant type is screened according to the inferred model of the localization trait. For example, to establish the BC1 segregation model, select the locus where only one parent is heterozygous, and establish the F2 segregation model, select the locus where both parents are heterozygous. point. According to the separation model, the Mendelian separation ratio was determined, and the chi-square test was carried out according to the separation ratio, and the p-values in the chi-square test results less than 0.001 were retained.

On the basis of Example 3, Example 4: performing partial separation degree analysis processing on the genotype variation information B in each data window, and the process of obtaining the partial separation degree information includes:

In each data window, count the frequency of the genotype variation information on the partial segregation site, and obtain the number of the partial segregation site according to the frequency;

The chi-square test is performed on the Mendelian separation ratio, and the variation information of the partial separation site is obtained according to the p value of the chi-square test result, wherein the p value is less than 0.001;

The number of the partial separation sites and the variation information of the partial separation sites are used as the partial separation degree information.

Specifically, the frequency of the genotype variation information at the partial segregation sites is counted in each data window, and the distribution map of the genome-wide partial segregation sites of the hybrid population is obtained by drawing, and the degree of partial segregation is calculated in each window, Get the degree of partial separation.

It should be understood that the variation information of the partial segregation site includes the location information of the partial segregation site on the chromosome, and the number is counted according to the 100kb window that has been divided into the genome, which is recorded as the partial segregation frequency of the window, which reflects the bias of the locus. Separation credibility. All the partial separation sites in each window have the characteristics of partial separation, and the degree of partial separation can be reflected according to the p value. In this embodiment, log10 is taken for p to reflect the degree of partial separation.

In the above embodiment, the chi-square test is performed on the Mendelian segregation ratio to obtain the variation information of the partial segregation site.

On the basis of Example 1, Example 5: dividing the descendants of the genetic population in the phenotype data to be located in the genetic population into at least two subgroups with different traits, using the obtained subgroups as the standard from The process of extracting the partial segregation effect removal variation file and the partial segregation effect increasing variant file of the relative traits from the genotype variation information includes:

Constructing a partial segregation effect removing group and constructing a partial segregation effect increasing group by using the phenotype data to be located in the genetic population;

Extracting the partial segregation effect-removed variation file and the partial segregation effect-increasing variation file of the relative trait from the genotype variation information using the partial segregation effect removal group and the partial segregation effect increase group as a standard.

In the above embodiment, the location candidate segment, that is, the phenotype partial segregation information of the genetic phenotype data to be located, is obtained through the information on the decrease in the degree of partial segregation and the information on the increase in the degree of partial segregation.

On the basis of Example 5, Example 6: the process of constructing a deviated segregation effect removing group and constructing a deviating segregation effect increasing group by using the phenotype data to be located in the genetic population includes:

Obtain a plurality of A phenotype population progeny information and a plurality of B phenotype population progeny information in the phenotype data to be located in the genetic population;

Select all the progeny information of the B phenotype population and randomly select the progeny information of the A phenotype population to construct a partial segregation effect removal group;

All the progeny information of the A phenotype population was selected to construct a population with increased segregation effect.

Specifically, the numbers corresponding to the progeny information of the A phenotype population and all the progeny information of the B phenotype population are randomly selected as m and n, and m>n, where the ratio of m:n must conform to the Mendelian genetic model. Chi-square test.

In the above-mentioned embodiment, multiple A phenotype population progeny information and multiple B phenotype population progeny information are obtained through the phenotype data to be located in the genetic population, thereby constructing and obtaining a partial segregation effect removal group and a partial segregation effect increasing group, through Partial segregation effect removal of taxa and partial segregation effect increase of taxa facilitate further processing to obtain a partial segregation trait location segment.

On the basis of Embodiment 1, Embodiment 7: the first partial separation degree information and the second partial separation degree information are compared with the to-be-compared partial separation degree information, and the partial separation is obtained according to the comparison result The process of locating segments of a trait includes:

Comparing the first partial separation degree information and the second partial separation degree information with the to-be-compared partial separation degree information to obtain partial separation degree decrease information and partial separation degree increase information;

The partial separation degree decreasing information and the partial separation degree increasing information are used to obtain a data window with overlapping data, and a partial separation trait location segment is obtained according to the data overlapping data window.

Specifically, pass the t-test method in the data window, and set a 99% confidence interval. After the t-test method shows that the degree of partial separation is significantly reduced, it is a window where the degree of partial separation is significantly reduced; similarly, pass the t-test in the data window. method, and set a 99% confidence interval. The t-test method shows that the degree of partial separation is significantly increased, which is the window where the degree of partial separation is significantly increased.

It should be understood that the statistics of multiple segregation effects remove the window in which the degree of partial segregation is significantly reduced compared with the hybrid population, and the statistical partial segregation effect increases the window in which the degree of partial segregation is significantly increased compared with the hybrid population, and the overlapping window is the positioning candidate area. segment, affecting phenotype biased segregation.

FIG. 2 is a schematic diagram of functional modules of an apparatus for locating a deviated separation trait according to an embodiment of the present invention.

Embodiment 8: a kind of device for positioning partial separation character, comprising:

The import module is used to import the phenotype data to be located in the genetic group, the genotype variation information and genome reference information of the parents and offspring of the genetic group;

a window division module, configured to divide the genome reference information based on the data window division method to obtain a plurality of data windows;

a processing module, used for performing partial separation degree analysis and processing on the genotype variation information in multiple data windows to obtain partial separation degree information;

Divide the genetic population progeny in the phenotype data to be located in the genetic population into at least two subgroups with different traits, and extract the partial segregation effect of relative traits from the genotype variation information using the subgroups obtained by division as a standard Remove variation files and add variation files with partial separation effects;

Perform partial separation degree analysis processing on the partial separation effect removal variation file through a plurality of the data windows to obtain the first partial separation degree information to be compared, and add a variation file for the partial separation effect through the multiple data windows Performing partial separation degree analysis and processing to obtain the second to-be-compared partial separation degree information;

A comparison module, configured to compare the first and second partial separation degree information to be compared with the partial separation degree information to obtain a first comparison result and a second comparison result, The first comparison result and the second comparison result are intersected to obtain a partial separation trait location segment.

Embodiment 9: a device for positioning biased separation traits, comprising a memory, a processor, and a computer program stored in the memory and executable on the processor, when the processor executes the computer program, A method to achieve the above-described localization biased segregation trait.

Embodiment 10: A computer-readable storage medium, where a computer program is stored in the computer-readable storage medium, and when the computer program is executed by a processor, the above-described method for locating a biased separation trait is implemented.

It should be understood that, in the above-mentioned embodiments 1 to 8, the data processing method is described by taking two traits as an example. If there are more than two traits, the data processing method is the same as the data processing method of "two traits", No longer.

The following is a concrete example to verify the effectiveness of this method:

The citrus genome and the citrus hybrid population were used to locate the citrus self-incompatibility traits. The citrus self-incompatibility traits were located in the range of 1-1.3mb on the citrus chromosome 1. The re-sequencing data of this population was used to construct the hybrid population. The genotype variation files of the parents and their offspring, because the segregation ratio of 1.7:1 for incompatibility and incompatibility is assumed to deviate from the 1:1 model. The compatibility traits are derived from the female parent, the compatibility is derived from the male parent, and the partial segregation is biased toward the male parent. The partial segregation of the relative traits of affinity and incompatibility is successfully detected. This example is based on the relative traits in the known positioning interval. It shows that the partial segregation detection is effective and can accurately locate the partial segregation traits.

It should be noted that, in this document, relational terms such as first and second are only used to distinguish one entity or operation from another entity or operation, and do not necessarily require or imply any relationship between these entities or operations. any such actual relationship or sequence exists. Moreover, the terms "comprising", "comprising" or any other variation thereof are intended to encompass a non-exclusive inclusion such that a process, method, article or device that includes a list of elements includes not only those elements, but also includes not explicitly listed or other elements inherent to such a process, method, article or apparatus.

The above are only preferred embodiments of the present invention and are not intended to limit the present invention. Any modifications, equivalent replacements, improvements, etc. made within the spirit and principles of the present invention shall be included in the protection of the present invention. within the range.

Claims (9)

1. A data processing method for positioning segregation traits is characterized by comprising the following steps:

introducing phenotype data to be located of the genetic group, genotype variation information of parents and offspring of the genetic group and genome reference information;

dividing the genome reference information based on a data window division method to obtain a plurality of data windows;

performing partial separation degree analysis processing on the genotype variation information in a plurality of data windows to obtain partial separation degree information to be compared;

dividing filial generations of the genetic population in the phenotype data to be located of the genetic population into subgroups with different traits, and extracting partial segregation effect removing variation files of relative traits and partial segregation effect increasing variation files of relative traits from the genotype variation information by taking the obtained subgroups as a standard;

performing partial separation degree analysis processing on the partial separation effect removal variant file through the plurality of data windows to obtain first partial separation degree information, and performing partial separation degree analysis processing on the partial separation effect addition variant file through the plurality of data windows to obtain second partial separation degree information;

and comparing the first partial separation degree information and the second partial separation degree information with the partial separation degree information to be compared, and obtaining a partial separation character positioning section according to a comparison result.

2. The data processing method for locating segregation traits as claimed in claim 1, wherein the dividing the genome reference information based on a data window division method to obtain a plurality of data windows comprises:

and carrying out window division on the genome reference information according to a preset step value to obtain a plurality of data windows, wherein the preset step value is 100kb in length.

3. The data processing method for locating segregation trait according to claim 1, further comprising a step of optimizing the genotype variation information before analyzing the segregation degree of the genotype variation information in a plurality of data windows, wherein the step comprises:

filtering out false positive sites of the offspring genotypes in the genotype variation information;

carrying out mutation type screening on the filtered genotype mutation information according to a preset Mendelian genetic theory model to obtain a Mendelian separation ratio;

the process of analyzing and processing the segregation degree of the genotype variation information in a plurality of data windows to obtain the segregation degree information comprises the following steps:

counting the frequency of the genotype variation information on the partial separation sites in each data window, and obtaining the number of the partial separation sites according to the frequency;

performing chi-square test on the Mendelian separation ratio, and obtaining variation information of partial separation sites according to a p value of a chi-square test result as a standard, wherein the p value is less than 0.001;

and taking the number of the partial separation sites and the variation information of the partial separation sites as partial separation degree information.

4. The data processing method for locating segregation traits as claimed in claim 1, wherein the process of dividing progeny of the genetic population in the phenotype data to be located of the genetic population into at least two subsets of different traits, and extracting segregation-effect-removing variation files of relative traits and segregation-effect-increasing variation files of relative traits from the genotype variation information by using the divided subsets as a standard comprises:

constructing a segregation effect removing class group and a segregation effect increasing class group through the phenotype data to be located of the genetic group;

and extracting a partial segregation effect removal variation file of relative characters and a partial segregation effect increase variation file of relative characters from the genotype variation information by taking the partial segregation effect removal cluster and the partial segregation effect increase cluster as standards.

5. The data processing method for locating segregation traits as claimed in claim 4, wherein the process of constructing segregation effect eliminating cluster and constructing segregation effect increasing cluster by the phenotype data to be located by the genetic population comprises:

acquiring a plurality of A phenotype population filial generation information and a plurality of B phenotype population filial generation information from the genetic population to-be-located phenotype data;

selecting all B phenotype population progeny information and randomly selecting A phenotype population progeny information to construct segregation-biased effect removal clusters;

and selecting all filial generation information of the A phenotype population to construct a segregation effect increasing class group.

6. The data processing method for locating segregation trait according to claim 1, wherein the step of comparing the first segregation degree information and the second segregation degree information with the segregation degree information to be compared to obtain a segregation trait locating section according to the comparison result comprises:

comparing the first partial separation degree information and the second partial separation degree information with the partial separation degree information to be compared to obtain partial separation degree reduction information and partial separation degree increase information;

and obtaining data overlapping data windows according to the partial separation degree reduction information and the partial separation degree increase information, and obtaining partial separation character positioning sections according to the data overlapping data windows.

7. A data processing apparatus for locating segregation traits, comprising:

the introduction module is used for introducing phenotype data to be positioned of the genetic group, genotype variation information of parents and filial generations of the genetic group and genome reference information;

the window division module is used for dividing the genome reference information based on a data window division method to obtain a plurality of data windows;

the processing module is used for analyzing and processing the segregation degree of the genotype variation information in a plurality of data windows to obtain segregation degree information;

dividing filial generations of the genetic population in the phenotype data to be located of the genetic population into at least two subgroups with different traits, and extracting partial segregation effect removing variation files of relative traits and partial segregation effect increasing variation files of relative traits from the genotype variation information by taking the obtained subgroups as a standard;

performing partial separation degree analysis processing on the partial separation effect removing variation file through the plurality of data windows to obtain first partial separation degree information to be compared, and performing partial separation degree analysis processing on the partial separation effect adding variation file through the plurality of data windows to obtain second partial separation degree information to be compared;

and the comparison module is used for respectively comparing the first partial separation degree information to be compared and the second partial separation degree information to be compared with the partial separation degree information to obtain a first comparison result and a second comparison result, and performing intersection processing on the first comparison result and the second comparison result to obtain a partial separation character positioning section.

8. A data processing apparatus for locating segregation traits, comprising a memory, a processor and a computer program stored in the memory and executable on the processor, characterized in that when the computer program is executed by the processor, a data processing method for locating segregation traits according to any one of claims 1 to 6 is implemented.

9. A computer-readable storage medium, in which a computer program is stored which, when being executed by a processor, carries out a data processing method for locating a segregation trait of any one of claims 1 to 6.

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