Method and device for detecting gradual gene introgression between biological populations

Abstract

The present invention relates to the fields of bioinformatics and genetics, and more particularly to a method and apparatus for detecting introgression between biological populations. The method comprises obtaining genetic information from at least three biological populations, scanning the genetic information, and determining the location and number of target genomic regions exhibiting introgression within the genetic information; and determining whether introgression exists between the biological populations based on the location and number of the target genomic regions within the genetic information. Compared to existing methods, the method of the present invention offers higher detection efficiency.

Description

Technical Field

[0001] The present invention relates to the fields of bioinformatics and genetics, and in particular to a method and device for detecting progressive gene introgression between biological populations. Background Art

[0002] In genetics (particularly plant genetics), introgression refers to the flow of genes between two populations or varieties. Genes are nucleotide sequences containing specific genetic information, known as deoxyribonucleic acid (DNA). They serve as the primary material for storing and transmitting genetic information and replicating cells. Genes carry out their functions by synthesizing corresponding functional proteins. Genetic information is transmitted from one individual to another through various chemical reactions, replicating in the form of replication, thereby preserving the information characteristics of the previous generation.

[0003] These hybrid genetic methods involve designed breeding of the overall genetic heritage of a population or variety. However, the genetic background of progressive introgression and the detailed information about the genes that control the relevant traits of this phenomenon are currently unknown. Only when the source of the alleles at the introgressed gene loci can be accurately identified and the background genotype can gene introgression be effectively carried out. The existing technology mainly uses genetic markers and major effect genes to determine whether progressive gene introgression occurs between two hybrid biological populations. However, these two current detection methods require long detection cycles and have low accuracy rates. Summary of the Invention

[0004] The present invention provides a method and device for detecting genetic introgression between biological populations, which are used to solve the technical problem of long detection cycles in the prior art when detecting whether genetic introgression exists between biological populations. In one aspect, the present invention provides a method for detecting genetic introgression between biological populations, comprising:

[0005] Obtain genetic information for at least three biological populations;

[0006] Scanning the genetic information to determine the location and number of target genomic regions with progressive introgression in the genetic information;

[0007] Determine whether there is a phenomenon of progressive gene introgression between the biological populations based on the position information and number of the target genomic region in the genetic information.

[0008] According to a method for detecting progressive gene introgression between biological populations provided by the present invention, scanning the genetic information to determine the position information and number of target genomic regions with progressive introgression in the genetic information includes:

[0009] Numbering the genomic sequence of the genetic information;

[0010] Scanning the genome sequence of the genetic information using a sliding window to obtain numbers corresponding to the starting window position and the ending window position of the target genome on the genome sequence, and determining the position information of the target genome region on the genome sequence according to the numbers;

[0011] The number of windows in which the target genomic region appears is obtained, and the number of the target genomic regions is determined according to the number of windows.

[0012] According to a method for detecting progressive gene introgression between biological populations provided by the present invention,

[0013] The determining whether there is a phenomenon of gene introgression between the biological populations according to the position information and number of the target genomic region in the genetic information includes:

[0014] determining a difference score between the two populations based on the number of the target genomic regions;

[0015] Determine whether there is a phenomenon of gradual gene introgression between the biological populations based on the difference.

[0016] In another aspect, the present invention further provides a device for detecting progressive gene introgression between biological populations, comprising:

[0017] An input module, used for inputting genetic information of at least three biological populations;

[0018] a calculation module, configured to scan the genetic information and determine the position information and number of target genomic regions with progressive introgression in the genetic information;

[0019] An output module is used to determine whether there is a phenomenon of progressive gene introgression between the biological populations based on the position information and number of the target genome region in the genetic information.

[0020] According to a device for detecting progressive gene introgression between biological populations provided by the present invention, the scanning of the genetic information to determine the position information and number of target genomic regions with progressive introgression in the genetic information includes:

[0021] Numbering the genomic sequence of the genetic information;

[0022] Scanning the genome sequence of the genetic information using a sliding window to obtain numbers corresponding to the starting window position and the ending window position of the target genome on the genome sequence, and determining the position information of the target genome region on the genome sequence according to the numbers;

[0023] The number of windows in which the target genomic region appears is obtained, and the number of the target genomic regions is determined according to the number of windows.

[0024] According to a biological population gene introgression detection device provided by the present invention, determining whether there is a phenomenon of progressive gene introgression between the biological populations based on the position information and number of the target genomic region in the genetic information includes:

[0025] determining a difference score between the two populations based on the number of the target genomic regions;

[0026] Determine whether there is a phenomenon of gradual gene introgression between the biological populations based on the difference.

[0027] On the other hand, the present invention also provides an electronic device comprising a memory, a processor, and a computer program stored in the memory and executable on the processor, wherein when the processor executes the program, it implements any of the above-described methods for detecting gene infiltration in biological populations.

[0028] On the other hand, the present invention also provides a non-transitory computer-readable storage medium having a computer program stored thereon, which, when executed by a processor, implements any of the biological population gene introgression detection methods described above.

[0029] On the other hand, the present invention also provides a computer program product, comprising a computer program, which, when executed by a processor, implements any of the biological population gene introgression detection methods described above.

[0030] According to the method for detecting introgression between biological populations provided by the present invention, genetic information from at least three biological populations is obtained and scanned to determine the location and number of target genomic regions exhibiting introgression within the genetic information. Based on the location and number of target genomic regions within the genetic information, whether introgression occurs between the biological populations is determined. Compared to existing methods, the method of the present invention offers higher detection efficiency. BRIEF DESCRIPTION OF THE DRAWINGS

[0031] In order to more clearly illustrate the technical solutions in the present invention or the prior art, a brief introduction is given below to the drawings required for use in the embodiments or the description of the prior art. Obviously, the drawings described below are some embodiments of the present invention. For ordinary technicians in this field, other drawings can be obtained based on these drawings without paying any creative work.

[0032] Figure 1 Schematic diagram of the process of detecting progressive gene introgression between biological populations provided by the present invention;

[0033] Figure 2 It is a schematic structural diagram of the device for detecting progressive gene introgression between biological populations provided by the present invention.

[0034] Figure 3 It is a structural schematic diagram of the electronic device provided by the present invention. DETAILED DESCRIPTION

[0035] To make the objectives, technical solutions, and advantages of the present invention more clear, the technical solutions of the present invention will be clearly and completely described below in conjunction with the accompanying drawings. Obviously, the embodiments described are only some of the embodiments of the present invention, not all of them. Based on the embodiments of the present invention, all other embodiments obtained by ordinary technicians in this field without making creative efforts shall fall within the scope of protection of the present invention.

[0036] The following combination Figure 1-Figure 3 The technical solution of the present invention is further described.

[0037] The present invention provides a method for detecting introgression between biological populations. The method involves obtaining genetic information from at least three biological populations; scanning the genetic information to determine the location and number of target genomic regions exhibiting introgression within the genetic information; and determining whether introgression exists between the biological populations based on the location and number of the target genomic regions within the genetic information. The method can rapidly determine whether introgression has occurred, improving detection efficiency.

[0038] Specifically, this embodiment uses a mobile window to scan the genome and calculates the relative offspring difference score (rIBD score) between populations in each window, thereby determining whether there is progressive gene introgression between populations based on the rIBD score, and can determine the regions and gene sites of the genome with significant progressive introgression.

[0039] Example 1:

[0040] like Figure 1 The present invention provides a flow chart of a method for detecting progressive introgression of genes between biological populations. The method specifically comprises:

[0041] Step 101: Obtain genetic information of at least three biological populations.

[0042] For example, when obtaining genetic information, the genetic material is first extracted, and then the genetic material is sequenced using a sequencer to obtain the regret information of the biological population.

[0043] For example, the three biological populations may be: two purebred species and one hybrid species, for example, the three populations are purebred South China tigers, purebred Siberian tigers, and hybrid tigers.

[0044] Step 102: Scan the genetic information to determine the location information and number of target genomic regions with progressive introgression in the genetic information.

[0045] For example, the genomic sequence of the genetic information is numbered; the genomic sequence of the genetic information is scanned using a sliding window to obtain numbers corresponding to the starting window position and the ending window position of the target genome on the genomic sequence, and the position information of the target genomic region on the genomic sequence is determined based on the numbers; the number of windows in which the target genomic region appears is obtained, and the number of target genomic regions is determined based on the number of windows.

[0046] The target gene segment region of this embodiment is generally a gene fragment with excellent biological characteristics shared by three species. Specifically, in this embodiment, before scanning the gene sequence, the gene sequence with significant offspring consistency is first numbered; when the gene sequence is window scanned, the numbers corresponding to the starting window position and the ending window position of the target genomic region are obtained, and the position information of the target genomic region is determined according to the numbers corresponding to the starting window position and the ending window position. At the same time, the number of windows that appear in the target genomic region is recorded by scanning, so as to determine the number and specific position of the target genomic region, and then all genomic window regions with significant progressive introgression are output, which include the position and location of the target genomic region.

[0047] For example, in this embodiment, the gene sequence of the biological population is obtained and converted into the required input file format. Then, a circular index method is used in the computer to search for the target genomic region with significant progressive introgression in a sliding window manner, and the number of the starting window position and the number of the ending window position of the target genomic region are recorded at the same time, and the specific position where the target genomic region appears is recorded.

[0048] Step 103: Determine whether there is progressive gene introgression between biological populations based on the location information and number of the target genomic region in the genetic information.

[0049] For example, the difference score (i.e., rIBD score) between two populations is determined based on the number of target genomic regions; and whether there is gene introgression between the biological populations is determined based on the difference score.

[0050] In this embodiment, the calculated rIBD score is used to determine whether there is significant gene introgression between biological populations and the exact location information of the relevant dominant genes.

[0051] For example, when it is determined that similar target genomic region sequences exist at positions with progeny consistency that are relatively close in the gene sequences of two biological populations, and the number of windows of such target genomic regions in the entire gene sequence is basically the same, the rIBD score between varieties of a population is calculated comprehensively based on the number of windows. The specific calculation method is as follows:

[0052] rIBD=IBD s1 -IBD s2

[0053] Among them, IBD s1 Indicates the ratio of IBD (Identity By Descent) between the genomes of source variety 1 and the hybrid population, IBD s2 Indicates the ratio of IBD between the genomes of source species 2 and the hybrid population. For example, for a purebred Siberian tiger, a purebred South China tiger, and a hybrid tiger, the IBD s1 Indicates the ratio of IBD between purebred Siberian tigers and hybrid tigers, IBD s2 Represents the ratio of IBD between purebred South China tigers and hybrid tigers.

[0054] If the rIBD score is greater than a preset value, generally, a person skilled in the art sets the preset value based on experience, then it is determined that there is significant gene introgression between the two biological populations.

[0055] According to the method for detecting progressive gene introgression between biological populations of this embodiment, it is possible to quickly determine whether there is significant progressive gene introgression between biological populations, as well as the window position information and number of the relevant target genomic regions.

[0056] This method can realize the sliding recognition of batches of progressive introgression maps of gene sequences, determine the genomic regions with significant progressive introgression phenomena and the window regions of their corresponding gene loci, and the application of the method of this embodiment can realize the accurate determination of the progressive genomic regions of the population. The use of corresponding computer tools will also greatly improve the calculation efficiency, reduce the time consumed by manual labor, and ultimately obtain accurate calculation results.

[0057] Example 2:

[0058] The device for detecting the gradual introgression of genes between biological populations provided by the present invention is described below. The device for detecting the gradual introgression of genes between biological populations described below and the method for detecting the gradual introgression of genes between biological populations described above can be referenced to each other.

[0059] This embodiment provides a device for detecting the progressive introgression of genes in biological populations. The detection device of this embodiment can also be understood as a detection platform, such as Figure 2This is a structural diagram of a device for detecting progressive introgression of genes in biological populations according to an embodiment of the present invention. The device includes: an input module 201, a calculation module 202, and an output module 203.

[0060] The input module 201 is used to input genetic information from at least three biological populations. The calculation module 202 is used to scan the genetic information and determine the location and number of target genomic regions with introgression within the genetic information. The output module 203 is used to determine whether introgression occurs between the biological populations based on the location and number of target genomic regions within the genetic information.

[0061] In another embodiment, the output module 203 of the apparatus for detecting introgression between biological populations is further configured to output the determination of whether introgression exists between biological populations. Furthermore, in other embodiments, the output module 203 is further configured to simultaneously output the location and number of target genomic regions.

[0062] For example, the calculation module 202 is used to number the genomic sequence of the genetic information; use a sliding window to scan the genomic sequence of the genetic information, obtain the numbers corresponding to the starting window position and the ending window position of the target genome on the genomic sequence, and determine the position information of the target genomic region on the genomic sequence based on the numbers; obtain the number of windows in which the target genomic region appears, and determine the number of target genomic regions based on the number of windows.

[0063] For example, when it is determined that similar target genomic region sequences exist at relatively close positions with offspring consistency in the gene sequences of two biological populations, and the number of windows of such target genomic regions in the entire gene sequence is basically the same, the average rIBD score between the varieties of a population is comprehensively calculated based on the number of windows. If the rIBD score is greater than a preset value, it is determined that there is significant progressive gene introgression between the two biological populations.

[0064] In this embodiment, the implementation method of each of the above functional modules is the same as that in the above embodiment 1 and will not be repeated here.

[0065] Example 3:

[0066] like Figure 3 An example of a physical structure diagram of an electronic device is shown below. Figure 3As shown, the electronic device may include: a processor 310, a memory 330, and a communication bus 340, wherein the processor 310 and the memory 330 communicate with each other via the communication bus 340. The processor 310 may call logic instructions in the memory 330 to execute a method for detecting progressive gene introgression between biological populations, the method comprising: obtaining genetic information of at least three biological populations; scanning the genetic information to determine the location information and number of target genomic regions with progressive introgression in the genetic information; and determining whether progressive gene introgression exists between the biological populations based on the location information and number of the target genomic regions in the genetic information.

[0067] In addition, the logic instructions in the above-mentioned memory 330 can be implemented in the form of a software functional unit and can be stored in a computer-readable storage medium when sold or used as an independent product. Based on this understanding, the technical solution of the present invention, or the part that contributes to the prior art, or the part of the technical solution, can be embodied in the form of a software product. The computer software product is stored in a storage medium and includes several instructions for enabling a computer device (which can be a personal computer, a server, or a network device, etc.) to perform all or part of the steps of the method described in each embodiment of the present invention. The aforementioned storage medium includes: various media that can store program codes, such as a USB flash drive, a mobile hard disk, a read-only memory (ROM), a random access memory (RAM), a magnetic disk or an optical disk.

[0068] On the other hand, the present invention also provides a computer program product, which includes a computer program, which can be stored on a non-transitory computer-readable storage medium. When the computer program is executed by a processor, the computer can perform the method for detecting progressive gene introgression between biological populations provided by the above methods, which includes: obtaining genetic information of at least three biological populations; scanning the genetic information to determine the position information and number of target genomic regions with progressive introgression in the genetic information; and determining whether there is progressive gene introgression between biological populations based on the position information and number of target genomic regions in the genetic information.

[0069] On the other hand, the present invention also provides a non-transitory computer-readable storage medium having a computer program stored thereon, which, when executed by a processor, is implemented to execute the method for detecting progressive gene introgression between biological populations provided by the above-mentioned methods, the method comprising: obtaining genetic information of at least three biological populations; scanning the genetic information to determine the position information and number of target genomic regions with progressive introgression in the genetic information; and determining whether there is progressive gene introgression between biological populations based on the position information and number of target genomic regions in the genetic information.

[0070] The device embodiments described above are merely illustrative. The units described as separate components may or may not be physically separate, and the components shown as units may or may not be physical units, that is, they may be located in one place or distributed across multiple network units. Some or all of the modules may be selected based on actual needs to achieve the objectives of this embodiment.

[0071] Through the description of the above embodiments, those skilled in the art can clearly understand that each embodiment can be implemented by means of software plus a necessary general hardware platform, or of course, by hardware. Based on this understanding, the essence of the above technical solution or the part that contributes to the existing technology can be embodied in the form of a software product. The computer software product can be stored in a computer-readable storage medium, such as ROM / RAM, a magnetic disk, an optical disk, etc., and includes a number of instructions for enabling a computer device (which can be a personal computer, a server, or a network device, etc.) to execute the methods described in each embodiment or certain parts of the embodiments.

[0072] Finally, it should be noted that the above embodiments are only used to illustrate the technical solutions of the present invention, rather than to limit it. Although the present invention has been described in detail with reference to the aforementioned embodiments, those skilled in the art should understand that they can still modify the technical solutions described in the aforementioned embodiments, or make equivalent replacements for some of the technical features therein. However, these modifications or replacements do not deviate the essence of the corresponding technical solutions from the spirit and scope of the technical solutions of the various embodiments of the present invention.

Claims

1. A method for detecting progressive gene introgression between biological populations, characterized in that: include: Obtaining genetic information of at least three biological populations, the three biological populations being two purebred organisms and one hybrid organism; Scanning the genetic information to determine the location and number of target genomic regions with progressive introgression in the genetic information; Scanning the genetic information to determine the location information and number of target genomic regions with progressive introgression in the genetic information includes: Numbering the genomic sequence of the genetic information; Scanning the genomic sequence of the genetic information using a sliding window, obtaining numbers corresponding to the starting window position and the ending window position of the target genomic region on the genomic sequence, and determining the position information of the target genomic region on the genomic sequence according to the numbers; Obtaining the number of windows in which the target genomic region appears, and determining the number of the target genomic regions according to the number of windows; determining whether there is gene introgression between the biological populations based on the position information and number of the target genomic region in the genetic information; Determining whether there is gene introgression between the biological populations based on the position information and number of the target genomic region in the genetic information includes: Determining a difference score between two populations based on the number of target genomic regions, wherein the difference score is a rIBD score; The presence of gene introgression between the biological populations is determined based on the difference score.

2. A device for detecting progressive gene introgression between biological populations, characterized in that: include: An input module, configured to input genetic information of at least three biological populations, wherein the three biological populations are two purebred organisms and one hybrid organism; A calculation module is used to scan the genetic information to determine the position information and number of target genomic regions with progressive introgression in the genetic information; the scanning of the genetic information to determine the position information and number of target genomic regions with progressive introgression in the genetic information includes: numbering the genomic sequence of the genetic information; scanning the genomic sequence of the genetic information using a sliding window to obtain the numbers corresponding to the starting window position and the ending window position of the target genomic region on the genomic sequence, and determining the position information of the target genomic region on the genomic sequence according to the numbers; obtaining the number of windows in which the target genomic region appears, and determining the number of the target genomic regions according to the number of windows; An output module is used to determine whether there is progressive gene introgression between the biological populations based on the position information and number of the target genomic region in the genetic information; the determining whether there is progressive gene introgression between the biological populations based on the position information and number of the target genomic region in the genetic information includes: determining a difference score between the two populations based on the number of the target genomic regions, the difference score being a rIBD score; and determining whether there is progressive gene introgression between the biological populations based on the difference score.

3. An electronic device comprising a memory, a processor, and a computer program stored in the memory and executable on the processor, wherein: When the processor executes the program, it implements the method for detecting gradual gene introgression between biological populations as described in claim 1.

4. A non-transitory computer-readable storage medium having a computer program stored thereon, characterized in that: When the computer program is executed by a processor, the method for detecting gradual gene introgression between biological populations as described in claim 1 is implemented.

5. A computer program product comprising a computer program, characterized in that When the computer program is executed by a processor, the method for detecting gradual gene introgression between biological populations as described in claim 1 is implemented.

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