Method for identifying gender antagonism hot spot region on pig autosome and application

Abstract

The invention relates to a method for identifying a sex antagonism hot spot region on a pig autosome and application. The method provided by the invention comprises the following specific steps: constructing three generations of domestic pig hybrid population F0, F1 and F2, performing genome sequencing and SNP (Single Nucleotide Polymorphism) identification, transmitting and tracking genetic materials in a hybrid population family, and identifying a gender antagonism hot spot region. According to the method disclosed by the invention, the Chr3: 121M window is identified to be a gender proportion directional regulation molecular marker beneficial to the generation of male offspring in a large white / Min pig genotype individual. According to the method disclosed by the invention, the sex of the swinery can be predicted, regulated and controlled, multiple generations are obtained by continuous cross-crossing on the basis of not introducing exogenous blood relationship through screening and optimal mating of parent genotypes before mating, and the sex of the swinery can be predicted and controlled under the condition that all genotypes of each generation are kept on the group level. The proportion of genotypes beneficial to male or female can reach the maximum value of dynamic planning, and then the gender proportion of offspring piglet groups can be dynamically regulated and controlled.

Description

Technical Field

[0001] The present invention relates to the field of molecular breeding technology, and in particular to a method for identifying sex antagonistic hotspot regions on pig autosomes and applications thereof. Background Art

[0002] The sex ratio of live pigs is an important economic trait in the pig farming industry. Male and female pigs have different characteristics and economic values ​​in the industry. Male pigs grow fast and have a high lean meat rate, making them suitable for breeding pig production; sows have strong reproductive capacity and good meat quality, making them suitable for commercial pig production. It is of great significance to achieve sex control of live pigs, which can not only improve economic benefits, but also improve production efficiency. It can also better optimize genetics in genetic breeding applications and prevent the occurrence of sex-linked genetic diseases.

[0003] Existing methods for sex control include: (1) semen sorting: using the difference in DNA content between X sperm and Y sperm, the semen is stained and X and Y sperm are separated according to fluorescence intensity using a flow cytometer. This method has problems such as high cost and high sperm deformity rate; (2) embryo sex identification: by identifying the sex of the embryo, the embryo is artificially selected to interfere with the sex ratio at birth. This method has problems such as potential embryo loss, difficulty in operation, and difficulty in large-scale promotion; (3) external regulation: by controlling the external environment of pig fertilization (such as hormone levels) to affect sex, there are problems such as high randomness and unstable results.

[0004] At present, genetic selection has become a new method. This method requires the identification of relevant genetic markers and the selection of individuals with relevant genetic markers (such as specific genotypes) for directional breeding, thereby expanding the pig population of a specific sex. With the increasing maturity of genetic technology, the cost of genetic technology has also dropped significantly, making it possible to promote it on a large scale in production applications. The sex determination of pigs is chromosomal sex determination. Like most mammals, when the sex chromosome is XX type, it is female, and when the sex chromosome is XY, it is male. In fact, in the mammalian genome, the sex chromosome is only the master switch for sex determination, which contains a complex sex development regulatory network. Studies have found that in higher mammals, the transcription factor SRY encoded by the Y chromosome triggers the early gonadal development into testis (male) by activating the expression of the SOX9 gene. If there is no SRY expression during early gonadal development, it develops into ovary (female).

[0005] Traditionally, it is believed that sex is determined by the combination of sex chromosomes, but existing studies have found that autosomes can also participate in sex determination. Looking back at the long process of pig domestication, female and male pigs were selected to have different phenotypic characteristics, and a large number of sex-antagonistic gene loci have accumulated on the autosomes of Asian domestic pigs. Sex-antagonistic hotspot regions have different effects on the fitness of males and females, thereby affecting the ratio of males to females in the population. If sex-antagonistic hotspot regions that affect sex can be screened out from autosomes, the sex ratio of offspring can be regulated in a targeted manner during breeding, but no relevant research has been reported so far. Summary of the invention

[0006] In order to solve the above problems, the present invention proposes a method and application for identifying sex antagonistic hotspot regions on pig autosomes.

[0007] The method for identifying sex antagonistic hotspot regions on pig autosomes provided by the present invention comprises the following specific steps:

[0008] S1. Constructing a hybrid pig population of three generations: F0, F1, and F2: Using two homozygous pigs of different breeds, A and B, as the F0 generation, hybridizing two purebred pigs of the F0 generation to obtain the F1 generation, and cross-crossing the F1 generation without introducing exogenous blood to obtain the F2 generation;

[0009] S2. Genome sequencing and SNP identification: DNA of all the above-mentioned generations of individuals is collected, and the genome information and SNP site variation information of the autosomes of all individuals from F0 to F2 generations are obtained through genome sequencing and SNP identification;

[0010] S3. Tracking the transmission of genetic material in the hybrid population family: Cut all autosomal genomic information from 0 into 1Mb non-overlapping fragments in sequence, and define each fragment as a window. Combine pedigree information, the gene transmission law of father-mother-offspring, and the SNP site variation information obtained in S2, and analyze the genetic transmission pathway of F0 generation gene fragments in F1 and F2 generations in units of windows, determine the source of alleles inherited in each window of F2 generation, and count the number of male and female individuals with different genotypes to obtain the observed value (N);

[0011] S4. Identify sex-antagonistic hotspots: Analyze the differences in the number of male and female individuals with different genotypes in the F2 generation in units of windows. Set a statistic (NHWED), and compare the differences between the observed values (N) and the expected values (E) of the number of male and female individuals with different genotypes in each window of the F2 generation. The formula is NHWED = (N - E) / E. Classify the male and female NHWED values. When NHWED > N, it means the actual number of individuals is higher than the expected number, and vice versa when NHWED < N. If the male and female NHWED values in a window are both positive or both negative, it means the sex selection directions in this window are the same, which is defined as sex-synergistic selection (SSS). If the male and female NHWED values in a window are one positive and one negative, it means the sex selection directions in this window are opposite, which is defined as sex-antagonistic selection (SAS). Analyze the windows of all individuals with different genotypes in the F2 generation in turn, and divide the windows into SAS windows and SSS windows. Find the SAS windows with significantly higher absolute values of NHWED and identify them as sex-antagonistic hotspots.

[0012] Furthermore, the calculation method of the expected value is as follows:

[0013] In units of windows, N is the observed value described in S3. Let N(male) represent the total number of male individuals in this window, represent the number of male individuals with genotype A / A, represent the number of male individuals with genotype A / B, represent the number of male individuals with genotype B / A, represent the number of male individuals with genotype B / B; Let N(female) represent the total number of female individuals in this window, represent the number of female individuals with genotype A / A, represent the number of female individuals with genotype A / B, represent the number of female individuals with genotype B / A, represent the number of female individuals with genotype B / B; Let represent the expected value of the number of male individuals with genotype A / A in this window, represent the expected value of the number of male individuals with genotype A / B in this window, represent the expected value of the number of male individuals with genotype B / A in this window, represent the expected value of the number of male individuals with genotype B / B in this window; Let represent the expected value of the number of female individuals with genotype A / A in this window, represent the expected value of the number of female individuals with genotype A / B in this window, represent the expected value of the number of female individuals with genotype B / A in this window, It indicates the expected number of females with genotype B / B in this window. The calculation formula of the above expected value is as follows:

[0014]

[0015]

[0016] The method for identifying sex antagonistic hotspot regions on pig autosomes provided by the present invention is applied in pig hybrid breeding.

[0017] Preferably, the method for the sex antagonism hotspot region on the pig autosome provided by the present invention is applied to pig hybrid breeding, and the sex ratio of the offspring pig herd is directional regulated by the specific selection of parent pigs with genotypes having the sex antagonism hotspot region.

[0018] The present invention also provides a molecular marker for directional regulation of the sex ratio of pigs. In the hybrid breeding of Large White and Min pigs, in the F2 generation and the subsequent generation pigs, when the paternal chromosome of the individual is a Large White genotype and the maternal chromosome is a Min pig genotype, the Chr3:121M window is a molecular marker for directional regulation of the sex ratio that is beneficial to the production of male offspring in individuals with the Large White / Min pig genotype. The Chr3:121M window is a sex antagonistic hotspot region identified by the above method, and the whole genome version is Sscrofa11.

[0019] The pig sex ratio directional control molecular marker provided by the present invention can realize directional control of the sex ratio of the offspring pig group by specific selection of parent pigs with genotypes in the Chr3:121M window in pig hybrid breeding.

[0020] The beneficial effects of the present invention are as follows:

[0021] 1. The present invention provides a method for identifying sex antagonistic hotspot regions related to directional regulation of sex ratio on pig autosomes. The sex antagonistic hotspot regions obtained according to the method of the present invention can be used as molecular markers, and different genotypes of the molecular markers can be used to produce different regulatory effects on male and female individuals, thereby achieving sex ratio control in pig breeding.

[0022] 2. The present invention is based on sequencing data, and it is found that in the three-generation Eurasian domestic pig hybrid system, the transmission of the genotype of the genetic material at a specific window position of the chromosome has a sex genetic skewness, and thus the method of the present invention is developed. The method of the present invention can predict and regulate the sex of the pig group. For example, in some cases, a specific genotype may be beneficial to the survival of males. Therefore, by increasing the proportion of the genotype in the parents, the proportion of the offspring boars in the overall group can be increased. In actual production, if more boars or sows are desired, the genotypes of the parents can be screened and optimized before mating, and multiple generations can be obtained by continuous cross-crossing without introducing exogenous blood. Under the condition that all the genotypes of each generation are retained at the group level, the proportion of genotypes that are beneficial to males or females can be achieved to the maximum value of dynamic programming, thereby realizing dynamic regulation of the sex ratio of the offspring piglet group. BRIEF DESCRIPTION OF THE DRAWINGS

[0023] Figure 1 It is a schematic diagram of the technical process of the present invention;

[0024] Figure 2 It is a tracer of the transmission of genetic material in the lineage of a hybrid population;

[0025] Figure 3 This is a scatter plot of the correlation analysis of the male-female frequency of LW / MIN genotypes in the whole genome;

[0026] Figure 4 This is the percentage of males with LW / MIN genotype in the chromosome 3 window;

[0027] Figure 5 This is the P value peak graph after correction of the LW / MIN genotype of chromosome 3 in the simulated population. DETAILED DESCRIPTION

[0028] The present invention will be further described below with reference to the embodiments.

[0029] Example 1: A method for identifying sex antagonistic hotspot regions on pig autosomes:

[0030] The following steps are involved:

[0031] S1. Construct the three generations of F0, F1, and F2 of the domestic pig hybrid population: Use homozygous European domestic pigs and homozygous Asian domestic pigs as the F0 generation. The European domestic pigs used in the construction are selected from male homozygous Large White pigs (LW), and the Asian domestic pigs are selected from female homozygous Min pigs (MIN). In the first step, 5 Large White boars and 16 Min pig sows were selected as the F0 generation; in the second step, the F0 generation was mated, and a total of 9 F1 generation boars and 45 F1 generation sows were produced; in the third step, the F1 generation individuals were mated, and 284 F2 generation sows and 294 F2 generation boars were produced. Through the above steps, the Eurasian domestic pig hybrid genetic system was successfully established. The individuals in this system include 653 pigs in the F0, F1 and F2 generations, and all pigs in this family are grown under the same feeding conditions.

[0032] S2. Genome sequencing and SNP identification: Ear tissue samples of all generations were collected, and genomic DNA of ear samples was extracted from all individuals using the phenol-chloroform method. All samples were genotyped using Illumina Porcine SNP60Bead Chips. The Porcine SNP60 chip data was used to infer the autosomal haplotypes of all family individuals, and the autosomal genomic information and SNP site variation information of all individuals from the F0, F1 to F2 generations were obtained. In this process, family information was used to correct genotype errors and recombination breakpoint errors to improve the accuracy of haplotype inference. The whole genome version is Sscrofa11.

[0033] S3. Tracking the transmission of genetic material in hybrid population families: The genomic information of all autosomes was cut into non-overlapping fragments of 1 Mb in size, and each fragment was defined as a window. The pedigree information, the gene transmission rules of father-mother-offspring, and the SNP site variation information obtained in S2 were combined to analyze the genetic transmission pathways of F0 generation gene fragments in F1 and F2 generations in units of windows, determine the source of alleles inherited in each window of the F2 generation, and count the number of male and female individuals of different genotypes in the F2 generation to obtain the observed value (N).

[0034] For example, the total base pairs of pig chromosome 5 are about 105Mb. If a window size of 1Mb is used, and the starting position of each window slides back 1Mb, then chromosome 5 corresponds to 105 windows of 1Mb, generating a pair of mappings from the window number to the actual coordinates of the window on each chromosome in the genome. The specific window position information is represented as Chrx:yM, where x is the chromosome number and y is the window range, such as Chr1:2M, i.e. Chr1:2000000-2999999.

[0035] Combined with the pedigree information, the gene transmission law of male parent-female parent-offspring, and the SNP locus variation information obtained from S2, analyze the genetic transmission pathways of F0-generation gene fragments in F1-generation and F2-generation in units of windows, determine the allelic origin inherited by each window in F2-generation, and count the number of male and female individuals with different genotypes in F2-generation to obtain the observed value (N). Pedigree analysis includes the genetic relationships of F2 from F1 and F1 from F0 to establish a pedigree genetic map.

[0036] Specifically, infer the autosomal haplotypes of offspring by combining pedigree information and the genomic transmission of male parent-female parent-offspring. By comparing the two autosomal haplotypes of F2 with the four autosomal haplotypes of F1 parents, use the principle and method of dynamic programming to identify the haplotype sequence compositions inherited by F2 from F1 male parent and F1 female parent respectively. Using the same method, the haplotype sequences inherited by each F1 from F0 parents can be identified. By integrating the inheritance information of F2 from F1 and the inheritance information of F1 from F0, the sequences of the F0-generation large white boar and F0-generation Min pig sow included in the haplotypes inherited by F2 from the male parent and female parent respectively can be inferred, and the analysis is shown in Figure 2 .

[0037] In this embodiment, according to different sources and genomic information, all window genotypes in F2-generation are divided into four types. According to the coding order of paternal homologous chromosomes / maternal homologous chromosomes, the four genotypes are respectively denoted as "Large White / Large White" (LW / LW), "Large White / Min Pig" (LW / MIN), "Min Pig / Large White" (MIN / LW), and "Min Pig / Min Pig" (MIN / MIN). Count the number of male and female individuals with different genotypes in F2-generation to obtain the observed value (N).

[0038] S4. Identify sex-antagonistic hotspots: Analyze the differences in the number of male and female individuals with different genotypes in F2-generation in units of windows, set a statistic (NHWED), and compare the differences between the observed value (N) and the expected value (E) of the number of male and female individuals with different genotypes in each window of F2-generation respectively. The formula is NHWED = (N - E) / E; classify the male and female NHWED values. When NHWED > N, it means that the actual number of individuals is higher than the expected number of individuals, and vice versa when NHWED < N; if the male and female NHWED values of a window are both positive or both negative, it means that the sex selection directions of this window are the same, which is defined as sex-cooperative selection (SSS); if the male and female NHWED values of a window are one positive and one negative, it means that the sex selection directions of this window are opposite, which is defined as sex-antagonistic selection (SAS); analyze the windows of all individuals with different genotypes in F2-generation in turn, and divide the windows into SAS windows and SSS windows; find the SAS windows with significantly higher absolute values of NHWED and identify them as sex-antagonistic hotspots.

[0039] Let LW be A, MIN be B, and take a window with genotype A / B as an example. The frequency of LW(A) allele from the father is recorded as p, and the frequency of MIN(B) allele from the mother is recorded as q. According to the Harwin equilibrium, theoretically, the frequency of A / B should be p×q×n, where n represents the size of the male or female population actually observed. In males, the frequency of A allele on the paternal chromosome is recorded as p(male1), the frequency of B allele on the paternal chromosome is recorded as p(male2), the frequency of A allele on the maternal chromosome is recorded as q(male1), and the frequency of B allele on the maternal chromosome is recorded as q(male2), then:

[0040]

[0041] Therefore, in this embodiment, assuming that LW is A and MIN is B, the expected value is calculated as follows:

[0042] Taking the window as the unit, N is the observation value described in S3, and N(male) represents the total number of male individuals in the window. represents the number of male individuals with genotype A / A, represents the number of male individuals with genotype A / B, represents the number of male individuals with genotype B / A, represents the number of male individuals with genotype B / B; N(female) represents the total number of female individuals in this window. represents the number of female individuals with genotype A / A, represents the number of female individuals with genotype A / B, represents the number of female individuals with genotype B / A, represents the number of female individuals with genotype B / B; It indicates the expected number of males with genotype A / A in this window. It indicates the expected number of males with genotype A / B in this window. It indicates the expected number of males with genotype B / A in this window. represents the expected number of males with genotype B / B in this window; It indicates the expected number of females with genotype A / A in this window. It indicates the expected number of females with genotype A / B in this window. It indicates the expected number of females with genotype B / A in this window. It indicates the expected number of females with genotype B / B in this window. The calculation formula of the above expected value is as follows:

[0043]

[0044] By analyzing the windows of all individuals of different genotypes in the F2 generation in turn, a total of 1154 SAS windows and 1279 SSS windows were obtained. The absolute value of NHWED indicates the degree of deviation from the Harwin equilibrium and reflects the intensity of selection. Searching for SAS windows with significantly high absolute values ​​of NHWED within the above 1154 SAS windows, it was found that there was a strong SAS window Chr3:121M on chromosome 3 of the LW / MIN genotype, confirming that there was obvious sex antagonism on chromosome 3 of the LW / MIN genotype.

[0045] In addition, in the entire window range of the F2 generation, except for the MIN / MIN genotype, a strong negative correlation between the male and female frequencies of the genotypes in the 1Mb sliding window was observed, among which the LW / MIN genotype had R = -0.13; P < 1.7 x 10 -9 (See Figure 3 ). Among them, R is the Pearson correlation coefficient, which is used to measure the linear correlation between two variables. The formula is:

[0046]

[0047] Here, the correlation between the frequencies of male and female LW / MIN genotypes was calculated, where x is the frequency of male LW / MIN, y is the frequency of female LW / MIN, and n is the number of paired male LW / MIN frequencies and female LW / MIN frequencies. The calculation of the R value is based on all data points of the frequencies of male LW / MIN and female LW / MIN, where the frequency calculation of male LW / MIN = the number of male individuals with the LW / MIN genotype in this window / the number of male individuals with all genotypes in this window; the frequency calculation of female LW / MIN = the number of female individuals with the LW / MIN genotype in this window / the number of female individuals with all genotypes in this window.

[0048] The p-value is used to test the significance of the R-value, that is, to determine whether the observed correlation may be due to random factors. The p-value is calculated by performing a statistical test on the R-value, specifically a test based on the t-distribution:

[0049]

[0050] n, R can be obtained from the previous

[0051] Based on the calculated t value and degrees of freedom (n-2), the corresponding p value can be obtained by looking up a table or calculating.

[0052] Based on the data of the real population, a graph of the number of males and females of chromosome 3 of the LW / MIN genotype was drawn (i.e., the gender ratio graph, see Figure 4 ), and found that there was a significant gender difference in the Chr3:121M window (Chr3:121000000-121999999). The data of the real population of this site were further extracted, and it was found that the female proportion of the "Large White / Min Pig" (LW / MIN) genotype was 36.43%, while the female proportion was relatively high under the other three genotypes: the female proportion of the "Large White / Large White" (LW / LW) genotype was 55.65%, the female proportion of the "Min Pig / Large White" (MIN / LW) genotype was 52.17%, and the female proportion of the "Min Pig / Min Pig" (MIN / MIN) genotype was 42.86%, which shows that Chr3:121M is a hot spot for sex antagonism, and this hot spot for sex antagonism is beneficial to males under the LW / MIN genotype (see Table 1).

[0053] Table 1: Sex ratio of four genotypes in the Chr3:121M window of the real population

[0054]

[0055] The deviation from warm-temperature equilibrium was analyzed in the sex antagonistic hotspot area Chr3:121M (see Table 2). The NHWED statistic of females with the "Large White / Min Pig" (LW / MIN) genotype was -0.04550729, which was negatively correlated, and its absolute value was significantly greater than the NHWED statistics of females with the other three genotypes, indicating that in this window, females with the "Large White / Min Pig" genotype were negatively regulated and the selection intensity was greater than that of the other three genotypes, further confirming the existence of a sex selection effect at this point.

[0056] Table 2: Deviation of Chr3:121M site from the warm equilibrium value

[0057]

[0058] Example 2: Verification and analysis of the effectiveness of the gender antagonistic hotspot regions identified by the method of the present invention:

[0059] Statistical methods were used to test whether the genotype frequency difference of the male and female sex antagonistic hotspot regions obtained in Example 1 reached a significant level, that is, to determine whether the significant difference in the male and female sex ratio under the genotype was not caused by other random factors. The specific method is as follows:

[0060] 1) Construction and comparison of simulated populations: The paternal genomes of all male and female individuals of the four genotypes in all windows of the F2 generation were taken as a whole, and extracted from them using the sampling method without replacement to obtain a set of simulated male paternal genomes. The remaining parts were used as simulated female paternal genomes. This process ensured that there were differences between the paternal genomes of the male and female simulated populations, while also maintaining the randomness of the sampling process. Ensure that the population size of the simulated males and simulated females obtained after sampling is consistent with the population size in the real F2 population. The same method was applied to sampling without replacement from the maternal genome. The genotype frequency of the Chr3:121M window in the male and female simulated populations was calculated based on the extracted paternal and maternal genomes. This simulation method was used for 10 8 Simulations were performed to study in how many times the genotypic differences between males and females in the simulated populations reached or exceeded the differences between males and females in the real F2 population, and to detect the probability of occurrence of genotypic differences between males and females in the real population, thereby obtaining the P values ​​of the four genotypes in all autosomal windows.

[0061] The formula for calculating the P value is:

[0062] P = the number of times the difference observed in the simulation is greater than or equal to the real population difference / total number of simulations; 2) P value peaks of chromosome 3 were plotted based on the simulated P values, and it was determined that there was a sex antagonistic hotspot on chromosome 3, which was consistent with the results of the real population analysis. The P values ​​of the four genotypes were FDR corrected, and a significant window (FDR < 0.05) was found in the "LW / MIN" genotype, which was Chr3:121M (see Figure 5 ), the position of the significant point is consistent with the analysis results of the real population, which fully demonstrates that the Chr3:121M window is related to sex selection. The P value of the simulated deviation was analyzed and calculated, and it can be seen that the P value of the simulated deviation of the "Large White / Min Pig" (LW / MIN) genotype is significantly lower than the simulated P values ​​of the other three (see Table 3), which determines that the sex difference in genotype frequency is a non-random effect, and there is an internal mechanism that effectively affects the sex ratio of the pig population.

[0063] Table 3: P values ​​of the simulated population of the F2 parents in the Chr3:121M window

[0064]

[0065] In summary, through the method of identifying the sex antagonistic hotspot region on the pig autosome of the present invention, the autosomal molecular markers for the directional regulation of the pig sex ratio can be found, and by adjusting the genotype ratio that is favorable to males in the parental generation, the dynamic programming method can be used to achieve the maximization goal, thereby regulating the sex ratio of the Eurasian hybrid pig herd. Similarly, this method is also applicable to regulating the female sex ratio.

[0066] The present invention obtains a sex antagonism hotspot region on a pig autosome through the method, which is the Chr3:121M window, and is a directional regulation molecular marker for sex ratio in Large White / Min pig genotype individuals that is beneficial to the production of male offspring. Through the specific selection of parent pigs with the genotype of the Chr3:121M window, directional regulation of the sex ratio of the offspring pig herd can be achieved.

[0067] It will be apparent to those skilled in the art that the present invention is not limited to the details of the exemplary embodiments described above and that the present invention can be implemented in other specific forms without departing from the spirit or essential features of the present invention. Therefore, the embodiments should be considered exemplary and non-restrictive in all respects, and the scope of the present invention is defined by the appended claims rather than the above description, and it is intended that all changes falling within the meaning and scope of the equivalent elements of the claims be included in the present invention.

[0068] In addition, it should be understood that although the present specification is described according to implementation modes, not every implementation mode contains only one independent technical solution. This description of the specification is only for the sake of clarity. Those skilled in the art should regard the specification as a whole. The technical solutions in each embodiment may also be appropriately combined to form other implementation modes that can be understood by those skilled in the art.

Claims

1. A method for identifying sex antagonistic hotspot regions on pig autosomes, characterized in that: It includes the following specific steps: S1. Construct three generations of domestic pig hybrid populations F0, F1, and F2: Use two different purebred pig breeds A and B as the F0 generation, where A is the boar and B is the sow. Cross the two purebred pigs of the F0 generation to obtain the F1 generation, and perform inbreeding within the F1 generation without introducing exogenous bloodlines to obtain the F2 generation; S2. Genome sequencing and SNP identification: Collect the DNA of all individuals in the above generations. Through genome sequencing and SNP identification, obtain the genomic information of the autosomes and the SNP locus variation information of all individuals from F0 to F2 generations; S3. Tracking the transmission of genetic material in the hybrid population pedigree: Cut the genomic information of all autosomes into non-overlapping fragments of 1 Mb in size starting from 0 in sequence, and define each fragment as a window. Combine the pedigree information, the gene transmission rules of father-mother-offspring, and the SNP locus variation information obtained in S2. Analyze the genetic transmission pathways of the F0 generation gene fragments in the F1 and F2 generations in units of windows, determine the source of the alleles inherited by each window in the F2 generation, and count the number of male and female individuals with different genotypes to obtain the observed value (N); S4. Identify sex-antagonistic hotspots: Analyze the differences in the number of male and female individuals with different genotypes in the F2 generation in units of windows, set the statistic (NHWED), and compare the differences between the observed value (N) and the expected value (E) of the number of male and female individuals with different genotypes in each window of the F2 generation respectively. The formula is NHWED = (N - E) / E; Classify the male and female NHWED values. When NHWED > N, it means that the actual number of individuals is higher than the expected number of individuals, and vice versa when NHWED < N; If the male and female NHWED values of a window are both positive or both negative, it means that the sex selection directions of this window are the same, which is defined as sex-cooperative selection (SSS); If the male and female NHWED values of a window are one positive and one negative, it means that the sex selection directions of this window are opposite, which is defined as sex-antagonistic selection (SAS); Analyze the windows of all individuals with different genotypes in the F2 generation in turn, and divide the windows into SAS windows and SSS windows; Find the SAS windows with significantly higher absolute values of NHWED and identify them as sex-antagonistic hotspots.

2. The method for identifying sex antagonistic hotspot regions on pig autosomes according to claim 1, characterized in that: The calculation method of the expected value is as follows: Taking the window as the unit, N is the observation value described in S3, and N(male) represents the total number of male individuals in the window. represents the number of male individuals with genotype A / A, represents the number of male individuals with genotype A / B, represents the number of male individuals with genotype B / A, represents the number of male individuals with genotype B / B; N(female) represents the total number of female individuals in this window. represents the number of female individuals with genotype A / A, represents the number of female individuals with genotype A / B, represents the number of female individuals with genotype B / A, represents the number of female individuals with genotype B / B; It indicates the expected number of males with genotype A / A in this window. It indicates the expected number of males with genotype A / B in this window. It indicates the expected number of males with genotype B / A in this window. represents the expected number of males with genotype B / B in this window; It indicates the expected number of females with genotype A / A in this window. It indicates the expected number of females with genotype A / B in this window. It indicates the expected number of females with genotype B / A in this window. It indicates the expected number of females with genotype B / B in this window. The calculation formula of the above expected value is as follows:

3. Application of the method for identifying sex-antagonistic hotspots on pig autosomes according to claim 1 or 2 in pig crossbreeding.

4. Application of the method for identifying sex antagonistic hotspot regions on pig autosomes according to claim 1 or 2 to directional control of sex ratio of offspring pigs in pig crossbreeding, characterized in that: Through specific breeding of the parental pigs with the genotype of the sex-antagonistic hotspot region, the sex ratio of the offspring pig population can be regulated directionally.

5. A molecular marker for directional regulation of pig sex ratio, characterized in that: In the crossbreeding of Large White and Min pigs, in the F2 generation and subsequent generations of pigs, when the paternal chromosome of an individual is of the Large White genotype and the maternal chromosome is of the Min pig genotype, the Chr3:121M window is a molecular marker for directional regulation of the sex ratio that is beneficial to the production of male offspring in individuals with the Large White / Min pig genotype. The Chr3:121M window is a sex-antagonistic hotspot region identified by the method described in claim 2, and the whole genome version is Sscrofa11.

6. The use of the molecular marker for directional regulation of pig sex ratio according to claim 5 for directional regulation of sex ratio of F2 generation and subsequent generations of pigs in pig crossbreeding, characterized in that: Through the specific selection of parent pigs with the genotype of the Chr3:121M window, targeted regulation of the sex ratio of the offspring pig herd can be achieved.

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