Method for identifying sex antagonistic hot spot region on pig autosomes and application thereof

Abstract

The present application relates to a method for identifying a sex antagonistic hotspot region on a pig autosomal chromosome and application thereof. The method provided by the present application comprises the following specific steps: constructing a hybrid population F0, F1, F2 three generations, genome sequencing and SNP identification, transmission tracking of genetic material in the hybrid population pedigree, and identifying a sex antagonistic hotspot region. The method of the present application identifies that the Chr3:121M window is a sex ratio directional regulation molecular marker that is beneficial to the generation of male offspring in the Large White / Mini pig genotype individual. According to the method of the present application, the pig population sex can be predicted and regulated, and by screening and optimal mating of the genotype of the parent before mating, a plurality of generations is obtained by continuous cross without introducing exogenous blood relationship, so that the maximum value of the proportion of the genotype beneficial to the male or female is achieved under the condition that all genotypes of each generation are retained at the population level, and then the dynamic regulation of the sex ratio of the offspring pig population is achieved.

Description

Technical Field

[0001] This invention relates to the field of molecular breeding technology, specifically to a method and its application for identifying sex antagonistic hotspot regions on pig autosomes. Background Technology

[0002] The sex ratio of pigs is an important economic trait in the pig farming industry. Boars and sows each have different characteristics and economic value in the industry. Boars grow faster and have a higher lean meat percentage, making them suitable for breeding pig production; sows have stronger reproductive capabilities and better meat quality, making them suitable for commercial pig production. Achieving sex control in pigs is of great significance, as it can improve economic efficiency and production efficiency, and also better optimize genetics in breeding applications, preventing 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 by flow cytometry based on fluorescence intensity. This method has problems such as high cost and high sperm abnormality rate; (2) Embryo sex identification: by identifying the sex of the embryo, the embryo is artificially selected to intervene in the sex ratio at birth. This method has problems such as potential embryo loss, high operational difficulty, and difficulty in large-scale promotion; (3) External regulation: by controlling the external environment (such as hormone levels) of domestic pig fertilization to affect sex, there are problems such as high randomness and unstable effectiveness.

[0004] Currently, genetic selection has emerged as a new method. This method requires identifying relevant genetic markers and selecting individuals with relevant genetic markers (such as specific genotypes) for targeted breeding, thereby expanding the pig population of a specific sex. With the increasing maturity of gene technology, its cost has also decreased significantly, making its large-scale application in production possible. Pigs determine sex through chromosomes. Like most mammals, XX sex chromosomes result in females, and XY sex chromosomes result in males. In fact, within the mammalian genome, sex chromosomes are merely the master switch for sex determination, containing a complex network regulating sex development. Studies have found that in higher mammals, the transcription factor SRY encoded by the Y chromosome triggers early gonadal development into testes (male) by activating the expression of the SOX9 gene; if SRY expression is absent during early gonadal development, ovaries develop (female).

[0005] Traditionally, sex was thought to be determined by the combination of sex chromosomes, but current research has found that autosomes can also play a role in sex determination. Looking back at the long domestication process of pigs, female and male pigs were selected for different phenotypic traits, and a large number of sex-antagonistic gene loci have accumulated on the autosomes of Asian domestic pigs. These sex-antagonistic hotspots have different effects on the fitness of males and females, thus affecting the male-to-female ratio in the population. If these sex-antagonistic hotspots could be screened from autosomes, it would be possible to target and regulate the sex ratio of offspring during breeding, but currently, no relevant research has been reported. Summary of the Invention

[0006] To address the above problems, this invention proposes a method and its application for identifying sex antagonistic hotspot regions on pig autosomes.

[0007] The method for identifying sex antagonistic hotspot regions on porcine autosomes provided by this invention includes the following specific steps:

[0008] S1. Construct three generations of domestic pig hybrid population: F0, F1 and F2. Two different breeds of purebred pigs, A and B, are used as F0 generation. The purebred pigs of the two F0 generation are crossed to obtain F1 generation. Without introducing foreign bloodlines, crossbreeding is carried out within F1 generation to obtain F2 generation.

[0009] S2. Genome sequencing and SNP identification: Collect DNA from all the above generations of individuals, and obtain the genomic information of autosomes and SNP site variation information of all individuals from F0 to F2 through genome sequencing and SNP identification.

[0010] S3. Tracing the transmission of genetic material in hybrid population families: Starting from 0, the genomic information of all autosomes is sequentially cut into 1Mb segments that are not overlapping. Each segment is defined as a window. Combining pedigree information, the gene transmission pattern of the father-mother-offspring line, and the SNP site variation information obtained in S2, the genetic transmission pathway of F0 generation gene segments in F1 and F2 generations is analyzed in units of windows. The source of alleles inherited by each window in F2 generation is determined, and the number of male and female individuals with different genotypes is counted to obtain the observation value (N).

[0011] S4. Identify sex-antagonistic hotspots: Analyze the differences in the numbers 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 numbers 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 of a window are both positive or both negative, it indicates that the sex selection directions of this window are the same, defined as sex-synergistic selection (SSS); if the male and female NHWED values of a window are one positive and one negative, it indicates that the sex selection directions of this window are opposite, defined as sex-antagonistic selection (SAS); sequentially analyze the windows of all individuals with different genotypes in the F2 generation, 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] Further, 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; take 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; take 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, This represents the expected number of females with genotype B / B appearing in this window; the formula for calculating this expected value is as follows:

[0014]

[0015]

[0016] The method for identifying sex antagonistic hotspot regions on pig autosomes provided by this invention is applied in pig crossbreeding.

[0017] Preferably, the method for identifying sex antagonistic hotspot regions on pig autosomes provided by the present invention is applied to pig crossbreeding. By specifically selecting parent pigs with genotypes containing the sex antagonistic hotspot regions, the sex ratio of offspring pig herds can be directionally regulated.

[0018] This invention also provides a molecular marker for the targeted regulation of sex ratio in pigs. In crossbreeding between 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 the targeted regulation of sex ratio in Large White / Min pig genotype individuals that is conducive to the production of male offspring. The Chr3:121M window is a sex antagonistic hotspot region identified using the above method, and its whole genome version is Sscrofa11.

[0019] The molecular marker for targeted regulation of pig sex ratio provided by this invention can achieve targeted regulation of the sex ratio of offspring pig populations in pig hybridization breeding by specifically selecting parent pigs with the genotype of Chr3:121M.

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

[0021] 1. This invention provides a method for identifying sex antagonistic hotspot regions on pig autosomes related to targeted regulation of sex ratio. The sex antagonistic hotspot regions obtained by this method can be used as molecular markers. Different genotypes of these molecular markers can exert different regulatory effects on male and female individuals, thereby achieving control of sex ratio in pig breeding.

[0022] 2. This invention is based on sequencing data that revealed a sex-biased inheritance pattern in the transmission of genotypes at specific chromosomal window locations in a three-generation Eurasian pig hybrid system. The method developed based on this invention can predict and regulate the sex ratio of pig herds. For example, in certain situations, specific genotypes may favor male survival; therefore, increasing the proportion of this genotype in the parents can increase the proportion of boars in the overall population. In actual production, if more boars or sows are desired, pre-breeding genotype screening and optimal mating can be performed. Multiple generations can be obtained through continuous crossbreeding without introducing exogenous bloodlines. This allows for the dynamic programming of the proportion of genotypes favorable to males or females to their maximum value while maintaining all genotypes in each generation at the population level, thereby achieving dynamic regulation of the sex ratio of offspring piglets. Attached Figure Description

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

[0024] Figure 2 A tracing diagram of the transmission of genetic material in a hybrid family;

[0025] Figure 3 Scatter plot of correlation analysis of male and female frequencies of LW / MIN genotypes across the whole genome;

[0026] Figure 4 A graph showing the percentage of males with the LW / MIN genotype under the chromosomal window on chromosome 3;

[0027] Figure 5 P-value peak diagram for simulated population chromosome 3 LW / MIN genotype after genotype correction. Detailed Implementation

[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] Includes the following steps:

[0031] S1. Constructing a three-generation (F0, F1, F2) crossbred pig population: Purebred European and Asian domestic pigs were used as the F0 generation. The European domestic pigs selected were male purebred Large White (LW) pigs, and the Asian domestic pigs selected were female purebred 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, producing 9 F1 boars and 45 F1 sows. In the third step, the F1 individuals were mated, producing 284 F2 sows and 294 F2 boars. Through these steps, a Eurasian crossbred pig genetic system was successfully established. This system comprises 653 pigs across the F0, F1, and F2 generations, all raised under identical conditions.

[0032] S2. Genome Sequencing and SNP Identification: Ear tissue samples were collected from all generations of individuals. Genomic DNA was extracted from the ear samples using the phenol-chloroform method. Genotypic analysis was performed on all samples using Illumina Porcine SNP60 Bead Chips. Autosomal haplotype inference was performed on all families using Porcine SNP60 chip data, obtaining autosomal genomic information and SNP locus variation information for all individuals in generations F0, F1, and F2. During 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 was Sscrofa11.

[0033] S3. Tracing the transmission of genetic material in hybrid population families: The genomic information of all autosomes is cut into 1Mb non-overlapping fragments, each fragment is defined as a window. Combining pedigree information, the gene transmission pattern of the father-mother-offspring line, and the SNP locus variation information obtained in S2, the genetic transmission pathway of F0 generation gene fragments in F1 and F2 generations is analyzed in units of windows. The source of alleles inherited by each window in F2 generation is determined, and the number of male and female individuals with different genotypes in F2 generation is counted to obtain the observed value (N).

[0034] For example, pig chromosome 5 has approximately 105 Mb of base pairs. If we use 1 Mb as a window size, and each window moves forward by 1 Mb, then chromosome 5 corresponds to 105 1 Mb windows, creating a mapping from 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 relationship of F2 from F1 and F1 from F0 to establish a pedigree genetic map.

[0036] Specifically, combine the pedigree information and the genomic transmission of male parent - female parent - offspring to infer the autosomal haplotypes of 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 composition inherited by F2 from the F1 male parent and F1 female parent respectively. Using the same method, the haplotype sequence 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. For the analysis, see Figure 2 .

[0037] In this embodiment, according to the different sources and genomic information, all window genotypes of 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. When NHWED > N, it means the actual number of individuals is higher than the expected number of individuals, and when NHWED < N, it is the opposite; if the male and female NHWED values of a window are both positive or both negative, it means the sex - selection directions of this window are the same, defined as sex - coordinated selection (SSS); if the male and female NHWED values of a window are one positive and one negative, it means the sex - selection directions of this window are opposite, defined as sex - antagonistic selection (SAS); successively analyze all windows of individuals with different genotypes in F2 - generation, 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 and MIN be B. Taking a window with genotypes A / B as an example, let p be the frequency of the LW(A) allele from the father and q be the frequency of the MIN(B) allele from the mother. According to Hardy-Wen equilibrium, theoretically, the frequency of A / B should be p × q × n, where n represents the size of the observed male or female population. In the males, let p(male1) be the frequency of the paternal A allele and p(male2) be the frequency of the paternal B allele, q(male1) be the frequency of the maternal A allele and q(male2) be the frequency of the maternal B allele, then:

[0040]

[0041] Therefore, in this embodiment, let LW be A and MIN be B, the method for calculating the expected value is as follows:

[0042] Using a window as the unit, N represents the observation value described in S3, and N(male) represents the total number of male individuals within that window. This indicates the number of male individuals with genotype A / A. This indicates the number of male individuals with genotype A or B. This indicates the number of male individuals with genotype B / A. This represents the number of male individuals with genotype B / B; N (female) represents the total number of female individuals within this window. This indicates the number of female individuals with genotype A / A. This indicates the number of female individuals with genotype A or B. This indicates the number of female individuals with genotype B / A. This indicates the number of female individuals with genotype B / B; This indicates the expected number of males with genotype A / A appearing in this window. This indicates the expected number of males with genotype A / B appearing in this window. This indicates the expected number of males with genotype B / A appearing in this window. This indicates the expected number of males with genotype B / B appearing in this window; This indicates the expected number of females with genotype A / A appearing in this window. This indicates the expected number of females with genotype A / B appearing in this window. This indicates the expected number of females with genotype B / A appearing in this window. This represents the expected number of females with genotype B / B appearing in this window; the formula for calculating this expected value is as follows:

[0043]

[0044] By sequentially analyzing the windows of all individuals with different genotypes in the F2 generation, a total of 1154 SAS windows and 1279 SSS windows were obtained. The absolute value of NHWED indicates the degree of deviation from Haven equilibrium, reflecting the intensity of selection. Within these 1154 SAS windows, a search was conducted to identify SAS windows with significantly high absolute NHWED values. A strong SAS window, Chr3:121M, was found on chromosome 3 of the LW / MIN genotype, confirming a significant sex antagonism on chromosome 3 of the LW / MIN genotype.

[0045] Furthermore, across the entire window range of the F2 generation, except for the MIN / MIN genotype, a strong negative correlation was observed between the sex frequencies of genotypes within a 1Mb sliding window, with the LW / MIN genotype showing R = -0.13 and P < 1.7 x 10. -9 (See Figure 3 Where R is the Pearson correlation coefficient, used to measure the linear correlation between two variables, and the formula is:

[0046]

[0047] The correlation between the frequencies of male and female LW / MIN genotypes was calculated here, where x is the frequency of male LW / MIN, y is the frequency of female LW / MIN, and n is the number of pairs of male and female LW / MIN frequencies. The R-value was calculated based on all data points of both male and female LW / MIN frequencies, where the male LW / MIN frequency was calculated as the number of male individuals with the LW / MIN genotype in that window divided by the total number of male individuals with all genotypes in that window; and the female LW / MIN frequency was calculated as the number of female individuals with the LW / MIN genotype in that window divided by the total number of female individuals with all genotypes in that window.

[0048] The p-value is used to test the significance of the R-value, that is, to determine whether the observed correlation is likely 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 and R can be obtained from the previous information.

[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 by calculation.

[0052] A sex ratio diagram (i.e., a diagram showing the proportion of males and females on chromosome 3 of the LW / MIN genotype) was drawn based on data from the actual population. Figure 4 The study found significant sex differences within the Chr3:121M window (Chr3:121000000-121999999). Further data from real-world populations at this locus revealed a female prevalence of 36.43% for the "LW / MIN" genotype, while the female prevalence was relatively higher for the other three genotypes: 55.65% for the "LW / LW" genotype, 52.17% for the "MIN / LW" genotype, and 42.86% for the "MIN / MIN" genotype. This indicates that Chr3:121M is a sex antagonistic hotspot region, and in the LW / MIN genotype, this hotspot region is favorable to males (see Table 1).

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

[0054]

[0055] A Hardy-Wen balance deviation analysis was performed on the sex antagonistic hotspot region Chr3:121M (see Table 2). The NHWED statistic for females with the "LW / MIN" genotype was -0.04550729, indicating a negative correlation. Moreover, the absolute value was significantly greater than that of females with the other three genotypes. This suggests that under this window, females with the "LW / MIN" 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 Haven equilibrium value

[0057]

[0058] Example 2: Verification and analysis of the utility of the gender antagonism hotspot region identified by the method of the present invention:

[0059] Statistical methods were applied to test whether the differences in genotype frequencies in the sex antagonism hotspot regions obtained in Example 1 reached a significant level, i.e., to determine whether the significant difference in the sex ratio under this 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 with all four genotypes in the F2 generation were treated as a whole. A set of simulated male paternal genomes was extracted from this genome using sampling without replacement. The remaining genomes were used as simulated female paternal genomes. This process ensured that the paternal genomes of the male and female simulated populations were distinct, while also maintaining the randomness of the sampling process. The population sizes of the simulated males and females obtained after sampling were ensured to be consistent with the population sizes in the real F2 population. The same method was applied to the sampling without replacement from the maternal genome. The genotype frequencies of the Chr3:121M window in the male and female simulated populations were calculated based on the extracted paternal and maternal genomes. This simulation method was used for 10... 8 The simulation was conducted to investigate how many simulated populations the genotypic differences between males and females reached or exceeded the differences between males and females in the real F2 population, and to detect the probability of the occurrence of genotypic differences between males and females in the real population, thereby obtaining the P-values ​​for all four genotypes in the autosomal window.

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

[0062] P = Number of times the observed difference in the simulation was greater than or equal to the difference in the real population / Total number of simulations; 2) Based on the simulated P values, a peak diagram of the P values ​​of chromosome 3 was plotted to confirm the presence of a sex antagonistic hotspot on chromosome 3, consistent with the results of the real population analysis. The P values ​​of the four genotypes were corrected for FDR. A significant window (FDR < 0.05) was found in the "Large White / Min Pig" (LW / MIN) genotype, namely Chr3:121M (see...). Figure 5 The significant point locations are consistent with the results of the actual population analysis, fully demonstrating that the Chr3:121M window is related to sex selection. Analysis of the simulated bias p-value shows that the simulated bias p-value for the "Large White / Min Pig" (LW / MIN) genotype is significantly lower than that for the other three genotypes (see Table 3). This indicates that the sex difference in genotype frequency is a non-random effect, with an intrinsic mechanism effectively influencing the sex ratio of the pig population.

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

[0064]

[0065] In summary, the method of identifying sex-antagonistic hotspot regions on pig autosomes using this invention can locate autosomal molecular markers that directionally regulate the sex ratio in pigs. By adjusting the proportion of male-favorable genotypes in the parental generations, dynamic programming can be used to maximize the target, thereby regulating the sex ratio of Eurasian hybrid pig populations. Similarly, this method is also applicable to regulating the female sex ratio.

[0066] This invention obtains a sex antagonistic hotspot region on a pig autosome, namely the Chr3:121M window, which is a molecular marker for targeted regulation of sex ratio in Large White / Min pig genotype individuals that favors the production of male offspring. Through specific breeding of parent pigs with the Chr3:121M window genotype, targeted regulation of the sex ratio of offspring pig herds 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 invention can be implemented in other specific forms without departing from the spirit or essential characteristics of the invention. Therefore, the embodiments should be considered in all respects as exemplary and non-limiting, and the scope of the invention is defined by the appended claims rather than the foregoing description. Thus, it is intended that all variations falling within the meaning and scope of equivalents of the claims be included within the present invention.

[0068] Furthermore, it should be understood that although this specification describes embodiments, not every embodiment contains only one independent technical solution. This narrative style is merely for clarity. Those skilled in the art should consider the specification as a whole, and the technical solutions in each embodiment can also be appropriately combined to form other embodiments 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 male pig and B is the female pig. Cross the two purebred pigs of the F0 generation to obtain the F1 generation, and perform inbred mating 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 from the three generations of F0 to F2 above. 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 allelic origin 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. When NHWED > N, it means that the actual number of individuals is higher than the expected number of individuals, and the opposite is true 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-synergistic 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 porcine autosomes according to claim 1, characterized in that, The calculation method of the expected value is as follows: Using a window as the unit, N represents the observation value described in S3, and N(male) represents the total number of male individuals within that window. N represents the number of male individuals with genotype A / A. N represents the number of male individuals with genotype A / B. N represents the number of male individuals with genotype B / A. This represents the number of male individuals with genotype B / B; N(female) represents the total number of female individuals within this window. N represents the number of female individuals with genotype A / A. N represents the number of female individuals with genotype A / B. N represents the number of female individuals with genotype B / A. This indicates the number of female individuals with genotype B / B; denoted by E (male / female). E(male) represents the expected number of males with genotype A / A appearing in this window. E(male) represents the expected number of males with genotype A / B appearing in this window. E(male) represents the expected number of males with genotype B / A appearing in this window. The number of males with genotype B / B is represented by E(female). E(female) represents the expected number of females with genotype A / A appearing in this window. E(female) represents the expected number of females with genotype A / B appearing in this window. E(female) represents the expected number of females with genotype B / A appearing in this window. This indicates the expected number of females with genotype B / B appearing in this window; the formula for calculating the expected value is as follows: And(bad) )= × ×N(bad); And(bad) )= × ×N(bad); And(bad) )= × ×N(bad); And(bad) )= × ×N(bad); E(female )= × ×N(female); E(female )= × ×N(female); E(female )= × ×N(female); E(female )= × ×N(female)。 3. Application of the method for identifying sex-antagonistic hotspots on pig autosomes according to claim 1 or 2 in pig crossbreeding.

4. The application of the method for identifying sex antagonistic hotspot regions on pig autosomes as described in claim 1 or 2 in the targeted regulation of the sex ratio of offspring pigs in pig crossbreeding, characterized in that... By specifically selecting 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 targeted regulation of sex ratio in pigs, 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 application of the molecular marker for targeted regulation of pig sex ratio as described in claim 5 in pig crossbreeding for targeted regulation of the sex ratio of F2 and offspring pigs, characterized in that, By specifically selecting the parental pigs with the genotype of the Chr3:121M window, the sex ratio of the offspring pig population can be regulated directionally.

Images