SNP (Single Nucleotide Polymorphism) molecular marker related to chicken immune traits and application

Abstract

According to the invention, GWAS analysis is carried out on immune traits of Qingyuan partridge chicken infected with ALV-J, and SNP molecular markers related to immune traits such as spleen tissue index, pancreatic tissue index, IL-6 content in blood, IFN-beta content in blood and cloaca virus positive degree are screened and obtained; the SNP molecular markers can be applied to disease-resistant molecular marker assisted breeding of Qingyuan partridge chickens. Through molecular marker-assisted breeding, the spleen tissue index, the pancreatic tissue index, the IL-6 content and the IFN-beta content in blood of the Qingyuan partridge chicken can be increased, especially the IL-6 content and the IFN-beta content in the blood infected with ALV-J can be increased, the ALV-J infection resistance of the chicken is improved, and the immunity of the chicken is improved. Meanwhile, breeding is assisted through the molecular marker, the cloaca virus positive degree of the chickens infected with ALV-J can be reduced, the diseases infected with ALV-J and the ALV-J infection resisting capacity are relieved, and the immunity of the chickens is improved. Therefore, the medicine use cost of the chicken farm is reduced, the economic performance of the chicken farm is improved, and healthy breeding is promoted.

Description

Technical Field

[0001] The present invention relates to the technical fields of molecular markers and animal breeding, and particularly relates to an SNP molecular marker related to chicken immune traits and its application. Background Art

[0002] Qingyuan partridge chicken is a local high-quality chicken breed resource and one of the typical chicken breeds of yellow-feathered broilers. It has strong disease resistance, is a high-quality material for breeding disease-resistant lines, and has high economic value.

[0003] Immunity-related traits are important traits of Qingyuan partridge chicken in disease-resistant breeding. These traits are controlled by multiple genes, and their genetic laws and mechanisms are very complex. Comprehensively analyzing the molecular genetic mechanism of the immune traits of Qingyuan partridge chicken and excavating key candidate genes and molecular markers have important theoretical value and practical significance for its breed selection and genetic improvement. Traits such as spleen tissue index, pancreas tissue index, IL-6 content in blood, IFN-β content in blood, and the degree of cloacal virus positivity are important immune traits. By selecting these traits, the immunity and disease resistance of chickens can be improved.

[0004] The spleen is the largest immune organ of the body, accounting for 25% of the total amount of lymphoid tissue in the whole body. It contains a large number of lymphocytes and plasma cells, which play important roles in humoral immunity and cell-mediated immunity. The spleen tissue index can reflect the strength of the immune response. A high spleen tissue index indicates a strong immune response, and vice versa.

[0005] The pancreas is an important digestive organ and at the same time an endocrine gland, which is also closely related to immunity. The islet cells in the pancreas can secrete certain cytokines (such as IL-6, TNF-α) and participate in local immune regulation.

[0006] Interleukin 6 (IL-6) is a multifunctional cytokine that plays an important role in immune regulation, hematopoiesis, and inflammatory processes. IL-6 is mainly synthesized by activated T cells and B cells, monocytes-macrophages, endothelial cells, epithelial cells, and fibroblasts. In the immune response, IL-6 can promote the proliferation and differentiation of B cells, thereby enhancing the body's immune response to antigens. In addition, IL-6 also participates in regulating the inflammatory response, promoting cell proliferation, differentiation, oxidative stress, and immune regulation by activating signal pathways such as JAK-STAT and RAS-RAF. The higher the IL-6 content in the blood, the stronger the immune response during virus infection and the stronger its resistance to the virus.

[0007] Interferon-β (IFN-β) is a key type I interferon cytokine that plays a crucial role in coordinating the innate immune response against various challenges, including infections, tumor development, and inflammatory stimuli. The higher the IFN-β content in the blood, the stronger the immune response during viral infection, the stronger the resistance to the virus, and the better the disease resistance.

[0008] After a chicken is infected with a virus, the degree of virus positivity in the cloaca can be detected to evaluate the replication of the virus in the chicken, and then the immunity and disease resistance of the chicken can be evaluated. Generally, the lower the degree of virus positivity in the cloaca, the lower the virus replication and the better the disease resistance of the chicken.

[0009] Avian Leukosis Virus (ALV) can induce tumors in chickens, affecting the production performance of chickens, such as reducing egg production rate and egg quality, causing growth retardation, and even leading to death. Subgroup J avian leukosis virus (ALV-J) is a subgroup of ALV virus, with strong pathogenicity and wide spread. ALV virus has caused huge economic losses to the poultry industry. Breeding chickens with higher disease resistance to improve the disease resistance of the population is an effective way to solve ALV infection.

[0010] Genome-wide association study (GWAS) is a powerful tool for mining effective genetic information of target traits. Many studies have successfully identified key genes or loci of target traits in livestock and poultry through GWAS. By mining important candidate genes and molecular markers and carrying out molecular marker-assisted breeding, it is of great significance to improve individual immunity and enhance the disease resistance of the population, and will provide important reference basis for disease-resistant breeding of poultry. Summary of the Invention

[0011] The object of the present invention is to provide an SNP molecular marker related to chicken immune traits, which can be applied to disease-resistant molecular marker-assisted breeding of Qingyuan partridge chickens through this SNP molecular marker. By preventing the occurrence of ALV-J at the genomic level, the efficiency of disease-resistant breeding of Qingyuan partridge chickens can be significantly improved, the breeding process can be accelerated, and at the same time, the cost of immune prevention can be reduced, having good application prospects.

[0012] According to the first aspect of the present invention, there is provided an SNP molecular marker related to chicken immune traits, and the immune traits include any one or more of spleen tissue index, pancreas tissue index, IL-6 content in blood, IFN-β content in blood, and the degree of cloacal virus positivity. The SNP molecular marker includes any one or more of the following molecular markers: the G>T mutation at the 12931235bp site on chromosome 7 of the chicken genome, the C>T mutation at the 59309366bp site on chromosome 3 of the chicken genome, the T>C mutation at the 59309189bp site on chromosome 3 of the chicken genome, the G>A mutation at the 59308643bp site on chromosome 3 of the chicken genome, the A>G mutation at the 1331279bp site on chromosome 25 of the chicken genome, the A>G mutation at the 1331316bp site on chromosome 25 of the chicken genome, the G>A mutation at the 878099bp site on chromosome 21 of the chicken genome, the C>T mutation at the 114656880bp site on chromosome 1 of the chicken genome, the A>G mutation at the 69131730bp site on chromosome 1 of the chicken genome, and the C>T mutation at the 11372457bp site on chromosome 4 of the chicken genome. Thus, by applying the above SNP molecular marker to molecular marker-assisted breeding of chickens, the disease resistance and immunity of chickens can be improved, especially the ability to resist ALV-J infection. On the one hand, the occurrence of ALV-J can be prevented, and on the other hand, the symptoms after ALV-J infection can be alleviated, the mortality rate and the impact of ALV-J virus on the production performance of chickens can be reduced, the drug use cost of chicken farms can be reduced, and the economic benefits of chicken farms can be improved.

[0013] According to a second aspect of the present invention, there is provided an application of SNP molecular markers in the breeding of chicken immune traits. The immune traits include any one or more of the spleen tissue index, pancreas tissue index, IL-6 content in blood, IFN-β content in blood, and the degree of cloacal virus positivity. The SNP molecular markers include any one or more of the following molecular markers: the G>T mutation at the 12,931,235bp locus on chromosome 7 of the chicken genome, the C>T mutation at the 59,309,366bp locus on chromosome 3 of the chicken genome, the T>C mutation at the 59,309,189bp locus on chromosome 3 of the chicken genome, the G>A mutation at the 59,308,643bp locus on chromosome 3 of the chicken genome, the A>G mutation at the 1,331,279bp locus on chromosome 25 of the chicken genome, the A>G mutation at the 1,331,316bp locus on chromosome 25 of the chicken genome, the G>A mutation at the 878,099bp locus on chromosome 21 of the chicken genome, the C>T mutation at the 114,656,880bp locus on chromosome 1 of the chicken genome, the A>G mutation at the 69,131,730bp locus on chromosome 1 of the chicken genome, and the C>T mutation at the 11,372,457bp locus on chromosome 4 of the chicken genome. Thus, through this application, the disease resistance and immunity of chickens can be improved, especially the ability to resist ALV-J infection. On the one hand, the occurrence of ALV-J can be prevented, and on the other hand, the symptoms after ALV-J infection can be alleviated, the mortality rate and the impact of ALV-J virus on the production performance of chickens can be reduced, the drug use cost of chicken farms can be reduced, and the economic benefits of chicken farms can be increased.

[0014] According to the third aspect of the present invention, there is provided an application of a product for detecting SNP molecular markers in the breeding of chicken immune traits. The immune traits include any one or more of the spleen tissue index, pancreatic tissue index, IL-6 content in blood, IFN-β content in blood, and the degree of cloacal virus positivity. The SNP molecular markers include any one or more of the following molecular markers: the G>T mutation at the 12931235bp site on chromosome 7 of the chicken genome, the C>T mutation at the 59309366bp site on chromosome 3 of the chicken genome, the T>C mutation at the 59309189bp site on chromosome 3 of the chicken genome, the G>A mutation at the 59308643bp site on chromosome 3 of the chicken genome, the A>G mutation at the 1331279bp site on chromosome 25 of the chicken genome, the A>G mutation at the 1331316bp site on chromosome 25 of the chicken genome, the G>A mutation at the 878099bp site on chromosome 21 of the chicken genome, the C>T mutation at the 114656880bp site on chromosome 1 of the chicken genome, the A>G mutation at the 69131730bp site on chromosome 1 of the chicken genome, and the C>T mutation at the 11372457bp site on chromosome 4 of the chicken genome. Thus, by using the product for detecting SNP molecular markers, the molecular markers in the chicken flock can be detected efficiently and conveniently, the advantageous genotypes of immune traits can be screened out, the frequency of advantageous alleles can be increased, and the disease resistance and immunity of the chicken flock, especially the ability to resist ALV-J infection, can be gradually improved. On the one hand, the occurrence of ALV-J can be prevented, on the other hand, the symptoms after ALV-J infection can be alleviated, the mortality rate and the impact of ALV-J virus on the production performance of chickens can be reduced, the drug use cost of the chicken farm can be reduced, and the economic benefits of the chicken farm can be increased.

[0015] In some embodiments, the product for detecting SNP molecular markers refers to primers or probes capable of detecting the said SNP molecular markers or a kit prepared from the said primers or probes.

[0016] According to the fourth aspect of the present invention, there is provided an application of an SNP molecular marker in breeding chicken breeds with high immunity traits. The SNP molecular marker includes any one or more of the following molecular markers: the G>T mutation at the 12931235bp locus on chromosome 7 of the chicken genome, the C>T mutation at the 59309366bp locus on chromosome 3 of the chicken genome, the T>C mutation at the 59309189bp locus on chromosome 3 of the chicken genome, the G>A mutation at the 59308643bp locus on chromosome 3 of the chicken genome, the A>G mutation at the 1331279bp locus on chromosome 25 of the chicken genome, the A>G mutation at the 1331316bp locus on chromosome 25 of the chicken genome, the G>A mutation at the 878099bp locus on chromosome 21 of the chicken genome, the C>T mutation at the 114656880bp locus on chromosome 1 of the chicken genome, the A>G mutation at the 69131730bp locus on chromosome 1 of the chicken genome, and the C>T mutation at the 11372457bp locus on chromosome 4 of the chicken genome. Thus, through marker-assisted breeding, chicken breeds with high immunity traits can be bred, which can efficiently resist virus infections, especially ALV-J infections, improve the immunity of chicken breeds, thereby reducing the drug use cost of chicken farms and increasing the economic benefits of chicken farms.

[0017] According to the fifth aspect of the present invention, there is provided an application of a product for detecting SNP molecular markers in breeding chicken breeds with high immunity traits. The SNP molecular marker includes any one or more of the following molecular markers: the G>T mutation at the 12931235bp locus on chromosome 7 of the chicken genome, the C>T mutation at the 59309366bp locus on chromosome 3 of the chicken genome, the T>C mutation at the 59309189bp locus on chromosome 3 of the chicken genome, the G>A mutation at the 59308643bp locus on chromosome 3 of the chicken genome, the A>G mutation at the 1331279bp locus on chromosome 25 of the chicken genome, the A>G mutation at the 1331316bp locus on chromosome 25 of the chicken genome, the G>A mutation at the 878099bp locus on chromosome 21 of the chicken genome, the C>T mutation at the 114656880bp locus on chromosome 1 of the chicken genome, the A>G mutation at the 69131730bp locus on chromosome 1 of the chicken genome, and the C>T mutation at the 11372457bp locus on chromosome 4 of the chicken genome. Thus, through the efficient detection of molecular markers by the product for detecting molecular markers, superior genotypes can be screened out, chicken breeds with high immunity traits can be bred, which can efficiently resist virus infections, especially ALV-J infections, improve the immunity of chicken breeds, thereby reducing the drug use cost of chicken farms and increasing the economic benefits of chicken farms.

[0018] In some embodiments, the product for detecting the SNP molecular marker refers to a primer or a probe capable of detecting the said SNP molecular marker, or a kit prepared from the said primer or probe.

[0019] According to the sixth aspect of the present invention, there is provided an application of an SNP molecular marker in improving the immune traits of chickens. The SNP molecular marker includes any one or more of the following molecular markers: the G>T mutation at the 12,931,235 bp locus on chromosome 7 of the chicken genome, the C>T mutation at the 59,309,366 bp locus on chromosome 3 of the chicken genome, the T>C mutation at the 59,309,189 bp locus on chromosome 3 of the chicken genome, the G>A mutation at the 59,308,643 bp locus on chromosome 3 of the chicken genome, the A>G mutation at the 1,331,279 bp locus on chromosome 25 of the chicken genome, the A>G mutation at the 1,331,316 bp locus on chromosome 25 of the chicken genome, the G>A mutation at the 878,099 bp locus on chromosome 21 of the chicken genome, the C>T mutation at the 114,656,880 bp locus on chromosome 1 of the chicken genome, the A>G mutation at the 69,131,730 bp locus on chromosome 1 of the chicken genome, and the C>T mutation at the 11,372,457 bp locus on chromosome 4 of the chicken genome. Thus, through marker-assisted breeding, the immune traits of the chicken flock can be improved, the immune performance of the chicken flock can be enhanced, the disease resistance of the chicken flock can be increased, especially the ability to resist ALV-J infection, and the immunity of the chicken flock can be improved, thereby reducing the drug usage cost of the chicken farm and increasing the economic benefit of the chicken farm.

[0020] According to the seventh aspect of the present invention, there is provided an application of a product for detecting SNP molecular markers in improving the immune traits of chickens. The SNP molecular markers include any one or more of the following molecular markers: the G>T mutation at the 12931235bp locus on chromosome 7 of the chicken genome, the C>T mutation at the 59309366bp locus on chromosome 3 of the chicken genome, the T>C mutation at the 59309189bp locus on chromosome 3 of the chicken genome, the G>A mutation at the 59308643bp locus on chromosome 3 of the chicken genome, the A>G mutation at the 1331279bp locus on chromosome 25 of the chicken genome, the A>G mutation at the 1331316bp locus on chromosome 25 of the chicken genome, the G>A mutation at the 878099bp locus on chromosome 21 of the chicken genome, the C>T mutation at the 114656880bp locus on chromosome 1 of the chicken genome, the A>G mutation at the 69131730bp locus on chromosome 1 of the chicken genome, and the C>T mutation at the 11372457bp locus on chromosome 4 of the chicken genome. Thus, by efficiently detecting the molecular markers with the product for detecting molecular markers, selecting superior genotypes and eliminating inferior genotypes, and gradually increasing the frequency of superior alleles, the immune traits of the chicken flock can be improved, the immune performance and disease resistance of the chicken flock can be enhanced, especially the ability to resist ALV-J infection, and the immunity of the chicken flock can be improved, thereby reducing the drug use cost of the chicken farm and increasing the economic benefits of the chicken farm.

[0021] In some embodiments, the product for detecting SNP molecular markers refers to primers or probes that can detect the aforementioned SNP molecular markers or a kit prepared from the primers or probes.

[0022] According to the eighth aspect of the present invention, there is provided an application of an SNP molecular marker in improving the pancreatic tissue index trait of chickens. The SNP molecular marker is the G>T mutation at the 12931235bp locus on chromosome 7 of the chicken genome. The application includes the following steps:

[0023] 1) Detect the aforementioned SNP molecular marker in candidate breeding chickens;

[0024] 2) Select individuals with the TT genotype detected in step 1) as breeding chickens and eliminate individuals with the GG and GT genotypes, which can improve the pancreatic tissue index of chickens. Thus, through this application, the pancreatic tissue index of chickens can be improved, and further the immune response during virus infection can be enhanced.

[0025] According to the ninth aspect of the present invention, there is provided an application of an SNP molecular marker in improving the spleen tissue index trait of chickens. The SNP molecular marker is a C>T mutation at the 59309366bp locus on chromosome 3 of the chicken genome, or a T>C mutation at the 59309189bp locus on chromosome 3 of the chicken genome, or a G>A mutation at the 59308643bp locus on chromosome 3 of the chicken genome. The application includes the following steps:

[0026] 1) Detect the said SNP molecular marker in candidate breeding chickens;

[0027] 2) Select and retain individuals with the TT and CT genotypes at the 59309366bp locus on chromosome 3 detected in step 1) as breeding chickens, and eliminate individuals with the CC genotype, which can improve the spleen tissue index of chickens and thus enhance the immune response during virus infection;

[0028] Or select and retain individuals with the CC and TC genotypes at the 59309189bp locus on chromosome 3 detected in step 1) as breeding chickens, and eliminate individuals with the TT genotype, which can improve the spleen tissue index of chickens and thus enhance the immune response during virus infection;

[0029] Or select and retain individuals with the AA and GA genotypes at the 59308643bp locus on chromosome 3 detected in step 1) as breeding chickens, and eliminate individuals with the GG genotype, which can improve the spleen tissue index of chickens. Thus, through this application, the spleen tissue index of chickens can be improved, and the immune response during virus infection can be enhanced.

[0030] According to the tenth aspect of the present invention, there is provided an application of an SNP molecular marker in increasing the content of IL6 in chicken blood. The SNP molecular marker is an A>G mutation at the 1331279bp locus on chromosome 25 of the chicken genome, or an A>G mutation at the 1331316bp locus on chromosome 25 of the chicken genome. The application includes the following steps:

[0031] 1) Detect the said SNP molecular marker in candidate breeding chickens;

[0032] 2) Select and retain individuals with the AA genotype at the 1331279bp locus on chromosome 25 detected in step 1) as breeding chickens, and eliminate individuals with the GG and AG genotypes, which can increase the content of IL6 in chicken blood and thus enhance the immune response during virus infection;

[0033] Alternatively, select the individuals with the AA and AG genotypes at the 1331316bp locus on chromosome 25 detected in step 1) as breeding chickens, and eliminate the individuals with the GG genotype, which can increase the IL6 content in chicken blood. Thus, through this application, the IL6 content in chicken blood can be increased, especially the IL6 content in blood after infection with ALV-J. The higher the IL-6 content, the stronger its resistance to the virus and the stronger the immune response. It can also alleviate the symptoms after infection with ALV-J, reduce the impact of the virus on chicken production performance, lower the mortality rate of chickens, and improve the disease resistance and immunity of chickens.

[0034] According to the eleventh aspect of the present invention, there is provided an application of an SNP molecular marker in increasing the IFN-β content in chicken blood. The SNP molecular marker is a G>A mutation at the 878099bp locus on chromosome 21 of the chicken genome. The application includes the following steps:

[0035] 1) Detect the said SNP molecular marker in the candidate breeding chickens;

[0036] 2) Select the individuals with the AA genotype of the allele detected in step 1) as breeding chickens, and eliminate the individuals with the GG and GA genotypes, which can increase the IFN-β content in chicken blood and further enhance the immune response during virus infection. Thus, through this application, the IFN-β content in chicken blood can be increased, especially the IFN-β content in blood after infection with ALV-J. The higher the IFN-β content, the stronger its resistance to the virus and the stronger the immune response. It can also alleviate the symptoms after infection with ALV-J, reduce the impact of the virus on chicken production performance, lower the mortality rate of chickens, and improve the disease resistance and immunity of chickens.

[0037] According to the twelfth aspect of the present invention, there is provided an application of an SNP molecular marker in reducing the positive degree of cloacal virus in chickens. The SNP molecular marker is a C>T mutation at the 114656880bp locus on chromosome 1 of the chicken genome, or an A>G mutation at the 69131730bp locus on chromosome 1 of the chicken genome, or a C>T mutation at the 11372457bp locus on chromosome 4 of the chicken genome. The application includes the following steps:

[0038] 1) Detect the said SNP molecular marker in the candidate breeding chickens;

[0039] 2) Select the individuals with the CC and CT genotypes of the allele at the 114656880bp locus on chromosome 1 detected in step 1) as breeding chickens, and eliminate the individuals with the TT genotype, which can reduce the positive degree of cloacal virus in chickens and improve the ability of chickens to resist ALV-J virus;

[0040] Alternatively, select and retain the individuals with the AA and AG genotypes at the 69131730bp locus on chromosome 1 detected in step 1) as breeding chickens, and eliminate the individuals with the GG genotype, which can reduce the positive degree of chicken cloacal virus and improve the ability of chickens to resist ALV-J virus;

[0041] Alternatively, select and retain the individuals with the CC and CT genotypes at the 11372457bp locus on chromosome 4 detected in step 1) as breeding chickens, and eliminate the individuals with the TT genotype, which can reduce the positive degree of chicken cloacal virus and improve the ability of chickens to resist ALV-J virus. Thus, through this application, the positive degree of chicken cloacal virus can be reduced, especially the positive degree of chicken cloacal virus after infection with ALV-J. The lower the positive degree of cloacal virus, the lower the virus replication, the better the disease resistance of chickens, the higher the ability of chickens to resist ALV-J virus, and it can also alleviate the symptoms after infection with ALV-J, reduce the impact of this virus on the production performance of chickens, reduce the mortality rate of chickens, and improve the disease resistance of chickens.

[0042] Beneficial effects of the present invention:

[0043] Through GWAS analysis of the immune traits of Qingyuan partridge chickens infected with ALV-J, the present invention screened and obtained SNP molecular markers related to immune traits such as spleen tissue index, pancreas tissue index, IL-6 content in blood, IFN-β content in blood, and the positive degree of cloacal virus. These SNP molecular markers can be applied to molecular marker-assisted breeding for disease resistance in Qingyuan partridge chickens. Through molecular marker-assisted breeding, the spleen tissue index, pancreas tissue index, IL-6 content, and IFN-β content in the blood of Qingyuan partridge chickens can be improved, especially the IL-6 content and IFN-β content in the blood after infection with ALV-J, further improving the ability to resist ALV-J infection and the immunity of chickens. At the same time, through molecular marker-assisted breeding, the positive degree of cloacal virus after chickens are infected with ALV-J can also be reduced, alleviating the disease symptoms and the ability to resist ALV-J infection, and improving the immunity of chickens. Therefore, through the assisted selection of molecular markers, the ability of chickens to prevent the occurrence of ALV-J and the ability of chickens to resist ALV-J infection can be improved at the genomic level, the immunity of Qingyuan partridge chickens can be significantly improved, the efficiency of disease resistance breeding in Qingyuan partridge chickens can be enhanced, the breeding process can be accelerated, and at the same time, the cost of immunoprophylaxis can be reduced, having good application prospects. Description of the drawings

[0044] Figure 1 It is a flow chart of whole-genome resequencing;

[0045] Figure 2Manhattan plot of genome-wide association analysis for pancreatic tissue index traits: Among them, the abscissa represents the chromosome number, and the ordinate represents the -logP value. The arrow indicates the corresponding SNP molecular marker screened out;

[0046] Figure 3 Manhattan plot of genome-wide association analysis for spleen tissue index traits: Among them, the abscissa represents the chromosome number, and the ordinate represents the -logP value. The arrow indicates the corresponding SNP molecular marker screened out;

[0047] Figure 4 Manhattan plot of genome-wide association analysis for the trait of IL6 content in blood: Among them, the abscissa represents the chromosome number, and the ordinate represents the -logP value. The arrow indicates the corresponding SNP molecular marker screened out;

[0048] Figure 5 Manhattan plot of genome-wide association analysis for the trait of IFN-β content in blood: Among them, the abscissa represents the chromosome number, and the ordinate represents the -logP value. The arrow indicates the corresponding SNP molecular marker screened out;

[0049] Figure 6 Manhattan plot of genome-wide association analysis for the trait of the positive degree of cloacal virus: Among them, the abscissa represents the chromosome number, and the ordinate represents the -logP value. The arrow indicates the corresponding SNP molecular marker screened out. Detailed implementation mode

[0050] The invention will be further described in detail below with reference to the accompanying drawings.

[0051] Example 1. Screening of SNP molecular markers related to chicken immune traits

[0052] (1) Select 240 15-day-old Qingyuan partridge chickens infected with ALV-J, collect blood samples from the wing vein, and collect thymus, spleen, bursa of Fabricius, pancreas and cloacal swab samples after slaughtering. Weigh the collected tissues and organs, calculate the tissue index using the formula "tissue index = tissue weight / body weight", detect the IL-6 content and IFN-β content in the blood using an ELISA kit, and detect the p27 protein of avian leukosis virus in the virus culture solution and cloacal swabs according to the instructions of the avian leukosis virus ELISA antigen detection kit (Harbin Guosheng Biotechnology Co., Ltd., NEE83500) to obtain the positive degree of cloacal virus. Collect wing vein blood and store it in a sodium citrate anticoagulant tube at -20 °C for blood DNA extraction; collect thymus, spleen and bursa of Fabricius tissues and store them at -80 °C.

[0053] (2) Extract the DNA of the chicken flock: Extract the DNA according to the instructions of the blood DNA extraction kit. The general steps are: sample preparation → digestion → washing → drying → elution. Send the qualified DNA to BGI Genomics Co., Ltd. in Shenzhen for whole-genome resequencing (sequencing strategy: PE150, average sequencing depth 10X). The sequencing process is as Figure 1 shown.

[0054] (3) Construct a DNA library and perform whole-genome sequencing;

[0055] (4) Use the software fastp (version 0.23.4) to process the adapters and perform Q30 filtering on the raw sequencing data, and at the same time complete the merging of paired-end reads. Use the software BWA (version 0.7.17) and SAMtools (version 1.18) to align the sequencing data to the 7th version of the chicken genome (bGalGal1.mat.broiler.GRCg7b), and perform sorting, merging, indexing, etc. on the SAM (sequence alignment / map) file and convert the format to a BAM (Binary Alignment / Map format) file. Subsequently, use the software GATK for variant detection and merge the population genotype gVCF files. Finally, use beagle (version 5.4) for genotype imputation. Use the software plink (version 1.90b4.6) to convert the population gVCF file to a binary format, and at the same time set filtering parameters to retain SNPs with a minor allele genotype missing rate less than 0.1, a minor allele frequency greater than 0.05, and a Hardy-Weinberg equilibrium test P value greater than 0.000001.

[0056] (5) Use the software GEMMA (version 0.98.5) to perform a genome-wide association study (GWAS) on a total of 5 immune traits, including spleen tissue index, pancreas tissue index, IL-6 content in blood, IFN-β content in blood, and the degree of cloacal virus positivity. Subsequently, use ANNOVAR to annotate the SNPs at the significant level to obtain information related to significant SNP molecular markers.

[0057] (6) By performing a GWAS analysis on the immune traits of 240 Qingyuan partridge chickens infected with ALV-J, significant SNPs were identified. Among the five immune-related traits (spleen tissue index, pancreas tissue index, IL-6 content in blood, IFN-β content in blood, and cloacal virus positivity), there were 10 SNP molecular markers with a relatively high allele frequency (MAF < 0.5), namely chr7_12931235, chr25_1331279, chr25_1331316, chr3_59309366, chr1_114656880, chr3_59309189, chr3_59308643, chr4_11372457, chr1_69131730, and chr21_878099. The mutations at these 10 SNP molecular marker sites had a significant impact on the immune traits of Qingyuan partridge chickens. The specific information of the 10 SNP molecular markers related to chicken immune traits screened out is shown in Table 1 as follows:

[0058] Table 1 Gene frequency statistics of SNP molecular markers related to chicken immune traits

[0059]

[0060]

[0061] 1.1 SNP molecular markers related to the pancreas tissue index trait

[0062] The chr7_12931235 SNP molecular marker is a G>T mutation located at the 12931235bp site on chromosome 7 of the chicken genome, and it is significantly correlated with the pancreas tissue index trait of chickens. The GWAS analysis results of this site are as Figure 2 shown: The arrow in the figure indicates the chr7_12931235 SNP molecular marker.

[0063] The correlation analysis between the chr7_12931235 SNP molecular marker and the pancreas tissue index is shown in Table 2:

[0064] Table 2 Correlation analysis between the chr7_12931235 SNP molecular marker and the pancreas tissue index

[0065]

[0066]

[0067] Note: In the table, the same letters above the same column of numbers indicate no significant difference (P > 0.05), and different letters indicate significant difference (P < 0.05).

[0068] According to Table 2, the chr7_12931235 SNP molecular marker is significantly associated with the pancreatic tissue index trait (P < 0.05). Among them, the pancreatic tissue index of the TT genotype is significantly greater than that of the GG and GT genotypes (P < 0.05), while there is no significant difference in the pancreatic tissue index between the GG genotype and the GT genotype (P > 0.05). This indicates that the TT genotype is the dominant genotype at this locus, and T is the dominant allele at this locus. Selecting the TT dominant genotype at this SNP locus and eliminating the GG and GT genotypes can gradually increase the frequency of the dominant allele T at this locus, which can significantly improve the pancreatic tissue index of the chicken population. The pancreas is an important digestive organ and also an endocrine gland, which is closely related to immunity. Islet cells in the pancreas can secrete certain cytokines (such as IL-6, TNF-α) and participate in local immune regulation. The higher the pancreatic tissue index, the stronger the immune response of the chicken, thus improving the immunity of the chicken.

[0069] 1.2 SNP molecular markers related to the spleen tissue index trait

[0070] The chr3_59309366 SNP molecular marker is a C>T mutation at the 59309366bp site on chromosome 3 of the chicken genome, and it is significantly associated with the spleen tissue index trait of chickens. The GWAS analysis results of this locus are as Figure 3 shown: The blue arrow in the figure indicates the chr3_59309366 SNP molecular marker.

[0071] The chr3_59309189 SNP molecular marker is a T>C mutation at the 59309189bp site on chromosome 3 of the chicken genome, and it is significantly associated with the spleen tissue index trait of chickens. The GWAS analysis results of this locus are as Figure 3 shown: The yellow arrow in the figure indicates the chr3_59309189 SNP molecular marker.

[0072] The chr3_59308643 SNP molecular marker is a G>A mutation at the 59308643bp site on chromosome 3 of the chicken genome, and it is significantly associated with the spleen tissue index trait of chickens. The GWAS analysis results of this locus are as Figure 3 shown: The red arrow in the figure indicates the chr3_59308643 SNP molecular marker.

[0073] The correlation analysis of the chr3_59309366 SNP molecular marker, chr3_59309189 SNP molecular marker, and chr3_59308643 SNP molecular marker with the spleen tissue index is shown in Table 3:

[0074] Table 3 Correlation analysis between SNP molecular markers chr3_59309366, chr3_59309189, chr3_59308643 and spleen tissue index

[0075]

[0076] Note: In the table, the same letter above the numbers in the same column indicates no significant difference (P>0.05), and different letters indicate significant difference (P<0.05).

[0077] As can be seen from Table 3, the SNP molecular marker chr3_59309366 is significantly correlated with the spleen tissue index trait (P<0.05). Among them, the spleen tissue index of the TT genotype is significantly greater than that of the CC and CT genotypes (P<0.05), and the spleen tissue index of the CT genotype is significantly greater than that of the CC genotype (P<0.05). This indicates that T is the dominant allele at this locus. Selecting the TT and CT dominant genotypes and eliminating the CC genotype at this SNP locus to gradually increase the frequency of the dominant allele T at this locus can significantly increase the spleen tissue index of the chicken population. The spleen is the largest immune organ in the body, accounting for 25% of the total lymphoid tissue in the body, and contains a large number of lymphocytes and plasma cells, which play important roles in humoral immunity and cell-mediated immunity. The spleen tissue index can reflect the strength of the immune response. A high spleen tissue index indicates a strong immune response, and vice versa. The higher the spleen tissue index, the stronger the immune response of the chicken and the higher its immunity.

[0078] As can be seen from Table 3, the SNP molecular marker chr3_59309189 is significantly correlated with the spleen tissue index trait (P<0.05). Among them, the spleen tissue index of the CC genotype is significantly greater than that of the TT and TC genotypes (P<0.05), and the spleen tissue index of the TC genotype is significantly greater than that of the TT genotype (P<0.05). This indicates that C is the dominant allele at this locus. Selecting the CC and TC dominant genotypes and eliminating the TT genotype at this SNP locus to gradually increase the frequency of the dominant allele C at this locus can significantly increase the spleen tissue index of the chicken population. The spleen is the largest immune organ in the body, accounting for 25% of the total lymphoid tissue in the body, and contains a large number of lymphocytes and plasma cells, which play important roles in humoral immunity and cell-mediated immunity. The spleen tissue index can reflect the strength of the immune response. A high spleen tissue index indicates a strong immune response, and vice versa. The higher the spleen tissue index, the stronger the immune response of the chicken and the higher its immunity.

[0079] According to Table 3, the chr3_59308643 SNP molecular marker is significantly associated with the spleen tissue index trait (P < 0.05). Among them, the spleen tissue index of the AA genotype is significantly greater than that of the GG and GA genotypes (P < 0.05), and the spleen tissue index of the GA genotype is significantly greater than that of the GG genotype (P < 0.05), indicating that A is the dominant allele at this locus. Selecting the AA and GA dominant genotypes and eliminating the GG genotype at this SNP locus can gradually increase the frequency of the dominant allele A at this locus, which can significantly increase the spleen tissue index of the chicken population. The spleen is the largest immune organ of the body, accounting for 25% of the total lymphoid tissue in the body, and contains a large number of lymphocytes and plasma cells, which play important roles in humoral immunity and cellular immunity. The spleen tissue index can reflect the strength of the immune response. A high spleen tissue index indicates a strong immune response, and vice versa indicates a weak immune response. Moreover, the higher the spleen tissue index, the stronger the immune response of the chicken and the higher the immunity of the chicken.

[0080] 1.3 SNP molecular markers associated with the IL6 content trait in blood

[0081] The chr25_1331279 SNP molecular marker is an A > G mutation at the 1331279bp locus on chromosome 25 of the chicken genome, and it is significantly associated with the IL6 content trait of chickens. The GWAS analysis results of this locus are as Figure 4 shown: The blue arrow in the figure indicates the chr25_1331279 SNP molecular marker.

[0082] The chr25_1331316 SNP molecular marker is an A > G mutation at the 1331316bp locus on chromosome 25 of the chicken genome, and it is significantly associated with the IL6 content trait of chickens. The GWAS analysis results of this locus are as Figure 4 shown: The yellow arrow in the figure indicates the chr25_1331316 SNP molecular marker.

[0083] The correlation analysis of the chr25_1331279 and chr25_1331316 SNP molecular markers with the IL6 content is shown in Table 4:

[0084] Table 4 Correlation analysis of the chr25_1331279 and chr25_1331316 SNP molecular markers with the IL6 content

[0085]

[0086]

[0087] Note: In the table, the same letters above the same column of numbers indicate no significant difference (P > 0.05), and different letters indicate significant difference (P < 0.05).

[0088] According to Table 4, the molecular marker chr25_1331279 was significantly associated with the IL6 content trait (P < 0.05). Among them, the IL6 content in the blood of the AA genotype was significantly higher than that of the GG genotype (P < 0.05), but there was no significant difference between the AA genotype and the AG genotype (P > 0.05), and there was also no significant difference in the IL6 content in the blood between the AG genotype and the GG genotype (P > 0.05). This indicates that A is the dominant allele at this locus. Selecting the AA dominant genotype and eliminating the GG and AG genotypes at this SNP locus can gradually increase the frequency of the dominant allele A at this locus, which can significantly increase the IL6 content in the chicken population blood. IL-6 is a multifunctional cytokine that plays an important role in immune regulation, hematopoiesis, and inflammation processes. IL-6 is mainly synthesized by activated T cells and B cells, monocytes-macrophages, endothelial cells, epithelial cells, and fibroblasts, etc. In the immune response, IL-6 can promote the proliferation and differentiation of B cells, thereby enhancing the immune response of the body to antigens. In addition, IL-6 is also involved in regulating the inflammatory response, promoting cell proliferation, differentiation, oxidative stress, and immune regulation by activating signal pathways such as JAK-STAT and RAS-RAF. Therefore, the higher the IL-6 content in the blood, the stronger its resistance to viruses. And the higher the IL6 content in the blood, the stronger the immune response of chickens and the higher the immunity of chickens.

[0089] According to Table 4, the molecular marker chr25_1331316 was significantly associated with the IL6 content trait (P < 0.05). Among them, the IL6 content of the AA genotype was significantly higher than that of the GG and AG genotypes (P < 0.05), and the IL6 content of the AG genotype was significantly higher than that of the GG genotype (P < 0.05). This indicates that A is the dominant allele at this locus. Selecting the AA and AG dominant genotypes and eliminating the GG genotype at this SNP locus can gradually increase the frequency of the dominant allele A at this locus, which can significantly increase the IL6 content of the chicken population. IL-6 is a multifunctional cytokine that plays an important role in immune regulation, hematopoiesis, and inflammation processes. IL-6 is mainly synthesized by activated T cells and B cells, monocytes-macrophages, endothelial cells, epithelial cells, and fibroblasts, etc. In the immune response, IL-6 can promote the proliferation and differentiation of B cells, thereby enhancing the immune response of the body to antigens. In addition, IL-6 is also involved in regulating the inflammatory response, promoting cell proliferation, differentiation, oxidative stress, and immune regulation by activating signal pathways such as JAK-STAT and RAS-RAF. Therefore, the higher the IL-6 content in the blood, the stronger its resistance to viruses. And the higher the IL6 content, the stronger the immune response of chickens and the higher the immunity of chickens.

[0090] 1.4 SNP molecular markers related to the IFN-β content trait in the blood

[0091] The chr21_878099 SNP molecular marker is a G>A mutation at the 878099bp locus on chromosome 21 of the chicken genome, and it is significantly associated with the IFN-β content trait in chickens. The GWAS analysis results of this locus are as Figure 5 shown: The arrow in the figure indicates the chr21_878099 SNP molecular marker.

[0092] The correlation analysis between the chr21_878099 SNP molecular marker and the IFN-β content is shown in Table 5:

[0093] Table 5 Correlation analysis between the chr21_878099 SNP molecular marker and the IFN-β content

[0094]

[0095] Note: In the table, the same letters above the numbers in the same column indicate no significant difference (P>0.05), and different letters indicate significant difference (P<0.05).

[0096] According to Table 5, the chr21_878099 molecular marker is significantly associated with the IFN-β content trait (P<0.05). Among them, the IFN-β content of the AA genotype is significantly higher than that of the GG genotype (P<0.05), but there is no significant difference from the GA genotype (P>0.05), and there is also no significant difference between the GA genotype and the GG genotype (P>0.05). This indicates that A is the dominant allele at this locus. Selecting the AA dominant genotype and eliminating the GG and GA genotypes at this SNP locus to gradually increase the frequency of the dominant allele A at this locus can significantly increase the IFN-β content in the blood of the chicken population. IFN-β is a key type I interferon cytokine that plays a crucial role in coordinating the innate immune response against various challenges, including infection, tumor development, and inflammatory stimuli. The higher the IFN-β content in the blood, the stronger its resistance to viruses and the better its disease resistance. Moreover, the higher the IFN-β content in the blood, the stronger the immune response of the chicken and the higher its immunity.

[0097] 1.5 SNP molecular markers related to the degree of cloacal virus positivity

[0098] The chr1_114656880 SNP molecular marker is a C>T mutation at the 114656880bp locus on chromosome 1 of the chicken genome, and it is significantly associated with the degree of virus positivity trait in chickens. The GWAS analysis results of this locus are as Figure 6 shown: The blue arrow in the figure indicates the chr1_114656880 SNP molecular marker.

[0099] The chr1_69131730 SNP molecular marker is an A>G mutation at the 69131730 bp locus on chromosome 1 of the chicken genome, and it is significantly associated with the trait of the degree of virus positivity in chickens. The GWAS analysis results of this locus are as Figure 6 shown: The yellow arrow in the figure indicates the chr1_69131730 SNP molecular marker.

[0100] The chr4_11372457 SNP molecular marker is a C>T mutation at the 11372457 bp locus on chromosome 4 of the chicken genome, and it is significantly associated with the trait of the degree of virus positivity in chickens. The GWAS analysis results of this locus are as Figure 6 shown: The red arrow in the figure indicates the chr4_11372457 SNP molecular marker.

[0101] The correlation analysis of the chr1_114656880, chr1_69131730, and chr4_11372457 SNP molecular markers with the degree of virus positivity is shown in Table 6:

[0102] Table 6 Correlation analysis of the chr1_114656880, chr1_69131730, and chr4_11372457 SNP molecular markers with the degree of cloacal virus positivity

[0103]

[0104] Note: In the table, the same letters above the numbers in the same column indicate no significant difference (P>0.05), and different letters indicate significant difference (P<0.05).

[0105] According to Table 6, the chr1_114656880 molecular marker is significantly associated with the trait of the degree of cloacal virus positivity (P<0.05). Among them, the degree of cloacal virus positivity of the CC and CT genotypes is significantly lower than that of the TT genotype (P<0.05), but there is no significant difference between the CC genotype and the CT genotype (P>0.05). This indicates that C is the dominant allele at this locus. Selecting the CC and CT dominant genotypes and eliminating the TT genotype at this SNP locus to gradually increase the frequency of the dominant allele C at this locus can significantly reduce the degree of cloacal virus positivity in the chicken population. By detecting the degree of cloacal virus positivity, the replication of the virus in chickens can be evaluated, and then the immunity and disease resistance of chickens can be evaluated. Generally, the lower the degree of cloacal virus positivity, the lower the virus replication and the better the disease resistance of chickens. And the lower the degree of cloacal virus positivity, the higher the ability of the chicken flock to resist ALV-J virus, thereby improving the disease resistance of chickens.

[0106] As can be seen from Table 6, the molecular marker chr1_69131730 was significantly associated with the trait of the positive degree of cloacal virus (P < 0.05). Among them, the positive degree of cloacal virus in the AA genotype was significantly lower than that in the AG and GG genotypes (P < 0.05), and the positive degree of cloacal virus in the AG genotype was significantly lower than that in the GG genotype (P < 0.05). This indicates that A is the dominant allele at this locus. Selecting the AA and AG dominant genotypes and eliminating the GG genotype at this SNP locus to gradually increase the frequency of the dominant allele A at this locus can significantly reduce the positive degree of cloacal virus in the chicken population. By detecting the positive degree of cloacal virus, the replication of the virus in chickens can be evaluated, and then the immunity and disease resistance of chickens can be evaluated. Generally, the lower the positive degree of cloacal virus, the lower the virus replication and the better the disease resistance of chickens. Moreover, the lower the positive degree of cloacal virus, the higher the ability of the chicken flock to resist ALV-J virus, thereby improving the disease resistance of chickens.

[0107] As can be seen from Table 6, the molecular marker chr4_11372457 was significantly associated with the trait of the positive degree of cloacal virus (P < 0.05). Among them, the content of the positive degree of cloacal virus in the CC genotype was significantly lower than that in the CT and CC genotypes (P < 0.05), and the positive degree of cloacal virus in the CT genotype was significantly lower than that in the TT genotype (P < 0.05). This indicates that C is the dominant allele at this locus. Selecting the CC and CT dominant genotypes and eliminating the TT genotype at this SNP locus to gradually increase the frequency of the dominant allele C at this locus can significantly reduce the positive degree of cloacal virus in the chicken population. By detecting the positive degree of cloacal virus, the replication of the virus in chickens can be evaluated, and then the immunity and disease resistance of chickens can be evaluated. Generally, the lower the positive degree of cloacal virus, the lower the virus replication and the better the disease resistance of chickens. Moreover, the lower the positive degree of cloacal virus, the higher the ability of the chicken flock to resist ALV-J virus, thereby improving the disease resistance of chickens.

[0108] Example 2: Application of SNP molecular markers of chr7_12931235, chr25_1331279, chr25_1331316, chr3_59309366, chr1_114656880, chr3_59309189, chr3_59308643, chr4_11372457, chr1_69131730, chr21_878099 in the breeding of chicken immune traits.

[0109] By detecting the SNP molecular markers of chr7_12931235, chr25_1331279, chr25_1331316, chr3_59309366, chrl_114656880, chr3_59309189, chr3_59308643, chr4_11372457, chr1_69131730, chr21_878099, selecting and retaining the dominant alleles and dominant genotypes of the corresponding SNP loci, eliminating the poor genotypes, the breeding of chicken immune traits can be achieved through molecular marker-assisted breeding technology, especially the breeding of immune traits such as spleen tissue index, pancreas tissue index, IL-6 content in blood, IFN-β content in blood, and positive degree of cloacal virus, and chickens with high immune performance can be obtained.

[0110] Or according to the loci of chr7_12931235, chr25_1331279, chr25_1331316, chr3_59309366, chr1 _ 114656880, chr3_59309189, chr3_59308643, chr4_11372457, chr1_69131730, chr21_878099 SNP molecular markers on the chicken genome chromosomes, primers or probes are designed to detect the SNP molecular markers, the dominant alleles and dominant genotypes of the corresponding SNP loci are selected and retained, the poor genotypes are eliminated, and the breeding of chicken immune traits can be achieved through molecular marker-assisted breeding technology, especially the breeding of immune traits such as spleen tissue index, pancreas tissue index, IL-6 content in blood, IFN-β content in blood, and positive degree of cloacal virus, and chickens with high immune performance can be obtained.

[0111] Example 3. Application of chr7_12931235, chr25_1331279, chr25_1331316, chr3_59309366, chr1_114656880, chr3_59309189, chr3_59308643, chr4_11372457, chr1_69131730, chr21_878099 SNP molecular markers in breeding chicken breeds with high immunity traits.

[0112] By detecting the SNP molecular markers of chr7_12931235, chr25_1331279, chr25_1331316, chr3_59309366, chrl_114656880, chr3_59309189, chr3_59308643, chr4_11372457, chr1_69131730, chr21_878099, selecting the individuals with the dominant genotypes at the corresponding SNP loci as breeding chickens for mating, then detecting the molecular markers of the hatched chicks, selecting the individuals with the dominant genotypes at the corresponding SNP loci, eliminating the poor genotypes, gradually increasing the frequency of the dominant alleles, and finally a chicken breed with high immunity traits can be obtained.

[0113] Or according to the loci of the SNP molecular markers of chr7_12931235, chr25_1331279, chr25_1331316, chr3_59309366, chr1_114656880, chr3_59309189, chr3_59308643, chr4_11372457, chr1_69131730, chr21_878099 on the chicken genome chromosomes, designing primers or probes to detect the SNP molecular markers, selecting the individuals with the dominant genotypes at the corresponding SNP loci as breeding chickens for mating, then detecting the molecular markers of the hatched chicks, selecting the individuals with the dominant genotypes at the corresponding SNP loci, eliminating the poor genotypes, gradually increasing the frequency of the dominant alleles, and finally a chicken breed with high immunity traits can be obtained.

[0114] Example 4: Application of the SNP molecular markers of chr7_12931235, chr25_1331279, chr25_1331316, chr3_59309366, chr1_114656880, chr3_59309189, chr3_59308643, chr4_11372457, chr1_69131730, chr21_878099 in improving chicken immune traits.

[0115] By detecting the SNP molecular markers of chr7_12931235, chr25_1331279, chr25_1331316, chr3_59309366, chr1_114656880, chr3_59309189, chr3_59308643, chr4_11372457, chr1_69131730, chr21_878099, selecting and retaining individuals with the dominant genotype at the corresponding SNP locus as breeding chickens for mating, then detecting the molecular markers of the hatched chicks, selecting and retaining individuals with the dominant genotype at the corresponding SNP locus, eliminating the poor genotypes, and gradually increasing the frequency of the dominant allele, the immune traits of chickens can be improved ultimately.

[0116] Or according to the loci of the SNP molecular markers of chr7_12931235, chr25_1331279, chr25_1331316, chr3_59309366, chr1_114656880, chr3_59309189, chr3_59308643, chr4_11372457, chr1_69131730, chr21_878099 on the chicken genome chromosomes, designing primers or probes to detect the SNP molecular markers, selecting and retaining individuals with the dominant genotype at the corresponding SNP locus as breeding chickens for mating, then detecting the molecular markers of the hatched chicks, selecting and retaining individuals with the dominant genotype at the corresponding SNP locus, eliminating the poor genotypes, and gradually increasing the frequency of the dominant allele, the immune traits of chickens can be improved ultimately.

[0117] Example 5: Application of the chr7_12931235 SNP molecular marker in improving the chicken pancreas tissue index trait.

[0118] Detect the chr7_12931235 SNP molecular marker for the candidate breeding chickens; select and retain the individuals with the detected allele genotype of TT genotype as the breeding chickens, and eliminate the GG and GT genotype individuals, which can improve the chicken pancreas tissue index and thus enhance the immune response during virus infection.

[0119] Example 6: Application of the chr3_59309366, chr3_59309189, chr3_59308643 SNP molecular markers in improving the chicken spleen tissue index trait.

[0120] Detect the chr3_59309366 SNP molecular marker for the candidate breeding chickens; select and retain the individuals with the detected allele genotypes of TT and CT genotypes as the breeding chickens, and eliminate the CC genotype individuals, which can improve the chicken spleen tissue index and thus enhance the immune response during virus infection.

[0121] Or detect the chr3_59309189 SNP molecular marker in the candidate breeding chickens; select the individuals with the detected allele genotypes of CC and TC genotypes as the breeding chickens, and eliminate the individuals with the TT genotype, which can increase the spleen tissue index of the chickens and thus enhance the immune response during virus infection.

[0122] Or detect the chr3_59308643 SNP molecular marker in the candidate breeding chickens; select the individuals with the detected allele genotypes of AA and GA genotypes as the breeding chickens, and eliminate the individuals with the GG genotype, which can increase the spleen tissue index of the chickens and thus enhance the immune response during virus infection.

[0123] Example 7: Application of chr25_1331279 and chr25_1331316 SNP molecular markers in increasing the IL6 content in chicken blood.

[0124] Detect the chr25_1331279 SNP molecular marker in the candidate breeding chickens; select the individuals with the detected allele genotype of AA as the breeding chickens, and eliminate the individuals with the GG and AG genotypes, which can increase the IL6 content in chicken blood and thus enhance the immune response during virus infection.

[0125] Or detect the chr25_1331316 SNP molecular marker in the candidate breeding chickens; select the individuals with the detected allele genotypes of AA and AG as the breeding chickens, and eliminate the individuals with the GG genotype, which can increase the IL6 content in chicken blood and thus enhance the immune response during virus infection.

[0126] Example 8: Application of chr21_878099 SNP molecular marker in increasing the IFN-β content in chicken blood.

[0127] Detect the chr21_878099 SNP molecular marker in the candidate breeding chickens; select the individuals with the detected allele genotype of AA as the breeding chickens, and eliminate the individuals with the GG and GA genotypes, which can increase the IFN-β content in chicken blood and thus enhance the immune response during virus infection.

[0128] Example 9: Application of chr1_114656880, chr1_69131730, and chr4_11372457 SNP molecular markers in reducing the positive degree of cloacal virus in chickens.

[0129] Detect the chr1_114656880 SNP molecular marker in the candidate breeding chickens; select the individuals with the detected allele genotypes of CC and CT as the breeding chickens, and eliminate the individuals with the TT genotype, which can reduce the positive degree of cloacal virus in chickens and improve the ability of chickens to resist ALV-J virus.

[0130] Or detect the chr1_69131730 SNP molecular marker in the candidate breeding chickens; select and retain the individuals with the detected allelic genotypes of AA and AG as breeding chickens, and eliminate the individuals with the GG genotype, which can reduce the positive degree of chicken cloacal virus and improve the ability of chickens to resist ALV-J virus.

[0131] Or detect the chr4_11372457 SNP molecular marker in the candidate breeding chickens; select and retain the individuals with the detected allelic genotypes of CC and CT as breeding chickens, and eliminate the individuals with the TT genotype, which can reduce the positive degree of chicken cloacal virus and improve the ability of chickens to resist ALV-J virus.

Claims

1. SNP molecular markers related to chicken immune traits, wherein, The immune traits include any one or more of spleen tissue index, pancreatic tissue index, IL-6 content in blood, IFN-β content in blood, and the positive degree of cloacal virus. The SNP molecular markers include any one or more of the following molecular markers: the G>T mutation at the 12931235bp locus on chromosome 7 of the chicken genome, the C>T mutation at the 59309366bp locus on chromosome 3 of the chicken genome, the T>C mutation at the 59309189bp locus on chromosome 3 of the chicken genome, the G>A mutation at the 59308643bp locus on chromosome 3 of the chicken genome, the A>G mutation at the 1331279bp locus on chromosome 25 of the chicken genome, the A>G mutation at the 1331316bp locus on chromosome 25 of the chicken genome, the G>A mutation at the 878099bp locus on chromosome 21 of the chicken genome, the C>T mutation at the 114656880bp locus on chromosome 1 of the chicken genome, the A>G mutation at the 69131730bp locus on chromosome 1 of the chicken genome, and the C>T mutation at the 11372457bp locus on chromosome 4 of the chicken genome.

2. Use of the SNP molecular marker described in claim 1 in the breeding of chicken immune traits, wherein, The immune traits include any one or more of spleen tissue index, pancreatic tissue index, IL-6 content in blood, IFN-β content in blood, and the positive degree of cloacal virus.

3. Use of a product for detecting the SNP molecular marker described in claim 1 in the breeding of chicken immune traits, wherein, The immune traits include any one or more of spleen tissue index, pancreatic tissue index, IL-6 content in blood, IFN-β content in blood, and the positive degree of cloacal virus.

4. The application according to claim 3, wherein, The product for detecting the SNP molecular markers described in claim 1 refers to primers or probes that can detect the SNP molecular markers or a kit prepared from the primers or probes.

5. The application of the SNP molecular markers described in claim 1 in breeding chicken breeds with high immune traits, or the application of the product for detecting the SNP molecular markers described in claim 1 in breeding chicken breeds with high immune traits, or the application of the SNP molecular markers described in claim 1 in improving chicken immune traits, or the application of the product for detecting the SNP molecular markers described in claim 1 in improving chicken immune traits.

6. Use of an SNP molecular marker in improving the index traits of chicken pancreatic tissue, wherein, The SNP molecular marker is the G>T mutation at the 12931235bp locus on chromosome 7 of the chicken genome. The application includes the following steps: 1) Detect the SNP molecular marker in candidate breeding chickens. 2) Select and retain the individuals with the TT genotype detected in step 1) as breeding chickens, and eliminate the GG and GT genotype individuals, which can increase the pancreatic tissue index of chickens and thus enhance the immune response during virus infection.

7. Use of an SNP molecular marker in improving the index trait of chicken spleen tissue, wherein, The SNP molecular markers are the C>T mutation at the 59309366bp locus on chromosome 3 of the chicken genome, the T>C mutation at the 59309189bp locus on chromosome 3 of the chicken genome, or the G>A mutation at the 59308643bp locus on chromosome 3 of the chicken genome. The application includes the following steps: 1) Detect the SNP molecular markers in the candidate breeding chickens; 2) Select the individuals with the TT and CT genotypes at the 59309366bp locus on chromosome 3 detected in step 1) as the breeding chickens, and eliminate the individuals with the CC genotype, which can increase the spleen tissue index of chickens and further enhance the immune response during virus infection; Or select the individuals with the CC and TC genotypes at the 59309189bp locus on chromosome 3 detected in step 1) as the breeding chickens, and eliminate the individuals with the TT genotype, which can increase the spleen tissue index of chickens and further enhance the immune response during virus infection; Or select the individuals with the AA and GA genotypes at the 59308643bp locus on chromosome 3 detected in step 1) as the breeding chickens, and eliminate the individuals with the GG genotype, which can increase the spleen tissue index of chickens and further enhance the immune response during virus infection.

8. Use of an SNP molecular marker in increasing the content of IL6 in chicken blood, wherein, The SNP molecular marker is the A>G mutation at the 1331279bp locus on chromosome 25 of the chicken genome or the A>G mutation at the 1331316bp locus on chromosome 25 of the chicken genome. The application includes the following steps: 1) Detect the SNP molecular markers in the candidate breeding chickens; 2) Select the individuals with the AA genotype at the 1331279bp locus on chromosome 25 detected in step 1) as the breeding chickens, and eliminate the individuals with the GG and AG genotypes, which can increase the IL6 content in the blood of chickens; Or select the individuals with the AA and AG genotypes at the 1331316bp locus on chromosome 25 detected in step 1) as the breeding chickens, and eliminate the individuals with the GG genotype, which can increase the IL6 content in the blood of chickens and further enhance the immune response during virus infection.

9. Use of an SNP molecular marker in increasing the content of IFN-β in chicken blood, wherein, The SNP molecular marker is the G>A mutation at the 878099bp locus on chromosome 21 of the chicken genome. The application includes the following steps: 1) Detect the SNP molecular markers in the candidate breeding chickens; 2) Select the individuals with the AA genotype detected in step 1) as the breeding chickens, and eliminate the individuals with the GG and GA genotypes, which can increase the IFN-β content in the blood of chickens and further enhance the immune response during virus infection.

10. Use of an SNP molecular marker in reducing the positive degree of chicken cloacal virus, wherein, The SNP molecular marker is the C>T mutation at the 114656880bp locus on chromosome 1 of the chicken genome or the A>G mutation at the 69131730bp locus on chromosome 1 of the chicken genome or the C>T mutation at the 11372457bp locus on chromosome 4 of the chicken genome. The application includes the following steps: 1) Detect the SNP molecular markers in the candidate breeding chickens; 2) Select the individuals with the CC and CT genotypes at the 114656880bp locus on chromosome 1 detected in step 1) as the breeding chickens, and eliminate the individuals with the TT genotype, which can reduce the positive degree of cloacal virus in chickens and improve the ability of chickens to resist ALV-J virus; Alternatively, retain the individuals with the AA and AG genotypes at the 69131730 bp locus on chromosome 1 detected in step 1) as breeding chickens, and eliminate the individuals with the GG genotype, which can reduce the positive degree of chicken cloacal virus and improve the ability of chickens to resist ALV-J virus; Alternatively, retain the individuals with the CC and CT genotypes at the 11372457 bp locus on chromosome 4 detected in step 1) as breeding chickens, and eliminate the individuals with the TT genotype, which can reduce the positive degree of chicken cloacal virus and improve the ability of chickens to resist ALV-J virus.

Images