SNP (Single Nucleotide Polymorphism) molecular marker for influencing 49-day-old weight of chicken by influencing GCNT7 gene expression and application of SNP molecular marker

Abstract

The invention discloses an SNP (Single Nucleotide Polymorphism) molecular marker for influencing 49-day-old chicken body weight by influencing GCNT7 gene expression and application thereof, and belongs to the fields of molecular genetics and agricultural animal breeding, the SNP molecular marker is located at the position of 12292590bp of a chicken 20 # chromosome, a reference genome version is GRCg7b, a basic group at the position has A / G polymorphism, and the SNP molecular marker can be used for identifying the chicken 49-day-old body weight. The individual with the genotype of GG or GA at the position has a higher 49-day-old body weight character than the individual with the genotype of AA. A molecular marker system which is remarkably related to the GCNT7 expression level and can be used for early prediction and selection of the 49-day-old chicken weight character is constructed, and a feasible technical path is provided for broiler chicken breeding practice.

Description

Technical Field

[0001] This invention relates to the fields of molecular genetics and agricultural animal breeding, specifically to an SNP molecular marker that affects the body weight of chickens at 49 days of age by influencing the expression of the GCNT7 gene and its application. Background Technology

[0002] With the continuous advancement of livestock and poultry genetic breeding technology in my country, the broiler industry plays a vital role in ensuring the supply of animal protein and promoting rural economic development. Body weight, as a core economic trait for measuring broiler production performance, directly affects feed conversion efficiency, time to market, and end-market value, making it one of the key target traits in broiler breeding. Especially in yellow-feathered broilers with short breeding cycles and rapid metabolic growth, body weight at 49 days of age is often used as an important indicator of growth rate and breeding value. Although traditional family selection and phenotypic selection have achieved some success in improving body weight, limitations such as significant environmental interference and low breeding efficiency make it difficult to achieve further precision selection. Therefore, it is urgent to utilize molecular breeding methods to identify and apply functional genes and genetic markers closely related to body weight regulation to accelerate the breeding process of superior germplasm.

[0003] Among numerous candidate genes, GCNT7 (β-1,6-N-acetylglucosamine transferase 7), as an important enzyme in the glycosylation process, plays a crucial role in the regulation of cell proliferation, differentiation, and signal transduction. Previous studies have shown that GCNT7 participates in regulating metabolism and tissue development in various animals, and it may have important functions in poultry muscle development and energy metabolism. Recent studies suggest that the GCNT7 gene exhibits high expression levels during chicken embryonic development and early growth stages, and its expression level is significantly correlated with body weight phenotype, implying that genetic variations in this gene may play an important role in regulating early growth and development in chickens. Therefore, identifying regulatory SNP sites around the GCNT7 gene and assessing their impact on body weight at 49 days of age holds promise for providing new molecular targets for broiler breeding.

[0004] Single nucleotide polymorphisms (SNPs), as third-generation molecular markers, have become important tools for genetic improvement and molecular-assisted selection breeding due to their large number, wide distribution, and high genetic stability. Genome-wide association studies (GWAS) can systematically uncover the associations between SNP loci and complex quantitative traits. Combining next-generation sequencing and low-depth resequencing strategies to conduct GWAS studies at the population level can achieve large-sample, high-density whole-genome marker scanning at a lower cost, thus significantly improving the efficiency and accuracy of molecular marker discovery.

[0005] Against this backdrop, identifying and verifying functional SNP sites that affect the body weight of chickens at 49 days of age, especially regulatory genetic variations related to GCNT7 gene expression, is of great significance for conducting molecular marker-assisted selection breeding of chicken body weight. Summary of the Invention

[0006] The technical problem to be solved by this invention is to provide an SNP site that is significantly associated with the body weight of chickens at 49 days of age and its application in molecular marker-assisted breeding.

[0007] The technical solution of the present invention is: the application of SNP molecular markers in the assisted selection of chicken weight traits at 49 days of age. The SNP molecular markers are located at position 12292590bp on chicken chromosome 20, with the reference genome version being GRCg7b. The bases at this position have A / G polymorphism. Individuals with the genotype GG or GA at this position have a higher weight trait at 49 days of age than individuals with the AA genotype.

[0008] The application of a substance for detecting SNP site polymorphism or genotype in assisted breeding of chickens at 49 days of age. The SNP site is located at position 12292590bp on chicken chromosome 20, with a reference genome version of GRCg7b. The bases at this position exhibit A / G polymorphism. The substance is used to detect the genotype of the SNP site. Individuals with the genotype GG or GA at this position have a higher 49-day-old weight trait than individuals with the AA genotype.

[0009] The application of substances for detecting SNP site polymorphism or genotype in the preparation of a breeding kit for weight traits in chickens at 49 days of age. The SNP site is located at position 12292590bp on chicken chromosome 20, with the reference genome version being GRCg7b. The bases at this position exhibit A / G polymorphism. Individuals with the genotype GG or GA at this position have a higher weight trait at 49 days of age than individuals with the AA genotype.

[0010] Compared with the prior art, the present invention has the following beneficial effects:

[0011] This invention provides a functional SNP locus associated with the weight trait of chickens at 49 days of age. This locus is located at Chr20:12292590 in chicken genome version GRCg7b, with a reference allele of A and a mutant allele of G. This SNP significantly affects the mRNA expression level of the GCNT7 gene: the G allele significantly upregulates GCNT7 expression. The allele substitution effect of the mutant allele G relative to the reference allele A is 7.27441g. A molecular marker system significantly correlated with GCNT7 expression levels has been constructed and can be used for early prediction and selection of weight traits in chickens at 49 days of age, providing a practical technical approach for broiler breeding practices. Attached Figure Description

[0012] Figure 1 Co-location of GCNT1 eQTL with GWAS of chickens at 49 days of age.

[0013] Figure 2 Comparison of body weight at 49 days of age for three genotypes at the SNP locus. Detailed Implementation

[0014] Unless otherwise specified, the experimental methods used in the following embodiments are conventional methods. Unless otherwise specified, the experimental materials used in the following embodiments were all purchased from commercial channels.

[0015] Example 1: Mining of SNP Molecular Markers

[0016] Low-depth whole-genome resequencing and body weight phenotypic data collection were performed on a broiler chicken population (12,952 individuals). Genome-wide association analysis (GWAS) was then conducted, and a mutation signal significantly associated with body weight at 49 days of age was detected at the Chr20:12292590 locus (reference genome version GRCg7b), named 20_12292590_A_G. The reference allele is A, and the mutant allele is G, with corresponding genotypes including A / A, A / G, and G / G. In the studied broiler chicken population, the frequency of the mutant allele at this locus was 0.7070. The allele substitution effect of the mutant allele G relative to the reference allele A was 7.27441g (Table 1). Figure 2 ).

[0017] Table 1. Basic information on genetic marker loci

[0018] mutation location Reference / Mutant Alleles Mutant gene frequency Mutation effect Chr20:12292590 A / G 0.7070 7.27441g

[0019] Further eQTL analysis showed that this SNP significantly affected the mRNA expression level of the GCNT7 gene: the G allele significantly upregulated GCNT7 expression. Colocalization analysis revealed that this site was highly colocalized with a quantitative trait locus (eQTL) for GCNT7 gene expression. Figure 1 The posterior probability (PPH4) was as high as 0.973615, which is significantly higher than the threshold (generally 0.8) that is usually considered to have evidence of colocalization. This indicates that this site is likely to affect the weight performance of chickens at 49 days of age by regulating the expression level of the GCNT7 gene.

[0020] Example 2: Detection of SNP molecular markers

[0021] Sample collection: Collect blood or other usable tissues from the sample chicken population, ensuring that the samples are uncontaminated, and label each sample with a number.

[0022] DNA extraction: Genomic DNA was extracted from the collected samples using commercial DNA extraction kits (such as Tiangen, QIAGEN, etc.) to ensure that the DNA quality met the requirements for PCR amplification.

[0023] Primer design: Design specific primers corresponding to the target SNP site. Online tools (such as Primer3, Primer-BLAST, etc.) are usually used to design primers to ensure that the primers can effectively amplify the target region.

[0024] PCR amplification: PCR amplification is performed using well-designed primers to ensure that the SNP sites of each sample are amplified under appropriate temperature and time conditions.

[0025] PCR product purification: After the PCR reaction is completed, primers, dNTPs and other impurities in the reaction system are removed using a DNA purification kit to obtain purified PCR products.

[0026] Genotyping: Using appropriate detection methods, such as restriction fragment length polymorphism (RFLP), high-resolution melting curve analysis (HRM), Sanger sequencing, etc., genotyping of PCR products is performed to determine the genotype of each sample at the target SNP locus.

[0027] Example 3: Application of SNP molecular markers

[0028] This molecular marker was used in chicken breeding populations for assisted selection to improve the body weight of chickens at 49 days of age.

[0029] (1) The genotype of the SNP locus in the chicken samples was detected. Individuals with the genotype GG or GA at this location had a higher 49-day weight than those with the AA genotype.

[0030] (2) The substance used to detect the genotype at this site can be prepared into a kit for the selection of early weight in chickens.

Claims

1. Application of SNP molecular markers in assisted breeding of chicken weight traits at 49 days of age. The SNP molecular marker is located at position 12292590bp on chicken chromosome 20, with the reference genome version being GRCg7b. The bases at this position exhibit A / G polymorphism. Individuals with the genotype GG or GA at this position have a higher weight trait at 49 days of age than individuals with the AA genotype.

2. Application of a substance for detecting SNP site polymorphism or genotype in assisted breeding of chickens at 49 days of age. The SNP site is located at 12292590 bp on chicken chromosome 20, with a reference genome version of GRCg7b. The bases at this site exhibit A / G polymorphism. The substance is used to detect the genotype of the SNP site. Individuals with the genotype GG or GA at this site have a higher 49-day-old weight trait than individuals with the AA genotype.

3. Application of substances for detecting SNP site polymorphism or genotype in the preparation of a chicken 49-day-old weight trait-assisted breeding kit. The SNP site is located at position 12292590bp on chicken chromosome 20, with the reference genome version being GRCg7b. The bases at this position exhibit A / G polymorphism. Individuals with the genotype GG or GA at this position have a higher 49-day-old weight trait than individuals with the AA genotype.

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