SNP (Single Nucleotide Polymorphism) molecular marker for chicken weight selective breeding and application

Abstract

The invention discloses an SNP (Single Nucleotide Polymorphism) molecular marker for chicken weight selective breeding and application, and belongs to the field of molecular biology, the SNP molecular marker is located at 169, 712 and 797 bp positions of a chicken chromosome 1, and is located at the upstream of an HTR2A gene. Whole genome association analysis results show that the SNP site presents A / T polymorphism, and A in high-weight chickens of multiple weeks old is a dominant allele. For the site, genotype statistical analysis is carried out in other high-weight and low-weight chicken populations to further verify that the A / A genotype is a dominant genotype of high-weight chickens, and the proportion of the A / A genotype in the high-weight chickens is obviously higher than that of low-weight chickens. Therefore, the chicken of which the site is the A / A genotype can be preferably selected, and early selection of high-weight chickens is expected to be performed, so that high-yield breeding of the chickens is accelerated.

Description

Technical Field

[0001] This invention belongs to the field of molecular biology, specifically relating to a SNP molecular marker associated with the body weight of chickens at 4, 6, 8, 10, and 12 weeks of age and its application. Background Technology

[0002] Chicken is a major source of animal protein globally, widely popular due to its high protein, low fat, and short growth cycle. In recent years, with the upgrading of dietary structures in my country, chicken production and consumption have continued to grow, making improving broiler yield and growth efficiency a key direction in breeding. Among these traits, the weekly weight of chickens is a core characteristic for measuring their production performance and genetic improvement potential. Selecting individuals with fast growth and high weight can significantly improve the economic benefits of the flock.

[0003] Traditional breeding methods mainly rely on phenotypic selection, which has drawbacks such as long cycle time, high cost, and low accuracy. With the development of genomics and high-throughput sequencing technologies, genome-wide association analysis (GWAS) has become an important tool for elucidating the genetic basis of complex traits. This method can identify single nucleotide polymorphisms (SNPs) that are significantly associated with target traits across the entire genome, providing a scientific basis for marker-assisted selection (MAS).

[0004] SNPs are a rich, widely distributed, and stable type of genetic variation with significant potential applications in animal molecular breeding. Utilizing SNP markers closely related to chicken weight at week 18 can enable early molecular prediction and precise selection, significantly shortening the breeding cycle and improving breeding efficiency. However, the number of functional SNPs currently proven to significantly affect chicken weight traits remains relatively limited.

[0005] Therefore, identifying and validating key SNP molecular markers that are significantly associated with chicken weight at age 1 week not only helps to elucidate the genetic mechanism of weight formation, but also provides new technical support for establishing an efficient molecular-assisted breeding system, laying the foundation for the breeding of high-yield and high-quality broilers. Summary of the Invention

[0006] The technical problem to be solved by this invention is to provide an SNP molecular marker related to the weight trait of chickens at multiple weeks of age and its application.

[0007] The technical solution of the present invention is: the application of SNP molecular markers in the assisted breeding of chicken weight traits. The SNP molecular marker is located at position 169,712,797 bp on chicken chromosome 1. The SNP name is rs317496170, and the reference genome version is GRCg6a. The bases at this position have an A / T state. Individuals with the genotype AA at this position have a higher weight trait than other genotypes.

[0008] The application of substances that detect SNP site polymorphism or genotype in chicken weight-related breeding, wherein the SNP site is located at position 169,712,797 bp on chicken chromosome 1, and the bases at this position have A / T polymorphism. Individuals with the genotype AA at this position have higher weight traits than other genotypes. The reference genome version is GRCg6a.

[0009] Furthermore, the substance is a primer pair, and the nucleotide sequences of the primer pair are shown in SEQ ID No. 2 and SEQ ID No. 3.

[0010] The application of substances for detecting SNP site polymorphism or genotype in the preparation of a chicken weight trait-assisted breeding kit, wherein the SNP site is located at position 169,712,797 bp on chicken chromosome 1, and the bases at this position have A / T polymorphism. Individuals with the genotype AA at this position have higher weight trait than other genotypes. The reference genome version is GRCg6a.

[0011] Furthermore, the substance is a primer pair, and the nucleotide sequences of the primer pair are shown in SEQ ID No. 2 and SEQ ID No. 3.

[0012] Compared with the prior art, the present invention has the following beneficial effects:

[0013] Association analysis of the SNP molecular markers of this invention with the body weight of chickens at 4, 6, 8, 10, and 12 weeks of age revealed that this locus was significantly associated with body weight at all these ages, and the dominant allele for high body weight was A. Therefore, chickens with the A / A genotype at this locus can be preferentially selected, potentially enabling early selection of high-weight chickens and accelerating genetic breeding of chickens. Attached Figure Description

[0014] Figure 1 The association between SNPs on chromosome 1 and body weight of chickens at multiple weeks of age. Detailed Implementation

[0015] Unless otherwise specified, the experimental methods used in the following examples are conventional methods. Unless otherwise specified, the experimental materials used in the following examples were all purchased from commercial sources.

[0016] Example 1: Genome-wide association analysis of body weight phenotype over multiple weeks of age

[0017] Resequencing technology was used to sequence individuals in a hybrid chicken population. Genome-wide association analysis was performed to identify SNPs, and quality control filtering was conducted to select one SNP locus significantly associated with the body weight of chickens at 4, 6, 8, 10, and 12 weeks of age. Figure 1 ).

[0018] The SNP is located at position 169,712,797 bp on chromosome 1 of genomic version GRCg6a (SNP name rs317496170), upstream of the HTR2A gene, and exhibits A / T polymorphism. This locus was detected and passed quality filtering in 1161, 1161, 1160, 1129, and 1072 chickens at 4, 6, 8, 10, and 12 weeks of age, respectively. The effect of this locus on body weight at different ages and the significance P-values ​​are shown in Table 1. The A allele showed a strong positive correlation with body weight, therefore A is dominant in high-weight chickens.

[0019]

[0020] Example 2: Validation of SNP molecular markers in high- and low-weight chicken populations

[0021] (1) Collection of experimental data

[0022] SNP data for 38 high-weight chicken breeds and 111 low-weight chicken breeds were collected from the Galbase database. High-weight breeds included: Guangxi chicken (n=6), Langshan chicken (n=10), Miyi chicken (n=5), Southern Xinjiang fighting chicken (n=8), and Luxi fighting chicken (n=9). Low-weight breeds included: Daweishan miniature chicken (n=8), Jinyang silky-feathered chicken (n=6), and Tibetan chicken (n=97).

[0023] (2) Genotype frequency analysis

[0024] SNP information for the Chr1: 169,712,797 locus in 38 high-weight chickens and 111 low-weight chickens was extracted from the Galbase database, and allele frequencies were calculated (as shown in Table 2).

[0025]

[0026] (3) Results Analysis

[0027] At the SNP locus Chr1:169,712,797, there was a significant difference in allele frequency between high- and low-weight chicken flocks (P = 5.30 × 10⁻⁻⁶). 5 The frequency of allele A was 0.64 in the high-weight flock and 0.37 in the low-weight flock, indicating that A is the dominant allele at this locus in the high-weight flock. Further genotypic analysis showed that the frequency of the A / A genotype was 0.45 in the high-weight flock and 0.21 in the low-weight flock, a significant difference (P = 0.0057). These results indicate that the A / A genotype is closely related to improved body weight.

[0028] Therefore, by prioritizing the selection of individuals carrying the A / A genotype during the breeding process, the weight trait of the flock can be effectively improved, thereby increasing production efficiency.

[0029] Example 3 Detection of SNP molecular markers

[0030] (1) Based on the upstream and downstream sequence information of the SNP molecular marker, primers for amplifying fragments containing the SNP site were designed;

[0031] Forward primer F: GTCAGCCTATCCACTCCA (SEQ ID No. 2)

[0032] Reverse primer R: AAGGACCCTGGAGAGAAG (SEQ ID No. 3)

[0033] (2) Extract genomic DNA from the chicken sample to be tested and perform PCR amplification using the primer pair designed in (1) to obtain an amplification product containing an SNP site with a size of 592 bp. The sequence is shown in SEQ ID No.1, and the SNP site is located at position 247 of the sequence shown in SEQ ID No.1.

[0034] (3) Perform Sanger sequencing on the amplified products to obtain the genotype of the SNP site.

Claims

1. Application of SNP molecular markers in chicken weight trait-assisted breeding: The SNP molecular marker is located at position 169,712,797 bp on chicken chromosome 1, with the reference genome version being GRCg6a. The bases at this position exhibit A / T polymorphism. Individuals with the genotype AA selected at this position have a higher weight trait than other genotypes.

2. Application of substances that detect SNP site polymorphism or genotype in chicken weight trait-assisted breeding, wherein the SNP site is located at position 169,712,797bp on chicken chromosome 1, and the bases at this position have A / T polymorphism. Individuals with the genotype AA at this position have higher weight trait than other genotypes. The reference genome version is GRCg6a.

3. The application according to claim 2, characterized in that, The substance is a primer pair, and the nucleotide sequences of the primer pair are shown in SEQ ID No. 2 and SEQ ID No.

3.

4. Application of substances for detecting SNP site polymorphism or genotype in the preparation of a chicken weight trait-assisted breeding kit, wherein the SNP site is located at position 169,712,797 bp on chicken chromosome 1, and the bases at this position have A / T polymorphism. Individuals with the genotype AA at this position have higher weight trait than other genotypes. The reference genome version is GRCg6a.

5. The application according to claim 4, characterized in that, The substance is a primer pair, and the nucleotide sequences of the primer pair are shown in SEQ ID No. 2 and SEQ ID No. 3.

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