SNP site related to feed conversion efficiency of Qingyuan partridge chickens and application of SNP site

Abstract

The invention relates to the technical field of animal breeding, in particular to an SNP site related to the feed conversion efficiency of Qingyuan partridge chickens and application of the SNP site. The feed efficiency characters of the Qingyuan partridge chickens are screened through whole genome association analysis, the SNP molecular marker remarkably related to the characters is obtained, the SNP molecular marker comprises at least one of 23 SNP sites, and the SNP molecular marker can be applied to molecular marker assisted breeding of the Qingyuan partridge chickens. According to the breeding method disclosed by the invention, early individual breeding is carried out on the genome level, dependence on phenotypic information is avoided, the selection efficiency is remarkably improved, the breeding process is accelerated, meanwhile, the feeding cost is reduced, and the breeding method has a good application prospect.

Description

Technical Field

[0001] The present invention relates to the technical field of animal breeding, and particularly relates to SNP loci related to the feed conversion efficiency of Qingyuan partridge chickens and their applications. Background Art

[0002] The breeding of traditional poultry mainly relies on artificial selection of phenotypes based on experience. Artificial breeding is time-consuming and does not delve deep into genomic information for long-term and high-precision selection. With the continuous development of high-throughput sequencing technology and genome-wide association study methods, genome-wide association analysis (GWAS) can be used as a new method for efficiently mining genetic variations related to feed efficiency and discovering related candidate genes, providing a theoretical basis for formulating molecular breeding plans for poultry feed efficiency, and combining locus detection technology to achieve the goal of improving target traits through genomic selection. After retrieval, there is no research on using GWAS to study genetic variations related to feed efficiency and discover related candidate genes in Qingyuan partridge chickens. Summary of the Invention

[0003] The purpose of the present invention is to overcome the shortcomings of the prior art and provide SNP loci related to the feed conversion efficiency of Qingyuan partridge chickens and their applications.

[0004] The purpose of the present invention is achieved through the following technical solutions: SNP loci related to the feed conversion efficiency of Qingyuan partridge chickens, including at least one of the 23 SNP loci:

[0005] The SNP locus chr9_18678989 is located on chromosome 9, its physical position is 18678989, and the alleles are T or A;

[0006] The SNP locus chr9_18679189 is located on chromosome 9, its physical position is 18679189, and the alleles are G or A;

[0007] The SNP locus chr9_18679446 is located on chromosome 9, its physical position is 18679446, and the alleles are G or C;

[0008] The SNP locus chr1_2115833 is located on chromosome 1, its physical position is 2115833, and the alleles are A or C;

[0009] The SNP locus chr1_2123033 is located on chromosome 1, its physical position is 2123033, and the alleles are C or G;

[0010] The SNP locus chr2_97064987 is located on chromosome 2, its physical position is 97064987, and the alleles are G or A;

[0011] The SNP locus chr2_97228041 is located on chromosome 2, with a physical position of 97228041, and the alleles are T or C;

[0012] The SNP locus chr2_97229574 is located on chromosome 2, with a physical position of 97229574, and the alleles are C or T;

[0013] The SNP locus chr2_97407483 is located on chromosome 2, with a physical position of 97407483, and the alleles are C or T;

[0014] The SNP locus chr15_1605736 is located on chromosome 15, with a physical position of 1605736, and the alleles are T or C;

[0015] The SNP locus chr2_97224498 is located on chromosome 2, with a physical position of 97224498, and the alleles are G or T; The SNP locus chr4_78686225 is located on chromosome 4, with a physical position of 78686225, and the alleles are C or T; The SNP locus chr4_83685073 is located on chromosome 4, with a physical position of 83685073, and the alleles are A or G; The SNP locus chr4_84775274 is located on chromosome 4, with a physical position of 84775274, and the alleles are T or C; The SNP locus chr8_21652832 is located on chromosome 8, with a physical position of 21652832, and the alleles are C or T; The SNP locus chr8_21652833 is located on chromosome 8, with a physical position of 21652833, and the alleles are A or G; The SNP locus chr2_136728505 is located on chromosome 2, with a physical position of 136728505, and the alleles are G or T; The SNP locus chr3_38080711 is located on chromosome 3, with a physical position of 38080711, and the alleles are T or C; The SNP locus chr3_38108306 is located on chromosome 3, with a physical position of 38108306, and the alleles are G or T; The SNP locus chr3_38108375 is located on chromosome 3, with a physical position of 38108375, and the alleles are T or A; The SNP locus chr3_38145227 is located on chromosome 3, with a physical position of 38145227, and the alleles are A or G; The SNP locus chr3_38145228 is located on chromosome 3, with a physical position of 38145228, and the alleles are A or G; The SNP locus chr3_38145908 is located on chromosome 3, with a physical position of 38145908, and the alleles are A or G.

[0016] A primer pair for detecting the above SNP loci related to the feed conversion efficiency of Qingyuan partridge chickens.

[0017] As a preferred technical solution,

[0018] The nucleotide sequences of the primer pairs for chr9_18678989 are shown in SEQ ID NO.1 and SEQ ID NO.2;

[0019] The nucleotide sequences of the primer pairs for chr9_18679189 are shown in SEQ ID NO.3 and SEQ ID NO.4;

[0020] The nucleotide sequences of the primer pairs for chr9_18679446 are shown in SEQ ID NO.5 and SEQ ID NO.6;

[0021] The nucleotide sequences of the primer pairs for chr1_2115833 are shown in SEQ ID NO.7 and SEQ ID NO.8;

[0022] The nucleotide sequences of the primer pairs for chr1_2123033 are shown in SEQ ID NO.9 and SEQ ID NO.10;

[0023] The nucleotide sequences of the primer pairs for chr2_97064987 are shown in SEQ ID NO.11 and SEQ ID NO.12;

[0024] The nucleotide sequences of the primer pairs for chr2_97228041 are shown in SEQ ID NO.13 and SEQ ID NO.14;

[0025] The nucleotide sequences of the primer pairs for chr2_97229574 are shown in SEQ ID NO.15 and SEQ ID NO.16;

[0026] The nucleotide sequences of the primer pairs for chr2_97407483 are shown in SEQ ID NO.17 and SEQ ID NO.18;

[0027] The nucleotide sequences of the primer pairs for chr15_1605736 are shown in SEQ ID NO.19 and SEQ ID NO.20;

[0028] The nucleotide sequences of the primer pairs for chr2_97224498 are shown in SEQ ID NO.21 and SEQ ID NO.22;

[0029] The nucleotide sequences of the primer pairs for chr4_78686225 are shown in SEQ ID NO.23 and SEQ ID NO.24;

[0030] The nucleotide sequences of the primer pairs for chr4_83685073 are shown in SEQ ID NO.25 and SEQ ID NO.26;

[0031] The nucleotide sequences of the primer pairs for chr4_84775274 are shown in SEQ ID NO.27 and SEQ ID NO.28;

[0032] The nucleotide sequences of the primer pairs for chr8_21652832 are shown in SEQ ID NO.29 and SEQ ID NO.30;

[0033] The nucleotide sequences of the primer pairs for chr8_21652833 are shown in SEQ ID NO.31 and SEQ ID NO.32;

[0034] The nucleotide sequences of the primer pairs for chr2_136728505 are shown in SEQ ID NO.33 and SEQ ID NO.34;

[0035] The nucleotide sequences of the primer pairs for chr3_38080711 are shown in SEQ ID NO.35 and SEQ ID NO.36;

[0036] The nucleotide sequences of the primer pairs for chr3_38108306 are shown in SEQ ID NO.37 and SEQ ID NO.38;

[0037] The nucleotide sequences of the primer pairs for chr3_38108375 are shown in SEQ ID NO.39 and SEQ ID NO.40;

[0038] The nucleotide sequences of the primer pairs for chr3_38145227 are shown in SEQ ID NO.41 and SEQ ID NO.42;

[0039] The nucleotide sequences of the primer pairs for chr3_38145228 are shown in SEQ ID NO.43 and SEQ ID NO.44;

[0040] The nucleotide sequences of the primer pairs for chr3_38145908 are shown in SEQ ID NO.45 and SEQ ID NO.46.

[0041] The application of the above SNP sites or the above primer pairs in the breeding of Qingyuan partridge chickens.

[0042] As a preferred technical solution, it includes the following steps:

[0043] S1. Extract the genomic DNA of the Qingyuan partridge chicken to be tested;

[0044] S2. Using the genomic DNA in step S1 as a template, perform amplification with the above primer pair;

[0045] S3. Perform gene typing on the tested Qingyuan partridge chickens to identify the genotypes of the tested Qingyuan partridge chickens, and select Qingyuan partridge chickens with genotypes having a low gene frequency at positive effect loci or / and a high gene frequency at negative effect loci.

[0046] As a preferred technical solution, the effector genes with a low gene frequency at positive effect loci are:

[0047] The effector allele of chr9_18678989 is T, the effector allele of chr9_18679189 is G, the effector allele of chr9_18679446 is G, the effector allele of chr1_2115833 is A, the effector allele of chr1_2123033 is C, the effector allele of chr2_97064987 is G, the effector allele of chr2_97228041 is T, the effector allele of chr2_97229574 is C, the effector allele of chr2_97407483 is C, the effector allele of chr15_1605736 is T, the effector allele of chr2_97224498 is G, the effector allele of chr4_78686225 is C, the effector allele of chr4_83685073 is A, the effector allele of chr4_84775274 is T, the effector allele of chr8_21652832 is C, the effector allele of chr8_21652833 is A, and the effector allele of chr2_136728505 is G.

[0048] As a preferred technical solution, the effector genes with a high gene frequency at negative effect loci are:

[0049] The effector allele of chr3_38080711 is T, the effector allele of chr3_38108306 is G, the effector allele of chr3_38108375 is T, the effector allele of chr3_38145227 is A, the effector allele of chr3_38145228 is A, and the effector allele of chr3_38145908 is A.

[0050] As a preferred technical solution, breed Qingyuan partridge chicken varieties with high feed efficiency.

[0051] The present invention has the following advantages: The present invention uses genome-wide association analysis to screen the feed efficiency traits of Qingyuan partridge chickens, and obtains SNP molecular markers significantly related to the traits, including at least one of 23 SNP loci, which can be applied to the molecular marker-assisted breeding of Qingyuan partridge chickens. By the breeding method disclosed in the present invention, early individual selection is carried out at the genome level, avoiding the dependence on phenotypic information, significantly improving the selection efficiency, accelerating the breeding process, reducing the feeding cost at the same time, and having good application prospects. BRIEF DESCRIPTION OF THE DRAWINGS

[0052] Figure 1 It is the Manhattan plot of genome-wide effect SNPs for RFI at 12-14 weeks of age, FCR at 12-14 weeks of age, FCR at 14-17 weeks of age, and FCR at 12-17 weeks of age of Qingyuan partridge chickens in Example 1; wherein, the abscissa represents the chromosome number; the ordinate represents the -logP value. DETAILED DESCRIPTION OF THE EMBODIMENTS

[0053] The present invention will be further described below in conjunction with the drawings and embodiments, and the protection scope of the present invention is not limited to the following; the animals, instruments, reagents, and kits used in the following embodiments can all be obtained by purchasing commercially.

[0054] Example 1:

[0055] 1. Collection of experimental population and phenotypic data:

[0056] Select 633 healthy Qingyuan partridge cocks and raise them individually in cages at the breeding base according to the "Broiler Management Standard" and "Poultry Production Technology Department Standard" of the Production Technology Department. Start the experiment at 12 weeks of age after a two-week environmental adaptation period, and end the experiment at 17 weeks of age. Stop feeding for 12 hours before weighing, and regularly record the body weight and feed intake of each individual at the 12th week, 14th week, and 17th week. In the later stage, calculate the average daily feed intake values (average daily feed intake from 12 weeks of age to 14 weeks of age, average daily feed intake from 14 weeks of age to 17 weeks of age, average daily feed intake from 12 weeks of age to 17 weeks of age), average daily weight gain (average daily weight gain from 12 weeks of age to 14 weeks of age, average daily weight gain from 14 weeks of age to 17 weeks of age, average daily weight gain from 12 weeks of age to 17 weeks of age) and mid-term metabolic body weight (mid-term metabolic body weight from 12 weeks of age to 14 weeks of age, mid-term metabolic body weight from 14 weeks of age to 17 weeks of age, mid-term metabolic body weight from 12 weeks of age to 17 weeks of age) at each stage. The calculation method of mid-term metabolic body weight is the 0.75th power of body weight. According to the above multiple data, calculate the FCR, predicted feed intake, and RFI at each stage.

[0057] The calculation method of FCR is the average daily feed intake in the corresponding period / the average daily weight gain in the corresponding period.

[0058] The calculation method of predicted feed intake is b0 +b 1 ×Mid - metabolic body weight during the corresponding period + b 2 ×Average daily gain, b 0 is the intercept of the linear regression equation, b 1 is the partial regression coefficient of the mid - metabolic body weight during the corresponding period, b 2 is the partial regression coefficient of average daily gain. The calculation method of RFI is the average daily feed intake during the corresponding period - the predicted feed intake during the corresponding period.

[0059] 2. Phenotypic data sorting and analysis:

[0060] All phenotypic data collected in step 1 were statistically analyzed, including minimum value, maximum value, average value, standard deviation, coefficient of variation (CV), and the results are shown in Table 1;

[0061] Table 1: Statistical analysis of phenotypic data of feed efficiency of Qingyuan partridge chickens

[0062]

[0063] 3. DNA extraction and sequencing:

[0064] Blood samples of the experimental chicken flock were collected at 17 weeks of age and genomic DNA was extracted, then sent to BGI Shenzhen Co., Ltd. for whole - genome re - sequencing. The sequencing platform was Illumina PE150, and the depth of re - sequencing was above 10×. To ensure data quality, preliminary quality control was performed on the FASTQ files, and the paired - end sequencing files were merged using fastp v0.23.4.

[0065] 4. Genome data alignment and variant detection:

[0066] The genomic data obtained by sequencing were aligned, analyzed, sorted, de - duplicated, and format - converted using bioinformatics analysis software BWA v0.7.17 and SAMtools v1.18; the reference genome for comparison was the seventh - edition reference genome of chicken (bGalGal1.mat.broiler.GRCg7b). Subsequently, variant detection was performed using GATK v4.4 and the population genotype VCF file was obtained by merging. Finally, genotype imputation was performed using beagle v5.4 to solve the problem of missing genotypes.

[0067] 5. SNP quality control and filtering:

[0068] The population VCF file was converted to binary format using Plink v1.90b5.3, and filtering parameters were set 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. After screening, a total of 11,442,036 SNPs from 663 chickens were retained for subsequent genome-wide association analysis.

[0069] 6. Genome-wide association analysis:

[0070] GEMMA v0.98.1 was used to establish the kinship matrix of the population for genome-wide association analysis using the mixed linear model in conjunction with phenotypic traits. The model is as follows:

[0071] Y = Xβ + Zkγk + ξ + e

[0072] Y is the phenotypic vector, Xβ is the population structure effect, Zkγk is the marker effect to be tested, ξ ∼ N(0, Kφ2) is the polygenic effect, and e ∼ N(0, Iσ2) is the residual effect. K in the polygenic effect is the kinship matrix inferred from the markers.

[0073] The results are as Figure 1 shown, which is the Manhattan plot obtained from the genome-wide association analysis of feed efficiency-related traits. From Figure 1 it can be seen that: a total of 3 significant molecular marker loci were identified in the FCR at 12 - 14 weeks of age; 7 significant molecular marker loci were identified in the FCR at 14 - 17 weeks of age; 6 significant molecular marker loci were identified in the FCR at 12 - 17 weeks of age; in addition, 7 significant molecular marker loci were identified in the RFI at 12 - 14 weeks of age.

[0074] 7. Screening and extraction of SNP molecular marker loci related to feed conversion traits:

[0075] The Bonferroni method was used to determine the genome-wide significant threshold line as 4.26×10 -9 and the recommended threshold line as 8.53×10 -8 . Finally, 23 SNP molecular marker loci were obtained, and the information of these loci is shown in Table 2.

[0076] Table 2: Information of 23 molecular marker loci

[0077]

[0078]

[0079]

[0080]

[0081]

[0082] Note: In the table, M is A or C, R is A or G, W is A or T / U, S is C or G, Y is C or T / U, K is G or T / U, D is A or G or T / U; not C.

[0083] Example 2: Breeding of Qingyuan Partridge Chickens

[0084] S1. Extract the genomic DNA of the Qingyuan partridge chickens to be tested; specifically the same as step 3 in Example 1;

[0085] S2. Using the genomic DNA in step S1 as a template, perform amplification with the primer pairs described in Table 3. The total volume of the PCR reaction system is 25 μL, including 1 - 2 μL (10 - 100 ng / μL) of genomic DNA template, 2.5 μL of 10×PCR buffer, 2 μL of dNTP mixture (2.5 mM each), 1 μL each of upstream primer and downstream primer (10 μM), 0.25 μL of Taq DNA polymerase (5 U / μL), and make up to 25 μL with sterile deionized water.

[0086] Design of PCR amplification primers for each molecular marker locus:

[0087] Download the DNA template sequence information from the NCBI website, and use Primer Premier 5 to design PCR amplification primers. The primer information is shown in Table 3.

[0088] Table 3: Primer information table for 23 molecular markers

[0089]

[0090]

[0091] S3. Perform genotyping on the Qingyuan partridge chickens to be tested, thereby identifying the genotypes of the Qingyuan partridge chickens to be tested, and select Qingyuan partridge chickens with low gene frequency of positive - effect loci or / and high gene frequency of negative - effect loci.

[0092] S31. Identification of genotypes at molecular marker loci:

[0093] After PCR amplification, send the obtained products to a biological company for first - generation sequencing, match the sequencing results of each locus to the sequences of the base fragments before and after the SNP molecular markers given in Table 2. The marked regions in the brackets are the mutation site regions, and use this to judge the genotypes of each molecular marker locus.

[0094] S32. Breeding:

[0095] In the production and breeding of Qingyuan partridge chickens, individual selection is carried out on the tested population according to the gene typing results. Qingyuan partridge chickens with genotypes having a low gene frequency at positive-effect loci or / and a high gene frequency at negative-effect loci are selected, that is, the gene frequency at positive-effect loci is gradually reduced. For example, the gene frequency of the effect allele T at the positive-effect locus chr9_18678989 is reduced; the gene frequency at negative-effect loci is increased. For example, the gene frequency of the effect allele T at the negative-effect locus chr3_38080711 is increased. In this way, the values of FCR and RFI are reduced, thereby improving the feed conversion rate of the offspring chicken flock and accelerating the breeding progress. Specifically, the effect genes with a low gene frequency at positive-effect loci are as follows:

[0096] The effect allele of chr9_18678989 is T, the effect allele of chr9_18679189 is G, the effect allele of chr9_18679446 is G, the effect allele of chr1_2115833 is A, the effect allele of chr1_2123033 is C, the effect allele of chr2_97064987 is G, the effect allele of chr2_97228041 is T, the effect allele of chr2_97229574 is C, the effect allele of chr2_97407483 is C, the effect allele of chr15_1605736 is T, the effect allele of chr2_97224498 is G, the effect allele of chr4_78686225 is C, the effect allele of chr4_83685073 is A, the effect allele of chr4_84775274 is T, the effect allele of chr8_21652832 is C, the effect allele of chr8_21652833 is A, the effect allele of chr2_136728505 is G.

[0097] The effect genes with a high gene frequency at negative-effect loci:

[0098] The effect allele of chr3_38080711 is T, the effect allele of chr3_38108306 is G, the effect allele of chr3_38108375 is T, the effect allele of chr3_38145227 is A, the effect allele of chr3_38145228 is A, the effect allele of chr3_38145908 is A.

[0099] As mentioned above, the above is only a preferred specific embodiment of the present invention, but the protection scope of the present invention is not limited thereto. Any person skilled in the art within the technical scope disclosed by the present invention, according to the technical solution of the present invention and its inventive concept, makes equivalent substitutions or changes, and all are covered by the protection scope of the present invention.

Claims

1. The SNP loci associated with Qingyuan Ma chicken feed conversion efficiency are characterized by: Includes at least one of the 23 SNP loci: The SNP locus chr9_18678989 is located on chromosome 9, its physical position is 18678989, and its alleles are T or A; The SNP locus chr9_18679189 is located on chromosome 9, its physical position is 18679189, and its allele is G or A; The SNP site chr9_18679446 is located on chromosome 9, its physical position is 18679446, and its allele is G or C; The SNP site chr1_2115833 is located on chromosome 1, its physical position is 2115833, and its allele is A or C; The SNP site chr1_2123033 is located on chromosome 1, its physical position is 2123033, and its allele is C or G; The SNP locus chr2_97064987 is located on chromosome 2, its physical position is 97064987, and its allele is G or A; The SNP locus chr2_97228041 is located on chromosome 2, its physical position is 97228041, and its allele is T or C; The SNP locus chr2_97229574 is located on chromosome 2, its physical position is 97229574, and its allele is C or T; The SNP locus chr2_97407483 is located on chromosome 2, its physical position is 97407483, and its allele is C or T; The SNP locus chr15_1605736 is located on chromosome 15, its physical position is 1605736, and its allele is T or C; The SNP locus chr2_97224498 is located on chromosome 2, its physical position is 97224498, and its allele is G or T; The SNP locus chr4_78686225 is located on chromosome 4, its physical position is 78686225, and its allele is C or T; The SNP locus chr4_83685073 is located on chromosome 4, its physical position is 83685073, and its allele is A or G; The SNP locus chr4_84775274 is located on chromosome 4, its physical position is 84775274, and its allele is T or C; The SNP locus chr8_21652832 is located on chromosome 8, its physical position is 21652832, and its allele is C or T; The SNP locus chr8_21652833 is located on chromosome 8, its physical position is 21652833, and its allele is A or G; The SNP locus chr2_136728505 is located on chromosome 2, its physical position is 136728505, and its allele is G or T; The SNP locus chr3_38080711 is located on chromosome 3, its physical position is 38080711, and its allele is T or C; The SNP locus chr3_38108306 is located on chromosome 3, its physical position is 38108306, and its allele is G or T; The SNP locus chr3_38108375 is located on chromosome 3, its physical position is 38108375, and its allele is T or A; The SNP locus chr3_38145227 is located on chromosome 3, its physical position is 38145227, and its allele is A or G; The SNP locus chr3_38145228 is located on chromosome 3, its physical position is 38145228, and its allele is A or G; The SNP site chr3_38145908 is located on chromosome 3, its physical position is 38145908, and its allele is A or G.

2. The detection primer pair is characterized in that: Detect the SNP site related to the feed conversion efficiency of Qingyuan Ma chicken as described in claim 1.

3. The detection primer pair according to claim 2, characterized in that: The nucleotide sequences of the primer pair of chr9_18678989 are shown in SEQ ID NO.1 and SEQ ID NO.2; The nucleotide sequences of the primer pair of chr9_18679189 are shown in SEQ ID NO.3 and SEQ ID NO.4; The nucleotide sequences of the primer pair of chr9_18679446 are shown in SEQ ID NO.5 and SEQ ID NO.6; The nucleotide sequences of the primer pair of chr1_2115833 are shown in SEQ ID NO.7 and SEQ ID NO.8; The nucleotide sequences of the primer pair of chr1_2123033 are shown in SEQ ID NO.9 and SEQ ID NO.10; The nucleotide sequences of the primer pair of chr2_97064987 are shown in SEQ ID NO.11 and SEQ ID NO.12; The nucleotide sequences of the primer pair of chr2_97228041 are shown in SEQ ID NO.13 and SEQ ID NO.14; The nucleotide sequences of the primer pair of chr2_97229574 are shown in SEQ ID NO.15 and SEQ ID NO.16; The nucleotide sequences of the primer pair of chr2_97407483 are shown in SEQ ID NO.17 and SEQ ID NO.18; The nucleotide sequences of the primer pair of chr15_1605736 are shown in SEQ ID NO.19 and SEQ ID NO.20; The nucleotide sequences of the primer pair of chr2_97224498 are shown in SEQ ID NO.21 and SEQ ID NO.22; The nucleotide sequences of the primer pair of chr4_78686225 are shown in SEQ ID NO.23 and SEQ ID NO.24; The nucleotide sequences of the primer pair of chr4_83685073 are shown in SEQ ID NO.25 and SEQ ID NO.26; The nucleotide sequences of the primer pair of chr4_84775274 are shown in SEQ ID NO.27 and SEQ ID NO.28; The nucleotide sequences of the primer pair of chr8_21652832 are shown in SEQ ID NO.29 and SEQ ID NO.30; The nucleotide sequences of the primer pair of chr8_21652833 are shown in SEQ ID NO.31 and SEQ ID NO.32; The nucleotide sequences of the primer pair of chr2_136728505 are shown in SEQ ID NO.33 and SEQ ID NO.34; The nucleotide sequences of the primer pair of chr3_38080711 are shown in SEQ ID NO.35 and SEQ ID NO.36; The nucleotide sequences of the primer pair of chr3_38108306 are shown in SEQ ID NO.37 and SEQ ID NO.38; The nucleotide sequences of the primer pair of chr3_38108375 are shown in SEQ ID NO.39 and SEQ ID NO.40; The nucleotide sequences of the primer pair of chr3_38145227 are shown in SEQ ID NO.41 and SEQ ID NO.42; The nucleotide sequences of the primer pair of chr3_38145228 are shown in SEQ ID NO.43 and SEQ ID NO.44; The nucleotide sequences of the primer pair for chr3_38145908 are shown in SEQ ID NO.45 and SEQ ID NO.

46.

4. Use of the SNP site described in claim 1 or the primer pair described in claim 2 or 3 in breeding Qingyuan Ma chicken.

5. The use according to claim 4, characterized in that: It includes the following steps: S1. Extracting genomic DNA of the Qingyuan Ma chicken to be tested; S2. Using the genomic DNA of step S1 as a template, amplifying using the primer pair according to claim 3; S3. Perform genotyping on the Qingyuan Ma chicken to be tested, thereby identifying the genotype of the Qingyuan Ma chicken to be tested, and selecting Qingyuan Ma chicken with a genotype having a low frequency of the gene at the positive effect site and / or a high frequency of the gene at the negative effect site.

6. The use according to claim 5, characterized in that: The effector gene with low gene frequency at the positive effect site is: The chr9_18678989 effect allele is T, the chr9_18679189 effect allele is G, the chr9_18679446 effect allele is G, the chr1_2115833 effect allele is A, the chr1_2123033 effect allele is C, the chr2_97064987 effect allele is G, the chr2_97228041 effect allele is T, the chr2_97229574 effect allele is C, and the chr2_9740748 3 effect allele is C, chr15_1605736 effect allele is T, chr2_97224498 effect allele is G, chr4_78686225 effect allele is C, chr4_83685073 effect allele is A, chr4_84775274 effect allele is T, chr8_21652832 effect allele is C, chr8_21652833 effect allele is A, and chr2_136728505 effect allele is G.

7. The use according to claim 5, characterized in that: Effector genes with high frequency of negative effect loci: The chr3_38080711 effect allele is T, the chr3_38108306 effect allele is G, the chr3_38108375 effect allele is T, the chr3_38145227 effect allele is A, the chr3_38145228 effect allele is A, and the chr3_38145908 effect allele is A.

8. The use according to claim 4, characterized in that: Cultivate the Qingyuan Ma chicken breed with high feed efficiency.

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