Application and methods of SNP loci related to chicken age at laying age in chicken breeding

Abstract

The application provides an application and method of a SNP site related to a chicken age at first egg trait in chicken breeding, and belongs to the technical field of biological breeding. The application discloses a SNP site related to a chicken age at first egg trait, which is located at the 28th chromosome of a chicken genome GGA6 version at the 2104764th position. According to the genotype of the SNP site, the age at first egg trait of sample chickens is selected and bred, and chickens with an age at first egg trait of restlessness can be obtained. The application can be popularized and applied in the selection and improvement of the age at first egg trait of chickens, has important significance for the broiler breeding industry, and has great potential commercial value.

Description

TECHNICAL FIELD

[0001] The application belongs to the technical field of biological breeding, and particularly relates to application and a method of a SNP site related to a chicken first egg laying age trait in chicken breeding. BACKGROUND

[0002] Molecular markers are important materials for genetic research. Single nucleotide polymorphism markers are widely used in human and animal and plant genetic research due to their large number, wide distribution and easy identification. Single nucleotide polymorphism (SNP) markers are the third generation of genetic markers, which refer to a polymorphism caused by a single base mutation in the genomic DNA sequence. The mutation includes single base transversion, transition, insertion and deletion. SNPs have the advantages of large number, high frequency and low mutation rate, and are widely used in genome analysis, automated biological information detection, genetic research of simple and complex diseases, livestock breeding markers and global ethnic genetics. SNP site assisted selection breeding is a selection of target traits at the molecular level, which can be unaffected by the environment, reduce linkage drag through genetic background selection, and thus accelerate the breeding process and precision.

[0003] The chicken first egg laying age refers to the age of the first egg laying of a hen, which marks the sexual maturity of the hen and is related to egg laying traits such as egg laying period and egg weight. At present, there is still no report on using SNP sites or SNP molecular markers for assisted selection breeding of laying hens. SUMMARY

[0004] In view of the above technical problems of the prior art, the purpose of the present application is to provide an application and a method of a SNP site related to a chicken first egg laying age trait in chicken breeding, which can select laying hens with superior allele genotypes by detecting the SNP site, so as to breed superior lines. The technical scheme of the present application is as follows:

[0005] In a first aspect, the present application provides an application of a SNP site related to a chicken first egg laying age trait in chicken breeding, wherein the SNP site is located at position 2104764 of chromosome 28 of chicken genome GGA6 version; and the first egg laying age trait of sample chickens is selected according to the genotype of the SNP site.

[0006] Further, the sample chicken includes but is not limited to at least one of the following: the ephedra chicken, the deer park chicken, the Tibetan chicken, the silk feather black-bone chicken, the Henan fighting chicken, the Qingyuan ephedra chicken, the Anyi white clay chicken, the big-bone chicken, the Guangxi three-yellow chicken, the Liyang chicken, the Xianju chicken, the tea flower chicken, the Beijing star yellow chicken dwarf foot line, the Qingjia ephedra chicken medium speed line, the border chicken, the Shouguang chicken, the Dongxiang green shell egg chicken, the Wenshang Luohua chicken, the Chongren ephedra chicken, the Wenchang chicken, the Jinhu black phoenix chicken, the Daweishan miniature chicken, the Huixiang chicken, the Xianju chicken, the tea flower chicken, the Gushi chicken, the Wolf Mountain chicken, the pot chicken, the white ear yellow chicken, the Beijing oil chicken, the Xiaoshan chicken, the Langya chicken, the Nandanyao chicken, the Macheng green shell egg chicken, the Rugao yellow chicken and the recessive white feather broiler.

[0007] In a second aspect, the present application provides a breeding method based on the SNP site related to the age of the first egg laying of a chicken, the method comprising:

[0008] Determining the frequency of the C allele genotype of the SNP site of the sample chicken, the SNP site being located at the 2104764th position of the 28th chromosome of the chicken genome GGA6 version; based on the frequency of the C allele genotype of the SNP site, the sample chicken is confirmed as the target chicken if the frequency is within a preset frequency range.

[0009] Further, the preset frequency range is 0.12-0.16.

[0010] Further, the method further comprises:

[0011] Determining the allele substitution effect value of the SNP site of the sample chicken; based on the allele substitution effect value of the SNP site, the sample chicken is confirmed as the target chicken if the allele substitution effect value is within a preset effect value range.

[0012] Further, the preset effect value range is -1.05 to -1.40.

[0013] Further, the method further comprises:

[0014] Extracting a blood sample of the sample chicken; obtaining the genome of the blood sample of the sample chicken by Tn5 transposase; performing Bonferroni correction on the genome by independent marker number; and according to the gene data of the SNP site, marking the SNP site in the corrected genome.

[0015] Further, the age of the first egg laying of the target chicken is 1-1.5 days earlier than the standard age of the first egg laying.

[0016] The curing agent provided by the present application has the following advantages and beneficial effects:

[0017] The sample chicken with the advantageous allele genotype is selected by the SNP site related to the age at first egg laying of the chicken, and the target chicken of the advantageous line is mainly characterized in that the age at first egg laying is earlier, so that the production cost can be saved and the genetic progress can be accelerated, and the target chicken is better applied to the breeding of the chicken, and has wide economic application and scientific research value. BRIEF DESCRIPTION OF DRAWINGS

[0018] Figure 1 is a relationship diagram of blood samples of female Ephedra vulgaris chickens and the age at first egg laying in the embodiment of the present application;

[0019] Figure 2 is a Manhattan plot of the SNP site related to the age at first egg laying in the embodiment of the present application. DETAILED DESCRIPTION

[0020] In order to facilitate the understanding of the present application, the present application will be described more fully below with reference to the related embodiments. The preferred embodiments of the present application are given in the embodiments. However, the present application can be realized in many different forms and is not limited to the embodiments described herein. On the contrary, the purpose of providing these embodiments is to make the disclosure of the present application more thorough and comprehensive.

[0021] Unless otherwise defined, all technical and scientific terms used herein have the same meaning as commonly understood by one of ordinary skill in the art to which the present application belongs. The terms used in the specification of the present application are only for the purpose of describing the specific embodiments and are not intended to limit the present application. The term "and / or" used herein includes any and all combinations of one or more related listed items.

[0022] In the description of the present application, it should be noted that, unless otherwise specified, the specific conditions in the embodiments are carried out according to the conventional conditions or the conditions recommended by the manufacturer. The reagents or instruments used are not specified by the manufacturer, and are all conventional products that can be purchased on the market.

[0023] The present application will be further described in detail below with reference to specific embodiments, which are an explanation of the present application rather than a limitation.

[0024] Embodiment 1

[0025] Embodiment 1 takes Ephedra vulgaris chickens as the research object, collects blood samples of 4527 female Ephedra vulgaris chickens and records the age at first egg laying phenotype, as shown in Table 1. Figure 1

[0026] (I) Chicken whole genome SNP typing and association analysis based on low-depth sequencing technology includes the following steps:

[0027] ​(1) A gene library of female ephedra chickens was established using Tn5 transposase, and whole-genome resequencing was performed. All genome samples were sequenced on a designated life science platform. The number of sequenced samples was 4527, and the sequencing depth was 0.94×. Sequencing depth refers to the ratio of the total number of bases (bp) obtained by sequencing to the genome size (Genome). The designated life science platform was the Basevar SNP detection platform.

[0028] (2) Genotyping and filling of all genome resequencing results in step (1) are performed to obtain the SNP site gene data of each female Ephedra chicken.

[0029] (3) Perform genome-wide association analysis on the laying age of all female ephedra chickens and the SNP locus gene data obtained in step (2).

[0030] (4) Using the number of independent markers to perform Bonferroni correction and detect significant loci at the genome level, a QTL region with a 5% genome-wide significance level at the Bonferroni correction for the age of chicken laying was obtained. The most significant Chr28:2104764 locus in the QTL region is a SNP locus associated with the age of laying trait. The Manhattan plot of the genome-wide association study (GWAS) analysis results of SNP loci associated with the age of laying trait is shown in Figure 2. Figure 2 The number of independent markers is calculated using the PLINK indep-pairwise command.

[0031] (2) Using Ephedra chicken as a sample chicken to be screened, a breeding method using a SNP site (Chr28:2104764) in the chicken laying age trait includes the following steps:

[0032] (1) Collect blood samples from 8,000 sample chickens.

[0033] (2) The genomes of all chicken blood samples were obtained using Tn5 transposase, and the genomes were Bonferroni corrected using the number of independent markers.

[0034] (3) Based on the genetic data of the SNP site (Chr28:2104764), the SNP sites related to the chicken laying age trait in the corrected genome were marked.

[0035] (4) With the SNP site (Chr28:2104764) as the center, the frequencies of different genotypes and the effect sizes of the alleles were statistically calculated. For example, the frequencies of different genotypes and the effect sizes of the alleles in a sample chicken were statistically calculated. The results are shown in Table 1.

[0036] Statistical calculation process is to carry out whole genome association analysis on unit point by using GCTA software mixed linear model (MLM) method. In the constructed additive genetic model, gender and batch are taken as fixed effect covariance, and mixed linear model is used to carry out unit point effect analysis and significance test on each site combined with egg laying age. The additive genetic model is constructed as follows: y=Xb+Za+e, wherein y represents the observation value of each phenotype; b represents the fixed effect vector, including batch, gender and other factors; a represents the additive genetic effect vector of individual; e represents the random residual vector; X and Z represent the association matrix of b and a respectively. b a b a

[0037] Table 1

[0038]

[0039] (5) Comparing the C allele frequency with the preset frequency range, and comparing the effect value of the allele with the preset effect value range.

[0040] (6) The results show that the allele C is a minor allele, the frequency is a low frequency of 0.14, the allele replacement effect is-1.21, and the chicken is selected as the target chicken for subsequent breeding according to the breeding conditions. Further, through the chicken egg laying age statistics, the target chicken egg laying age of the C allele can be about 1.21 days earlier than the standard chicken egg laying age.

[0041] The method of the application can also be applied to other sample chickens, including but not limited to at least one of the following: Luyuan chicken, Tibetan chicken, silk feather black-bone chicken, Henan Dou chicken, Qingyuan chicken, Anyi Vagray chicken, large-bone chicken, Guangxi Sanhuang chicken, Liyang chicken, Xianju chicken, tea flower chicken, Beijing Xinghuang chicken dwarf foot line, Qingjiaomachicken medium speed line, Bian chicken, Shouguang chicken, Dongxiang green shell egg chicken, Wenshang Luohua chicken, Chongren chicken, Wenchang chicken, Jinhu Wufeng chicken, Daweishan miniature chicken, Huixiang chicken, Xianju chicken, tea flower chicken, Gushi chicken, Langshan chicken, Pouchi chicken, Bai'er yellow chicken, Beijing oil chicken, Xiaoshan chicken, Langya chicken, Nandanyao chicken, Macheng green shell egg chicken, Rugao yellow chicken and recessive white feather broiler, and the specific application method is the same as that of Machong chicken, and the preset effect value range is-1.05 to-1.40.

[0042] ​​​​The above embodiments only express several implementation manners of the present application, and the description is more specific and detailed, but it should not be understood as a limitation on the patent scope of the present application. It should be noted that for ordinary skilled persons in the art, without departing from the concept of the present application, several modifications and improvements can be made, which are all within the protection scope of the present application. Therefore, the protection scope of the patent of the present application should be subject to the appended claims.

Claims

1. An application of a SNP locus related to the age-to-lay trait of chickens in chicken breeding, characterized by: The SNP site is located at position 2104764 of chromosome 28 of the chicken genome GGA6 version; Selecting and breeding the sample chickens for the age at which they lay eggs according to the genotype of the SNP site; The target chickens whose genotype of the SNP site is the C allele can start laying eggs 1.21 days earlier than the standard chickens.

2. The use of the SNP loci associated with the chicken laying age trait in chicken breeding according to claim 1, characterized in that: The sample chicken is Ephedra chicken.

3. A breeding method based on SNP loci related to the age-of-laying trait of chickens, characterized in that: include: Determine the frequency of the C allele of the SNP site in the sample chicken, wherein the SNP site is located at position 2104764 of chromosome 28 of the chicken genome GGA6 version; Based on the fact that the frequency of the C allele type of the SNP site is consistent with the preset frequency range, the sample chicken is confirmed as the target chicken; the preset frequency range is 0.12~0.

16.

4. The method according to claim 3, characterized in that The method further comprises: Determining the allele substitution effect value of the SNP site of the sample chicken; Based on the fact that the allele substitution effect value of the SNP site is consistent with the preset effect value range, the sample chicken is confirmed as the target chicken; the preset effect value range is -1.05~-1.

40.

5. The method according to claim 3 or 4, characterized in that The method further comprises: extracting a blood sample from the sample chicken; Obtaining the genome of the chicken blood sample by Tn5 transposase; The genome was subjected to Bonferroni correction using the number of independent markers; The SNP site in the genome after correction is marked according to the genetic data of the SNP site.

6. The method according to claim 3 or 4, characterized in that: The target chicken's first laying age is 1 to 1.5 days earlier than the standard laying age.

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