SNP molecular markers related to body size and weight traits in goats and their application

Abstract

The present invention relates to the field of molecular marker technology, and in particular to SNP molecular markers related to body size and weight traits of goats and applications thereof. The SNP molecular markers developed by the present invention have significant correlation with body size and weight traits of goats, can be used for molecular marker-assisted breeding of goats, are not limited by the age and gender of goats, can be used for breeding large-sized goat varieties, can accurately screen goats at birth, thereby significantly accelerating the breeding speed of large-sized goat varieties.

Description

Technical Field

[0001] The invention relates to the technical field of molecular markers, in particular to SNP molecular markers related to body size and weight traits of goats and applications thereof. Background Art

[0002] The Janus kinase (JAK)-signal transducer and activator of transcription (STAT) pathway is an evolutionarily conserved signaling pathway that mediates the effects of cytokines, hormones, and growth factors. These extracellular factors increase or inhibit the expression of certain genes through the JAK / STAT signaling pathway to control cell growth and differentiation. Activation of the JAK / STAT pathway can lead to diseases such as cancer and many immune-mediated inflammatory diseases. The JAK family includes JAK1, JAK2, JAK3, and tyrosine kinase 2 (TYK2). Among them, JAK3 is mainly expressed in hematopoietic cells, and the other three members have a wider tissue distribution in the organism. Cytokines play a major role in bone formation and remodeling, among which proinflammatory cytokines such as interleukin-6 (IL-6) and interleukin-1 (IL-1) are effective stimulants that affect bone resorption. Related studies have shown that mice with JAK1 functional deficiency die in the perinatal period and have significantly reduced body weight and size, which is interpreted as JAK1 may play a role in bone development. Furthermore, there is evidence that systemic activation of JAK1 in all JAK1-expressing cells results in clinical phenotypes similar to those of systemic lupus erythematosus (SLE) (eg, arthralgia, renal impairment) and increases bone resorption leading to osteopenia in the skeleton.

[0003] Goats are an important livestock resource in the world, and their body shape has an important impact on meat production, reproductive capacity, and disease resistance. China has rich goat breed resources and a long history of domestication. After a long period of natural and artificial breeding, it has gradually formed the breeds with a wide range of uses today. Body shape traits include weight, height, body length, chest circumference, and tube circumference. They are complex traits controlled by multiple genes and are one of the most important traits in the domestication and breeding process of livestock, including goats. Goat body shape is closely related to meat production performance and environmental adaptability, which is of great significance to the development of animal husbandry, and different goat breeds show amazing body shape variation.

[0004] With the improvement of people's living standards and the intensive development of breeding enterprises, the market demand for large-sized goat breeds is growing, which brings new challenges to the breeding industry. In order to meet consumers' demand for high-quality meat products, it is necessary to breed larger and stronger goats. The body development and muscle growth of goats is a complex process in which genes, feeding management and environmental factors work together. Effectively promoting body development and muscle growth can not only improve meat quality and meet market demand, but also improve breeding efficiency and bring greater economic benefits. In recent years, the development of molecular genetic technology has enabled DNA molecular marker technology to play an important role in the study of goat genetic diversity. In order to better develop and utilize the economic characteristics of excellent breeds, protect and rationally utilize breed resources, it is necessary to develop goat-specific molecular markers. The development of molecular markers related to goat body traits can be applied to the selection and breeding of large-sized goats and provide a theoretical basis for molecular breeding of large-sized goats. Summary of the invention

[0005] The invention provides SNP molecular markers related to goat body size and weight traits and applications thereof.

[0006] Specifically, the present invention provides the technical solution described below.

[0007] In a first aspect, the present invention provides a SNP molecular marker associated with body size and weight traits of goats, wherein the SNP molecular marker comprises a nucleotide sequence in which the polymorphism at position 183 of the sequence shown in SEQ ID NO: 1 is T / C.

[0008] In the sequence shown in SEQ ID NO:1, Y is T or C.

[0009] The polymorphic site of the SNP molecular marker described above is located at position 40379673 of chromosome 3 of the ARS1 version of the goat reference genome, and the polymorphism is T / C, that is, the rs663771497 molecular marker. The polymorphic site is located in the 7th exon of the JAK1 gene.

[0010] The SNP molecular marker of the present invention has a significant correlation with the body size and weight traits of goats, and can be used for early prediction of the body size and weight traits of goats and molecular marker-assisted breeding.

[0011] To facilitate detection, the present invention has developed primers for amplifying the SNP molecular marker based on the polymorphic site at position 40379673 of chromosome 3 of the ARS1 version goat reference genome and its upstream and downstream sequences. In combination with the upstream and downstream sequences of the polymorphic site, the present invention obtains the sequence shown in SEQ ID NO:1. It can be understood by those skilled in the art that based on the above-mentioned polymorphic site and its upstream and downstream sequences, sequence fragments of different lengths can be developed as SNP molecular markers for amplification and detection of the site. Therefore, the sequence shown in SEQ ID NO:1 does not constitute a limitation to the SNP molecular marker of the present invention, as long as the sequence fragments containing the polymorphic site at position 40379673 of chromosome 3 of the ARS1 version goat reference genome are within the protection scope of the SNP molecular marker of the present invention.

[0012] In some embodiments of the present invention, the nucleotide sequence of the SNP molecular marker is as shown in SEQ ID NO: 1, the polymorphic site is located at position 183 of the sequence shown in SEQ ID NO: 1, and the polymorphism is T / C.

[0013] The genotype of the polymorphic site of the SNP molecular marker mentioned above is CC, corresponding to the low body size and weight trait, and the genotype is TT, corresponding to the high body size and weight trait.

[0014] In a second aspect, the present invention provides primers for amplifying the above-mentioned SNP molecular markers related to the body size and weight traits of goats.

[0015] According to the location of the polymorphic site of the SNP molecular marker provided above and its upstream and downstream sequences, those skilled in the art can develop various types of primers for amplifying the SNP molecular marker. Therefore, the above primers can be any primers that can be used to detect the genotype of the SNP molecular marker.

[0016] In some embodiments of the present invention, the primers include primers whose sequences are shown in SEQ ID NO: 2-3.

[0017] In a third aspect, the present invention provides a kit, which comprises the primers described above.

[0018] The above-mentioned kit may also contain other reagents for PCR amplification, including but not limited to PCR reaction buffer, DNA polymerase, probe, dNTP, Mg 2+ , water, etc.

[0019] In a fourth aspect, the present invention provides any one of the following 1)-8) applications of the above-mentioned SNP molecular markers, the primers or the kit:

[0020] 1) Prediction of body size and weight traits of goats;

[0021] 2) Preparation of reagents for predicting body size and weight traits of goats;

[0022] 3) Screening or identification of goat strains with high body size and weight;

[0023] 4) Prepare reagents for screening or identifying high body size and weight goat strains;

[0024] 5) Breeding of goats based on their body size and weight;

[0025] 6) Molecular marker-assisted breeding related to body size and weight traits of goats;

[0026] 7) Breed improvement related to body size and weight traits of goats;

[0027] 8) JAK1 genotyping.

[0028] In a fifth aspect, the present invention provides any one of the following 1)-8) applications of a SNP molecular marker or a detection reagent for the SNP molecular marker:

[0029] 1) Prediction of body size and weight traits of goats;

[0030] 2) Preparation of reagents for predicting body size and weight traits of goats;

[0031] 3) Screening or identification of goat strains with high body size and weight;

[0032] 4) Prepare reagents for screening or identifying high body size and weight goat strains;

[0033] 5) Breeding of goats based on their body size and weight;

[0034] 6) Molecular marker-assisted breeding related to body size and weight traits of goats;

[0035] 7) Breed improvement related to body size and weight traits of goats;

[0036] 8) JAK1 genotyping;

[0037] The polymorphic site of the SNP molecular marker is located at the 40379673th site of chromosome 3 of the ARS1 version of the goat reference genome, and the polymorphism is T / C;

[0038] The genotype of the polymorphic site of the SNP molecular marker is CC, corresponding to the low body size and weight trait, and the genotype is TT, corresponding to the high body size and weight trait.

[0039] In some embodiments of the present invention, the SNP molecular marker contains a nucleotide sequence in which the polymorphism at position 183 of the sequence shown in SEQ ID NO: 1 is T / C.

[0040] In some embodiments of the present invention, the nucleotide sequence of the SNP molecular marker is as shown in SEQ ID NO: 1, the polymorphic site is located at position 183 of the sequence shown in SEQ ID NO: 1, and the polymorphism is T / C.

[0041] Preferably, the detection reagent for the SNP molecular marker includes a detection primer for the SNP molecular marker.

[0042] In some embodiments of the present invention, the detection primers for the SNP molecular markers include primers shown in SEQ ID NO: 2-3.

[0043] In the present invention, the reference sequence number of the JAK1 gene in NCBI is ENSCHIG00000012708.

[0044] In the present invention, the prediction of goat body size and weight traits is preferably an early prediction.

[0045] In a sixth aspect, the present invention provides a method for screening goats with high body size and weight traits, the method comprising: detecting SNP molecular markers related to goat body size and weight traits in goats to be screened, and determining goats with high body size and weight traits according to the genotype of the SNP molecular markers;

[0046] The polymorphic site of the SNP molecular marker is located at the 40379673th site of chromosome 3 of the ARS1 version of the goat reference genome, and the polymorphism is T / C;

[0047] The genotype of the polymorphic site of the SNP molecular marker is CC, corresponding to the low body size and weight trait, and the genotype is TT, corresponding to the high body size and weight trait.

[0048] In the above method, when the genotype of the detected SNP molecular marker is TT, the goat to be screened has the genetic trait of high body size and weight and is retained; when the genotype detected is CC or CT, the goat to be screened has the genetic trait of low body size and weight and is eliminated.

[0049] Preferably, the goat is a lamb.

[0050] In a seventh aspect, the present invention provides a method for breeding a goat strain with high body size and weight traits, the method comprising: detecting SNP molecular markers related to the body size and weight traits of goats, selecting individuals with the genotype of the SNP molecular marker being TT as seed goats; mating the male goats and female goats of the seed goats; detecting the SNP molecular markers of goats born from mating, retaining individuals with the genotype of the SNP molecular marker being TT, eliminating individuals with the genotype of CC or CT, and then breeding to obtain a goat strain with high body size and weight traits;

[0051] The polymorphic site of the SNP molecular marker is located at the 40379673th site of chromosome 3 of the ARS1 version of the goat reference genome, and the polymorphism is T / C;

[0052] The genotype of the polymorphic site of the SNP molecular marker is CC, corresponding to the low body size and weight trait, and the genotype is TT, corresponding to the high body size and weight trait.

[0053] In an eighth aspect, the present invention provides a method for breeding goats based on their body size and weight, comprising: detecting SNP molecular markers related to the body size and weight traits of goats, selecting individuals with a genotype of TT as breeding goats, and eliminating goat individuals with a genotype of CC or CT, so as to breed goats with high body size and weight traits as breeding goats, so as to achieve breeding of breeding goats based on their body size and weight traits;

[0054] The polymorphic site of the SNP molecular marker is located at the 40379673th site of chromosome 3 of the ARS1 version of the goat reference genome, and the polymorphism is T / C;

[0055] The genotype of the polymorphic site of the SNP molecular marker is CC, corresponding to the low body size and weight trait, and the genotype is TT, corresponding to the high body size and weight trait.

[0056] In a ninth aspect, the present invention provides a method for genetic improvement of goats, the method comprising: detecting SNP molecular markers related to body size and weight traits of goats, selecting individuals with a genotype of TT, and eliminating individuals with a genotype of CC or CT; using individuals with a genotype of TT as breeding goats, breeding, and continuing to select breeding goat individuals with a genotype of TT in the offspring, and eliminating individuals with a genotype of CC or CT; increasing the frequency of allele T in the offspring goat population generation by generation, thereby reducing the proportion of low body size and weight of the offspring breeding goats; the polymorphic site of the SNP molecular marker is located at the 40379673th site of chromosome 3 of the ARS1 version of the goat reference genome, and the polymorphism is T / C;

[0057] The genotype of the polymorphic site of the SNP molecular marker is CC, corresponding to the low body size and weight trait, and the genotype is TT, corresponding to the high body size and weight trait.

[0058] In the present invention, the body size and weight include weight, body length, body height, tube circumference and / or chest circumference. The low body size and weight traits are low weight, low body length, low body height, low tube circumference and / or low chest circumference; the high body size and weight traits are high weight, high body length, high body height, high tube circumference and / or high chest circumference.

[0059] The beneficial effects of the present invention include at least:

[0060] 1) The present invention screened and identified SNP molecular markers related to the body size and weight of goats. The body size and weight of goats with different genotypes of this molecular marker are extremely significantly different; the average height of goats with genotype TT is 67.03cm, the average weight is 44.16kg, and the average height of goats with genotype CC is 53.14cm, the average weight is 26.63kg. The T allele can significantly increase the body size and weight of goats and thus affect meat production. The TT genotype is a dominant genotype. By applying this molecular marker, the production performance of goats can be greatly improved, and the genetic improvement and breeding process of goats can be accelerated.

[0061] 2) By detecting the genotype of the SNP molecular marker of the present invention to assist in the breeding of goats, the goats with the TT genotype are selected, which can effectively improve the body size and weight of the goats, and facilitate subsequent comprehensive breeding.

[0062] 3) The SNP molecular markers of the present invention are applied to the breeding of goat body size and weight traits. The bred goats can significantly improve body size and weight, and then increase carcass weight. It can be used to breed large-sized goat varieties and improve the production performance of breeding goats.

[0063] 4) The SNP molecular markers of the present invention are applied to the breeding of goat strains with high body size and weight traits, so that goat strains with significantly increased body size and weight can be obtained, thereby increasing carcass weight and net meat weight, thereby improving the production performance of the goats of this strain and accelerating the genetic improvement and breeding process of breeding goats.

[0064] 5) Applying the SNP molecular marker of the present invention to the genetic improvement of goats can greatly shorten the years of genetic breeding, improve the goat slaughter rate, and accelerate the genetic improvement and breeding process of goats.

[0065] 6) The SNP molecular markers of the present invention are applied to the screening of lambs with genetic traits of high body size and weight, so that goats with high body size and weight traits can be screened out and retained at the lamb stage, thereby achieving accurate screening and breeding of goats with high body size and weight traits at the early stage of birth, without being restricted by the age and gender of the goats, greatly improving the breeding speed and breeding efficiency, and saving feeding costs. BRIEF DESCRIPTION OF THE DRAWINGS

[0066] In order to more clearly illustrate the technical solutions in the present invention or the prior art, the following briefly introduces the drawings required for use in the embodiments or the description of the prior art. Obviously, the drawings described below are some embodiments of the present invention. For ordinary technicians in this field, other drawings can be obtained based on these drawings without paying creative work.

[0067] Figure 1The phenotypic statistical diagram of weight, body length, height, tube circumference and chest circumference of the high body size group goats and the low body size group goats in Example 1 of the present invention; wherein, or Indicates P<0.01.

[0068] Figure 2 This is a Manhattan plot of the whole genome SNP effect distribution of goat body size and weight traits in Example 2 of the present invention; wherein, the upper figure is a Manhattan plot of the three selection signals of FST, XP-EHH and Piratio, wherein the selected position in the box represents the genomic position of the rs663771497 molecular marker of the JAK1 gene; the lower figure is a fine positioning map of the JAK1 gene, and the position indicated by the arrow is the rs663771497 molecular marker.

[0069] Figure 3 It is a Venn diagram of genes screened out by the three selection signal methods between the high body high group and the low body high group in Example 2 of the present invention; the three methods jointly identified 25 overlapping candidate regions, including 15 significantly correlated genes (including the JAK1 gene); the right figure shows that the overlapping genes of the five groups were further overlapped, and it was found that the five groups were jointly located to the JAK1 gene.

[0070] Figure 4 This is a gene locus frequency diagram between the low body height group and the high body height group in Example 2 of the present invention. The SNP site (rs663771497) has a significant difference between the low body height group and the high body height group (p<0.01). DETAILED DESCRIPTION

[0071] The present invention aims to provide a SNP molecular marker related to goat body size and weight and application thereof.

[0072] The present invention adopts the technical solution described below.

[0073] The invention provides a SNP molecular marker related to goat body size and weight. The SNP molecular marker is located at the 40379673bp position of chromosome 3 of the goat reference genome ARS1 version, and the polymorphism is a T>C base mutation (i.e., the rs663771497 molecular marker).

[0074] Therefore, by applying this molecular marker, the production performance of goats can be greatly improved. Through continuous selection and breeding, the body size and weight of goats can be increased, the meat production can be increased, and the genetic improvement and breeding process of goats can be accelerated.

[0075] In some specific embodiments, the upstream and downstream gene sequences of the polymorphic site of the SNP molecular marker are as shown in SEQ ID NO: 1 (wherein Y is T or C), and the polymorphic site of the SNP molecular marker is located at the 183rd position of the sequence shown in SEQ ID NO: 1, and the polymorphism is a T>C base mutation (i.e., the rs663771497 molecular marker).

[0076] The present invention also provides an application of a SNP molecular marker (rs663771497 molecular marker) in the breeding of goat body size and weight traits, wherein the SNP molecular marker is located at the 40379673bp position of chromosome 3 of the goat reference genome ARS1 version, and the polymorphism is a T>C base mutation; or the upstream and downstream gene sequences of the polymorphic site of the SNP molecular marker are as shown in SEQ ID NO:1, and the polymorphic site of the SNP molecular marker is located at the 183rd position of the sequence shown in SEQ ID NO:1, and the polymorphism is a T>C base mutation.

[0077] Therefore, by applying this molecular marker to the breeding of goats based on their body size and weight traits, the selected goats can greatly increase the proportion of goats with high body size and weight, thereby increasing their slaughter rate, improving economic benefits, and accelerating the genetic improvement and breeding process of breeding goats.

[0078] In some specific embodiments, the application includes the following steps: detecting the following SNP molecular marker (rs663771497 molecular marker) in breeding goats: the SNP molecular marker is located at the 40379673bp position of chromosome 3 of the ARS1 version of the goat genome, and the polymorphism is a T>C base mutation, or the upstream and downstream gene sequences of the polymorphic site of the SNP molecular marker are as shown in SEQ ID NO:1, and the polymorphic site of the SNP molecular marker is located at the 183rd position of the sequence shown in SEQ ID NO:1, and the polymorphism is a T>C base mutation.

[0079] The present invention also provides an application of a SNP molecular marker (rs663771497 molecular marker) in breeding a high body size and weight goat strain, wherein the SNP molecular marker is located at the 40379673bp position of chromosome 3 of the goat reference genome ARS1 version, and the polymorphism is a T>C base mutation, or the upstream and downstream gene sequences of the polymorphic site of the SNP molecular marker are as shown in SEQ ID NO:1, and the polymorphic site of the SNP molecular marker is located at the 183rd position of the sequence shown in SEQ ID NO:1, and the polymorphism is a T>C base mutation.

[0080] Therefore, by applying the above-mentioned molecular markers in breeding goat strains with high body size and weight, a goat strain with high body size and weight can be obtained, thereby increasing the slaughter rate of goats of this strain, improving the production performance of goats of this strain, and accelerating the genetic improvement and breeding process of breeding goats.

[0081] In some specific embodiments, the application comprises the following steps:

[0082] 1) The following SNP molecular marker (rs663771497 molecular marker) was detected in the breeding goats: the SNP molecular marker was located at the 40379673bp position of chromosome 3 of the goat reference genome ARS1 version, and the polymorphism was a T>C base mutation, or the upstream and downstream gene sequences of the polymorphic site of the SNP molecular marker were as shown in SEQ ID NO:1, and the polymorphic site of the SNP molecular marker was located at the 183rd position of the sequence shown in SEQ ID NO:1, and the polymorphism was a T>C base mutation;

[0083] 2) selecting the individuals with the TT genotype detected in step 1) as seed goats, and breeding the male and female seed goats;

[0084] 3) The goats born from the mating in step 2) are tested for the SNP molecular markers described in step 1), the TT genotype individuals are retained, the CC or CT genotype individuals are eliminated, and the breeding is performed to cultivate a large goat strain with high body size and weight during the fattening period.

[0085] The present invention also provides a method for genetic improvement of goats, wherein the method comprises the following steps:

[0086] 1) Detect the following SNP molecular marker (rs663771497 molecular marker) in goats: the SNP molecular marker is located at the 40379673bp position of chromosome 3 of the goat reference genome ARS1 version, and the polymorphism is a T>C base mutation, or the upstream and downstream gene sequences of the polymorphic site of the SNP molecular marker are as shown in SEQ ID NO:1, and the polymorphic site of the SNP molecular marker is located at the 183rd position of the sequence shown in SEQ ID NO:1, and the polymorphism is a T>C base mutation;

[0087] 2) Selecting and retaining the breeding goat individuals with the molecular marker genotype of TT in step 1) and eliminating the individuals with CC or CT genotype;

[0088] 3) The individuals selected in step 2) are used as breeding goats for breeding, and the breeding goat individuals with the molecular marker genotype of TT in step 1) are continued to be selected from the offspring, and the individuals with CC or CT genotypes are eliminated; so as to increase the frequency of allele T in the offspring goat population generation by generation, thereby reducing the proportion of small-sized goats in the offspring breeding goats.

[0089] Therefore, by applying the above molecular markers to the genetic improvement of goats, the genetic breeding period can be greatly shortened and the meat production rate of goats can be improved.

[0090] The present invention also provides an application of a SNP molecular marker (rs663771497 molecular marker) in screening lambs with high body size and weight genetic traits. Thus, by applying the molecular marker to screening lambs with high body size and weight genetic traits, goats with high body size and weight can be screened out at the lamb stage and selected, so as to achieve the selection of goats with high body size and weight traits at the lamb stage, which can greatly improve breeding efficiency, reduce feeding costs, and improve economic benefits.

[0091] In some specific embodiments, the application includes the following steps:

[0092] 1) Detect the following SNP molecular marker (rs663771497 molecular marker) in the lambs to be screened: the SNP molecular marker is located at the 40379673bp position of chromosome 3 of the goat reference genome ARS1 version, and the polymorphism is a T>C base mutation, or the upstream and downstream gene sequences of the polymorphic site of the SNP molecular marker are as shown in SEQ ID NO:1, and the polymorphic site of the SNP molecular marker is located at the 183rd position of the sequence shown in SEQ ID NO:1, and the polymorphism is a T>C base mutation;

[0093] 2) When the genotype of the molecular marker detected in step 1) is TT, the lamb to be screened has the genetic trait of high body size and weight and is retained; when the genotype is CC or CT, the lamb to be screened has the genetic trait of low body size and weight and is eliminated.

[0094] In order to make the purpose, technical solution and advantages of the present invention clearer, the technical solution of the present invention will be clearly and completely described below in conjunction with the drawings of the present invention. Obviously, the described embodiments are part of the embodiments of the present invention, not all of the embodiments. Based on the embodiments of the present invention, all other embodiments obtained by ordinary technicians in this field without creative work are within the scope of protection of the present invention.

[0095] Unless otherwise specified, the following examples were performed according to conventional experimental conditions, such as Sambrook J & Russell DW, Molecular Cloning: a Laboratory Manual, 2001, or according to the conditions recommended in the manufacturer's instructions.

[0096] Example 1 Acquisition of SNP Molecular Markers

[0097] 1. Based on the National Domestic Animal Germplasm Resource Bank, the goats were divided into high-weight group and low-weight group, high-body-height group and low-body-height group, high-body-length group and low-body-length group, high-chest-circumference group and low-chest-circumference group, high-chest-circumference group and low-chest-circumference group according to the five indicators of weight, height, body length, chest circumference and tube circumference. Ear tissue samples or blood samples were collected from each group of goat breeds, and total DNA was extracted. The DNA was quality controlled and sent to a sequencing company for high-depth whole-genome resequencing (BGI, T7 platform), with an average sequencing depth of about 10×. Phenotypic data such as body size and weight trait determination of each group of goat breeds were collected. Among them, the average weight of the high weight group was 44.16kg, the average weight of the low weight group was 26.63kg, the average height of the high height group was 67.03cm, the average height of the low height group was 53.14cm, the average body length of the high length group was 74.99cm, the average body length of the low length group was 57.27cm, the average chest circumference of the high chest circumference group was 85.71cm, the average chest circumference of the low chest circumference group was 65.95cm, the average tube circumference of the high tube circumference group was 8.60cm, and the average tube circumference of the low tube circumference group was 6.94cm ( Figure 1 ).

[0098] 2. Sort out the fastq files downloaded from the sequencing company. Eliminate reads that do not meet the standards and have poor quality. After quality control and filtering of the raw data, obtain high-quality sequencing data. Use the MEM algorithm of BWA (Version 0.7.15) software to align the Clean Data to the goat reference genome (ARS1) to obtain the initial bam file, and use SAMtools (Version 1.9) software to sort the bam file and remove PCR duplicates.

[0099] 3. First, use the HaplotypeCaller module of GATK (Version 4.1.4.0) software to detect variants in all individuals and generate gvcf files. Use the CombineGVCFs function of GATK software to merge the gvcf files of all individuals, and finally use GenotypeGVCFs for genotyping. Only autosomes were used for subsequent analysis, and the generated vcf files were initially filtered using the SelectVariants function. The SNP filtering conditions are as follows: QD60.0, MQ3.0, ReadPosRankSum<-8.0, MQRankSum<-12.5. Use GATK4 to detect variants in 76 samples, and then perform hard filtering (QD<-2.0||ReadPosRankSum<-8.0||FS>60.0||MD<40.0||SOR>3.0||efMQRa

[0100] nkSum<-12.5||QUAL<30). After quality control, 76 domestic goat breeds and 16,744,201 SNPs were used for subsequent genome-wide selection signal analysis.

[0101] Example 2 Verification of SNP molecular markers associated with body size and weight of goats

[0102] 1. The research population consisted of 76 domestic goat breeds, and the samples were from the National Domestic Animal Germplasm Resource Bank.

[0103] 2. Using VCFtools (Version 0.1.16) software, the FST of the high body high group and the low body high group was calculated, with the parameters of window length 50kb and step length 20kb. Using VCFtools (Version 0.1.16) software, the π-RATIO (--window-pi 10000) of the high body high group and the low body high group was calculated, and the tajimaD of the high body high group and the low body high group was calculated using Plink (Version 1.90) software. Using Selscan (Version 2.0.2) software, the XP-EHH of the high body high group and the low body high group was calculated. The top 1% windows with the strongest signal values ​​were screened as significant areas. The analysis results were visualized using ggplot2 (Version 3.4.4) software in R (Version 4.3.2) ( Figure 2 ). The three methods annotated 328, 428 and 351 genes respectively ( Figure 3 ). The intersection of the three screening methods annotated 15 significantly related genes. At the same time, the same method was used to perform co-localization in the body weight group, chest circumference group, tube circumference group and body length group. The body length group, chest circumference group, tube circumference group and body weight group co-localized to 37, 41, 32 and 22 overlapping regions respectively. Then the overlapping genes of the five groups were further overlapped, and it was found that the five groups co-localized to JAK1 ( Figure 3 The visualization results show that in chromosome 3, within the 40.3MB-40.5MB region, this gene region is selected in both the high body height group and the low body height group.

[0104] 3. Use Plink (Version 1.90) software to calculate the rs663771497 molecular marker site (located at JAK1 The genotype of the gene in exon 7 was significantly different between the high-body high group and the low-body high group. The results of Fisher test and chi-square test showed that the difference between the high-body high group and the low-body high group at this site was extremely significant (P<0.01) ( Figure 4). As shown in Table 1, this site has extremely significant differences in the other four body size and weight index groups (P<0.01).

[0105] Table 1 Significance test of SNP genotype distribution among different groups

[0106]

[0107] The SNP molecular marker rs663771497 is located at the 40379673bp position of chromosome 3 of the goat reference genome ARS1 version, and the polymorphism is a T>C base mutation; the upstream and downstream gene sequences of the polymorphic site of the SNP molecular marker are shown in SEQ ID NO:1, the polymorphic site is located at the 183rd position of the sequence shown in SEQ ID NO:1, and the polymorphism is a T>C base mutation.

[0108] The above results show that there are extremely significant differences in body size and weight among goats with different genotypes of SNP molecular marker rs663771497; the T allele can significantly increase the body size and weight of goats and thus affect meat production, and the TT genotype is the dominant genotype, corresponding to the high body size and weight trait.

[0109] Example 3 Application of SNP molecular markers in breeding goats for height, size and weight

[0110] The rs663771497 molecular marker is detected in the breeding goats; the individuals with the TT genotype obtained by the detection are selected as the breeding goats, and the CC or CT genotype breeding goats are eliminated. Goats with high body size and weight traits can be selected as breeding goats, so as to realize the selection of body size and weight traits of breeding goats.

[0111] Example 4 Application of SNP molecular markers in breeding goat strains with high body size and weight traits

[0112] The rs663771497 molecular marker is detected in the breeding goats; the individuals with the TT genotype obtained by the detection are selected as the breeding goats, and the male and female breeding goats are bred; the rs663771497 molecular marker is detected in the goats born from the breeding, the TT genotype individuals are retained, and the CC or CT genotype individuals are eliminated for breeding, so as to cultivate a high production performance goat strain with high body size and weight.

[0113] Example 5 A method for genetic improvement of goats

[0114] Detect the rs663771497 molecular marker in breeding goats; select breeding goat individuals with a genotype of TT and eliminate individuals with CC or CT genotypes; use the screened individuals as breeding goats for breeding, and continue to select breeding goat individuals with a genotype of TT for the rs663771497 molecular marker and eliminate individuals with CC or CT genotypes in the offspring, so as to increase the frequency of the allele T in the offspring goat population generation by generation, thereby increasing the body size and weight of the offspring breeding goats.

[0115] Example 6 Application of SNP molecular markers in screening goat lambs with high body size and weight traits

[0116] The rs663771497 molecular marker is detected in the lambs to be screened; when the genotype of the detected molecular marker is TT, the lambs to be screened have the genetic trait of high body size and weight and are retained; when the genotype is CC or CT, the lambs to be screened have the genetic trait of low body size and weight and are eliminated.

[0117] The goats used in the above Examples 3 to 6 are Chinese local specialty goats; the following primers are used to amplify the rs663771497 molecular marker, and the primer sequences are as follows:

[0118] Forward primer (SEQ ID NO: 2): 5′-CACGTGCTGCATAACTGTCC-3′;

[0119] Reverse primer (SEQ ID NO:3): 5′-TGGCTTCACTCTGTCGCTTA-3′.

[0120] The PCR amplification method of the rs663771497 molecular marker comprises the following steps:

[0121] 1) Extract genomic DNA from the goat to be tested;

[0122] 2) Using genomic DNA as a template, PCR amplification was performed using the primers shown in SEQ ID NO: 2-3;

[0123] 3) Analyze the PCR amplification products.

[0124] The amplification system used in the PCR reaction includes 50 μL of the following: 1 μL of 100 ng / μL template DNA, 1 μL of 10 pmol / μL forward primer and reverse primer, 1 μL of 10 mmol / L dNTP Mixture, 1 μL of 1.25 U / 25 μL TaKaRa Ex Taq DNA polymerase, 25 μL of 2× PCR reaction buffer, and the remainder is double distilled water.

[0125] The PCR reaction program was as follows: pre-denaturation at 95°C for 5 min; denaturation at 95°C for 30 s, annealing at 55°C or 60°C for 30 s, extension at 72°C for 1-2 min, for a total of 30-35 cycles; and insulation at 72°C for 2 min.

[0126] Finally, it should be noted that the above embodiments are only used to illustrate the technical solutions of the present invention, rather than to limit it. Although the present invention has been described in detail with reference to the aforementioned embodiments, those skilled in the art should understand that they can still modify the technical solutions described in the aforementioned embodiments, or make equivalent replacements for some of the technical features therein. However, these modifications or replacements do not deviate the essence of the corresponding technical solutions from the spirit and scope of the technical solutions of the embodiments of the present invention.

Claims

1. Any one of the following 1) to 7) of a SNP molecular marker or a primer for amplifying the SNP molecular marker or a kit containing the primer: 1) Prediction of body size and weight traits of goats; 2) Preparation of reagents for predicting body size and weight traits of goats; 3) Screening or identification of goat strains with high body size and weight; 4) Prepare reagents for screening or identifying high body size and weight goat strains; 5) Breeding of goats based on their body size and weight; 6) Molecular marker-assisted breeding related to body size and weight traits of goats; 7) Breed improvement related to body size and weight traits of goats; The nucleotide sequence of the SNP molecular marker is as shown in SEQ ID NO: 1, the polymorphic site is located at position 183 of the sequence shown in SEQ ID NO: 1, and the polymorphism is T / C; The genotype of the polymorphic site of the SNP molecular marker is CC, corresponding to the low body size and weight trait, and the genotype is TT, corresponding to the high body size and weight trait.

2. Any one of the following 1)-7) applications of the SNP molecular marker rs663771497 or a detection reagent for the SNP molecular marker: 1) Prediction of body size and weight traits of goats; 2) Preparation of reagents for predicting body size and weight traits of goats; 3) Screening or identification of goat strains with high body size and weight; 4) Prepare reagents for screening or identifying high body size and weight goat strains; 5) Breeding of goats based on their body size and weight; 6) Molecular marker-assisted breeding related to body size and weight traits of goats; 7) Breed improvement related to body size and weight traits of goats; The genotype of the polymorphic site of the SNP molecular marker is CC, corresponding to the low body size and weight trait, and the genotype is TT, corresponding to the high body size and weight trait.

3. A method for screening goats with high body size and weight traits, characterized in that: The method comprises: detecting SNP molecular markers related to body size and weight traits of goats in goats to be screened, and determining goats with high body size and weight traits according to the genotype of the SNP molecular markers; The SNP molecular marker is rs663771497; The genotype of the polymorphic site of the SNP molecular marker is CC, corresponding to the low body size and weight trait, and the genotype is TT, corresponding to the high body size and weight trait.

4. A method for breeding goat strains with high body size and weight traits, characterized in that: The method comprises: detecting SNP molecular markers related to body size and weight traits in goats, selecting individuals with genotype TT of the SNP molecular markers as seed goats; mating the male goats and female goats of the seed goats; detecting the SNP molecular markers of goats born from mating, retaining individuals with genotype TT of the SNP molecular markers, eliminating individuals with genotype CC or CT, and then breeding to obtain goat strains with high body size and weight traits; The SNP molecular marker is rs663771497; The genotype of the polymorphic site of the SNP molecular marker is CC, corresponding to the low body size and weight trait, and the genotype is TT, corresponding to the high body size and weight trait.

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