SNP molecular markers associated with chest girth traits in goats and their application

Abstract

The present invention relates to the technical field of molecular markers, and in particular to SNP molecular markers related to goat chest girth traits and applications thereof. The SNP molecular markers of the present invention have a significant correlation with the chest girth traits of goats, can be used for molecular marker-assisted breeding of large goat breeds, are not limited by the age and gender of goats, can be used for breeding large goat breeds, accelerate the establishment of goat populations with excellent body shape traits, and improve the speed of breeding of fine breeds.

Description

Technical Field

[0001] The invention relates to the technical field of molecular markers, in particular to SNP molecular markers related to goat chest circumference traits and applications thereof. Background Art

[0002] Bone morphogenetic proteins (BMPs) are an important class of cytokines in the transforming growth factor-β (TGF-β) superfamily, and have demonstrated osteogenic activity in many clinical and preclinical studies, including BMP2, which is widely used in the treatment of spinal fusion and tibial fractures. BMP type 1 receptor (BMPR1A) is a transmembrane cell surface receptor that belongs to the transforming growth factor β receptor superfamily and interacts with BMP-2 to exert protein activity. Related studies have shown that BMPR1A is involved in the formation of bone and cartilage, and the palmitoylation level of BMPR1a can lead to changes in BMP signaling by affecting the localization and transport of BMP signals. Mutants with the lowest efficacy in inducing BMPR1A-BMPR2 dimerization exhibit minimal chondrogenic and osteogenic activity, indicating that BMPR1A is necessary for chondrogenic and osteogenic differentiation. BMPR1A is also essential for the self-renewal of suture stem cells (SuSCs) and SuSC-mediated bone formation. SuSC-specific disruption of Bmpr1a in mice leads to premature cell differentiation, which in turn causes skull deformities at the midline of the suture, the stem cell niche. BMPR1A expression was shown to be downregulated in a mouse model used to study human idiopathic short stature. It is also involved in the regulation of adipogenesis, and variations in BMPR1A are associated with obesity in humans. Finally, another gene encoding a BMP2 / 4 receptor, BMPR1B, was identified as a candidate gene for changes in mature body size in sheep. In addition, GBA also identified 39 genes significantly associated with the gene network related to body size based on PA analysis. Priority genes were identified near all significant SNPs, including BMPR1A. In summary, understanding the role of BMPR1A in bone and cartilage formation and its impact on body size is of great significance to basic biological research and will help to breed large goat breeds.

[0003] Goats are an important livestock resource in the world, and their body shape characteristics directly affect meat production, reproductive capacity and disease resistance. China has rich goat breed resources, and after a long period of natural and artificial breeding, a variety of breeds have been formed. Body shape, including weight, height, body length, chest circumference, cannon circumference, etc., is a complex trait controlled by multiple genes and is one of the most important traits in the process of livestock domestication and breeding. As an important component of body shape, chest circumference has a significant impact on the slaughter rate and meat yield of goats. Goats with wide chest circumference are usually larger, have a higher slaughter rate, and have stronger meat production ability, which can meet the market demand for mutton and improve economic benefits.

[0004] With the increasing demand for high-quality meat products, especially in some regions with high consumption demand for mutton (such as the Middle East, Africa and some Asian countries), the market demand for large-sized goats is growing. Breeding large-sized goats can better meet these market demands and promote the development of the breeding industry. The body size and bone development of goats are the result of the combined effects of genetics, nutrition and environment. With the rapid development of molecular genetic technologies such as molecular marker-assisted selection, the study of the main effect genes of the main performance of goats has gradually become a hot topic. The use of polymorphic sites of candidate genes as molecular auxiliary markers of the genetic effects of goat traits and then breeding goats provides a new idea for improving various performances and goat breeding. Therefore, it is necessary to develop goat-specific molecular markers and apply them to the breeding of wide chest girth goats to provide a basis for molecular breeding of wide chest girth goats. The application of these molecular markers will improve the efficiency and accuracy of breeding, accelerate the process of genetic improvement, optimize gene combinations, and thus significantly improve the overall level and economic benefits of goat breeding. Summary of the invention

[0005] The invention provides a SNP molecular marker related to the chest circumference trait of a goat and an application 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 goat chest circumference traits, wherein the SNP molecular marker comprises a nucleotide sequence in which the polymorphism at position 151 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 the 4230081bp position of chromosome 28 of the ARS1 version of the goat reference genome, and the polymorphism is T / C, that is, the rs640136264 molecular marker. The polymorphic site is located on the BMPR1A gene.

[0010] The SNP molecular marker of the present invention has a significant correlation with the chest girth trait of goats, and can be used for early prediction of the chest girth trait of goats and molecular marker-assisted breeding, etc.

[0011] For the convenience of detection, the present invention has developed primers for amplifying the SNP molecular marker based on the polymorphic site located at the 4230081bp position of chromosome 28 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 the 4230081bp position of chromosome 28 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 151 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 described above is TT, corresponding to the narrow chest circumference trait, and the genotype is CC or CT, corresponding to the wide chest circumference trait.

[0014] In a second aspect, the present invention provides primers for amplifying the above-mentioned SNP molecular markers associated with goat chest circumference traits.

[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 chest girth of goats;

[0021] 2) Preparation of reagents for predicting chest girth traits in goats;

[0022] 3) Screening or identification of wide chest goat strains;

[0023] 4) Preparation of reagents for screening or identifying wide chest goat strains;

[0024] 5) Breeding of goat chest girth traits;

[0025] 6) Molecular marker-assisted breeding related to chest girth traits in goats;

[0026] 7) Breed improvement related to chest girth traits in goats;

[0027] 8) BMPR1A 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 chest girth of goats;

[0030] 2) Preparation of reagents for predicting chest girth traits in goats;

[0031] 3) Screening or identification of wide chest goat strains;

[0032] 4) Preparation of reagents for screening or identifying wide chest goat strains;

[0033] 5) Breeding of goat chest girth traits;

[0034] 6) Molecular marker-assisted breeding related to chest girth traits in goats;

[0035] 7) Breed improvement related to chest girth traits in goats;

[0036] 8) BMPR1A genotyping;

[0037] The polymorphic site of the SNP molecular marker is located at the 4230081bp position of chromosome 28 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 TT, corresponding to the narrow chest circumference trait, and the genotype is CC or CT, corresponding to the wide chest circumference trait.

[0039] In some embodiments of the present invention, the SNP molecular marker contains a nucleotide sequence in which the polymorphism at position 151 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 151 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 BMPR1A gene in NCBI is ENSG00000107779.

[0044] In the present invention, the prediction of the chest girth trait of goats is preferably an early prediction.

[0045] In the present invention, the prediction of the goat chest girth trait is preferably an early prediction of goat individuals having a wide chest girth trait.

[0046] In a sixth aspect, the present invention provides a method for screening goats with a wide chest circumference trait, the method comprising: detecting a SNP molecular marker associated with the goat chest circumference trait in the goats to be screened, and determining the goats with the wide chest circumference trait according to the genotype of the SNP molecular marker;

[0047] The polymorphic site of the SNP molecular marker is located at the 4230081bp position of chromosome 28 of the ARS1 version of the goat reference genome, and the polymorphism is T / C;

[0048] The genotype of the polymorphic site of the SNP molecular marker is TT, corresponding to the narrow chest circumference trait, and the genotype is CC or CT, corresponding to the wide chest circumference trait.

[0049] In the above method, when the genotype of the detected SNP molecular marker is CC or CT, the goat to be screened has a wide chest circumference genetic trait and is retained; when the detected genotype is TT, the goat to be screened has a narrow chest circumference genetic trait and is eliminated.

[0050] In the above method, the goat may be a lamb.

[0051] In a seventh aspect, the present invention provides a method for breeding a wide chest girth goat strain, the method comprising: detecting SNP molecular markers associated with the chest girth trait of goats, selecting individuals with the genotype of the SNP molecular marker being CC or CT as seed goats; breeding the male goats and female goats of the seed goats; detecting the SNP molecular markers of goats born from breeding, retaining individuals with the genotype of the SNP molecular marker being CC or CT, eliminating individuals with the genotype of TT, and then breeding to obtain a goat strain with a wide chest girth trait;

[0052] The polymorphic site of the SNP molecular marker is located at the 4230081bp position of chromosome 28 of the ARS1 version of the goat reference genome, and the polymorphism is T / C;

[0053] The genotype of the polymorphic site of the SNP molecular marker is TT, corresponding to the narrow chest circumference trait, and the genotypes are CC and CT, corresponding to the wide chest circumference trait.

[0054] In an eighth aspect, the present invention provides a method for selecting and breeding goats for chest girth traits, the method comprising: detecting SNP molecular markers related to the chest girth traits of goats in reserve goats; selecting individuals with a genotype of CC or CT as reserve goats, and eliminating individuals with a genotype of TT goats, that is, selecting goats with a wide chest girth trait as reserve goats, so as to achieve the selection and breeding of the chest girth traits of the seed goats;

[0055] The polymorphic site of the SNP molecular marker is located at the 4230081bp position of chromosome 28 of the ARS1 version of the goat reference genome, and the polymorphism is T / C;

[0056] The genotype of the polymorphic site of the SNP molecular marker is TT, corresponding to the narrow chest circumference trait, and the genotype is CC or CT, corresponding to the wide chest circumference trait.

[0057] In a ninth aspect, the present invention provides a method for genetic improvement of goats, the method comprising: detecting SNP molecular markers associated with the chest circumference trait of goats in reserve goats; selecting individuals with a genotype of CC or CT and eliminating individuals with a genotype of TT; using individuals with a genotype of CC or CT as seed goats for breeding, and continuing to select seed goat individuals with a genotype of CC or CT in the offspring, eliminating individuals with a genotype of TT, so as to increase the frequency of allele C in the offspring goat population generation by generation, thereby reducing the proportion of narrow chest circumference of the offspring seed goats;

[0058] The polymorphic site of the SNP molecular marker is located at the 4230081bp position of chromosome 28 of the ARS1 version of the goat reference genome, and the polymorphism is T / C;

[0059] The genotype of the polymorphic site of the SNP molecular marker is TT, corresponding to the narrow chest circumference trait, and the genotype is CC or CT, corresponding to the wide chest circumference trait.

[0060] The beneficial effects of the present invention include at least:

[0061] 1) The present invention screened and identified a molecular marker related to the chest girth trait of goats. The chest girth width of goats with different genotypes of this molecular marker was significantly different; the average chest girth of genotypes CC and CT was 85.71 mm, and the average chest girth of genotype TT was 65.95 mm. The C allele significantly increased the chest girth width. The CC and CT genotypes were dominant genotypes, corresponding to the wide chest girth trait. Therefore, by applying this molecular marker, the chest girth width of goats can be greatly improved, thereby increasing the slaughter rate and meat production of goats, affecting their production performance, and accelerating the genetic improvement and breeding process of goats.

[0062] 2) By detecting the genotype of the molecular marker related to the chest girth trait of goats of the present invention to assist in the breeding of goats, the chest girth of goats can be effectively improved by selecting CC or CT genotype goats, which is convenient for the comprehensive breeding of subsequent goats.

[0063] 3) By applying the molecular markers related to the chest girth trait of goats to the breeding of wide chest girth traits, the selected goats can greatly increase the chest girth width, thereby increasing the slaughter rate and meat yield, and improving the production performance of breeding goats.

[0064] 4) By applying the molecular markers related to the chest girth trait of goats of the present invention to the breeding of goat strains with wide chest girth traits, a goat strain with wide chest girth can be obtained, thereby improving the slaughter rate, meat production, etc. of the goats of this strain, improving the production performance of the goats of this strain, and accelerating the genetic improvement progress and breeding process of breeding goats.

[0065] 5) By applying the molecular markers related to the chest girth trait of goats to the genetic improvement of goats, the genetic breeding period can be greatly shortened, the goat slaughter rate can be improved, and the genetic improvement progress and breeding process of goats can be accelerated.

[0066] 6) By applying the molecular markers related to the chest girth trait of goats of the present invention to the screening of lambs with the genetic trait of wide chest girth, goats with wide chest girth can be screened out at the lamb stage and selected, thereby achieving the selection and breeding of the wide chest girth trait of goats at the lamb stage, which can greatly improve the breeding efficiency and save the feeding cost. BRIEF DESCRIPTION OF THE DRAWINGS

[0067] 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.

[0068] Figure 1 This is a chest circumference phenotype statistical diagram of the wide chest circumference group goats and the narrow chest circumference group goats in Example 1 of the present invention; wherein, Indicates P<0.01.

[0069] Figure 2 It is a Manhattan plot of the whole genome SNP effect distribution of the chest circumference trait of goats 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 π-Ratio, wherein the selected position in the box represents the genomic position of the rs640136264 molecular marker of the BMPR1A gene; the lower figure is a fine positioning map of the BMPR1A gene, and the position indicated by the arrow is the rs640136264 molecular marker.

[0070] Figure 3 It is a Venn diagram of genes screened out by the three selection signal methods between the wide chest circumference group and the narrow chest circumference group in Example 2 of the present invention; wherein the three methods jointly identified 22 overlapping candidate regions, including 18 significantly correlated genes (including the BMPR1A gene).

[0071] Figure 4 This is a gene locus frequency diagram between the wide chest circumference group and the narrow chest circumference group in Example 2 of the present invention. The SNP site (rs640136264) has a significant difference between the wide chest circumference group and the narrow chest circumference group (p<0.01). DETAILED DESCRIPTION

[0072] The present invention aims to provide a SNP molecular marker related to the chest girth trait of goats and application thereof.

[0073] The present invention adopts the technical solution described below.

[0074] The present invention provides a SNP molecular marker associated with the chest circumference trait of goats. The polymorphic site of the SNP molecular marker is located at the 4230081bp position of chromosome 28 of the goat reference genome ARS1 version, and the polymorphism is a T>C base mutation (i.e., the rs640136264 molecular marker).

[0075] Therefore, by applying this molecular marker, the chest circumference of goats can be greatly improved, thereby increasing their mutton yield, improving their production performance, and improving economic benefits. Through continuous breeding, the chest circumference of goats can be continuously expanded, and the genetic improvement and breeding process of breeding goats can be accelerated.

[0076] 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, the polymorphic site of the SNP molecular marker is located at position 151 of the sequence shown in SEQ ID NO: 1, and the polymorphism is a T>C base mutation (ie, the rs640136264 molecular marker).

[0077] The present invention also provides an application of a SNP molecular marker (rs640136264 molecular marker) in the selection of goat chest girth traits, wherein the polymorphic site of the SNP molecular marker is located at the 4230081bp position of chromosome 28 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 151st position of the sequence shown in SEQ ID NO:1, and the polymorphism is a T>C base mutation. Thus, by applying the molecular marker to the selection of goat chest girth traits, the selected goats can greatly increase their chest girth, thereby increasing their mutton yield and slaughter rate, etc., improving economic benefits, and accelerating the genetic improvement progress and breeding process of goats.

[0078] In some specific embodiments, the application includes the following steps: detecting the following SNP molecular marker (rs640136264 molecular marker) on the reserve goat: the polymorphic site of the SNP molecular marker is located at the 4230081bp position of chromosome 28 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 151st 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 (rs640136264 molecular marker) in breeding a wide chest girth goat strain, wherein the polymorphic site of the SNP molecular marker is located at the 4230081bp position of chromosome 28 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 151st 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 the breeding of wide chest circumference goat breeds, goat breeds with wide chest circumference can be obtained, thereby increasing the slaughter rate and mutton yield of this breed of goats, improving the production performance of this breed of goats, and accelerating the genetic improvement progress and breeding process of breeding goats.

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

[0082] 1) The following SNP molecular marker (rs640136264 molecular marker) was detected in the reserve goats: the polymorphic site of the SNP molecular marker was located at the 4230081bp position of chromosome 28 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 151st 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 CC or CT genotypes detected in step 1) as seed goats, and breeding the 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 CC or CT genotype individuals are retained, the TT genotype individuals are eliminated, and the breeding is performed to cultivate a goat strain with a wide chest circumference.

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

[0086] 1) Detect the following SNP molecular marker (rs640136264 molecular marker) in reserve goats: the polymorphic site of the SNP molecular marker is located at the 4230081bp position of chromosome 28 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 151st 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 CC or CT described in step 1), and eliminating the individuals with TT 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 CC or CT in step 1) are continued to be selected in the offspring, and the individuals with the TT genotype are eliminated; so as to increase the frequency of allele C in the offspring goat population generation by generation, thereby reducing the proportion of narrow chest circumference 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 chest width of goats can be increased.

[0090] The present invention also provides an application of a SNP molecular marker (rs640136264 molecular marker) in screening lambs with a wide chest girth genetic trait, wherein the polymorphic site of the SNP molecular marker is located at the 4230081bp position of chromosome 28 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 151st position of the sequence shown in SEQ ID NO:1, and the polymorphism is a T>C base mutation.

[0091] Therefore, by applying the molecular marker to the screening of lambs with the genetic trait of wide chest circumference, breeding goats with wide chest circumference can be screened out at the lamb stage and selected, thereby realizing the selection and breeding of breeding goats with wide chest circumference traits at the lamb stage, which can greatly improve breeding efficiency, reduce feeding costs, and improve economic benefits.

[0092] In some specific embodiments, the application includes the following steps:

[0093] 1) Detect the following SNP molecular marker (rs640136264 molecular marker) in the lambs to be screened: the polymorphic site of the SNP molecular marker is located at the 4230081bp position of chromosome 28 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 151st position of the sequence shown in SEQ ID NO:1, and the polymorphism is a T>C base mutation;

[0094] 2) When the genotype of the molecular marker detected in step 1) is CC or CT, the lamb to be screened has the genetic trait of wide chest circumference and is retained; when the genotype is TT, the lamb to be screened has the genetic trait of narrow chest circumference and is eliminated.

[0095] 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.

[0096] Unless otherwise specified, the following examples are all based on conventional experimental conditions, such as Sambrook et al. Molecular Cloning: a Laboratory Manual (Sambrook J & Russell DW, Molecular Cloning: a Laboratory Manual, 2001), or the conditions recommended by the manufacturer's instructions.

[0097] Example 1 Acquisition of SNP Molecular Markers

[0098] 1. Based on the National Domestic Animal Germplasm Resource Bank, ear tissue samples or blood samples of goat breeds in the wide chest circumference group and narrow chest circumference group were collected, total DNA was extracted, DNA quality control was performed, and the samples were 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 growth performance determination of the corresponding goat breeds were collected, among which the average chest circumference of the wide chest circumference group was 85.71mm, and the average chest circumference of the narrow chest circumference group was 65.95mm ( Figure 1 ).

[0099] 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.

[0100] 3. First, the HaplotypeCaller module of GATK (Version 4.1.4.0) software was used to detect variants in all individuals and generate gvcf files. The CombineGVCFs function of GATK software was used to merge the gvcf files of all individuals, and finally genotyping was performed using GenotypeGVCFs. Only autosomes were used for subsequent analysis, and the generated vcf files were initially filtered using the SelectVariants function. SNP filtering conditions: QD60.0, MQ3.0, ReadPosRankSum<-8.0, MQRankSum<-12.5. GATK4 was used to detect variants in 88 samples, and hard filtering was performed (QD<-2.0||ReadPosRankSum<-8.0||FS>60.0||MD<40.0||SOR>3.0||efMQRankSum<-12.5||QUAL<30). After quality control, 88 Chinese domestic goat breed individuals and 16,744,201 SNPs were used for subsequent genome-wide selection signal analysis.

[0101] Example 2 Validation of Molecular Markers Associated with Goat Chest Girth Traits

[0102] 1. The research population consisted of 88 goat breeds from China, and the samples were obtained from the National Livestock and Poultry Germplasm Resource Bank.

[0103] 2. Using VCFtools (Version 0.1.16) software, the FST of the wide chest circumference group and the narrow chest circumference 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 wide chest circumference group and the narrow chest circumference group was calculated, and Plink (Version 1.90) software was used to calculate TajimaD of the wide chest circumference group and the narrow chest circumference group. Using Selscan (Version 2.0.2) software, the XP-EHH of the wide chest circumference group and the narrow chest circumference group was calculated. The top 1% of windows with the strongest signal values ​​were selected 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 442, 645, and 617 salient regions, respectively ( Figure 3). The intersection of the three screening methods annotated 22 overlapping regions, including 18 genes (including BMPR1A gene). At the same time, the same method was used for co-localization in the height group, chest circumference group and tube circumference group. The height group, chest circumference group and tube circumference group co-localized to 21, 18 and 38 overlapping regions respectively. Then the overlapping genes of the three groups were further overlapped, and it was found that the three groups co-localized to BMPR1A ( Figure 3 The visualization results show that in chromosome 28, within the 4.17MB-4.32MB region, this gene region is under selection in the wide chest group and the narrow chest group.

[0104] 3. Plink (Version 1.90) software was used to calculate the genotype significance of the rs640136264 molecular marker locus (located in the second intron of the BMPR1A gene) between the wide chest circumference group and the narrow chest circumference group. The results of the Fisher test and the chi-square test showed that the difference in this locus between the wide chest circumference group and the narrow chest circumference group was extremely significant (P<0.01) ( Figure 4 ).

[0105] The above results showed that the chest width of goats with different genotypes of SNP molecular marker rs640136264 was significantly different. The C allele significantly increased the chest width. The CC and CT genotypes were dominant genotypes, corresponding to the wide chest circumference trait.

[0106] Example 3 Application of SNP molecular markers in goat breast circumference trait breeding

[0107] The rs640136264 molecular marker is detected in the reserve goats; the individuals with the CC or CT genotype obtained by the detection are selected as the reserve goats, and the TT genotype goat individuals are eliminated. Goats with wide chest circumference traits can be selected as reserve goats to achieve the selection of chest circumference traits in breeding goats.

[0108] Example 4 Application of SNP molecular markers in breeding goat strains with wide chest circumference traits

[0109] The rs640136264 molecular marker is detected in the reserve goats; the individuals with the CC or CT genotype obtained by the detection are selected as the reserve goats, and the male and female reserve goats are bred; the rs640136264 molecular marker is detected in the goats born from the breeding, the CC or CT genotype individuals are retained, and the TT genotype individuals are eliminated for breeding, so as to cultivate a high production performance goat strain with wide chest circumference trait.

[0110] Example 5 A method for genetic improvement of goats

[0111] Detect the rs640136264 molecular marker in reserve breeding goats; select breeding goat individuals with genotypes of CC and CT, and eliminate individuals with TT genotype; use the screened individuals as breeding goats for breeding, and continue to select breeding goat individuals with rs640136264 molecular marker genotypes of CC or CT in the offspring, and eliminate individuals with TT genotype; so as to increase the frequency of allele C in the offspring goat population generation by generation, thereby increasing the chest circumference of the offspring breeding goats.

[0112] Example 6 Application of SNP molecular markers in screening lambs for wide chest circumference traits

[0113] The rs640136264 molecular marker is detected in the lambs to be screened; when the genotype of the detected molecular marker is CC or CT, the lambs to be screened have the genetic trait of wide chest circumference and are retained; when the genotype is TT, the lambs to be screened have the genetic trait of narrow chest circumference and are eliminated.

[0114] The reserve goats used in the above Examples 3 to 6 are Chinese local specialty goats; the following primers are used to amplify the rs640136264 molecular marker.

[0115] Forward primer (SEQ ID NO: 2): 5′-TTAGAACGGCTTCTCCCCTG-3′;

[0116] Reverse primer (SEQ ID NO:3): 5′-CCTCTGACGATGACAAGACAAG-3′.

[0117] PCR amplification methods include:

[0118] 1) Extract genomic DNA from the goat to be tested;

[0119] 2) Using genomic DNA as a template, PCR amplification was performed using the primers shown in SEQ ID NO: 2-3;

[0120] 3) Analyze the PCR amplification products.

[0121] 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.

[0122] 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.

[0123] 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 8) of a SNP molecular marker associated with goat chest girth traits, or a primer for amplifying the SNP molecular marker, or a kit containing the primer: 1) Prediction of chest girth traits of goats; 2) Preparation of reagents for predicting chest girth traits in goats; 3) Screening or identification of wide chest goat strains; 4) Preparation of reagents for screening or identifying wide chest goat strains; 5) Breeding of goat chest girth traits; 6) Molecular marker-assisted breeding related to chest girth traits in goats; 7) Breed improvement related to chest girth traits in goats; 8) BMPR1A genotyping; The SNP molecular marker contains a nucleotide sequence in which the polymorphism at position 151 of the sequence shown in SEQ ID NO: 1 is T / C.

2. The use according to claim 1, characterized in that: The nucleotide sequence of the SNP molecular marker is shown in SEQ ID NO: 1, the polymorphic site is located at the 151st position of the sequence shown in SEQ ID NO: 1, and the polymorphism is T / C.

3. The use according to claim 1 or 2, characterized in that: The genotype of the polymorphic site of the SNP molecular marker is TT, corresponding to the narrow chest circumference trait, and the genotype is CC or CT, corresponding to the wide chest circumference trait.

4. The use according to claim 1, characterized in that: The primers include primers whose sequences are shown in SEQ ID NO: 2-3.

5. Any one of the following 1)-8) applications of a SNP molecular marker or a detection reagent for the SNP molecular marker: 1) Prediction of chest girth traits of goats; 2) Preparation of reagents for predicting chest girth traits in goats; 3) Screening or identification of wide chest goat strains; 4) Preparation of reagents for screening or identifying wide chest goat strains; 5) Breeding of goat chest girth traits; 6) Molecular marker-assisted breeding related to chest girth traits in goats; 7) Breed improvement related to chest girth traits in goats; 8) BMPR1A genotyping; The polymorphic site of the SNP molecular marker is located at the 4230081bp position of chromosome 28 of the ARS1 version of the goat reference genome, and the polymorphism is T / C; The genotype of the polymorphic site of the SNP molecular marker is TT, corresponding to the narrow chest circumference trait, and the genotype is CC or CT, corresponding to the wide chest circumference trait.

6. A method for screening goats with a wide chest trait, characterized in that: The method comprises: detecting SNP molecular markers related to the chest girth trait of goats to be screened, and determining goats with wide chest girth trait according to the genotype of the SNP molecular markers; The polymorphic site of the SNP molecular marker is located at the 4230081bp position of chromosome 28 of the ARS1 version of the goat reference genome, and the polymorphism is T / C; The genotype of the polymorphic site of the SNP molecular marker is TT, corresponding to the narrow chest circumference trait, and the genotype is CC or CT, corresponding to the wide chest circumference trait.

7. A method for breeding a wide chest girth goat strain, characterized in that: The method comprises: detecting SNP molecular markers related to the chest girth trait in goats, selecting individuals with the genotype of the SNP molecular marker being CC or CT 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 CC or CT, eliminating individuals with the genotype of TT, and then breeding to obtain a goat strain with a wide chest girth trait; The polymorphic site of the SNP molecular marker is located at the 4230081bp position of chromosome 28 of the ARS1 version of the goat reference genome, and the polymorphism is T / C; The genotype of the polymorphic site of the SNP molecular marker is TT, corresponding to the narrow chest circumference trait, and the genotype is CC or CT, corresponding to the wide chest circumference trait.

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