Dairy goat whole-genome 55k SNP chip and use thereof

Abstract

Provided are a dairy goat whole-genome 55K SNP chip and a use thereof. The chip has a total of 54344 SNP sites. The provided dairy goat whole-genome 55K SNP chip can be used for the identification and kinship analysis of imported dairy goat breeds and domestically bred dairy goat breeds, and can also be used in multiple fields such as dairy goat whole-genome association analysis, whole-genome selective breeding, population genetics analysis, and trait-related candidate gene and QTL site analysis and positioning, and has high value in both production applications and scientific research.

Description

A dairy goat whole genome 55K SNP chip and its application Technical Field

[0001] The present invention relates to the fields of molecular biology, functional genomics, bioinformatics and genome breeding technology, and in particular to a dairy goat whole genome 55K SNP chip and application thereof. Background Art

[0002] SNP, short for Single Nucleotide Polymorphism, refers to variations in a single nucleotide in the genome, resulting from the deletion, insertion, transversion, or substitution of a single base. As genetic markers, SNPs are numerous, densely distributed, and easily detected, making them ideal targets for genotyping and playing a crucial role in the genetic variation of complex traits. In particular, SNPs have become a key research topic in analyzing the mechanisms of genetic variation in quality traits, economic traits, and some complex disease traits in plant and animal genetics.

[0003] Whole-genome SNP chips are tools for high-throughput detection of SNP locus information. Currently, the mainstream formats are solid-phase chips and liquid-phase chips. SNP solid-phase chips are made by fixing a large number of fluorescently labeled DNA probes on a glass substrate through photoetching. The principle is to hybridize and bind the probe DNA chain with the target genomic DNA, and then use laser scanning after staining to perform SNP genotyping. SNP liquid-phase chips based on targeted capture sequencing are an emerging genetic testing technology. It uses targeted capture sequencing technology to select genomic regions of interest and perform high-throughput SNP detection in these regions through SNP liquid-phase chips. Unlike traditional SNP chips, SNP liquid-phase chips based on targeted capture sequencing can more flexibly and accurately select specific genomic regions for detection, thereby enabling more in-depth research on SNP variations related to specific genes or phenotypes.

[0004] Genomic selection (GS) is a modern breeding technique that uses genomic information and computer technology to assist breeding, achieving more efficient and accurate selection. Genomic selection is a breeding method based on molecular markers such as single nucleotide polymorphisms (SNPs). It can more accurately assess individual genetic backgrounds, genomic variation, and phenotypic traits, and optimize breeding strategies through computer simulation and analysis.

[0005] Compared with traditional breeding methods, genomic selection can more accurately assess the genetic background and phenotypic traits of individuals within a population, thereby selecting superior varieties that better meet breeding goals. Furthermore, genomic selection can significantly shorten the breeding cycle, reduce breeding costs, and improve breeding efficiency. Genomic selection can also promote the accumulation of genomic variation, accelerate the breeding process, and better meet market demand.

[0006] Currently, genomic selection is widely used in livestock production, including dairy cattle, beef cattle, and pigs, but its application in other animal breeding, such as sheep, is still in its infancy. Currently, the most widely used SNP array for goats is the Illumina Goat 50K SNP Array (GoatSNP50). However, as a broad-spectrum array for goats, it is less adaptable to dairy goats.

[0007] Therefore, it is necessary to develop a whole-genome chip for dairy goats.

[0008] Summary of the Invention

[0009] In order to solve one of the above technical problems existing in the prior art, the present invention provides a dairy goat whole genome 55KSNP chip and application thereof.

[0010] In a first aspect, the present invention provides a SNP molecular marker for the whole genome of a dairy goat, wherein the SNP molecular marker is selected from at least one of the markers shown in Table 2.

[0011] In a second aspect, the present invention provides a molecular probe for specifically identifying the SNP molecular marker described in the first aspect.

[0012] In a third aspect, the present invention provides a dairy goat whole genome SNP chip, wherein the SNP chip comprises probes targeting the SNP molecular markers described in the first aspect.

[0013] In some embodiments, the dairy goat whole genome SNP chip provided by the present invention is a dairy goat whole genome 55K SNP liquid phase chip.

[0014] The present invention provides a dairy goat whole genome SNP chip, in which SNP sites include four types of probes: the first type is SNP sites with good polymorphism screened by resequencing data of five dairy goat breeds (Saanen dairy goat, Toggenburg goat, Alpine goat, Guanzhong dairy goat, Laoshan dairy goat); the second type is functional gene sites and QTL sites reported by public databases (such as NCBI or QTL database) to be significantly associated with dairy goat production traits; the third type is SNP sites associated with important economic traits of dairy goats obtained by the inventors through genome-wide association analysis (GWAS) and selection signal research; the fourth type is SNP sites that use public database information to fill in the genomic segments that the first three types fail to cover. The above four types of probes contain a total of 54,344 SNP sites.

[0015] In some embodiments, the molecular marker is associated with one or more of milk production performance, milk quality traits, udder morphology, limb and hoof morphology, coat color, body shape, melatonin synthesis capacity, and diurnal variability of melatonin in dairy goats.

[0016] In some embodiments, the milk production performance comprises milk yield.

[0017] In some embodiments, the milk quality traits include milk protein rate, milk fat rate, lactose rate, and somatic cell count.

[0018] In a fourth aspect, the present invention provides a kit comprising the molecular probe described in the second aspect, or the SNP chip described in the third aspect.

[0019] In a fifth aspect, the present invention provides use of the molecular probe, or the SNP chip, or the kit in whole genome breeding of dairy goats.

[0020] In a sixth aspect, the present invention provides use of the molecular probe, or the SNP chip, or the kit in identifying kinship of dairy goats.

[0021] In a seventh aspect, the present invention provides use of the molecular probe, or the SNP chip, or the kit in identifying European dairy goat and Chinese dairy goat breeds.

[0022] In an eighth aspect, the present invention provides use of the molecular probe, or the SNP chip, or the kit in genotyping detection of dairy goats.

[0023] In a ninth aspect, the present invention provides use of the molecular probe, or the SNP chip, or the kit in genetic diversity analysis of a dairy goat population.

[0024] In a tenth aspect, the present invention provides use of the molecular probe, or the SNP chip, or the kit in the location analysis of QTL (quantitative trait loci) of target traits in dairy goats.

[0025] In an eleventh aspect, the present invention provides a method for preparing the SNP chip, using the specific probes of the dairy goat detection chip of the present invention, and then making the SNP chip by, for example, Infmium chip manufacturing technology.

[0026] In some embodiments, the SNP chip of the present invention is prepared by the following method:

[0027] (1) Dairy goats were selected as germplasm materials for resequencing, the sequencing results were quality controlled, compared with the reference genome, and the core candidate SNP sites were identified and filtered according to the SNP site attribute index to obtain the first type of SNP sites;

[0028] (2) Search the research results in public databases to obtain candidate genes and quantitative trait loci associated with important economic traits, compare them with the core candidate SNP loci, and obtain functional SNP loci as the second type of SNP loci;

[0029] (3) Using the phenotypic information of sequenced individuals and bioinformatics methods, functional SNP sites associated with milk production, milk quality, udder morphology, and melatonin synthesis capacity were obtained as the third category of SNP sites; and the SNP sites in the genome segments not covered by the first three categories were filled in using public database information as the fourth category of SNP sites;

[0030] (4) Based on the absolute position of the candidate SNP site on the chromosome and the score of the targeted capture sequencing primer design results, select the SNP site for chip development;

[0031] (5) Develop a whole-genome SNP chip for the dairy goat using targeted capture sequencing genotyping technology.

[0032] In some embodiments, step (1) comprises the following process:

[0033] S1. Representative dairy goat breeds widely raised in China and Europe were selected as germplasm materials. Ear margin tissue was collected for total DNA extraction and sequencing.

[0034] S2. Perform quality control on the raw sequencing data to obtain high-quality clean reads (filtered read lengths), which are then mapped to the reference genome to obtain alignment results for each sample;

[0035] S3. The alignment results were used to identify and extract SNP sites, and filtered according to the minimum allele frequency > 0.05, deletion rate < 1%, and heterozygosity rate < 5% to obtain core candidate SNP sites.

[0036] In some embodiments, in the process S1 of step (1), the germplasm material selected includes at least one of the following:

[0037] Chinese dairy goat breeds: Guanzhong dairy goat and Laoshan dairy goat;

[0038] European dairy goat breeds: Saanen dairy goat, Alpine goat and Toggenburg goat.

[0039] In some embodiments, in process S1 of step (1), the DNA library is constructed using the Illumina standard method, the DNA fragment length is 500 bp, the sequencing strategy is PE150, the sequencing depth is 30×, and finally 2.2 Tb of data is obtained.

[0040] In some embodiments, in step (1), the total number of SNP sites obtained is 33,716,044.

[0041] In some embodiments, step (2) comprises the following process:

[0042] S1. Search the NCBI (https: / / www.ncbi.nlm.nih.gov / ) and QTL database (https: / / www.animalgenome.org / QTLdb / ) databases to obtain candidate genes and quantitative trait loci associated with important economic traits such as growth traits, udder morphology, and limb and hoof morphology in dairy goats.

[0043] S2. Compare the candidate gene and quantitative trait locus information with the core candidate SNP loci and obtain the overlapping sites as functional SNP loci.

[0044] In some embodiments, in step (2), the number of SNP sites that can be used for chip development is 20,884.

[0045] In some embodiments, step (3) comprises the following process:

[0046] S1. Using XP-CLR, iHs, and Fst selection signal analysis and genome-wide association analysis, combined with dairy goat phenotypic information, we identified SNPs significantly associated with traits.

[0047] S2. Integrate the results of the above four analysis methods to obtain functional SNP sites.

[0048] The present invention adopts three selection signal analysis methods, XP-CLR, iHs and Fst, takes the intersection, performs comprehensive selection, and merges the results of the genome-wide association analysis method GWAS according to the selected index and threshold, adds the site obtained in step (2), and then uses the public database information to fill in the SNP sites that the aforementioned method fails to cover the genomic segment. The selection sites of the present invention have a strong correlation with the target trait, are more accurate, and are more suitable for breeding applications of Chinese dairy goats. For example, the milk production of dairy goats of different varieties is different, which will be reflected in the sequence and site, so the SNP sites related to milk production are added to the SNP sites of the present application as the SNP sites associated with the economic traits of dairy goats.

[0049] In some embodiments, in step (3), there are 35,869 SNP sites that can be used for chip development.

[0050] In some embodiments, step (4) comprises the following process:

[0051] S1. Select the SNP sites that evenly cover the 29 autosomes and the two contigs LWLT01000021.1 and LWLT01000027.1 of dairy goats from the SNP sites obtained in steps (2) and (3);

[0052] S2. Based on the location of the site on the chromosome, analyze its upstream and downstream sequences, design sequencing primers, and screen for SNP sites that can be used for chip development.

[0053] In some embodiments, in step (4), there are 64,011 SNP sites that can be used for chip development.

[0054] In some embodiments, step (5) comprises the following process:

[0055] S1. Based on the upstream and downstream sequences of the SNP site obtained in steps (2), (3), and (4), a liquid phase probe covering the target SNP is designed for each site to be tested and labeled with biotin;

[0056] S2. Based on the principle of complementary DNA base pairing, the probe is hybridized with the DNA sample of the genotype to be tested in solution, and complementary pairing with the target region of the genome forms a double strand;

[0057] S3. Using streptavidin-coated magnetic beads to adsorb and enrich the biotin-carrying DNA fragments to obtain DNA fragments containing the target SNP site;

[0058] S4. The DNA fragments obtained by capturing and enriching all sites in all tested strains are mixed, and the identification sequence is added. After amplification, library construction and second-generation sequencing, the genotyping results of each target SNP in a specific individual are obtained. The obtained probe sequence is the dairy goat SNP chip information.

[0059] In some embodiments, in step (5), the number of probe sequences obtained is 54,344.

[0060] In some embodiments, the SNP chip prepared by the present invention is a dairy goat whole genome 55K SNP liquid phase chip.

[0061] Compared with the prior art, the present invention has the following advantages:

[0062] The SNP marker sites provided by the present invention are evenly distributed across the 29 autosomes and two contigs of the X chromosome in the dairy goat genome, with uniform distribution and high coverage, ensuring the accuracy of dairy goat genome genetic assessment. The chip of the present invention collects significant sites associated with traits such as milk production performance, milk quality traits, udder morphology, and melatonin synthesis capacity in dairy goats, increasing the practicality of the chip. The sites of this chip are derived from SNP sites with good polymorphism in imported and local varieties of dairy goats widely raised in my country, meeting the scientific research needs of scientific researchers and being suitable for whole-genome molecular breeding.

[0063] The SNP sites of the dairy goat whole genome SNP chip of the present invention are screened and generated by the following four parts: the first part: selecting Saanen dairy goats, Toggenburg dairy goats, Alpine dairy goats, Guanzhong dairy goats, and Laoshan dairy goats as germplasm materials for resequencing, performing quality control on the predicted results, comparing with the reference genome, and identifying and screening candidate SNP sites with good breed polymorphism; the second part, screening the SNP sites obtained based on important functional genes and QTL sites in the public database; the third part, using whole genome association analysis and population selection signals to screen the SNP sites associated with important traits such as milk production, udder morphology, and melatonin synthesis capacity of dairy goats; the fourth part, using information from the public database to fill in the SNP sites in the genomic regions that cannot be evenly covered by the first three parts. The dairy goat whole genome 55K SNP chip provided by the present invention can be used for the identification and kinship analysis of imported dairy goats and domestically cultivated dairy goat varieties, and can also be used in multiple fields such as whole genome association analysis, whole genome selection breeding, population genetics analysis, and trait-related candidate gene and QTL site analysis and positioning, and has high value in production application and scientific research. BRIEF DESCRIPTION OF THE DRAWINGS

[0064] FIG1 is a distribution diagram of SNP sites of the present invention across the entire genome.

[0065] FIG2 is the distance between adjacent SNPs of the SNP molecular markers used for preparing the whole-genome 55K SNP chip of dairy goats according to the present invention (unit: Mb).

[0066] FIG3 shows the distribution of SNP sites at the whole genome level of the present invention.

[0067] FIG4 is the principal component analysis clustering result of 5 dairy goat breeds in Example 3 of the present invention. DETAILED DESCRIPTION

[0068] To make the objectives, technical solutions, and advantages of the present invention more clearly understood, the present invention will be further described in detail below with reference to the following examples. The specific embodiments described herein are intended only to illustrate the present invention and are not intended to limit the present invention in any way. In addition, in the following description, descriptions of known structures and technologies are omitted to avoid unnecessary confusion about the concepts of the present disclosure. Such structures and technologies are also described in many publications.

[0069] definition

[0070] Unless otherwise defined, all technical and scientific terms used in the present invention have the same meaning as commonly used in the field to which the present invention belongs. For the purpose of interpreting this specification, the following definitions will apply, and where appropriate, terms used in the singular will also include the plural form, and vice versa.

[0071] Unless the context clearly dictates otherwise, as used herein, the expressions "a" and "an" include plural references. For example, reference to "a cell" includes a plurality of such cells and equivalents thereof known to those skilled in the art, and so forth.

[0072] The following examples and accompanying drawings are provided to facilitate understanding of the present invention. However, it should be understood that these examples and accompanying drawings are intended to illustrate the present invention only and are not intended to limit the present invention in any way. The actual scope of protection of the present invention is set forth in the claims. It should be understood that any modifications and variations may be made without departing from the spirit of the present invention.

[0073] The technical solution of the present invention is not limited to the specific embodiments, and all technical variations made based on the technical solution of the present invention fall within the protection scope of the present invention.

[0074] Example 1: Acquisition of SNP Molecular Markers and Preparation of a 55K SNP Chip for the Whole Genome of Dairy Goats

[0075] (1) Dairy goats were selected as germplasm materials for resequencing, the sequencing results were quality controlled, compared with the reference genome, and the core candidate SNP sites were identified and filtered according to the SNP site attribute indicators;

[0076] The step (1) includes the following process:

[0077] S1. We selected 110 dairy goat germplasm samples from various representative dairy goat breeds widely raised in China and Europe. These included the Guanzhong and Laoshan dairy goats from China, and the Saanen, Alpine, and Toggenburg goats from Europe. We collected ear margin tissue to extract total DNA, which was then sequenced whole-genome. We constructed DNA libraries using the standard Illumina method, with a 500-bp DNA fragment length, a PE150 sequencing strategy, and a sequencing depth of 30×, ultimately yielding 2.2 Tb of data.

[0078] S2. Perform quality control on the raw sequencing data to obtain high-quality clean reads (filtered read lengths), which are then mapped to the reference genome to obtain alignment results for each sample;

[0079] S3. The alignment results were used to identify and extract SNP sites, and filtered according to minimum allele frequency (MAF) > 0.05, deletion rate < 1%, and heterozygosity rate < 5% to maximize site polymorphism and versatility, resulting in 33,716,044 core candidate SNP sites.

[0080] (2) Searching for research results in public databases to obtain candidate genes and quantitative trait loci associated with important economic traits, and comparing them with core candidate SNP loci to obtain functional SNP loci;

[0081] The step (2) includes the following process:

[0082] S1. Search the NCBI (https: / / www.ncbi.nlm.nih.gov / ) and QTL database (https: / / www.animalgenome.org / QTLdb / ) databases to obtain candidate genes and quantitative trait loci (QTLs) associated with important economic traits such as growth traits, udder morphology, and limb and hoof morphology in dairy goats.

[0083] S2. The candidate gene and quantitative trait loci were aligned with the core candidate SNP loci, combined with the resequencing results, duplicates were removed, and screening was performed based on a MAF value less than 0.05. 20,884 overlapping sites were obtained as functional SNP loci.

[0084] (3) Using the phenotypic information of sequenced individuals and bioinformatics methods, functional SNP sites associated with milk production, milk quality, udder morphology, and melatonin synthesis capacity were obtained;

[0085] The step (3) includes the following process:

[0086] S1. Phenotypic information was collected from five dairy goat breeds, primarily for important production traits such as melatonin synthesis capacity, diurnal variability of melatonin, milk yield, milk protein content, somatic cell count, coat color, body conformation, udder morphology, and hoof score. SNPs significantly associated with these traits were identified using XP-CLR, iHs, and Fst selection signal analysis, and genome-wide association studies (GWAS), combined with the dairy goat phenotypic information. The XP-CLR analysis selected sites within the top 1% of the scoring, while the iHs and Fst analyses selected sites with significant P values ​​(P < 0.05). The NCBI (https: / / www.ncbi.nlm.nih.gov / ) database was then used to obtain SNP information for genomic regions not covered by the aforementioned methods.

[0087] S2. Combining the results of the above four analysis methods, 35,869 functional SNP sites were obtained;

[0088] (4) Based on the absolute position of the candidate SNP site on the chromosome and the score of the targeted capture sequencing primer design results, select the SNP site for chip development;

[0089] The step (4) includes the following process:

[0090] S1. Select the SNP sites that evenly cover the 29 autosomes and the two contigs LWLT01000021.1 and LWLT01000027.1 of dairy goats from the SNP sites obtained in steps (2) and (3);

[0091] S2. Based on the location of the site on the chromosome, its upstream and downstream sequences were analyzed, and sequencing primers were designed to screen and obtain SNP sites that can be used for chip development. There are 64,011 SNP sites that can be used for chip development.

[0092] (5) Develop a whole-genome SNP chip for the dairy goat using targeted capture sequencing genotyping technology.

[0093] The step (5) includes the following process:

[0094] S1. Based on the upstream and downstream sequences of the SNP site obtained in steps (2), (3), and (4), a liquid phase probe covering the target SNP is designed for each site to be tested and labeled with biotin;

[0095] S2. Based on the principle of complementary DNA base pairing, the probe is hybridized with the DNA sample of the genotype to be tested in solution, and complementary pairing with the target region of the genome forms a double strand;

[0096] S3. Using streptavidin-coated magnetic beads to adsorb and enrich the biotin-carrying DNA fragments to obtain DNA fragments containing the target SNP site;

[0097] S4. The DNA fragments captured and enriched at all loci in all tested strains are mixed and labeled with recognition sequences. After amplification, library construction, and next-generation sequencing, the genotyping results for each target SNP in a specific individual are obtained. The resulting probe sequences constitute the dairy goat SNP array information, totaling 54,344 probe sequences. This results in the preparation of a dairy goat whole-genome 55K SNP liquid-phase array.

[0098] In this example, the whole genome of a dairy goat is approximately 2.7 Gb in length. To ensure that the SNPs selected by the chip are as uniform as possible and include more sites, the whole genome of the dairy goat is divided into 35 kb windows. Candidate sites are filtered based on the importance of the functional information contained in the site and the SNP site MAF value, resulting in 64,011 candidate SNP sites. The distribution of SNP sites across the whole genome is shown in Figure 1.

[0099] The designed SNP site information was submitted to the chip probe synthesis system of Compson for scoring, and sites with non-specific flanking sequences, typing errors, low polymorphism, and low detection rate were removed. For the deleted unqualified SNP sites, the SNP sites closest to them were selected for supplementation and scored again. According to the above steps, identification and screening were performed, and finally 54,344 final sites were obtained by total filtration. The distance (unit: Mb) between adjacent SNPs of the SNP molecular markers used to prepare the 55K SNP chip of the whole genome of dairy goats of the present invention is shown in Figure 2. The number of sites distributed on each chromosome of the whole genome SNP chip of dairy goats of the present invention is shown in Table 1.

[0100] Table 1 The number of SNP chip sites in the whole genome of dairy goats of the present invention distributed on each chromosome

[0101] As shown in Table 1, the 55K whole-genome SNP chip of the dairy goat of the present invention has a uniform distribution of sites, covers 29 autosomes and the contig representing the X chromosome, and has good whole-genome coverage.

[0102] The dairy goat whole-genome 55K SNP chip of the present invention has three main advantages: First, high design rationality: the SNP marker sites provided by the present invention are evenly distributed on the 29 autosomes and two contigs of the X chromosome of the dairy goat genome, with uniform distribution and high coverage, ensuring the accuracy of dairy goat genome genetic evaluation. The genome-wide distribution of SNP sites of the present invention is shown in Figure 3; Second, strong functional relevance: the chip collects significant sites related to traits such as milk production performance, milk quality traits, udder morphology and melatonin synthesis capacity of dairy goats, increasing the practicality of the chip; Third, high specificity: the characteristic sites of representative local dairy goat breeds in my country and highly selected commercial dairy goat breeds at home and abroad are compared and screened, and SNP sites unique to my country are specially added, which can specifically identify European dairy goats and Chinese dairy goats; Fourth, good applicability: the chip sites are derived from SNP sites with good polymorphism in imported dairy goat breeds and local fine breeds that are widely raised in my country, which not only meets the scientific research needs of scientific researchers but is also suitable for whole-genome molecular breeding.

[0103] Example 2 Process of Detecting Dairy Goat DNA Samples Using a 55K Whole Genome SNP Chip

[0104] (1) Sample collection and preservation

[0105] Samples for chip testing can be freshly collected goat ear tissue or peripheral venous blood. Ear tissue samples should be collected in a size similar to a soybean. Before collection, disinfect the sampling site with iodine and 75% ethanol. After collection, completely immerse the sample in 75% ethanol and store at -20°C. Peripheral venous blood should be collected using anticoagulant blood collection tubes with a volume of no less than 5ml. After collection, store at -20°C.

[0106] (2) DNA extraction gene

[0107] Genomic DNA was extracted from dairy goats using a genomic DNA extraction kit. The specific process was adjusted according to the sampling type (ear tissue or peripheral venous blood). The extracted genomic DNA should be stored at -20°C. DNA quality was verified using 1% agarose gel electrophoresis and a microspectrophotometer. Qualified samples had a clear main band, a total DNA (no RNA) content ≥1.0 μg, a concentration ≥20 ng / μL, a volume >50 μL, an OD260:OD280 ≤2.0 of 1.8, an OD260:OD230 ≥1.8, and no or slight degradation.

[0108] (3) Construction of dairy goat DNA library and chip detection

[0109] For dairy goat genomic DNA samples, library samples were prepared according to the high-throughput library development reaction kit process. After quality control, the library samples were ready for microarray testing. Microarray probes hybridized with the samples to capture the target loci. Sequencing was then performed on the sequencing machine, along with basic bioinformatics analysis. The target interval variation information for the sample was analyzed, allowing for genotyping.

[0110] Example 3 55K Whole-Genome SNP Genotyping Quality Assessment

[0111] According to the steps of Example 2, 200 Saanen dairy goats were genotyped using the dairy goat whole genome 55K SNP chip provided by the present invention, and the following quality evaluation was performed.

[0112] 1. Detection rate

[0113] The sample detection rate and site detection rate are important indicators for measuring the effectiveness of SNP chips, generally measured by the proportion of detections at a site depth greater than 5X for autosomes and chromosome X. In this example, the 200 Saanen dairy goats tested had an average sample detection rate of 98.82%, with the maximum and minimum individual detection rates being 99.33% and 98.61%, respectively. The average site detection rate reached 97.54%, with the maximum and minimum site detection rates being 99.28% and 97.13%, respectively. This demonstrates the effectiveness of the dairy goat 55K whole-genome SNP chip.

[0114] 2. Genotyping stability

[0115] SNP array genotyping stability refers to the consistency of results between two independent tests on the same sample. Six randomly selected Saanen dairy goat samples were thoroughly tested, and the results showed a genotype consistency of 98.72% and a correlation coefficient of 99.4%, demonstrating the high stability of the 55K whole-genome SNP array genotyping in dairy goats.

[0116] 3. Chip site accuracy

[0117] SNP liquid-phase microarray genotyping is based on targeted capture sequencing, with resequencing results used to assess the accuracy of the microarray results. Resequencing of 15 randomly selected Saanen goats from the 200 individuals identified above revealed an average of 98.02% agreement between the microarray loci and the resequencing results, demonstrating the high accuracy of the 55K whole-genome SNP microarray genotyping in dairy goats.

[0118] Example 4 Principal component analysis of five dairy goat breeds based on a 55K whole-genome SNP chip

[0119] The whole-genome 55K SNP array provided by the present invention was used to perform genotyping on DNA extracted from 15 Saanen goats (SN), 15 Alpine goats (AE), 15 Toggenburg goats (TU), 15 Laoshan goats (SD), and 15 Guanzhong goats (SX). Principal component analysis (PCA) was performed using Plink software and plotted, with the results shown in Figure 4. The results showed that among the five dairy goat breeds, domestically bred varieties could be significantly distinguished from imported varieties, demonstrating that the array provided by the present invention has a certain ability to identify and differentiate dairy goat breeds.

[0120] The dairy goat whole genome 55K SNP chip designed by the present invention contains 54,344 SNP sites. The position information of all SNP sites is shown in Table 2.

[0121] Table 2. SNP chip sites in the whole genome of dairy goats

Claims

1. A SNP molecular marker for the whole genome of dairy goats, characterized in that: The SNP molecular marker is selected from at least one of the markers shown in Table 2.

2. A molecular probe, characterized in that The molecular probe is used to specifically identify the SNP molecular marker described in claim 1.

3. A dairy goat whole genome SNP chip, characterized in that: The SNP chip comprises probes targeting the SNP molecular markers according to claim 1.

4. The dairy goat whole genome SNP chip according to claim 3, characterized in that: The molecular marker is associated with one or more of the milk production performance, milk quality traits, udder morphology, limb and hoof morphology, coat color, body shape, melatonin synthesis ability and diurnal variation rate of melatonin of dairy goats; Preferably, the milk production performance includes milk yield; Preferably, the milk quality traits include milk protein rate, milk fat rate, lactose rate, and somatic cell count.

5. A kit, characterized in that: The kit comprises the molecular probe according to claim 2, or the SNP chip according to claim 3 or 4.

6. Use of the molecular probe according to claim 2, or the SNP chip according to claim 3 or 4, or the kit according to claim 5 in whole genome breeding of dairy goats.

7. Use of the molecular probe according to claim 2, or the SNP chip according to claim 3 or 4, or the kit according to claim 5 in identifying the kinship of dairy goats.

8. Use of the molecular probe according to claim 2, or the SNP chip according to claim 3 or 4, or the kit according to claim 5 in identifying European dairy goat and Chinese dairy goat breeds.

9. Use of the molecular probe according to claim 2, or the SNP chip according to claim 3 or 4, or the kit according to claim 5 in genotyping detection of dairy goats.

10. Use of the molecular probe according to claim 2, or the SNP chip according to claim 3 or 4, or the kit according to claim 5 in genetic diversity analysis of dairy goat populations or QTL positioning analysis of target traits.

Images