CN117089635B - Molecular marker combination for analyzing goat reproductive performance and application - Google Patents
Molecular marker combination for analyzing goat reproductive performance and application Download PDFInfo
- Publication number
- CN117089635B CN117089635B CN202311361081.3A CN202311361081A CN117089635B CN 117089635 B CN117089635 B CN 117089635B CN 202311361081 A CN202311361081 A CN 202311361081A CN 117089635 B CN117089635 B CN 117089635B
- Authority
- CN
- China
- Prior art keywords
- goat
- reproductive performance
- application
- snp
- analyzing
- Prior art date
- Legal status (The legal status is an assumption and is not a legal conclusion. Google has not performed a legal analysis and makes no representation as to the accuracy of the status listed.)
- Active
Links
- 241000283707 Capra Species 0.000 title claims abstract description 97
- 230000001850 reproductive effect Effects 0.000 title claims abstract description 41
- 239000003147 molecular marker Substances 0.000 title abstract description 6
- 108090000623 proteins and genes Proteins 0.000 claims abstract description 39
- 238000000034 method Methods 0.000 claims abstract description 22
- 239000003068 molecular probe Substances 0.000 claims abstract description 13
- 238000009395 breeding Methods 0.000 claims abstract description 9
- 230000001488 breeding effect Effects 0.000 claims abstract description 9
- 238000011156 evaluation Methods 0.000 claims abstract description 7
- 239000000523 sample Substances 0.000 claims description 26
- 108020004414 DNA Proteins 0.000 claims description 13
- 238000004458 analytical method Methods 0.000 claims description 12
- 238000012216 screening Methods 0.000 claims description 4
- 102100027627 Follicle-stimulating hormone receptor Human genes 0.000 claims description 3
- 101150110792 GNRHR gene Proteins 0.000 claims description 3
- 102100035970 Growth/differentiation factor 9 Human genes 0.000 claims description 3
- 101000862396 Homo sapiens Follicle-stimulating hormone receptor Proteins 0.000 claims description 3
- 101001075110 Homo sapiens Growth/differentiation factor 9 Proteins 0.000 claims description 3
- 101000595526 Homo sapiens T-box brain protein 1 Proteins 0.000 claims description 3
- 102100036083 T-box brain protein 1 Human genes 0.000 claims description 3
- 238000002864 sequence alignment Methods 0.000 claims description 3
- 101100479039 Caenorhabditis elegans aars-1 gene Proteins 0.000 claims 1
- 230000002068 genetic effect Effects 0.000 abstract description 9
- 230000008569 process Effects 0.000 abstract description 5
- 101100163849 Arabidopsis thaliana ARS1 gene Proteins 0.000 abstract description 3
- 101100097319 Schizosaccharomyces pombe (strain 972 / ATCC 24843) ala1 gene Proteins 0.000 abstract description 3
- 238000001514 detection method Methods 0.000 description 12
- 102000053602 DNA Human genes 0.000 description 11
- 230000035558 fertility Effects 0.000 description 9
- 238000007796 conventional method Methods 0.000 description 7
- 230000008901 benefit Effects 0.000 description 5
- 239000002773 nucleotide Substances 0.000 description 5
- 125000003729 nucleotide group Chemical group 0.000 description 5
- 238000012163 sequencing technique Methods 0.000 description 5
- 241001465754 Metazoa Species 0.000 description 4
- 239000003153 chemical reaction reagent Substances 0.000 description 4
- 230000006872 improvement Effects 0.000 description 4
- 238000002360 preparation method Methods 0.000 description 4
- 238000011160 research Methods 0.000 description 4
- 108091028043 Nucleic acid sequence Proteins 0.000 description 3
- 238000012360 testing method Methods 0.000 description 3
- 239000000872 buffer Substances 0.000 description 2
- 238000006243 chemical reaction Methods 0.000 description 2
- 238000012217 deletion Methods 0.000 description 2
- 230000037430 deletion Effects 0.000 description 2
- 238000013461 design Methods 0.000 description 2
- 230000008030 elimination Effects 0.000 description 2
- 238000003379 elimination reaction Methods 0.000 description 2
- 238000005516 engineering process Methods 0.000 description 2
- 239000011521 glass Substances 0.000 description 2
- 230000003100 immobilizing effect Effects 0.000 description 2
- 239000012528 membrane Substances 0.000 description 2
- 238000005457 optimization Methods 0.000 description 2
- 210000005259 peripheral blood Anatomy 0.000 description 2
- 239000011886 peripheral blood Substances 0.000 description 2
- 241000894007 species Species 0.000 description 2
- 108700028369 Alleles Proteins 0.000 description 1
- 238000000018 DNA microarray Methods 0.000 description 1
- 108090000790 Enzymes Proteins 0.000 description 1
- 102000004190 Enzymes Human genes 0.000 description 1
- 102000003960 Ligases Human genes 0.000 description 1
- 108090000364 Ligases Proteins 0.000 description 1
- 108091092919 Minisatellite Proteins 0.000 description 1
- 239000000020 Nitrocellulose Substances 0.000 description 1
- 239000004677 Nylon Substances 0.000 description 1
- VYPSYNLAJGMNEJ-UHFFFAOYSA-N Silicium dioxide Chemical compound O=[Si]=O VYPSYNLAJGMNEJ-UHFFFAOYSA-N 0.000 description 1
- 238000012271 agricultural production Methods 0.000 description 1
- 230000003321 amplification Effects 0.000 description 1
- 239000011324 bead Substances 0.000 description 1
- 230000009286 beneficial effect Effects 0.000 description 1
- SESFRYSPDFLNCH-UHFFFAOYSA-N benzyl benzoate Chemical compound C=1C=CC=CC=1C(=O)OCC1=CC=CC=C1 SESFRYSPDFLNCH-UHFFFAOYSA-N 0.000 description 1
- 210000004369 blood Anatomy 0.000 description 1
- 239000008280 blood Substances 0.000 description 1
- 238000004364 calculation method Methods 0.000 description 1
- 230000000295 complement effect Effects 0.000 description 1
- 239000000470 constituent Substances 0.000 description 1
- 101150024923 da gene Proteins 0.000 description 1
- 230000008021 deposition Effects 0.000 description 1
- 238000011161 development Methods 0.000 description 1
- 238000010586 diagram Methods 0.000 description 1
- 230000000694 effects Effects 0.000 description 1
- 238000002474 experimental method Methods 0.000 description 1
- 230000004907 flux Effects 0.000 description 1
- 238000012215 gene cloning Methods 0.000 description 1
- 238000009396 hybridization Methods 0.000 description 1
- 238000003780 insertion Methods 0.000 description 1
- 230000037431 insertion Effects 0.000 description 1
- 230000004807 localization Effects 0.000 description 1
- 238000004519 manufacturing process Methods 0.000 description 1
- 238000013507 mapping Methods 0.000 description 1
- 239000003550 marker Substances 0.000 description 1
- 239000000463 material Substances 0.000 description 1
- 235000013372 meat Nutrition 0.000 description 1
- 239000008267 milk Substances 0.000 description 1
- 210000004080 milk Anatomy 0.000 description 1
- 235000013336 milk Nutrition 0.000 description 1
- 239000000203 mixture Substances 0.000 description 1
- 238000012986 modification Methods 0.000 description 1
- 230000004048 modification Effects 0.000 description 1
- 229920001220 nitrocellulos Polymers 0.000 description 1
- 238000003199 nucleic acid amplification method Methods 0.000 description 1
- 150000007523 nucleic acids Chemical group 0.000 description 1
- 229920001778 nylon Polymers 0.000 description 1
- 239000004033 plastic Substances 0.000 description 1
- 229920000307 polymer substrate Polymers 0.000 description 1
- 230000000644 propagated effect Effects 0.000 description 1
- 102000004169 proteins and genes Human genes 0.000 description 1
- 238000012253 re-sequencing analysis Methods 0.000 description 1
- 238000003753 real-time PCR Methods 0.000 description 1
- 238000007894 restriction fragment length polymorphism technique Methods 0.000 description 1
- 231100000241 scar Toxicity 0.000 description 1
- 230000035945 sensitivity Effects 0.000 description 1
- 238000007493 shaping process Methods 0.000 description 1
- 239000000741 silica gel Substances 0.000 description 1
- 229910002027 silica gel Inorganic materials 0.000 description 1
- 230000002194 synthesizing effect Effects 0.000 description 1
- 230000007704 transition Effects 0.000 description 1
- 238000013519 translation Methods 0.000 description 1
- 230000014616 translation Effects 0.000 description 1
Classifications
-
- C—CHEMISTRY; METALLURGY
- C12—BIOCHEMISTRY; BEER; SPIRITS; WINE; VINEGAR; MICROBIOLOGY; ENZYMOLOGY; MUTATION OR GENETIC ENGINEERING
- C12Q—MEASURING OR TESTING PROCESSES INVOLVING ENZYMES, NUCLEIC ACIDS OR MICROORGANISMS; COMPOSITIONS OR TEST PAPERS THEREFOR; PROCESSES OF PREPARING SUCH COMPOSITIONS; CONDITION-RESPONSIVE CONTROL IN MICROBIOLOGICAL OR ENZYMOLOGICAL PROCESSES
- C12Q1/00—Measuring or testing processes involving enzymes, nucleic acids or microorganisms; Compositions therefor; Processes of preparing such compositions
- C12Q1/68—Measuring or testing processes involving enzymes, nucleic acids or microorganisms; Compositions therefor; Processes of preparing such compositions involving nucleic acids
- C12Q1/6876—Nucleic acid products used in the analysis of nucleic acids, e.g. primers or probes
- C12Q1/6888—Nucleic acid products used in the analysis of nucleic acids, e.g. primers or probes for detection or identification of organisms
-
- C—CHEMISTRY; METALLURGY
- C12—BIOCHEMISTRY; BEER; SPIRITS; WINE; VINEGAR; MICROBIOLOGY; ENZYMOLOGY; MUTATION OR GENETIC ENGINEERING
- C12Q—MEASURING OR TESTING PROCESSES INVOLVING ENZYMES, NUCLEIC ACIDS OR MICROORGANISMS; COMPOSITIONS OR TEST PAPERS THEREFOR; PROCESSES OF PREPARING SUCH COMPOSITIONS; CONDITION-RESPONSIVE CONTROL IN MICROBIOLOGICAL OR ENZYMOLOGICAL PROCESSES
- C12Q1/00—Measuring or testing processes involving enzymes, nucleic acids or microorganisms; Compositions therefor; Processes of preparing such compositions
- C12Q1/68—Measuring or testing processes involving enzymes, nucleic acids or microorganisms; Compositions therefor; Processes of preparing such compositions involving nucleic acids
- C12Q1/6813—Hybridisation assays
- C12Q1/6834—Enzymatic or biochemical coupling of nucleic acids to a solid phase
- C12Q1/6837—Enzymatic or biochemical coupling of nucleic acids to a solid phase using probe arrays or probe chips
-
- C—CHEMISTRY; METALLURGY
- C40—COMBINATORIAL TECHNOLOGY
- C40B—COMBINATORIAL CHEMISTRY; LIBRARIES, e.g. CHEMICAL LIBRARIES
- C40B40/00—Libraries per se, e.g. arrays, mixtures
- C40B40/04—Libraries containing only organic compounds
- C40B40/06—Libraries containing nucleotides or polynucleotides, or derivatives thereof
-
- C—CHEMISTRY; METALLURGY
- C12—BIOCHEMISTRY; BEER; SPIRITS; WINE; VINEGAR; MICROBIOLOGY; ENZYMOLOGY; MUTATION OR GENETIC ENGINEERING
- C12Q—MEASURING OR TESTING PROCESSES INVOLVING ENZYMES, NUCLEIC ACIDS OR MICROORGANISMS; COMPOSITIONS OR TEST PAPERS THEREFOR; PROCESSES OF PREPARING SUCH COMPOSITIONS; CONDITION-RESPONSIVE CONTROL IN MICROBIOLOGICAL OR ENZYMOLOGICAL PROCESSES
- C12Q2600/00—Oligonucleotides characterized by their use
- C12Q2600/124—Animal traits, i.e. production traits, including athletic performance or the like
-
- C—CHEMISTRY; METALLURGY
- C12—BIOCHEMISTRY; BEER; SPIRITS; WINE; VINEGAR; MICROBIOLOGY; ENZYMOLOGY; MUTATION OR GENETIC ENGINEERING
- C12Q—MEASURING OR TESTING PROCESSES INVOLVING ENZYMES, NUCLEIC ACIDS OR MICROORGANISMS; COMPOSITIONS OR TEST PAPERS THEREFOR; PROCESSES OF PREPARING SUCH COMPOSITIONS; CONDITION-RESPONSIVE CONTROL IN MICROBIOLOGICAL OR ENZYMOLOGICAL PROCESSES
- C12Q2600/00—Oligonucleotides characterized by their use
- C12Q2600/156—Polymorphic or mutational markers
-
- Y—GENERAL TAGGING OF NEW TECHNOLOGICAL DEVELOPMENTS; GENERAL TAGGING OF CROSS-SECTIONAL TECHNOLOGIES SPANNING OVER SEVERAL SECTIONS OF THE IPC; TECHNICAL SUBJECTS COVERED BY FORMER USPC CROSS-REFERENCE ART COLLECTIONS [XRACs] AND DIGESTS
- Y02—TECHNOLOGIES OR APPLICATIONS FOR MITIGATION OR ADAPTATION AGAINST CLIMATE CHANGE
- Y02P—CLIMATE CHANGE MITIGATION TECHNOLOGIES IN THE PRODUCTION OR PROCESSING OF GOODS
- Y02P60/00—Technologies relating to agriculture, livestock or agroalimentary industries
- Y02P60/80—Food processing, e.g. use of renewable energies or variable speed drives in handling, conveying or stacking
- Y02P60/87—Re-use of by-products of food processing for fodder production
Landscapes
- Chemical & Material Sciences (AREA)
- Organic Chemistry (AREA)
- Life Sciences & Earth Sciences (AREA)
- Health & Medical Sciences (AREA)
- Proteomics, Peptides & Aminoacids (AREA)
- Engineering & Computer Science (AREA)
- Zoology (AREA)
- Wood Science & Technology (AREA)
- Analytical Chemistry (AREA)
- Molecular Biology (AREA)
- Biochemistry (AREA)
- Immunology (AREA)
- Microbiology (AREA)
- Physics & Mathematics (AREA)
- Biotechnology (AREA)
- Biophysics (AREA)
- Bioinformatics & Cheminformatics (AREA)
- General Engineering & Computer Science (AREA)
- General Health & Medical Sciences (AREA)
- Genetics & Genomics (AREA)
- Chemical Kinetics & Catalysis (AREA)
- General Chemical & Material Sciences (AREA)
- Medicinal Chemistry (AREA)
- Measuring Or Testing Involving Enzymes Or Micro-Organisms (AREA)
Abstract
The invention discloses a molecular marker combination for analyzing goat reproductive performance and application thereof, relates to the technical field of biology, and provides 414 molecular markers capable of analyzing goat reproductive performance characteristics, wherein physical position information of the molecular markers is determined based on genome sequence comparison of goat reference genome ARS1, and a molecular probe combination, a gene chip and a kit prepared from the 414 SNP molecular markers can be used for carrying out genetic evaluation on goat individuals, and carrying out individual selection on early goat reproductive performance which is difficult to measure, so that generation interval is shortened, breeding process is accelerated, and a large amount of breeding cost is saved.
Description
Technical Field
The invention relates to the technical field of biology, in particular to the technical field of biological detection, and more particularly relates to goat reproduction SNP locus combination and application thereof.
Background
Goats are one of the earliest domesticated domestic animals in world records, and have been supplied with meat, skin, milk, etc. from ancient times. The animal propagation character is taken as an important component of economic character, the performance of the animal propagation character is closely related to the cultivation benefit and the production cost, and the economic development of animal husbandry is directly influenced. Propagation traits are affected by a plurality of factors, and genes are taken as one of main acting factors, so that the contribution to the traits is great. Aiming at the current goats with various varieties and variable characters, how to rapidly screen the goats and distinguish the reproductive performance of the goats becomes the urgent problem to be solved, therefore, the design of the SNP chip which is applicable to the China goats and can rapidly and effectively detect the reproductive performance has very important significance.
Disclosure of Invention
In order to meet the requirements of the current goat variety research and agricultural production in China on the detection of the goat reproductive performance, the invention provides a molecular probe combination, a gene chip, a kit and application for analyzing the goat reproductive performance, and the site information provided by the invention can be used for rapidly and accurately realizing goat reproductive deposition evaluation, variety screening, variety identification, variety tracing and goat breeding, is beneficial to germplasm resource protection and germplasm resource improvement, and has the advantages of short time consumption, low cost and wide market benefit.
In order to achieve the technical purpose of the invention, the invention provides the following technical scheme:
in a first aspect, the present invention provides an application of 414 SNP site combinations in analysis of goat reproduction, wherein the physical positions of the 414 SNP site combinations are shown in table 1:
table 1 location information for 414 combinations of sites
Its physical location was determined based on goat reference genome ARS1 genome sequence alignment.
A second aspect provides a method of analyzing goat reproduction by comparing the genotype of 414 SNP sites of the genomic DNA of a goat to be tested with the genotype of the 414 SNP sites of the genomic DNA of a control goat;
wherein the 414 SNP loci are 414 SNP loci described in Table 1.
In a third aspect, there is provided a molecular probe set for analyzing goat reproduction, which detects SNP site combinations as shown in Table 1 in a sample to be tested, wherein physical position information of the site combinations in Table 1 is determined based on goat reference genome ARS1 genome sequence alignment.
In a fourth aspect, a gene chip for analyzing goat reproduction, the gene chip being loaded with the molecular probe combination according to the third aspect.
The fifth aspect is a kit for analyzing goat reproduction, which has the molecular probe set according to the third aspect or the gene chip according to the fourth aspect.
The sixth aspect is a method for analyzing goat reproduction, wherein the molecular probe combination of the third aspect or the gene chip of the fourth aspect or the kit of the fifth aspect is used for detecting a sample to be detected.
The molecular probe set according to the seventh aspect, the third aspect or the gene chip according to the fourth aspect or the kit according to the fifth aspect has any of the following uses:
(1) Application in goat reproductive performance evaluation;
(2) The application in screening the breeder's property variety of the goat;
(3) The application in the identification of the goat reproductive performance variety;
(4) The application in tracing the breeder's propagation performance variety;
(5) Use in goat breeding for reproductive performance;
(6) The application in germplasm resource protection of goats with reproductive performance;
(7) Use in improvement of germplasm resources for a reproductive performance goat;
(8) The application in goat pedigree reconstruction.
Advantageous effects
1. The SNP locus combination which only consists of 414 SNP loci and is used for analyzing the reproductive performance of goats is provided on the basis of researching genetic resources of a plurality of goats at home and abroad, the SNP locus combination provided by the invention has good domestic and foreign universality, can rapidly evaluate the early-stage non-obvious goat reproductive performance from the gene level, acquire more accurate breeding evaluation information, control the breeding process, and can also screen, identify and trace the goat varieties by utilizing the locus combination, thereby providing technical support for germplasm resource protection and germplasm resource improvement.
2. The probe combination, the gene chip and the kit for analyzing goat reproduction provided by the invention have the characteristics of small flux, low cost and easier analysis, and have wide universality and wide market prospect.
Drawings
FIG. 1 is a Manhattan plot of elimination analysis of a high and low fertility goat breed;
fig. 2 is a graph of the results of the present application for performing a significance test on the determination results of population threshold analysis.
Detailed Description
The invention will be further elucidated with reference to the following detailed description of specific embodiments, which are merely illustrative and are not to be construed as limiting the invention. Unless otherwise indicated, the techniques used in the examples are conventional and well known to those skilled in the art, and may be carried out with reference to the "bioinformatics and functional genomics" original third edition or related books, and the bioinformatics software and products used are also commercially available. The various processes and methods not described in detail are conventional methods known in the art, the source of the materials used, the trade names and those necessary to list the constituents are all indicated at the first occurrence, and the same reagents used thereafter, unless otherwise indicated, are all the same as the first indicated.
In addition, it should be noted that the site combination and application provided by the invention are accomplished by the inventor through hard creative work and optimization work.
The features and advantages described in the previous site combination section herein are equally applicable to the combination of molecular probes formed based on site combination, gene chips, kits and uses thereof, and are not described in detail herein.
The goat reproductive performance referred to in the present invention is divided according to the magnitude of fertility.
The SNP referred to in the present invention means a single nucleotide polymorphism (Single Nucleotide Polymorphism), mainly means a DNA sequence polymorphism caused by a variation of a single nucleotide including a variation caused by a single base transition, a transversion, an insertion or a deletion at the genome level.
It should be noted that the molecular marker of the present invention is any heritable and detectable DNA sequence or protein, including, but not limited to, molecular markers based on molecular hybridization, such as RFLP, minisatelliteDNA; molecular markers based on PCR technology, such as RAPD, STS, SSR and SCAR; DNA markers based on restriction and PCR techniques; molecular markers based on DNA chip technology, such as SNPs; analytical marking techniques developed based on EST databases, and the like. The molecular marker provided by the invention can be used for genome mapping, gene localization research, gene cloning based on a map, species genetic relationship, system classification and the like.
The probe referred to in the present invention is a nucleic acid sequence (DNA or RNA) with a known sequence complementary to the target gene, such as Taqman-MGB probe.
It should be noted that the kit of the present invention is any one of the kits conventionally used in the art, which contains reagents used for detection or experiment, and is convenient for operators to get rid of the heavy reagent preparation and optimization process. In one embodiment of the invention, the kit comprises a primer for amplifying the site information provided by the invention, a molecular marker or a probe or a gene chip for detecting the site information provided by the invention, an enzyme and a buffer used for amplification, or a fluorescent marker used for detection.
Example 1 obtaining of reproductive performance SNP site combinations
1. Selection of goat individuals
In order to realize more comprehensive coverage of domestic and foreign goat breeds, 361 individuals of 68 goat breeds in the global scope are re-sequenced, and each breed is:
the preparation method comprises the following steps of, menabe coat Mei Nabei Goat.
It should be noted that, some kinds of goats have no formal Chinese translations, and English names are still used at present.
2. Acquisition of Total SNP set of goat Whole Gene
The sample carrying genetic information from the individual goat in step 1 is collected using methods conventional in the art, including but not limited to blood, cells, tissue, skin, hair, excrement, etc. Genetic information (such as DNA) in the sample is extracted for high-depth sequencing, and comparison is carried out on a reference genome (obtained from NCBI) of a goat published in 2016 by using two modes of SAMtools and GATK, and a common result obtained by the comparison of the two modes forms a SNP set which contains 17,668,737 single nucleotide variations at the whole genome level. From these breeds, 39 goat individuals related to the breeding size were selected.
The genetic information (genetic information) referred to herein refers to information that an organism is to replicate the same thing as itself, is transferred from a parent to a progeny, or is transferred from a cell to a cell each time each cell divides.
It should be noted that, the high-depth sequencing by extracting genetic information (e.g., DNA) in the sample may be performed by a biological company, such as hua da gene company, illuminea company, etc., and the high-depth sequencing method is a conventional method in the art or a method of the biological company, and in one embodiment of the present invention, the high-depth sequencing is performed by using an average sequencing depth of about 25.7×, and using a re-sequencing analysis procedure.
3. Screening of candidate genes and located functional regions
All species individuals with high and low fertility are grouped according to the significant differences in fertility exhibited by goat breeds worldwide, and selection elimination analysis is performed by grouping high and low fertility into two groups, namely black bengal goat (Bengla black goat), jiing Gray goats, barberi goats (babari), naine goats, woyito_guti goats (Wo Yituo Gu Di) in groups.
It should be noted that, the fertility level may be adjusted according to market demands or research objectives, and the present invention is not limited thereto, and in one embodiment of the present invention, one goat is bred annually as a low fertility goat, and two or more goats are bred annually as high fertility goats.
The invention uses the nucleotide base polymorphism and locus allele frequency difference between two groups of goats swept by the calculated pi value and fst value to scanThe functional areas related to the propagation height are obtained by intersection of calculation results of the two methods, the functional areas related to the propagation height are screened out, manhattan diagrams which are generated by different groups of propagation height characters and are made through pi values and shown in the figure 1 are obtained, genes in the areas are screened by referring to the published gene research results, and finally 7 candidate genes which are related to the propagation performance and have very definite functions are determinedSENP7,SLC4A,TBR1,GnRHR,GDF9,FSHR,LHβ. And then determining the functional region corresponding to the candidate gene by perl script.
4. Acquisition of propagated SNP site combinations
Searching SNP loci corresponding to the functional regions of the candidate genes determined in the step 3 in the total SNP set by using bedtools to obtain the SNP loci corresponding to the functional regionsSENP7,SLC4A,TBR1,GnRHR,GDF9,FSHR,LHβA total of 7 reproductive performance related functional genes are associated and comprise only a reproductive performance site combination of 414 snp sites.
EXAMPLE 2 preparation of primer set and probe set Using reproductive-performance SNP site set
The technical personnel designs the primer according to the sequence information of each locus in the reproductive performance SNP locus combination provided by the invention, and carries out secondary structure evaluation and Tm value evaluation on the designed primer, so that the primer with good specificity and high sensitivity can be finally obtained, and the detection purpose can be realized under the same reaction condition.
The secondary structure and Tm value can be evaluated by any means commonly used in the art, for example, by using DNA shaping Form to evaluate the secondary structure, see (http:// unfold. Rna. Albany. Edu// q=mfold/DNA-shaping-Form), and then using software RaW-Probe to evaluate the Tm value.
The method is a conventional method, and the site information in the SNP site combination for propagation provided by the application can be obtained without creative labor, so that the primer obtained by the SNP site combination provided by the invention also belongs to the protection scope of the invention.
Likewise, probes prepared by using the SNP site combinations provided by the invention, such as tanqman probes, also belong to the scope of the invention.
Example 3 SNP site combination for analysis of goat reproductive performance for preparation of Gene chip
The SNP gene chip of the invention is obtained by immobilizing the primer or probe obtained in example 2 on a polymer substrate such as nylon membrane, nitrocellulose membrane, plastic, silica gel wafer, micro magnetic beads or the like by a conventional method, or immobilizing the probe on a glass plate, or directly synthesizing the primer or probe obtained in example 2 on a hard surface such as glass, and the method of using the SNP gene chip of the invention is the same as that of the conventional method.
It should be noted that, a person skilled in the art may prepare an SNP gene chip for detecting goat reproduction in any one of the ways, and may also entrust the biological company to prepare the SNP gene chip, but all SNP gene chips prepared based on the SNP locus combination for reproduction analysis provided in the application belong to the protection scope of the invention.
Example 4 analysis kit for goat reproductive performance
The SNP detection kit for propagation analysis provided by the application comprises a primer or a probe or a gene chip obtained based on the SNP locus combination obtained in example 1. Depending on the type of use, corresponding detection reagents are also included, such as buffers, ligases, aceQUniversal u+ Probe Master Mix V2, taqman probes, etc., conventionally used for fluorescent quantitative PCR reactions when Taqman probes are obtained based on the SNP site combinations obtained in example 1.
Different SNP kits for detecting goat reproductive performance are configured by a person skilled in the art according to different using modes, but the SNP kit for detecting goat reproductive performance based on the combination of reproductive performance SNP loci provided by the application belongs to the protection scope of the invention.
Example 5 detection of goat reproductive performance
Detection of reproduction of goats with known reproductive capacity based on analysis of SNP locus combinations of goat reproduction provided in example 1 of the application, and determination of detection accuracy based on detection results in combination with phenotypic traits of known reproductive capacity, specifically:
collecting peripheral blood of goats by adopting a conventional method, and extracting whole genome DNA (deoxyribonucleic acid) in the peripheral blood to obtain a whole genome DNA sample;
the gene chip is designed according to the site information in the SNP site combination provided by the invention by adopting a conventional method, a whole genome DNA sample of the goat is detected, a typing result of each site in the goat (namely, whether each site is homozygote, heterozygote, mutant homozygote or base deletion result) is obtained, the frequency value of the typing result of each site is calculated, the frequency value is compared with a population threshold value, and the comparison result shows that the gene detection result is consistent with the corresponding goat reproductive performance phenotype.
The population threshold value is obtained by analyzing populations with different fertility, and the method is the same as the above.
The method has the advantages that the significance test (independent sample Manwhitney U test) is carried out on the judging result of the analysis of the high-fertility goat population and the low-fertility goat population, the result is shown in figure 2, according to the result in the figure, P is less than 0.01, the difference is extremely remarkable, and the accuracy and the effectiveness of the judging result by adopting the method are obvious.
Industrial application
The SNP probe combination, the gene chip and the kit for analyzing goat reproduction, which can be prepared by the SNP locus combination for analyzing goat reproduction only consisting of 414 SNP loci, can analyze the reproduction of goat individuals on the genome level, evaluate genetic information, screen varieties, identify varieties, control the breeding process, and can be applied to the tracing of goat varieties, the reconstruction of goat pedigree, the protection of germplasm resources and the improvement of germplasm resources.
The above description is only for the purpose of aiding in understanding the preferred embodiments of the present invention and is not intended to limit the present invention, and various changes and modifications may be made to the present invention by those skilled in the art without departing from the spirit of the present invention, and it should also be considered that the present invention shall fall within the scope of the present invention.
Claims (7)
- Application of 1.414 SNP locus combinations in analysis of goat reproductive performance, wherein the 414 SNP locus combinations are derived fromSENP7,SLC4A,TBR1,GnRHR,GDF9,FSHR,LHβThe physical positions of the genes are shown in the following table:；its physical location is determined based on genomic sequence alignment of goat reference genome ARS 1.
- 2. A method for analyzing goat reproductive performance, which compares the genotype of 414 SNP loci of genomic DNA of a goat to be detected with the genotype of the 414 SNP loci of genomic DNA of a control goat;wherein the 414 SNP sites are 414 SNP sites as set forth in claim 1.
- 3. A molecular probe combination for analyzing goat reproductive performance, which detects the SNP site combination as set forth in claim 1 in a sample to be tested.
- 4. A gene chip for analyzing goat reproductive performance, the gene chip being loaded with the molecular probe combination of claim 3.
- 5. A kit for analyzing goat reproductive performance, which has the molecular probe set according to claim 3 or the gene chip according to claim 4.
- 6. A method for analyzing goat reproductive performance, which comprises detecting a sample to be detected using the molecular probe set of claim 3 or the gene chip of claim 4 or the kit of claim 5.
- 7. The molecular probe combination of claim 3 or the gene chip of claim 4 or the kit of claim 5 has the following uses:(1) Application in goat reproductive performance evaluation;(2) Application in screening goat reproductive performance varieties;(3) Application in the identification of goat reproductive performance varieties;(4) The application in tracing goat reproductive performance varieties;(5) Application in goat breeding;(6) The application in goat pedigree reconstruction.
Priority Applications (1)
| Application Number | Priority Date | Filing Date | Title |
|---|---|---|---|
| CN202311361081.3A CN117089635B (en) | 2023-10-20 | 2023-10-20 | Molecular marker combination for analyzing goat reproductive performance and application |
Applications Claiming Priority (1)
| Application Number | Priority Date | Filing Date | Title |
|---|---|---|---|
| CN202311361081.3A CN117089635B (en) | 2023-10-20 | 2023-10-20 | Molecular marker combination for analyzing goat reproductive performance and application |
Publications (2)
| Publication Number | Publication Date |
|---|---|
| CN117089635A CN117089635A (en) | 2023-11-21 |
| CN117089635B true CN117089635B (en) | 2024-03-01 |
Family
ID=88770270
Family Applications (1)
| Application Number | Title | Priority Date | Filing Date |
|---|---|---|---|
| CN202311361081.3A Active CN117089635B (en) | 2023-10-20 | 2023-10-20 | Molecular marker combination for analyzing goat reproductive performance and application |
Country Status (1)
| Country | Link |
|---|---|
| CN (1) | CN117089635B (en) |
Citations (3)
| Publication number | Priority date | Publication date | Assignee | Title |
|---|---|---|---|---|
| CN101338340A (en) * | 2008-08-29 | 2009-01-07 | 中国农业科学院北京畜牧兽医研究所 | Method for detecting goat fertility |
| CN105274094A (en) * | 2014-07-11 | 2016-01-27 | 深圳华大农业与循环经济科技有限公司 | Snp marker and application thereof |
| CN116814813A (en) * | 2023-08-16 | 2023-09-29 | 湖北省农业科学院畜牧兽医研究所 | Molecular marker related to lambing number in goat 3BHSD gene and application thereof |
-
2023
- 2023-10-20 CN CN202311361081.3A patent/CN117089635B/en active Active
Patent Citations (3)
| Publication number | Priority date | Publication date | Assignee | Title |
|---|---|---|---|---|
| CN101338340A (en) * | 2008-08-29 | 2009-01-07 | 中国农业科学院北京畜牧兽医研究所 | Method for detecting goat fertility |
| CN105274094A (en) * | 2014-07-11 | 2016-01-27 | 深圳华大农业与循环经济科技有限公司 | Snp marker and application thereof |
| CN116814813A (en) * | 2023-08-16 | 2023-09-29 | 湖北省农业科学院畜牧兽医研究所 | Molecular marker related to lambing number in goat 3BHSD gene and application thereof |
Non-Patent Citations (3)
| Title |
|---|
| 促黄体素β基因多态性及其与济宁青山羊产羔数的关系;狄冉等;畜牧兽医学报;第40卷(第8期);第1171-1178页 * |
| 兰蓉等.山羊产羔数全基因组关联分析.畜牧兽医学报.2015,第46卷(第4期),第549-554. * |
| 运用全基因组重测序对大足黑山羊体型与繁殖性状的GWAS分析;古博文;中国硕士学位论文电子期刊农业科技;摘要、结论、第14-16页、第33-35页 * |
Also Published As
| Publication number | Publication date |
|---|---|
| CN117089635A (en) | 2023-11-21 |
Similar Documents
| Publication | Publication Date | Title |
|---|---|---|
| CN113278712B (en) | Gene chip, molecular probe combination, kit and application for analyzing sheep hair color | |
| CN112695107B (en) | Growth performance SNP locus combination of meat sheep and application thereof | |
| CN113278716B (en) | Gene chip for analyzing characters for sheep wool, molecular probe combination, kit and application | |
| CN115029451B (en) | Sheep liquid phase chip and application thereof | |
| CN112695108B (en) | Reproductive performance SNP (single nucleotide polymorphism) locus combination of meat sheep and application thereof | |
| CN113265476B (en) | Gene chip, molecular probe combination, kit and application for analyzing milk production performance of sheep | |
| CN113795597B (en) | Soybean SNP (Single nucleotide polymorphism) typing detection chip and application thereof in molecular breeding and basic research | |
| WO2023001209A1 (en) | Gene chip, molecular probe combination, test kit and application for analyzing sheep fat tails | |
| CN111088382A (en) | Corn whole genome SNP chip and application thereof | |
| CN114790483B (en) | SNP locus combination related to fuzzing rate of fine wool sheep and application thereof | |
| CN114959059A (en) | SNP locus combination related to diameter variation coefficient of fine wool sheep wool fiber and application thereof | |
| CN113293220B (en) | Gene chip for analyzing ear size of sheep, molecular probe combination, kit and application | |
| CN113278714B (en) | Gene chip for analyzing whether sheep has horns or not, molecular probe combination, kit and application | |
| CN104769133A (en) | Method of improving microarray performance by strand elimination | |
| CN117089635B (en) | Molecular marker combination for analyzing goat reproductive performance and application | |
| CN117089633B (en) | Molecular marker combination for analyzing existence of goat fluff and application | |
| CN117089634B (en) | Molecular marker combination for analyzing goat milk performance and application | |
| CN117089636B (en) | Molecular marker combination for analyzing goat meat performance and application | |
| CN117126948B (en) | Molecular marker combination for analyzing goat ear characters and application thereof | |
| CN117106936B (en) | Molecular marker combination for analyzing goat hair color character and application | |
| CN114292924A (en) | Sika deer whole genome SNP molecular marker combination, SNP chip and application | |
| CN117106935A (en) | Molecular marker combination for analyzing angular character of goat and application thereof | |
| CN112011629A (en) | Jinfen white pig whole genome high-density SNP chip detection kit and application thereof | |
| CN113278713B (en) | Gene chip, molecular probe combination, kit and application of sheep multi-angle character | |
| CN113278715A (en) | Gene chip for analyzing sheep papilla number, molecular probe combination, kit and application |
Legal Events
| Date | Code | Title | Description |
|---|---|---|---|
| PB01 | Publication | ||
| PB01 | Publication | ||
| SE01 | Entry into force of request for substantive examination | ||
| SE01 | Entry into force of request for substantive examination | ||
| GR01 | Patent grant | ||
| GR01 | Patent grant |