CN114250307B - Molecular marker for evaluating age of pigs reaching 100kg body weight and application thereof - Google Patents
Molecular marker for evaluating age of pigs reaching 100kg body weight and application thereof Download PDFInfo
- Publication number
- CN114250307B CN114250307B CN202011025130.2A CN202011025130A CN114250307B CN 114250307 B CN114250307 B CN 114250307B CN 202011025130 A CN202011025130 A CN 202011025130A CN 114250307 B CN114250307 B CN 114250307B
- Authority
- CN
- China
- Prior art keywords
- pig
- pigs
- age
- snp
- snp marker
- 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
- 241000282887 Suidae Species 0.000 title claims abstract description 67
- 230000037396 body weight Effects 0.000 title claims abstract description 44
- 239000003147 molecular marker Substances 0.000 title description 3
- 239000003550 marker Substances 0.000 claims abstract description 51
- 238000000034 method Methods 0.000 claims abstract description 33
- 238000009395 breeding Methods 0.000 claims abstract description 28
- 230000001488 breeding effect Effects 0.000 claims abstract description 28
- 239000002773 nucleotide Substances 0.000 claims abstract description 25
- 125000003729 nucleotide group Chemical group 0.000 claims abstract description 25
- 210000000349 chromosome Anatomy 0.000 claims abstract description 22
- 238000012216 screening Methods 0.000 claims abstract description 22
- 239000003795 chemical substances by application Substances 0.000 claims abstract description 14
- 239000000126 substance Substances 0.000 claims abstract description 10
- 108020004414 DNA Proteins 0.000 claims description 12
- 238000012408 PCR amplification Methods 0.000 claims description 9
- 239000003153 chemical reaction reagent Substances 0.000 claims description 7
- 244000001582 Canarium odontophyllum Species 0.000 claims description 4
- 235000016299 Canarium odontophyllum Nutrition 0.000 claims description 4
- 239000012634 fragment Substances 0.000 claims description 4
- 108091028043 Nucleic acid sequence Proteins 0.000 claims description 3
- 238000012239 gene modification Methods 0.000 claims description 2
- 230000005017 genetic modification Effects 0.000 claims description 2
- 235000013617 genetically modified food Nutrition 0.000 claims description 2
- 241000255969 Pieris brassicae Species 0.000 claims 1
- 241000282898 Sus scrofa Species 0.000 abstract description 84
- 230000002068 genetic effect Effects 0.000 abstract description 17
- 230000008901 benefit Effects 0.000 abstract description 7
- 230000035772 mutation Effects 0.000 abstract description 3
- 108700028369 Alleles Proteins 0.000 description 7
- 239000011159 matrix material Substances 0.000 description 7
- 238000001514 detection method Methods 0.000 description 6
- 230000000694 effects Effects 0.000 description 6
- 238000004519 manufacturing process Methods 0.000 description 6
- 238000012098 association analyses Methods 0.000 description 5
- 238000003205 genotyping method Methods 0.000 description 5
- 108090000623 proteins and genes Proteins 0.000 description 5
- 230000003321 amplification Effects 0.000 description 3
- 238000012937 correction Methods 0.000 description 3
- 238000005516 engineering process Methods 0.000 description 3
- 238000003199 nucleic acid amplification method Methods 0.000 description 3
- 238000003908 quality control method Methods 0.000 description 3
- 238000012360 testing method Methods 0.000 description 3
- 210000001519 tissue Anatomy 0.000 description 3
- FWMNVWWHGCHHJJ-SKKKGAJSSA-N 4-amino-1-[(2r)-6-amino-2-[[(2r)-2-[[(2r)-2-[[(2r)-2-amino-3-phenylpropanoyl]amino]-3-phenylpropanoyl]amino]-4-methylpentanoyl]amino]hexanoyl]piperidine-4-carboxylic acid Chemical compound C([C@H](C(=O)N[C@H](CC(C)C)C(=O)N[C@H](CCCCN)C(=O)N1CCC(N)(CC1)C(O)=O)NC(=O)[C@H](N)CC=1C=CC=CC=1)C1=CC=CC=C1 FWMNVWWHGCHHJJ-SKKKGAJSSA-N 0.000 description 2
- 238000007400 DNA extraction Methods 0.000 description 2
- 238000004458 analytical method Methods 0.000 description 2
- 230000009286 beneficial effect Effects 0.000 description 2
- 201000010099 disease Diseases 0.000 description 2
- 208000037265 diseases, disorders, signs and symptoms Diseases 0.000 description 2
- 244000144972 livestock Species 0.000 description 2
- 238000005259 measurement Methods 0.000 description 2
- 235000013372 meat Nutrition 0.000 description 2
- 210000001087 myotubule Anatomy 0.000 description 2
- 235000015277 pork Nutrition 0.000 description 2
- 238000011160 research Methods 0.000 description 2
- 238000012163 sequencing technique Methods 0.000 description 2
- 238000007619 statistical method Methods 0.000 description 2
- 238000005303 weighing Methods 0.000 description 2
- 102000016928 DNA-directed DNA polymerase Human genes 0.000 description 1
- 108010014303 DNA-directed DNA polymerase Proteins 0.000 description 1
- 239000000654 additive Substances 0.000 description 1
- 230000000996 additive effect Effects 0.000 description 1
- 238000013459 approach Methods 0.000 description 1
- 210000004027 cell Anatomy 0.000 description 1
- 238000000546 chi-square test Methods 0.000 description 1
- 238000010219 correlation analysis Methods 0.000 description 1
- 238000013461 design Methods 0.000 description 1
- 238000011161 development Methods 0.000 description 1
- 238000009826 distribution Methods 0.000 description 1
- 238000011156 evaluation Methods 0.000 description 1
- 238000001914 filtration Methods 0.000 description 1
- 230000006870 function Effects 0.000 description 1
- 238000001502 gel electrophoresis Methods 0.000 description 1
- 230000007614 genetic variation Effects 0.000 description 1
- 238000012165 high-throughput sequencing Methods 0.000 description 1
- 238000012986 modification Methods 0.000 description 1
- 230000004048 modification Effects 0.000 description 1
- 238000004091 panning Methods 0.000 description 1
- 238000003752 polymerase chain reaction Methods 0.000 description 1
- 244000144977 poultry Species 0.000 description 1
- 238000000513 principal component analysis Methods 0.000 description 1
- 238000007894 restriction fragment length polymorphism technique Methods 0.000 description 1
- 210000003765 sex chromosome Anatomy 0.000 description 1
- 238000013179 statistical model Methods 0.000 description 1
- 238000006467 substitution reaction Methods 0.000 description 1
- 238000001196 time-of-flight mass spectrum Methods 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
- 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
Landscapes
- Chemical & Material Sciences (AREA)
- Life Sciences & Earth Sciences (AREA)
- Analytical Chemistry (AREA)
- Proteomics, Peptides & Aminoacids (AREA)
- Organic Chemistry (AREA)
- Zoology (AREA)
- Wood Science & Technology (AREA)
- Health & Medical Sciences (AREA)
- Engineering & Computer Science (AREA)
- Microbiology (AREA)
- Immunology (AREA)
- Molecular Biology (AREA)
- Biotechnology (AREA)
- Biophysics (AREA)
- Physics & Mathematics (AREA)
- Biochemistry (AREA)
- Bioinformatics & Cheminformatics (AREA)
- General Engineering & Computer Science (AREA)
- General Health & Medical Sciences (AREA)
- Genetics & Genomics (AREA)
- Measuring Or Testing Involving Enzymes Or Micro-Organisms (AREA)
Abstract
The invention discloses a SNP marker related to the age of pigs reaching 100kg body weight and application thereof, a substance for detecting polymorphism or genotype of the SNP marker, a method for identifying or assisting in identifying the growth rate of pigs, a method for screening or assisting in screening pig varieties reaching 100kg body weight and having low age of pigs, and a genetic improvement method of pigs. The SNP marker related to the age of 100kg body weight of pigs is positioned at nucleotide 7,185,799 of chromosome 4 of 10.2 version of the pig reference genome, A/G mutation exists, and the genotype of the SNP marker is that the age of 100kg body weight of pigs with AA is obviously lower than that of AG and GG genotype individuals. The SNP marker related to the weight of 100kg of pigs can carry out marker assisted selection, shortens the breeding period of pigs, obviously improves the growth speed of pigs and promotes the breeding of pig varieties with low weight of 100kg and day age; the disclosed genetic improvement method for pigs can accelerate the genetic progress of pigs reaching 100kg body weight and age, reduce the breeding time of pig growth traits and effectively improve the economic benefit of pig breeding.
Description
Technical Field
The invention belongs to the technical field of molecular biology, and particularly relates to SNP markers related to pig correction of up to 100kg body weight and day-age, and a detection method and application thereof.
Background
In China, the pork consumption accounts for about 68% of the total meat, and the increase of population and the increase of pork demand mean that the pig industry has a larger potential market. Among many factors affecting the production efficiency of pig industry, genetic factors of pig breeds play a leading role, and the maximum yield and benefit of pig raising production can be obtained only by fully utilizing the existing pig breeds resources and cultivating breeds or strains with excellent production performance under the same raising conditions and investment. Therefore, genetic improvement of swine breeds is particularly important.
To improve productivity of a population, the genetic value of each individual in the population must be assessed in each generation, and the ideal individual must be selected as a sire, thereby ensuring that the genetic level of the population progresses in the desired direction. The daily age of 100kg body weight is obtained by measuring the body weight of a target pig group to be detected when the weight of the target pig group to be detected is within the range of 80-105kg and then calculating according to a daily age correction formula of 100kg body weight. The trait can reflect the growth speed of individual pigs and can be used as an important index of the growth trait of meat production rate.
At present, SNP (single nucleotide polymorphism) chips developed based on high-throughput sequencing technology make whole genome-associated analysis (genome-wideassociation studies, GWAS) a mainstream strategy for identifying important candidate genes of economic traits of livestock and poultry. GWAS refers to the association analysis of single nucleotide mutations in the genome as molecular markers with some diseases and complex traits on humans and livestock, thereby identifying genetic variations associated with the target traits. In 1996 as early as Risch et al proposed the concept of whole genome association analysis for the first time. The basic principle is as follows: and selecting a case group or a control group from a specific group, comparing the genotype frequencies of SNP loci in the whole genome range with the differences among different groups, if the genotype of a locus is obvious in the differences among the different groups, considering the locus to be related to the target property, and deducing candidate genes according to the physical positions of the locus.
At present, in the genetic improvement of pigs, the research on genes related to the age of pigs reaching 100kg body weight is insufficient, and SNP markers related to the age of pigs reaching 100kg body weight, which have definite functions and obvious effects and can be directly used for breeding, are lacking.
Disclosure of Invention
In order to overcome the above problems, the present inventors have made intensive studies and have proposed a SNP marker related to the age of pigs up to 100kg body weight per day and uses thereof, a substance for detecting polymorphism or genotype of the SNP marker and uses thereof, a method for identifying or assisting in identifying the growth rate of pigs, a method for screening or assisting in screening a variety of pigs up to 100kg body weight per day of low age, a method for genetic improvement of pigs, and the like. The SNP marker related to the age of 100kg body weight of pigs is positioned at nucleotide 7,185,799 of chromosome 4 of 10.2 version of the pig reference genome, A/G mutation exists, and the genotype of the SNP marker is that the age of 100kg body weight of pigs with AA is obviously lower than that of AG and GG genotype individuals. The SNP marker can be used for marker-assisted selection, shortens the pig breeding period, remarkably improves the growth speed of pigs, accelerates the genetic progress of the pigs and effectively improves the economic benefit of pig breeding, thereby completing the invention.
In particular, it is an object of the present invention to provide the following aspects:
the invention provides an SNP marker which is one SNP locus on the genome of a pig, wherein the SNP marker is related to the age of the pig in days when the body weight of the pig reaches 100 kg.
Wherein the SNP marker is positioned at a nucleotide 7,185,799 of chromosome 4 of the 10.2 version of the pig reference genome, and the base type is A or G.
Wherein the genotypes of the SNP markers are AA, AG and GG,
Pigs with genotype AA of SNP markers were significantly lower in weight and day-age than AG and GG genotype individuals for 100 kg.
The invention also provides a substance for detecting polymorphism or genotype of the SNP marker, wherein the substance is as follows:
A primer pair for amplifying the pig genome DNA fragments including the SNP markers;
PCR amplification reagents comprising the above primer pairs; or (b)
Kit comprising the above primer pair or PCR amplification reagent.
Wherein, the primer pair is P1 and P2, and the nucleotide sequences of the primer pair are respectively shown in SEQ ID NO:1 and SEQ ID NO: 2.
The invention also provides an application of the SNP marker or a substance for detecting polymorphism or genotype of the SNP marker, wherein the application is at least one of the following (1) to (6):
(1) Identifying or aiding in identifying the growth rate of the pig;
(2) Screening or auxiliary screening pig breeds with weight of 100kg and day-old age;
(3) Breeding pigs;
(4) Preparing a product for identifying or assisting in identifying the growth rate of pigs;
(5) Preparing and screening or auxiliary screening products of pig breeds with weight of 100kg and day-old age;
(6) And (5) preparing a pig breeding product.
Wherein the pig is one or more of Duroc pig, changbai pig and Dabai pig.
The invention also provides a method for identifying or aiding in the identification of the growth rate of a pig, wherein the method comprises the step of detecting the polymorphism or genotype of the SNP marker at nucleotide 7,185,799 of chromosome 4 of version 10.2 of the pig reference genome.
The invention also provides a method for screening or assisting in screening pig breeds with a weight of up to 100kg and a day-old age, wherein the method comprises the following steps:
pig reference genome 10.2 version 4 pig with genotype AA of SNP marker at nucleotide 7,185,799 of chromosome 4 was selected for breeding.
The invention also provides a genetic improvement method of pigs, which comprises the following steps:
Determining SNP markers at nucleotide 7,185,799 of a chromosome 4 of a breeding pig in a breeding pig core group, and making corresponding selection according to the pig SNP markers.
The invention has the beneficial effects that:
(1) The SNP marker obviously related to the weight of 100kg of pigs in daily age can carry out marker-assisted selection, shortens the breeding period of pigs, obviously improves the growth speed of pigs and promotes the breeding of pig varieties with low weight of 100kg in daily age;
(2) The SNP marker obviously related to the age of 100kg of body weight of pigs provided by the invention has the advantages that the polymorphism is directly expressed in a DNA form, can be detected in each tissue and each development stage of the pigs, and is beneficial to more conveniently and rapidly predicting the age of 100kg of body weight of pigs;
(3) The genetic improvement method of the pigs can accelerate the genetic progress of the pigs to 100kg of body weight and age in days, and reduce the breeding time of the growth traits of the pigs, thereby effectively improving the economic benefit of pig breeding.
Drawings
FIG. 1 shows a Manhattan plot of a LEA (Lion Eyes Area) full genome association analysis of 100kg day old as described in example 1 of the present invention.
Detailed Description
The invention is further illustrated by the following preferred embodiments and examples. The features and advantages of the present invention will become more apparent from the description.
The word "exemplary" is used herein to mean "serving as an example, embodiment, or illustration. Any embodiment described herein as "exemplary" is not necessarily to be construed as preferred or advantageous over other embodiments.
In a first aspect of the present invention, there is provided a SNP marker which is a SNP site on the genome of a pig and which is significantly associated with the age of pigs up to 100kg body weight per day.
According to a preferred embodiment of the invention, the SNP marker is located at nucleotide 7,185,799 of chromosome 4 of version 10.2 of the porcine reference genome, the base type is A or G, designated WU_10.2_4_7185799.
In a further preferred embodiment, the genotypes of the SNP markers are AA, AG and GG,
100Kg body weight of pigs with genotype AA of SNP markers is significantly lower in age than those of AG and GG genotypes.
Wherein the AA genotype is homozygous type of SNP marker A in the pig genome, the GG genotype is homozygous type of SNP marker G in the pig genome, and the AG genotype is heterozygous type of SNP marker A and G in the pig genome.
The inventor researches and discovers that the SNP locus at the nucleotide 7,185,799 of the chromosome 10.2 version 4 of the pig reference genome is in a known QTL region such as the weight of the head, the total myofiber number, the myofiber number per unit area and the like, and the genotype of the locus is detected to provide scientific basis for the selection of the age of 100kg body weight of the pig in days.
In order to eliminate the mis-panning and mis-selection of the excellent genes of pigs by the factors of feeding environment, feed, diseases and the like in the phenotype selection, the SNP loci need to be genotyped so as to enhance the accuracy of target selection.
The genotyping method has various methods, such as a direct sequencing method, a restriction fragment length polymorphism polymerase chain reaction, a time-of-flight mass spectrum, a chip technology and the like, and the high-density SNP chip technology is preferably adopted for genotyping, so that a large number of SNPs can be typed in a short time period, the efficiency is high, and the cost is low.
Preferably, SNP 80K chip (Neogen _POPOD80K) of Newton's company is used for genotyping in the present invention.
In a second aspect of the present invention, there is provided a substance for detecting a polymorphism or genotype of the above SNP marker, the substance being:
A primer pair for amplifying the pig genome DNA fragments including the SNP markers;
PCR amplification reagents comprising the above primer pairs; or (b)
Kit comprising the above primer pair or PCR amplification reagent.
According to a preferred embodiment of the present invention, the primer pair is P1 and P2, the nucleotide sequences of which are set forth in SEQ ID NOs: 1 and SEQ ID NO: 2.
In a further preferred embodiment, the PCR amplification reagents comprise a PCR buffer, dNTPs, a primer pair, and a DNA polymerase.
In a third aspect of the present invention, there is provided use of the SNP marker of the first aspect or the substance for detecting a polymorphism or genotype of a SNP marker of the second aspect in any one of the following (1) to (6):
(1) Identifying or aiding in identifying the growth rate of the pig;
(2) Screening or auxiliary screening pig breeds with weight of 100kg and day-old age;
(3) Breeding pigs;
(4) Preparing a product for identifying or assisting in identifying the growth rate of pigs;
(5) Preparing and screening or auxiliary screening products of pig breeds with weight of 100kg and day-old age;
(6) And (5) preparing a pig breeding product.
According to a preferred embodiment of the invention, the pig is one or more of a duroc pig, a long white pig and a big white pig.
In a fourth aspect of the invention, there is provided a method of identifying or aiding in the identification of the growth rate of a pig, the method comprising the step of detecting the polymorphism or genotype of a SNP marker at nucleotide 7,185,799 of chromosome 4 in the reference genome of the pig.
Wherein the growth rate of the pig is preferably expressed by a daily age of up to 100kg body weight.
Preferably, the method for detecting the polymorphism or genotype of the SNP marker at the nucleotide 7,185,799 of chromosome 10.2 version 4 of the reference genome of the pig to be detected can adopt a direct sequencing method or adopt the primer pair to carry out allele-specific amplification on the pig to be detected.
More preferably, the method comprises the steps of:
Step 1, extracting genome DNA of a pig to be detected;
Step 2, performing PCR amplification by taking genomic DNA as a template;
step 3, determining the genotype of the SNP marker of the pig to be detected;
and step 4, determining the growth speed of the pig to be tested according to the genotype.
In the step 2, PCR amplification is performed by using the primer pair P1 and P2, and the amplified nucleotide fragment comprises the SNP marker.
In the step 4, if the genotype of the SNP locus of the pig to be tested is AA, the weight of the pig to be tested reaching 100kg is low in day-age;
if the genotype of the SNP locus of the pig to be tested is AG or GG, the weight of the pig to be tested reaching 100kg is high in day-age.
In a fifth aspect of the invention, there is provided a method of screening or assisting in screening of pig breeds of low age in the day up to 100kg body weight, the method comprising the steps of:
pig reference genome 10.2 version 4 pig with genotype AA of SNP marker at nucleotide 7,185,799 of chromosome 4 was selected for breeding.
In a sixth aspect of the present invention there is provided a method of genetic modification of pigs, the method comprising the steps of:
Determining the SNP markers of the breeding pigs in the breeding pig core group, and making corresponding selection according to the SNP markers of the pigs.
Preferably, the offspring of the breeding pigs breeds individuals with the genotype AA of the SNP marker at nucleotide 7,185,799 of chromosome 4 of version 10.2 of the reference genome of the pig, and the AG and GG individuals at the locus are eliminated, so that the frequency of the allele A at the locus is increased in a generation-by-generation manner, and the weight of the offspring pigs reaching 100kg is reduced.
Examples
The invention is further described below by means of specific examples, which are however only exemplary and do not constitute any limitation on the scope of protection of the invention.
EXAMPLE 1 SNP site discovery related to age of pigs reaching 100kg body weight
1. Test population
The test pig population employed in this example was 1,173 pigs from the Hebei American Shen stock pig farm, wherein, duroc boar was 23, duroc sow was 177, changbai boar was 15, changbai sow was 363, changbai boar was 2, and Changbai sow was 593.
2. Determination of phenotypic Properties
Fasted for 12 hours before weighing, weighed using an electronic weighing station, and the weight of the pigs and the actual age of the day when measured were recorded. Then correcting the actual day age of the pig reaching 100kg body weight, correcting the phenotype data of the collected data by using the genetic evaluation character measurement procedure of the pig farm production performance measurement technical procedure of the Hebei province local standard (DB-13/T2065-2014) file,
Specifically, the method is carried out according to the following correction formula:
corrected day age = measured day age (d) - [ (measured body weight (kg) -100)/CF ]
Wherein, the boar CF value= [ measured body weight (kg)/measured age of days (d) ]x 1.826040;
Sow CF value= [ measured body weight (kg)/measured age of day (d) ]x 1.714615.
Quality control of the measured phenotypic data: individuals with a loss of phenotype values were cleared, and individuals with a deviation from the mean value of greater than 3 standard deviations were cleared.
3. Genomic DNA extraction
In the embodiment, a DP1902 model cell/tissue genome DNA extraction kit of Beijing Baitaike biotechnology Co is adopted to extract DNA from pig ear tissues, an ultraviolet spectrophotometer and gel electrophoresis are used for DNA quality detection, and the DNA which is qualified in detection is stored at the temperature of minus 20 ℃ for subsequent typing determination.
4. Genotyping
And taking the DNA which is qualified in detection, and carrying out genotyping by utilizing Neogen _POR80K chips of Newton company.
5. Quality control of phenotypic and genotypic data
Quality control criteria for phenotypic data: clearing individuals with a loss of phenotype values; individuals with deviations from the mean that were greater than 3 standard deviations were cleared.
Filtration criteria for SNP chip typing: removing SNP loci with genotype detection rate less than 95%; clearing individuals with detection rate less than 95%; less than 1% of individuals with minimal allele frequency (Minimum Allele Frequency, MAF) clearance; clearing SNP loci with a Hardy-Wenberg equilibrium (Hardy-Weinberg Equilibrium, HWE) chi-square test P value less than 1.0E-4; the SNP site on the sex chromosome is cleared.
6. Whole genome association analysis
The whole genome correlation analysis was performed using the R language package GAPIT Version (developed by washington university), the statistical model of which was a compressed hybrid linear model, GAPIT designed to accurately perform GWAS and genome predictions on large datasets. The hybrid linear model (Mixed Liner Model, MLM) includes both fixed and random effects, including individuals as random effects enables the MLM to integrate information about relationships between individuals. This information about relationships is passed through a relative (K) matrix, which is used in MLM as a variance-covariance matrix between individuals. When genetic marker-based relatives matrix (K) is used with population structures (commonly referred to as "Q" matrices, and may be analyzed by structure or principal component analysis), the statistical power of the "q+k" matrix approach is higher than that of the "Q" matrix alone. The MLM can be described using a matrix representation of Henderson, as follows:
The statistical analysis model is:
y＝Xβ+Zμ+e
Wherein y is the value of the observed phenotype; beta is an unknown value containing fixed effects, including genetic markers, population structure (Q matrix) and intercept; μ is the unknown value of the random additive genetic effect from multiple background QTLs of an individual or line; x and Z are known design matrices; e is the residual vector that is not observed.
A mixed linear model of GAPIT statistical analysis software is adopted to carry out 100kg body weight age-of-day association analysis on all typing SNP loci, and the statistical analysis model is the same as the above.
The results are shown in FIG. 1, and as can be seen from FIG. 1: SNP locus WU_10.2_4_7185799 (A/G; chr2:7,185,799) has a significant correlation with the age of 100kg body weight per day (1.86E-03).
Example 2 effect analysis of SNP position WU_10.2_4_7185799
The sequence of the polymorphic site (wu_10.2_4_7185799) was extracted by R language and its genotype frequency and gene frequency distribution were counted, and the results are shown in table 1:
Wherein the AA genotype is homozygous type with the SNP locus at nucleotide 7,185,799 of chromosome 10.2 version 4 of the pig reference genome being A, the GG genotype is homozygous type with the SNP locus at nucleotide 7,185,799 of chromosome 10.2 version 4 of the pig reference genome being G, and the AG genotype is heterozygous type with the SNP locus at nucleotide 7,185,799 of chromosome 10.2 version 4 of the pig reference genome being A and G.
As can be seen from Table 1, allele A was found to have a frequency of 43.99%, allele G was found to have a frequency of 56.01%, AG genotype was the dominant genotype of the experimental population, and G was the dominant allele.
Further, the significance test of 100kg body weight age difference between individuals with different genotypes at SNP sites was carried out by using Rstudio software on genotype data and phenotype data and using Kruskal-Wallis method, P-value < 0.01 shows that the difference is very significant, and the result is shown in Table 2.
TABLE 2
Table 2 shows the effect of WU_10.2_4_7185799 site A/G on the age of 100kg body weight in a swine population, as can be seen: there was a very significant correlation (P < 0.01) between wu_10.2_4_7185799 locus and 100kg body weight age per day, of which 100kg body weight age per day was significantly smaller in individuals of wu_10.2_4_7185799 different genotypes than in individuals of AG type and GG type.
Therefore, in the pig population, the AA type individuals at the WU_10.2_4_7185799 locus are bred in a secondary mode, and the weight of 100kg can be gradually reduced. If all GG individuals of SNP markers related to 100kg body weight day old are bred into AA individuals, the average body weight day old of each pig can be reduced by 12.6 days, the growth speed of the pigs is obviously improved, and the production benefit of the pigs is improved.
The invention has been described in detail in connection with the specific embodiments and exemplary examples thereof, but such description is not to be construed as limiting the invention. It will be understood by those skilled in the art that various equivalent substitutions, modifications or improvements may be made to the technical solution of the present invention and its embodiments without departing from the spirit and scope of the present invention, and these fall within the scope of the present invention.
SEQUENCE LISTING
<110> Institute of agricultural genome of China academy of agricultural sciences
<120> Molecular marker for evaluating age of 100kg body weight of pig in days and application thereof
<130> 2020
<160> 2
<170> PatentIn version 3.5
<210> 1
<211> 21
<212> DNA
<213> Amplification primer P1 (Artificial sequence)
<400> 1
ggggaagctt tacccaagac a 21
<210> 2
<211> 21
<212> DNA
<213> Amplification primer P2 (Artificial sequence)
<400> 2
ggcaaggagc ctggatttag a 21
Claims (5)
1. An application of a substance for detecting polymorphism or genotype of SNP marker,
It is characterized in that the method comprises the steps of,
The SNP marker is one SNP locus on the genome of the pig, the SNP marker is related to the age of the pig reaching 100kg body weight,
The SNP marker is positioned at a nucleotide 7,185,799 of chromosome 4 of the 10.2 version of the pig reference genome, the base type is A or G,
Pig with the genotype of AA marked by SNP at the nucleotide 7,185,799 of chromosome 4 of 10.2 version 4 of pig reference genome is selected for breeding,
The substances are as follows:
A primer pair for amplifying the pig genome DNA fragments including the SNP markers;
PCR amplification reagents comprising the above primer pairs; or (b)
A kit comprising the above primer pair or PCR amplification reagent;
the primer pair is P1 and P2, and the nucleotide sequences of the primer pair are respectively shown in SEQ ID NO:1 and SEQ ID NO:2 is shown in the figure;
The application is at least one of the following (1) to (6):
(1) Identifying or aiding in identifying the growth rate of the pig;
(2) Screening or auxiliary screening pig breeds with weight of 100kg and day-old age;
(3) Breeding pigs;
(4) Preparing a product for identifying or assisting in identifying the growth rate of pigs;
(5) Preparing and screening or auxiliary screening products of pig breeds with weight of 100kg and day-old age;
(6) Preparing a pig breeding product;
the pig is one or more of Duroc pig, changbai pig and Dabai pig.
2. The use according to claim 1, wherein the genotypes of the SNP markers are AA, AG and GG,
Pigs with genotype AA of SNP markers were significantly lower in weight and day-age than AG and GG genotype individuals for 100 kg.
3. A method of identifying or aiding in the identification of the growth rate of a pig, the method comprising the step of detecting the polymorphism or genotype of a SNP marker on nucleotide 7,185,799 of chromosome 4 of version 10.2 of a reference genome of the pig, said SNP marker being a SNP locus on the genome of the pig, said SNP marker being associated with a weight of up to 100kg for the age of the pig, said pig being one or more of a doloken pig, a long white pig and a large white pig;
the SNP marker is positioned at nucleotide 7,185,799 of chromosome 4 of the 10.2 version of the pig reference genome, and the base type is A or G.
4. A method of screening or assisting in screening a breed of pig of age-of-day of up to 100kg body weight, the method comprising the steps of:
Pig with the genotype of AA marked by SNP at the nucleotide 7,185,799 of chromosome 4 of 10.2 version 4 of pig reference genome is selected for breeding,
The SNP marker is one SNP locus on a pig genome, the SNP marker is related to the age of pigs reaching 100kg body weight and age of days, and the pigs are one or more of Duroc pigs, changbai pigs and Dabai pigs.
5. A method of genetic modification of pigs, the method comprising the steps of:
Determining SNP markers at nucleotide 7,185,799 of a chromosome 4 of a breeding pig in a core group of the breeding pig, and making corresponding selection according to the SNP markers of the pig,
The SNP marker is positioned at a nucleotide 7,185,799 of chromosome 4 of the 10.2 version of the pig reference genome, the base type is A or G,
The SNP marker is one SNP locus on a pig genome, the SNP marker is related to the age of pigs reaching 100kg body weight and age of days, and the pigs are one or more of Duroc pigs, changbai pigs and Dabai pigs.
Priority Applications (1)
| Application Number | Priority Date | Filing Date | Title |
|---|---|---|---|
| CN202011025130.2A CN114250307B (en) | 2020-09-25 | 2020-09-25 | Molecular marker for evaluating age of pigs reaching 100kg body weight and application thereof |
Applications Claiming Priority (1)
| Application Number | Priority Date | Filing Date | Title |
|---|---|---|---|
| CN202011025130.2A CN114250307B (en) | 2020-09-25 | 2020-09-25 | Molecular marker for evaluating age of pigs reaching 100kg body weight and application thereof |
Publications (2)
| Publication Number | Publication Date |
|---|---|
| CN114250307A CN114250307A (en) | 2022-03-29 |
| CN114250307B true CN114250307B (en) | 2024-05-14 |
Family
ID=80789247
Family Applications (1)
| Application Number | Title | Priority Date | Filing Date |
|---|---|---|---|
| CN202011025130.2A Active CN114250307B (en) | 2020-09-25 | 2020-09-25 | Molecular marker for evaluating age of pigs reaching 100kg body weight and application thereof |
Country Status (1)
| Country | Link |
|---|---|
| CN (1) | CN114250307B (en) |
Citations (4)
| Publication number | Priority date | Publication date | Assignee | Title |
|---|---|---|---|---|
| CN107828897A (en) * | 2017-11-14 | 2018-03-23 | 中国农业大学 | To pig up to the related SNP marker of 100kg body weight age in days characters and its application |
| WO2019113818A1 (en) * | 2017-12-13 | 2019-06-20 | 中国农业大学 | Whole swine genome 50k snp chip and application thereof |
| CN110317880A (en) * | 2019-07-12 | 2019-10-11 | 天津诺禾致源生物信息科技有限公司 | Molecular labeling relevant to pannage conversion ratio, identification and its application |
| CN110541038A (en) * | 2019-08-23 | 2019-12-06 | 华南农业大学 | SNP molecular marker located on pig No.1 chromosome and related to daily gain of pig and application |
Family Cites Families (2)
| Publication number | Priority date | Publication date | Assignee | Title |
|---|---|---|---|---|
| US20070186298A1 (en) * | 2006-01-04 | 2007-08-09 | Blowe Charlotte D | Follistatin gene as a genetic marker for reproductive and performance traits in pigs |
| US20170159122A1 (en) * | 2014-03-28 | 2017-06-08 | Kunming Institute of Zoology, Chinese Acadermy of Sciences | Methods and kits for detecting genetic markers for litter size in pigs |
-
2020
- 2020-09-25 CN CN202011025130.2A patent/CN114250307B/en active Active
Patent Citations (4)
| Publication number | Priority date | Publication date | Assignee | Title |
|---|---|---|---|---|
| CN107828897A (en) * | 2017-11-14 | 2018-03-23 | 中国农业大学 | To pig up to the related SNP marker of 100kg body weight age in days characters and its application |
| WO2019113818A1 (en) * | 2017-12-13 | 2019-06-20 | 中国农业大学 | Whole swine genome 50k snp chip and application thereof |
| CN110317880A (en) * | 2019-07-12 | 2019-10-11 | 天津诺禾致源生物信息科技有限公司 | Molecular labeling relevant to pannage conversion ratio, identification and its application |
| CN110541038A (en) * | 2019-08-23 | 2019-12-06 | 华南农业大学 | SNP molecular marker located on pig No.1 chromosome and related to daily gain of pig and application |
Non-Patent Citations (1)
| Title |
|---|
| rs323787335.《UCSC Genome Browser》.2014,第1页. * |
Also Published As
| Publication number | Publication date |
|---|---|
| CN114250307A (en) | 2022-03-29 |
Similar Documents
| Publication | Publication Date | Title |
|---|---|---|
| CN110218798B (en) | SNP molecular marker located on pig chromosome 7 and related to eye muscle area and eye muscle thickness and application | |
| CN108676897B (en) | SNP marker influencing daily gain traits of pigs and application thereof | |
| KR101929391B1 (en) | Novel SNP marker for discriminating increasedthe number of nipples of pigs and use thereof | |
| CN110541038A (en) | SNP molecular marker located on pig No.1 chromosome and related to daily gain of pig and application | |
| CN107164463A (en) | It is a kind of to be used for the SNP marker of measure and/or genetic improvement pig growth traits | |
| KR101595011B1 (en) | Novel SNP marker for discriminating number of nipple of Pig and use thereof | |
| CN106906303A (en) | One SNP marker for influenceing quality character of pork and its application | |
| CN113249492B (en) | SNP marker for evaluating pig eye muscle area and application method thereof | |
| CN112941198B (en) | SNP marker for detecting pig eye muscle area and application thereof | |
| CN112481385B (en) | SNP marker for detecting pig backfat thickness and application thereof | |
| CN114150068B (en) | SNP (Single nucleotide polymorphism) marker related to pig backfat thickness and application thereof | |
| CN108004332B (en) | It is a kind of to influence the molecular labeling and its application that the main hoof of pig is grown | |
| CN114350818B (en) | Prolactin gene SNP molecular marker related to egg laying traits of Muscovy ducks and application thereof | |
| CN114250307B (en) | Molecular marker for evaluating age of pigs reaching 100kg body weight and application thereof | |
| CN113355427B (en) | SNP (single nucleotide polymorphism) marker related to pig backfat thickness and utilization method thereof | |
| CN114250306B (en) | Method for evaluating pig age of 100kg body weight by GLRX3 gene and application | |
| CN114134233B (en) | SNP (Single nucleotide polymorphism) related to age of pigs reaching 100kg day and eye muscle area | |
| CN114250305B (en) | GLRX3 gene-based method for detecting pig birth number and piglet birth litter size and application | |
| CN114231639B (en) | Method for identifying or assisting in identifying area of porcine eye muscle and application thereof | |
| CN113736890A (en) | SNP molecular marker related to Jian' er number and survival rate and application thereof | |
| CN112458183B (en) | Copy number variation molecular marker on pig No. 3 chromosome and related to daily gain and weight and age on market of pig and application thereof | |
| CN111808974B (en) | SNP molecular marker located on pig chromosome 9 and related to scrotal hernia and application | |
| CN113355428B (en) | SNP (Single nucleotide polymorphism) marker related to day age of up to 100kg body weight and application method thereof | |
| CN112266968B (en) | Copy number variation molecular marker influencing weight age in days and daily gain on pig chromosome 13 and application | |
| CN116162714B (en) | Haplotype molecular marker related to intramuscular fat traits of pigs in SYK gene 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 |