CN108893543B - SNP molecular marker related to average birth weight of newborn piglets of pigs, identification and application thereof - Google Patents
SNP molecular marker related to average birth weight of newborn piglets of pigs, identification and application thereof Download PDFInfo
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Abstract
The invention discloses an SNP locus related to the average birth weight of a newborn pig, wherein the SNP locus is positioned in an NM-214019.2 intron region of a pig DHRS4 gene, in particular to Chr7:75253401 of a reference genome Scrofa11.1, and two alleles of the SNP locus are A and T; three genotypes corresponding to the SNP loci are AA, TT and TA respectively, and compared with pigs with the genotypes of TT and AA, pigs with the genotypes of TA have higher birth weight of newly born piglets. The DHRS4 gene and the determination of the relevance of the SNP locus thereof and the average birth weight of the newborn piglets can be effectively used for identifying or assisting in identifying the pig species with high average birth weight of the newborn piglets, and are beneficial to achieving the purpose of improving the production level and the economic benefit of the pig industry.
Description
Technical Field
The invention relates to the field of pig breeding, in particular to an SNP molecular marker related to the average birth weight of newborn piglets of pigs and identification thereof, wherein the SNP molecular marker is used for improving the pig breeding efficiency.
Background
Reproductive performance is one of the key factors affecting the economic benefit of the pig industry. An important indicator of reproductive traits in sows is whether a heavier birth weight can be produced. The average birth weight is large, the variation coefficient is small, the litter regularity is good, the survival rate of piglets is improved, and the average birth weight can stimulate sows to produce more milk. The birth weight heritability of the piglets is very strong, if the birth weight of the piglets is light and the piglets born in a litter are uneven, the survival rate and the weaning weight of the piglets before weaning can be seriously influenced, and the slaughtering weight and the economic benefit of the fattening pigs are directly influenced.
The reproductive capacity of sows is affected by a number of factors, including sow breed, parity, placental efficiency, hormone levels, nutritional levels, mating work, etc. Among them, steroid hormones including adrenocortical hormone and sex hormones (male hormone and female hormone) play important roles in regulating the reproductive capacity of sows and maintaining normal pregnancy. The cognition of the action and the molecular mechanism of the hormone synthesis, particularly the exploration of the action of a new regulatory gene or enzyme in the hormone synthesis process and the influence on the reproduction, has very important guiding significance for guiding the application of exogenous reproductive hormone in the reproduction production process, improving the reproduction production efficiency and breeding the sows with high fertility. Meanwhile, the identification of the genes related to the average birth weight of the newly born pigs and piglets can provide important clues for explaining the genetic mechanism of the growth and development of the fetuses of the pigs and other mammals and provide theoretical basis for the genetic improvement of the breeding traits of the pigs.
Finding out the relation between genes and traits through correlation analysis between the genes and traits is an important means for researching gene functions. At present, the most widely used method for screening related SNP sites (single nucleotide polymorphism sites) is genome-wide association analysis (GWAS). GWAS is a method for scanning a population to be researched by screening high-density molecular markers in a genome-wide range and analyzing the correlation between molecular marker data obtained by scanning and phenotypic traits. However, the method of GWAS is used for searching SNP sites related to the pig litter size trait, the obtained results are numerous and jumbled and disordered, and most of gene variation is not related to the target trait. It is quite difficult to select the relevant SNP site in the result of this bulky disorder. Therefore, it is necessary to select a specific gene in advance and determine the relevant SNP site located on the specific gene in combination with the GWAS method.
The existing method for obtaining the pigs with high birth weight of piglets mainly focuses on genome editing, and realizes accurate modification of the genome by editing target genes, including knocking out specific DNA fragments, introducing specific mutations, transferring fixed-point DNA fragments and the like. However, people increasingly pay attention to the effect of pig breeding methods on pig quality and the influence on human health while the requirement on pork yield is improved. Because of the difficulty of the scientific community in verifying that transgenic animals have no side effects on human health in a short time and the insufficient cognition of the transgenic animals by the broad masses, people have a strong desire to eat non-transgenic animals. Apart from genome editing techniques, the realization of other breeding theories also requires knowledge of the pig genome. However, the understanding and recognition of the pig genome is far from sufficient, and the control of genes affecting the breeding efficiency of pigs is still insufficient, so that further research is necessary to meet the requirements of pig breeding methods.
Therefore, the invention aims to define a gene related to the average birth weight of the newborn piglets of the pigs, provide an SNP molecular marker related to the average birth weight of the newborn piglets of the pigs, identify the SNP molecular marker and application thereof, and search the SNP molecular marker related to the characteristics of the piglets by performing the association analysis of the gene polymorphism of a specific gene and the average birth weight of the newborn piglets, thereby being beneficial to realizing the promotion of the breeding theory and the technical level of the pigs in China.
Disclosure of Invention
Aiming at the problems in the pig breeding method, the inventor carries out intensive research, carries out association analysis on the polymorphism of the DHRS4 gene and important breeding traits by using a whole genome association analysis method, finds out SNP molecular markers related to the birth weight of the newborn piglets in the pig gene for the first time, enriches SNP sites influencing the pig breeding efficiency, and can improve the pig breeding efficiency (the birth weight of the newborn piglets), thereby completing the invention.
The object of the present invention is to provide the following:
(1) an SNP locus related to the average birth weight of a newborn piglet of a pig is positioned in an NM-214019.2 intron region of a DHRS4 gene of the pig, particularly Chr7:75253401 of a reference genome Scrofa11.1, and two alleles of the SNP locus are A and T.
(2) According to the SNP locus in the step (1), the three genotypes corresponding to the SNP locus are AA, TT and TA genotypes respectively, and compared with the pigs with the genotypes of TT and AA, the pigs with the genotypes of TA have higher birth weight of newborn piglets.
(3) The SNP site according to (1) above, wherein the method for detecting genotyping of the SNP site involves a PCR amplification reaction in which an amplification primer P is present1And P2The nucleotide sequences of (A) are respectively shown as SEQ ID NO.1 and SEQ ID NO. 2.
(4) The SNP site according to (1) above, wherein the method for detecting genotyping of said SNP site involves a single base extension reaction in which the nucleotide sequence of the extension primer is shown in SEQ ID NO. 3.
(5) The SNP site according to (1), wherein the kit for detecting the SNP site comprises a set of amplification primers P1And P2The amplification primer P1And P2The nucleotide sequences of (A) respectively comprise sequences shown in SEQ ID NO.1 and SEQ ID NO. 2;
the kit for detecting the SNP locus comprises an extension primer, wherein the nucleotide sequence of the extension primer comprises a sequence shown in SEQ ID NO. 3;
the kit for detecting the SNP locus also comprises a PCR reaction reagent and a PCR product purification reagent.
(6) A method for identifying or assisting in identifying the average primary weight of a newborn piglet comprises the steps of detecting whether deoxyribonucleotide at Chr7:75253401 of a reference genome Ssicrofa 11.1 of the piglet is A, T or A and T so as to determine the genotype of the piglet to be detected is AA, TT or TA, and determining the average primary weight of the newborn piglet of the piglet according to the genotype: compared with the pigs with the genotype of TT or AA, the pigs with the genotype of TA have higher birth weight of newly born piglets,
wherein, the AA genotype is the homozygote of the DNA of the SNP locus of the pig; the TT genotype is the homozygote of the pig with the deoxyribonucleotide of the SNP site as T; the TA genotype is a heterozygote of T and A of deoxyribonucleotide of the SNP site of the pig.
(7) A breeding method of high-birth piglet average birth weight pigs comprises the step of selecting pigs with TA genotype at Chr7:75253401 of reference genome Sscrofa11.1 as parents for breeding.
(8) The use of the SNP locus of (1) in the identification or auxiliary identification of the average birth weight of a newly born pig piglet;
use of the amplification primer for detecting the SNP site of (3) above or the extension primer for detecting the SNP site of (4) above in identification or assisted identification of the birth weight of a newborn piglet of a pig;
the application of the gene typing method for detecting the SNP locus in the (1) in the aspect of identification or auxiliary identification of the average birth weight of the newly born piglet of the pig.
According to the SNP molecular marker related to the average birth weight of the newborn piglets of the pigs, the identification and the application thereof, the invention has the following beneficial effects:
the inventor selects a specific DHRS4 gene from a plurality of genes to carry out pig breeding character relevance analysis, discovers that the relevance exists between a specific SNP locus in the gene and the birth weight of a newborn piglet for the first time, can be effectively used for identifying or assisting in identifying the pig with the high birth weight of the newborn piglet, accelerates the breeding process of the pig with the high birth weight of the newborn piglet through artificial breeding, avoids the problem of low acceptance caused by insufficient cognition of transgenic animals by the masses, and has better economic prospect.
Detailed Description
The features and advantages of the present invention will become more apparent and appreciated from the following detailed description of the invention. The word "exemplary" is used exclusively 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.
The invention uses a genome-wide association analysis (GWAS) method to search SNP sites related to the pig litter size traits. The GWAS method for searching the SNP locus related to the birth weight of the newly born pig piglets has the disadvantages that a huge disorder result is easily obtained, and most of gene variation is not related to target characters; there is great difficulty in selecting the relevant SNP site in this result of bulky disorder. Therefore, it is necessary to select a specific gene in advance and determine the relevant SNP site located on the specific gene by combining with the GWAS method.
Therefore, the specific gene is selected from a plurality of genes to be screened, so that the SNP locus on the gene is determined, and the success rate of determining the related SNP locus is greatly improved. In the present invention, the specific gene is DHRS4 gene.
Research shows that NRDR (coenzyme II dependent retinol resistant dehydrogenation/reductase) encoded by DHRS4 gene not only participates in vivo retinoic acid synthesis, but also shows different catalytic activities on steroid hormones, vitamin K3, isatin and other substances. The result of high-throughput detection of gene differential expression of embryonic development and tumor cells and normal cells shows that the DHRS4 gene is up-regulated in the development process of embryonic limbs. In this regard, the present inventors considered that the DHRS4 gene may be involved in intracellular signaling by affecting the synthesis of factors such as retinoic acid, and is involved in the occurrence of proliferative differentiation of embryonic cells.
Animal breeding trait research shows that the expression of DHRS4 gene in pig testis with high androgen is higher than that of pig testis with low androgen, but no other intensive research results are found after the discovery. The inventors consider that the DHRS4 gene is involved in the synthesis of steroid hormones. However, the mechanism of action of the specific DHRS4 gene in regulating steroid hormone synthesis is not clear and further studies are needed.
Among the existing studies, DHRS4 gene research has mainly focused on analyzing its expression in different tissues. The gene has less research in pigs, and the relationship between the gene and upstream and downstream genes in a breeding related pathway still needs to be disclosed in the aspects of a molecular mechanism for regulating and controlling the breeding performance of the pigs and the like. The inventor carries out association analysis on the polymorphism of the gene and important reproductive traits by using a whole genome association analysis method, and determines SNP sites related to litter traits in the gene for the first time through a large amount of researches.
The GWAS method is combined with the screened specific gene by the inventor, and a SNP site related to the average birth weight of the newborn piglets of the pigs in the DHRS4 gene is provided, the SNP site is positioned in an NM-214019.2 intron region of the DHRS4 gene, in particular to Chr7:75253401 of a reference genome Scrofa11.1, and two alleles of the SNP site are A and T. The gene frequency of deoxyribonucleotide A was 0.844, and the gene frequency of deoxyribonucleotide T was 0.156.
Three genotypes corresponding to the SNP locus are AA, TT and TA respectively, wherein the AA genotype is a homozygote of the pig with the deoxyribonucleotide of the SNP locus as A; the TT genotype is the homozygote of the pig with the deoxyribonucleotide of the SNP site as T; the TA genotype is a heterozygote of T and A of deoxyribonucleotide of the SNP site of the pig.
The inventor finds that compared with pigs with the genotypes of TT and AA, pigs with the genotype of TA have higher birth weight of newly born piglets.
In the invention, the genotyping utilizes matrix-assisted laser desorption ionization time-of-flight mass spectrometry (MALDI-TOF MS) technology: firstly, PCR amplifies the target sequence, then adds SNP sequence specific extension primer, and extends 1 base on the SNP site. The prepared sample analytes were co-crystallized with the chip matrix and subjected to transient nanosecond (10) in a vacuum tube of a mass spectrometer-9s) strong laser excitation, nucleic acid molecule desorption and conversion into metastable state ion, ion flight time in electric field is inversely proportional to ion mass, and the flight time of nucleic acid molecule in vacuum tube is detected by flight time detector to obtain accurate molecular weight of sample analyte, thereby detecting SNP site information.
As described above, the SNP site genotyping measurement involves steps such as extraction of DNA from pig genome, PCR amplification reaction, and single base extension reaction.
Wherein, the amplification primer P in the PCR amplification reaction1And P2The nucleotide sequences of (A) are respectively shown as SEQ ID NO.1 and SEQ ID NO. 2.
Wherein the nucleotide sequence of the extension primer in the single base extension reaction is shown as SEQ ID NO. 3.
Correspondingly, the invention provides a detection method for SNP locus genotyping related to the average birth weight of newborn piglets of pigs, which comprises the following steps:
(1) extracting the genomic DNA of the pig;
(2) and (3) taking the genome DNA of the pig to be detected as a template, and utilizing an amplification primer and an extension primer to carry out Sequenom MassArray detection to determine the genotype of the genotype at the Chr7:75253401 of the reference genome Sscrofa11.1 of the pig.
Wherein the amplification primer (P) in the PCR amplification reaction1And P2) As shown in SEQ ID NO.1 and SEQ ID NO. 2; the extension primer is shown as SEQ ID NO. 3.
The detection method for SNP locus genotyping related to the average birth weight of the newborn piglets of the pigs also comprises a direct sequencing method or a kit determination method.
The kit comprises (1) a PCR amplification primer P1And P2(ii) a Preferably, the kit also comprises (2) PCR reaction reagents: comprises PCR buffer solution, dNTP, PfuDNA polymerase and SNaPshot mixed solution; (3) PCR extension primer of SNP locus; (4) PCR product purification reagents: including exonuclease, shrimp-alkaline phosphatase, and buffer for purification.
The use method of the detection kit provided by the invention comprises the following steps: extracting a DNA sample from pig ear or other tissue cells; preparing a PCR reaction system, carrying out PCR amplification and purifying a PCR product; simultaneously carrying out extension reaction on the PCR product and the extension primer of the SNP locus; performing capillary electrophoresis analysis on the extension product; SNP locus analysis, and further gene typing information can be obtained. The SNP site analysis can adopt, but is not limited to, an ABI3730XL automatic sequencer.
The invention provides a method for identifying or assisting in identifying the average primary weight of a newborn pig, which comprises the steps of detecting whether deoxyribonucleotide at the position of Chr7:75253401 of a pig reference genome Scrofa11.1 is A or T or A and T so as to determine whether the genotype of a gene locus is AA, TT or TA, predicting the level of the average primary weight of the newborn pig according to the genotype: compared with pigs with the genotypes of TT and AA, pigs with the genotype of TA have higher birth weight of newly born piglets.
Wherein, the AA genotype is the homozygote of the DNA of the SNP locus of the pig; the TT genotype is the homozygote of the pig with the deoxyribonucleotide of the SNP site as T; the TA genotype is a heterozygote of T and A of deoxyribonucleotide of the SNP site of the pig.
The invention provides a breeding method of high-birth piglets and newborn piglets, which comprises the step of selecting pigs with the genotype TA at the Chr7:75253401 of a reference genome Sscrofa11.1 as parents for breeding. Specifically, the method comprises the following steps:
step 1, selecting pigs with the Chr7:75253401 genotype TA of a reference genome Ssicrofa 11.1 as parents (F0) for mating to obtain first-generation (F1 generation) piglets;
step 2, carrying out genotype analysis on the F1 generation piglets, breeding piglets with the genotype of TA at Chr7:75253401 of the reference genome Ssicrofa 11.1, and continuously breeding after the piglets grow up to obtain F2 generation piglets;
and 3, carrying out genotype analysis on the F2 generation piglets, breeding piglets with the genotypes of TA at Chr7:75253401 of the reference genome Ssicrofa 11.1, and continuously breeding after the piglets grow up to obtain the F3 generation piglets.
And (3) repeating the step (2) or the step (3) to finally obtain the high-birth piglet birth weight heredity pig breed with the genotype TA. The method follows natural propagation and obtains the pig breed with high initial piglet average birth weight through less manual intervention; meanwhile, the breeding method is a non-transgenic method, the acceptance of the masses is higher, the development of the pig industry can be effectively promoted, and the core competitiveness of the pig breeding industry in China is improved.
The invention also provides application of the SNP locus in identification or auxiliary identification of the average birth weight of newly-born piglets of pigs.
The invention also provides application of the extension primer or the amplification primer for detecting the SNP locus in identification or auxiliary identification of the average birth weight of the newborn piglets of the pigs.
The invention also provides an application of the genotyping method for detecting the SNP locus in the aspect of identification or auxiliary identification of the average birth weight of the newly born piglets of the pigs.
Examples
EXAMPLE 1 obtaining molecular markers for SNPs
1. Experimental sample Collection
234 big white pigs from certain pig farms in Shandong were used for SNP typing of the DHRS4 gene. Ear tissue samples were collected one by one, placed in 75% alcohol and stored at-20 ℃ for DNA extraction.
2. SNP typing of DHRS4 gene
2.1 extraction and detection of pig genomic DNA
(1) Cutting a proper amount of pig ear tissues, and putting the cut pig ear tissues into a 1.5mL Axgen tube;
(2) taking a 50mLBD centrifuge tube, uniformly mixing proteinase K with the final concentration of 0.4mg/mL and lysis buffer solution, and adding 0.5mL of lysis solution into a 1.5mL centrifuge tube filled with pig ear tissues for lysis;
(3) the centrifuge tubes were placed in parallel and uniformly on a rocking plate of a constant temperature hybridization oven (the tube caps were tightly sealed to prevent liquid from leaking out). Standing at 55 deg.C for more than 6 hr (it is important to mix the sample completely during digestion process, and the judgment is based on no obvious macroscopic pig ear tissue, and the digested mixture is milky);
(4) after the sample is fully cracked, taking out the centrifuge tube, adding 0.3mL of saturated sodium chloride solution into each tube, reversing and fully mixing for 6-8 times, then placing on ice, and carrying out ice bath for 15 minutes;
(5) after ice-cooling, centrifuge at 12000rpm for 15 minutes at room temperature, carefully and slowly transfer the supernatant to a new 1.5mL Axgen centrifuge tube (care was taken to avoid the pellet from pouring out with the supernatant, keeping the pouring procedure consistent, keeping the amount of supernatant poured out of each tube the same);
(6) adding 0.7mL of isopropanol (the amount of isopropanol added varies with the amount of supernatant poured off, and the two are equal in volume) to each tube, and inverting until flocculent precipitate appears in the solution (if there is no flocculent precipitate, the solution can be left in a refrigerator at-20 ℃ for 2 hours or at 4 ℃ overnight);
(7) centrifugation at 12000rpm for 15 minutes at room temperature removed the supernatant (during which time the tube was carefully observed for white DNA pellet at the bottom of the tube and was not decanted with the supernatant);
(8) 0.5mL of 70% ethanol was added to each tube and inverted gently to wash the precipitated DNA thoroughly;
(9) centrifugation at 10000rmp for 30s, and aspiration of ethanol from the centrifuge tube with a 200. mu.L micropipette to leave the precipitated DNA in the tube (when one is not concerned with aspirating the DNA precipitate from the tube, the tip used in this step may not be replaced when operating between centrifuge tubes);
(10) naturally air-drying the DNA for 10 minutes;
(11) taking 0.1mL of TE buffer solution by a pipette, dissolving the DNA precipitate again, placing the DNA precipitate at 55 ℃ for 2 hours, and shaking for several times to fully dissolve the DNA;
(12) after the DNA is fully dissolved, measuring the extracted concentration (the concentration and OD value of the DNA of a standard sample are needed for genotyping, the concentration of the DNA is 15-20 ng/mu L, the volume is 30 mu L, A260/230 is between 1.5 and 2.3), and detecting the extracted mass (a single visible band) by agarose gel electrophoresis;
(13) the DNA solution was left at 4 ℃ overnight, and 1. mu.L of the DNA solution was subjected to PCR the next day (if the extracted DNA was used within several weeks, it could be stored at 4 ℃ C.; if it was not used for a long time, it was left at-20 ℃ C.).
2.2 genotype determination and quality control of genotype data for SNP chip
DNA samples of 234 white pigs and related information of SNP are submitted to Sequenom MassArray nucleic acid mass spectrometry sequencing by Beijing Conpson organism Limited.
Adding PCR amplification primer (P) with sample DNA as template1And P2) And carrying out PCR amplification reaction on the single base extension primer, purifying a reaction product, co-crystallizing the reaction product with a mass spectrum chip, detecting and parting by using a flight mass spectrometry, and detecting the SNP locus of the target gene.
2.3 data collation and analysis
1) Phenotypic data analysis
And performing descriptive statistical analysis on the birth character of the initial birth and the birth character measured value of the multiparous (2-8 times) pig by using SAS9.2 statistical analysis software, wherein the descriptive statistical analysis comprises calculation of the average value, standard deviation, maximum value and minimum value of the characters.
2) Haplotype analysis
The calculation of the genotype and the allele frequency of the single nucleotide polymorphism is carried out using PopTene 3.2. The TLM process in SAS9.2 software is used for analyzing the correlation analysis of SNP, litter size and other characters, and the fixed effect model is as follows:
y＝μ+gi+mk+e
y is a phenotypic record of reproductive traits; μ is the total average of the traits; gi is the genotype effect; mk is the production month effect; e is the random error. Data are presented as probability values and mean ± standard deviation, # with P value < 0.05 indicating that the difference is statistically significant, and # with P value < 0.001 indicating that the difference is highly statistically significant.
2.4 analysis of results
The SNP typing results of DHRS4 gene of the white pig were obtained by Sequenom MassArray as described above, and are shown in Table 1.
TABLE 1
The research finds that the DHRS4 gene has a SNP locus rs326982309 which is obviously related to the reproductive trait of the sow and is positioned at Chr7:75253401 of a reference genome Sscrofa 11.1. The detection result of the rs326982309 genotype shows that: the 164 pig genotype is AA genotype, the 3 pig genotype is TT genotype, and the 64 pig genotype is TA genotype. The results of detecting the genotype frequency of the pig DHRS4 gene in the swinery are as follows: the AA genotype frequency is 0.701, the TT genotype frequency is 0.013, the TA genotype frequency is 0.286, the AA genotype frequency is higher than that of TT and TA, and the AA allele is the dominant gene.
And (3) carrying out statistical analysis on the genotype and the reproductive traits of the sows by using SAS9.2 software, and carrying out multiple comparison among samples. The results are shown in Table 2.
TABLE 2
As can be seen from Table 2, the difference of the birth weight of the newborn piglets among different genotypes at the locus rs326982309 is extremely obvious. In the initial production data, the nest weight and the average fetal weight of the TA type are higher than those of the AA type and the TT type, and the average fetal weight has statistical significance; in the menstruation yield data, the litter size, the litter weight and the average fetal weight of the TT type are all higher than those of the AA type and the TA type, but no statistical significance exists.
In conclusion, the SNP locus (rs326982309) obviously has an influence on the birth weight of a pig, and in the actual pig breeding, a pig with a TA genotype has higher birth weight of a piglet.
Therefore, the genotype of a pig individual in TA or TT and AA can be determined by determining the deoxyribonucleotide of the rs326982309 locus of the pig DHRS4 gene, so as to assist in identifying the average primary weight of a newborn piglet: the AA genotype pig has higher birth weight of newborn piglets.
The AA genotype is homozygote of nucleotide A at site rs326982309 of pig.
The TA genotype is a heterozygote of T and A in the nucleotide of the site rs326982309 of the pig;
the nucleotide with TT genotype of pig rs326982309 locus is T homozygote.
The invention has been described in detail with reference to specific embodiments and illustrative examples, but the description is not intended to be construed in a limiting sense. Those skilled in the art will appreciate 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, which fall within the scope of the present invention. The scope of the invention is defined by the appended claims.
Sequence listing
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Claims (5)
1. The method for identifying or assisting in identifying the average primary weight of the newborn piglets is characterized by comprising the steps of detecting whether deoxyribonucleotide at Chr7:75253401 of a pig reference genome Scrofa11.1 is A or T or A and T so as to determine the genotype of the pigs to be detected is AA, TT or TA, and determining the average primary weight of the newborn piglets of the pigs according to the genotype: compared with pigs with the genotype of TT or AA, the pigs with the genotype of TA have higher initial piglet initial weight, the reference number of the SNP locus positioned at the Chr7:75253401 of the pig reference genome Sscrofa11.1 is rs326982309,
wherein, the AA genotype is the homozygote of the DNA of the SNP locus of the pig; the TT genotype is the homozygote of the pig with the deoxyribonucleotide of the SNP site as T; the TA genotype is a heterozygote of T and A of deoxyribonucleotide of the SNP site of the pig.
2. A breeding method of high-early-birth piglets and newborn piglets is characterized by comprising the step of selecting pigs with TA genotypes at Chr7:75253401 of a reference genome Sscrofa11.1 as parents for breeding, wherein the reference number of SNP loci at Chr7:75253401 of the reference genome Sscrofa11.1 of the pigs is rs 326982309.
The application of the SNP locus in the aspect of identifying or assisting in identifying the average birth weight of a newborn piglet of a pig, wherein the SNP locus is positioned at Chr7:75253401 of a pig reference genome Sscrofa11.1, two alleles of the SNP locus are A and T, and the NCBI reference number of the SNP locus is rs 326982309;
the three genotypes corresponding to the SNP loci are AA, TT and TA genotypes respectively, and compared with the pigs with the genotypes of TT and AA, the pigs with the genotypes of TA have higher birth weight of newly born piglets.
4. Use of an amplification primer for detecting SNP sites or an extension primer for detecting said SNP sites for identifying or assisting in identifying the average birth weight of newborn piglets of pigs, wherein
The SNP locus is positioned at Chr7:75253401 of a pig reference genome Sscrofa11.1, two alleles of the SNP locus are A and T, and the NCBI reference number of the SNP locus is rs 326982309;
three genotypes corresponding to the SNP loci are AA, TT and TA genotypes respectively, and compared with pigs with the genotypes of TT and AA, pigs with the genotypes of TA have higher birth weight of newly born piglets;
the method for detecting the SNP locus genotyping involves a PCR amplification reaction in which an amplification primer P is used1And P2The nucleotide sequences of (A) are respectively shown as SEQ ID NO.1 and SEQ ID NO. 2;
the method for detecting SNP locus genotyping involves single base extension reaction, wherein the nucleotide sequence of an extension primer in the single base extension reaction is shown as SEQ ID NO. 3.
5. The application of the genotyping method for detecting the SNP locus in the aspect of identifying or assisting in identifying the average birth weight of the newly born piglet of the pig; wherein
The SNP locus is positioned at Chr7:75253401 of a pig reference genome Sscrofa11.1, two alleles of the SNP locus are A and T, and the NCBI reference number of the SNP locus is rs 326982309;
the three genotypes corresponding to the SNP loci are AA, TT and TA genotypes respectively, and compared with the pigs with the genotypes of TT and AA, the pigs with the genotypes of TA have higher birth weight of newly born piglets.
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