CN113637768B - SNP molecular marker related to number of sow-produced malformed piglets on chromosome 13 of pig and application thereof - Google Patents
SNP molecular marker related to number of sow-produced malformed piglets on chromosome 13 of pig and application thereof Download PDFInfo
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Abstract
The invention provides an SNP molecular marker related to the number of malformed piglets produced by sows on a chromosome 13, wherein the site of the SNP molecular marker is a 128894716 nucleotide site on a chromosome 13 of an international pig reference genome 11.1 version 13, and the base of the site is T or G. The base polymorphism of the locus causes the difference of the number of the piglets which are produced by the sow and are malformed. According to the invention, the dominant allele of the SNP is optimized, so that the dominant allele frequency can be increased generation by generation, the number of malformed piglets produced by the sow is reduced, the progress of genetic improvement of the pig is accelerated, and the economic benefit of breeding of the sow is effectively improved.
Description
Technical Field
The invention relates to an SNP molecular marker related to the number of abnormal piglets produced by sows on chromosome 13 of pigs and application thereof.
Background
In pig raising production, the reproductive capacity of sows is one of the important factors influencing the production capacity of a pig farm, and the reproductive performance determines the economic benefit of the whole pig farm. Therefore, improvement of sow reproductive traits such as increase of total litter size, number of live births and the like has been attracting attention of breeding researchers. However, unpredictable situations often occur throughout the pig raising process, such as malformations of piglets, which can occur anywhere in and out of the pig body, mainly include: the incidence rate of anus locking, leg bending, palate cracking, cryptorch, congenital tremor and the like is generally about 0.11-4.96%. Because of its low incidence, it is often difficult to pay attention to the breeding workers, resulting in slow progress of research. According to statistics of 'Chinese agricultural annual survey 2018', the stock quantity of sows which can be bred in the end of 2017 in the whole country is 4471.5 ten thousand, and about 2682.9 ten thousand piglets are lost in each year in the whole country according to average litter size of 2 litter per year, average litter size of 15 litter size and average incidence rate of deformity of 2 percent. This number visually shows the huge economic loss of deformity to the pig farming industry. At present, for the production management of the current large-scale pig farm, mature vaccination and administration procedures, the phenomenon of sow dysgenesis still occurs, so that the influence of genetic factors on the dysgenesis is not negligible. Therefore, to resolve the genetic mechanisms that lead to the malformation of sows, it is extremely important to identify quantitative trait loci (Quantitative trait loci, QTL) and functional genes that affect the number of malformations on the genome.
In recent years, a plurality of important economic traits of pigs are subjected to certain genetic progress in the breeding process by means of conventional breeding technology, such as lean meat percentage, feed conversion rate, growth speed and the like. However, the propagation property inheritance of sow is about 0.06-0.3, which belongs to the middle-low genetic property, the genetic progress obtained by conventional breeding based on phenotype value is not satisfactory, and the genetic mechanism of malformation cannot be fundamentally analyzed obviously. With the rapid development of molecular biotechnology, molecular breeding provides a new research strategy for animal breeding. The marker assisted selection technique can realize the conversion from phenotype selection to influencing the genetic variation of the character and the identification of the functional genes through genetic markers. However, QTL located by previous research results often uses microsatellite markers with low density, and has a large confidence interval, including more than ten genes. Therefore, it is difficult to accurately anchor functional genes related to the target trait in these regions. With the continuous penetration of sequencing technology, genome-wide association analysis (Genome-wide association study, GWAS) is becoming a mainstream strategy for identifying important candidate genes for economic traits of livestock and poultry. By detecting single nucleotide polymorphisms (Single nucleotide polymorphisms, SNPs) on the whole genome of pigs, the localization area can be further reduced in combination with GWAS technology, and QTL, functional genes and related genetic variation sites affecting the number of abnormalities can be finally identified. In the application, a single SNP locus is identified in a Duroc pig group by adopting a GWAS strategy, and the result shows that the single SNP locus has a certain correlation with the pig malformation number.
Disclosure of Invention
In order to overcome the defects and the shortcomings of the prior art, the invention provides an SNP molecular marker related to the number of malformed piglets produced by a sow on chromosome 13 of the pig and application thereof, and also provides a primer pair and a kit for detecting the SNP molecular marker.
In order to achieve the above purpose, the following technical scheme is adopted: a SNP molecular marker related to the number of malformed piglets of sow on chromosome 13, the locus of the SNP molecular marker is 128894716 nucleotide locus on chromosome 13 of international swine reference genome 11.1 version, and the base of the locus is T or G. The base polymorphism of the locus causes the difference of the number of the piglets which are produced by the sow and are malformed.
Preferably, the sequence of the SNP molecular marker is shown as SEQ ID NO:1, the sequence of SEQ ID NO:1 is T or G from the 5' end to the 120 th base. I.e. M in the sequence is G or T. The locus of SNP molecular marker is the nucleotide mutation of G120-T120 with the labeling position of 120 in SEQ ID NO:1 sequence.
Preferably, the sow comprises duroc and its synthetic lines. More preferably, the sow is a S22-line Duroc pig and its synthetic line.
The invention provides a primer pair for detecting the SNP molecular marker, and the nucleic acid sequence of the primer pair is shown as SEQ ID NO:2 and SEQ ID NO: 3.
The invention provides a kit for detecting the SNP molecular marker, which comprises the primer pair.
The invention provides a method for screening pig breeds with low number of malformed piglets, which comprises the following steps:
detecting the genotype of 128894716 nucleotide locus on chromosome 11.1 version 13 of the international swine reference genome of swine, and selecting TT type individuals of 128894716 nucleotide locus as breeding swine.
Preferably, the method for detecting the genotype of 128894716 nucleotide site on chromosome 11.1 version 13 of the international swine reference genome of swine comprises the steps of:
(1) Extracting genome DNA of a pig to be detected;
(2) Carrying out PCR amplification on the genome DNA of the pig to be detected by adopting the primer pair or the kit so as to obtain a PCR amplification product;
(3) Sequencing the PCR amplification product so as to obtain a sequencing result;
(4) And determining the genotype of the SNP molecular marker of the pig to be tested based on the sequencing result.
Preferably, the breeding pigs comprise doloque and synthetic lines thereof.
The present invention provides a method for genetic modification of pigs, said method comprising the steps of:
determining the locus of SNP molecular markers related to the number of malformed piglets produced by sows on the chromosome 13 of the breeding pigs in the breeding pig core group, and making corresponding selection according to the molecular markers: and selecting a boar individual with TT and GT genotypes at a 128894716 site on chromosome No. 13 of the international pig reference genome 11.1 version 13 from the boar core group, and eliminating the boar individual with GG genotype at a 128894716 site so as to increase the frequency of allele T at the site generation by generation, thereby reducing the number of malformed piglets of the sow.
The invention provides application of the SNP molecular marker, the primer pair or the kit in identifying pig malformation number-related characters, screening pig varieties with low malformation number of piglets, reducing the malformation number of piglets of sows or genetic breeding of pigs.
The beneficial effects are that:
(1) The invention researches and determines that the molecular marker related to the number of the malformed piglets which affect the sow is positioned on a nucleotide sequence on chromosome 13 of the pig, verifies the influence effect of the molecular marker on the malformed number character, finally establishes a high-efficiency accurate molecular marker assisted breeding technology, and applies the molecular marker assisted breeding technology to the genetic improvement of the malformed piglets which reduce the sow, thereby improving the number of the live piglets which produce the sow, reducing the breeding loss, improving the production benefit, improving the economic profit of enterprises and increasing the core competitiveness. By optimizing the dominant allele of the SNP, the dominant allele frequency can be increased generation by generation, the number of malformed piglets produced by the sow is reduced, and the progress of genetic improvement of the pig is accelerated, so that the economic benefit of breeding of the sow is effectively improved.
(2) The invention provides a primer pair for identifying SNP molecular markers on the chromosome 13 of the sow and related to the number of malformed piglets, and by the primer pair, a high-efficiency and accurate molecular marker assisted breeding technology can be established, so that the malformed piglets of the sow can be rapidly and accurately subjected to reduced breeding improvement, and the breeding process is accelerated.
Drawings
FIG. 1 is a Manhattan plot of genome-wide association analysis of Duroc on chromosome 13 for the S22 line with respect to malformation number traits; wherein: the abscissa indicates chromosome number of pigs; the ordinate represents the-logP value.
FIG. 2 is a graph of analysis of the results of the number of malformations in pigs of different genotypes.
Detailed Description
For a better description of the objects, technical solutions and advantages of the present invention, the present invention will be further described with reference to the following specific examples.
Example 1
(1) Experimental animal
The experimental swinery group used in the invention is pure S22-family Duroc sow 536 head of Wen food group stock pig division company, which is a core group of pig division company.
The experiment selects S22 Duroc sows in the resource group, the swinery freely ingests and drinks water, and the whole feeding mode, feeding conditions and the like are always consistent, so that the method is a conventional method.
(2) Sample collection
Collecting the pigtail and ear tissues, soaking in 75% ethanol solution, and storing in a refrigerator at-20deg.C.
(3) Pig whole genome 50K SNP judgement
Ear tissue or tail tissue collected from each individual of 536 Duroc pigs selected from the above resource population, whole genome DNA was extracted by a standard phenol-chloroform method, and the DNA concentration and OD ratio (OD 260/280, OD 260/230) of each sample were accurately determined by a Nanodrop2000/2000C nucleic acid protein detector. And detecting a qualified DNA sample by a Nanodrop2000/2000C nucleic acid protein detector, and diluting the DNA to about 50 ng/. Mu.L according to the detected concentration. And mixing 6 mu L of the extracted DNA sample to be detected with 2 mu L of Loading Buffer, loading the mixture into agarose gel with the mass-volume ratio of 1%, carrying out electrophoresis for 25min at 150V, and observing and photographing under an ultraviolet spectrophotometer and gel imaging equipment to observe the integrity of the DNA.
DNA samples were sent to the New Biotechnology (Shanghai) Inc., and genotype determination was performed on a pig whole genome 50K SNP chip (Illumina, USA) on a Illumina Beadstration platform according to the company standard procedure. Performing quality control on 50K chip scanning typing data of all samples by using a checkmarker in an R language GenABEL package, and removing and detecting that the individual rate is lower than 90%, the family Mendelian error rate is higher than 0.1, the minimum allele frequency is lower than 0.05 and the Hay-Wenberg equilibrium significance level is higher than 10 -6 And finally obtaining the effective genotype data of 39506 SNPs.
(4) Whole genome association (GWAS) analysis
In order to eliminate the layering effect of the population, the invention adopts linear mixed model single-point regression analysis and combines R language GenABEL software package to carry out GWAS analysis, and the layering effect is corrected by utilizing the similarity of genome among individuals in an analysis model. Determining a significance threshold of the association degree of the SNP and the effective total nipple number trait by adopting a Bonferrini method, wherein the genome level significance threshold is 0.05 divided by the effective SNP locus number, namely the genome significance level threshold is 1.26E-06, namely 0.05/39506 (the effective SNP number); the chromosome level significance threshold was 1 divided by the number of effective SNP sites, i.e., the chromosome level significance threshold was 2.53E-05, i.e., 1/39506 (number of effective SNPs).
The GWAS analysis results are shown in fig. 1. As can be seen from FIG. 1, in Duroc pigs, there is a site in chromosome 13 that significantly affects the number of malformations, and the strongest associated SNP is g.120G > T (P value 3.59E-06).
(5) Correlation analysis of different genotypes and malformed number phenotypes of the locus (rs 81298366)
According to Table 1, it is known that the SNP locus g.120G > T of the molecular marker (nucleotide 120 in SEQ NO.1, namely, G > T mutation 128894716 on chromosome 13 corresponding to the 11.1 version reference sequence of the International pig genome) is extremely obviously related to the malformation number character (P < 0.001), which indicates that the molecular marker obviously affects the malformation piglet number character of the sow, and the number of malformation piglets of the sow in the group can be reduced by auxiliary selection of the SNP locus of the sow, so that the reproductive performance of the sow is improved and the breeding process is accelerated.
As is clear from table 1 and fig. 2, the number of malformations in TT type and GT type is smaller than those in GG type. The average number of malformed piglets of TT type sows is 0.8 times less than that of the average malformed piglets of GG type sows, and the difference between the average malformed piglets of TT type sows and the average malformed piglets of GG type sows is extremely remarkable (P is less than 0.001). The result shows that the GG type sow is gradually removed in breeding, so that the frequency of the allele T of the locus is increased by each generation, the number of the malformed piglets produced by the sows in the group can be obviously reduced, and more economic benefits are brought to breeding enterprises.
TABLE 1 correlation analysis of SNP loci g.120G > T of molecular markers and malformations number
Example 2 amplification and sequencing of the DNA sequence of interest
(1) Primer design
The DNA sequence of SEQ ID NO.1 on chromosome 13 of pigs was downloaded via the Ensembl website (http:// asia. Ensembl. Org/index. Html). And primers were designed using primer premier 6.0. The DNA sequence of the designed primer is as follows:
P001-F：5’-GCTGCATTGGCCATCAAGGT-3’，
P002-R：5’-TGTGAAACGAGGAGGCAGGA-3’；
(2) PCR amplification
1. Mu.L of DNA template, 3.4. Mu.L of double distilled water, 2X Tag PCR StanMix with Loading Dye. Mu.L, and 0.3. Mu.L of each of the primers P001-F and P002-R were added to 10. Mu.L of the reaction system. The PCR reaction conditions were: after pre-denaturation at 94℃for 5min, denaturation at 94℃for 30s, annealing at 60℃for 30s, extension at 72℃for 30s,35 cycles, and extension at 72℃for 5min.
(3) DNA sequencing
Sequencing and identifying DNA sequences: the gene fragment was tested for both positive and negative responses in Shenzhen Dacron Gene technology Co. The sequence thus determined was aligned with the NCBI genomic sequence to give a mutation at the corresponding SNP site. The sequencing results are shown below:
note that: m marked in the sequence listing is a mutation site, shown by underline (mutation base in brackets, allelic mutation), and shown by thickening at the beginning and end of the sequence as a designed primer sequence position.
EXAMPLE 3 analysis of SNP site g.120G > T Effect of molecular marker
As can be seen from Table 1, the effect of SNP locus g.120G > T dominant allele type (TT) was significantly reduced by 0.8 from the average of GG type phenotypes for the number of deformities. Therefore, by molecular marker assisted selection, the pigs with the genotype GG in the group are gradually eliminated, so that the allele frequency of the allele T can be obviously improved, the probability of producing malformed piglets by the sow is reduced, the breeding loss is reduced, the animal welfare is improved, the improvement progress of the genetic defect of the pigs is accelerated, and the economic benefit of breeding the sow is effectively improved
The invention provides a new molecular marker for the auxiliary selection of the molecular marker of the pig by detecting the 120 th base mutation site in the SEQ ID NO.1 sequence and preliminarily carrying out the correlation analysis between the genotype and the number of the abnormal piglets produced by the sow.
Finally, it should be noted that the above embodiments are only for illustrating the technical solution of the present invention and not for limiting the scope of the present invention, and although the present invention has been described in detail with reference to the preferred embodiments, it should be understood by those skilled in the art that the technical solution of the present invention may be modified or substituted equally without departing from the spirit and scope of the technical solution of the present invention.
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Claims (4)
1. A method of screening a sow breed having a low number of malformed piglets, comprising the steps of:
detecting the genotype of 128894716 nucleotide locus on chromosome 11.1 version 13 of the international swine reference genome of swine, and selecting TT type individuals of 128894716 nucleotide locus as breeding swine, wherein the sow is S22-line Duroc.
2. The method of claim 1, wherein the method of detecting the genotype of nucleotide position 128894716 on chromosome 11.1 version 13 of the international swine reference genome of swine comprises the steps of:
(1) Extracting genome DNA of a pig to be detected;
(2) Performing PCR amplification on genome DNA of the pig to be detected by adopting a primer pair, wherein the nucleic acid sequence of the primer pair is shown as SEQ ID NO:2 and SEQ ID NO:3 in order to obtain PCR amplification products;
(3) Sequencing the PCR amplification product so as to obtain a sequencing result;
(4) And determining the genotype of the pig to be tested based on the sequencing result.
3. A method for genetic modification of a sow, comprising the steps of: selecting a boar individual with TT and GT genotypes at a 128894716 site on chromosome 11.1 version 13 of an international pig reference genome from a boar core group, eliminating the boar individual with GG genotype at the 128894716 site, and increasing the frequency of allele T at the site generation by generation so as to reduce the number of malformed piglets of sows, wherein the sows are S22-line Duroc.
4. Use of a primer pair for detecting the genotype of nucleotide 128894716 on chromosome 11.1 version 13 of the international swine reference genome of swine in screening sow breeds with low number of malformed piglets, wherein the sow is S22 duroc.
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Citations (5)
| Publication number | Priority date | Publication date | Assignee | Title |
|---|---|---|---|---|
| WO1994014064A1 (en) * | 1992-12-09 | 1994-06-23 | University Of Guelph | Methodology for developing a superior line of domesticated animals |
| WO2010066118A1 (en) * | 2008-12-11 | 2010-06-17 | 江西农业大学 | Muc13 molecular marker for identifying the f4ac adhesin-caused diarrhea resistance of the weanling pig and the use thereof |
| CN107988388A (en) * | 2017-12-11 | 2018-05-04 | 华南农业大学 | A kind of and relevant SNP marker of pig dewclaw undue growth character and application thereof |
| CN110106255A (en) * | 2019-03-29 | 2019-08-09 | 华南农业大学 | Molecular labeling relevant to duroc daily gain character and application on No. 7 chromosomes of pig |
| CN112011623A (en) * | 2020-08-25 | 2020-12-01 | 华中农业大学 | Molecular marker related to sow live litter size and effective live litter size traits |
-
2021
- 2021-08-06 CN CN202110905687.3A patent/CN113637768B/en active Active
Patent Citations (5)
| Publication number | Priority date | Publication date | Assignee | Title |
|---|---|---|---|---|
| WO1994014064A1 (en) * | 1992-12-09 | 1994-06-23 | University Of Guelph | Methodology for developing a superior line of domesticated animals |
| WO2010066118A1 (en) * | 2008-12-11 | 2010-06-17 | 江西农业大学 | Muc13 molecular marker for identifying the f4ac adhesin-caused diarrhea resistance of the weanling pig and the use thereof |
| CN107988388A (en) * | 2017-12-11 | 2018-05-04 | 华南农业大学 | A kind of and relevant SNP marker of pig dewclaw undue growth character and application thereof |
| CN110106255A (en) * | 2019-03-29 | 2019-08-09 | 华南农业大学 | Molecular labeling relevant to duroc daily gain character and application on No. 7 chromosomes of pig |
| CN112011623A (en) * | 2020-08-25 | 2020-12-01 | 华中农业大学 | Molecular marker related to sow live litter size and effective live litter size traits |
Non-Patent Citations (2)
| Title |
|---|
| Detection of genomic regions associated malformations in newborn piglets: a machine-learning approach;Siroj Bakoev 等;《PeerJ》;第7卷;第1-21页 * |
| 影响母猪繁殖性能的几种因素研究;刘彬 等;《西南农业学报》;第32卷(第8期);第1950-1955页 * |
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