CN111154889B - SNP molecular marker related to pig body weight and application and acquisition method thereof - Google Patents
SNP molecular marker related to pig body weight and application and acquisition method thereof Download PDFInfo
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- CN111154889B CN111154889B CN202010048151.XA CN202010048151A CN111154889B CN 111154889 B CN111154889 B CN 111154889B CN 202010048151 A CN202010048151 A CN 202010048151A CN 111154889 B CN111154889 B CN 111154889B
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Abstract
The invention relates to the technical field of molecular markers, in particular to a pig weight-related SNP molecular marker and an application and acquisition method thereof, the method obtains genotype data by extracting total DNA of pigs, performing quality control and analysis on the total DNA, and obtains genotyping data by comparing a pig reference genome sequence to obtain a pig weight-related molecular marker, wherein the nucleotide sequence of the marker is shown as SEQ ID NO:1, an allelic mutation of T/G at the 51 st base of the sequence, resulting in polymorphism in the nucleotide of the sequence as shown, when the nucleotide sequence of SEQ ID NO: when the 51 st nucleotide in 1 is T, the weight of the pig is heavier.
Description
[ technical field ] A method for producing a semiconductor device
The invention relates to the technical field of pig molecular marker screening, in particular to a pig weight-related SNP molecular marker and application thereof.
[ background of the invention ]
In production, the weight of pigs is closely related to economic benefit, and some important production cost is calculated by taking each pig as a unit, such as part of environmental management cost, and the heavier the weight of slaughtered pigs, the part of cost can be saved. Research shows that the weight of the pig is related to meat quality and carcass properties, and the weight of the pig is in extremely obvious positive correlation with the eye muscle area in a certain period. Meanwhile, researches find that the weight of the sow is related to the reproductive performance, and the proper weight can ensure the highest reproductive performance of the sow. Therefore, the exploration and discovery of the molecular markers related to the weight of the pigs are beneficial to actual production and better development of breeding research of the pigs.
And (4) genome-wide association analysis, namely searching variation sites, namely Single Nucleotide Polymorphisms (SNPs) on a genome-wide range, and screening the SNPs associated with the phenotypic traits. With the completion of whole genome sequencing of various organisms and the continuous research and development of high-throughput chips, GWAS is widely applied to the research of human disease traits and economic traits of livestock, poultry and plants, and has made a new progress. At present, the research on the growth, meat quality and other properties of the GWAS in the pig is newly progressed, and the applicability of the GWAS in the pig research is proved.
The method screens SNP molecular markers related to the weight by integrating the re-sequencing data of 469 pigs containing 58 breeds disclosed in NCBI databases (SRA, http:// www.ncbi.nlm.nih.gov/SRA /) and European bioinformatics institute (EMBL-EBI, https:// www.ebi.ac.uk /), using MVP software and using a Mixed Linear Model (MLM), provides a new molecular marker basis for auxiliary selection and prediction improvement of the weight of the pigs, and has important significance for pig breeding.
The SNP molecular marker screened by the invention is obviously related to the weight of the pig, and provides a new genetic resource for the research on the weight of the pig.
[ summary of the invention ]
In view of the above, there is a need to provide a pig weight-related SNP molecular marker, and the application and acquisition method thereof, the 43416507 nucleic acid locus of chromosome 14; is A > C mutation, and a primer for amplifying the molecular marker and a probe for identifying the molecular marker can be designed according to the mutation; and further applied to screening pigs with high body weight, and provides a new molecular marker basis for selection and improvement of the body weight of the Duroc pigs.
In order to achieve the purpose, the technical scheme adopted by the invention is as follows:
the SNP molecular marker related to the pig weight is characterized in that the molecular genetic marker is positioned at 43416507 th nucleic acid site of No. 14 chromosome of a pig, the base of the site is T or G, and the site corresponds to the 51 st nucleic acid site of a nucleic acid sequence table SEQ ID NO. 1.
The application also includes primers for amplifying the molecular genetic marker or probes for identifying the molecular genetic marker.
The application also includes kits containing the primers or probes.
The application also comprises the application of the molecular genetic marker in breeding or breeding assisting in breeding of high or low weight varieties or strains.
A method for breeding or assisting in breeding pigs with heavier weights comprises the following steps: extracting pig DNA, detecting 43416507 th deoxyribonucleotide of 14 th chromosome of pig, detecting 43416507 th ribonucleotide sequence as T or G, determining the genotype of pig to be detected as TT type or GG type, and selecting TT type gene pig for further breeding.
Further, the TT genotype is a homozygote of 43416507 th deoxyribonucleotide of the 14 th chromosome of the pig which is T; the GG genotype is a homozygote of G at the 43416507 th deoxyribonucleotide of chromosome 14.
Further, the method comprises the following steps: extracting total DNA of the pig, and performing quality control and analysis on the total DNA to obtain genotype data; counting the individual weight data of the pig as phenotype, and utilizing the whole genome correlation analysis technologyObtaining SNP obviously related to the weight of the pig; the quality control standard is as follows: by ` QUAL ` using GATK (V4.0.3.0) software<30.0||QD<2.0||FS>60.0||MQ<40.0||SOR>4.0||ReadPosRankSum<-8.0' command for quality control; the whole genome association analysis adopts a mixed linear model as follows: y ═ X β + Z μ + e, where y represents the phenotypic value of the individual, β represents the fixing effect including the principal component, and μ represents the obedient distribution
G in the distribution represents the affinity matrix calculated from the SNPs of the corresponding individuals. X and Z represent the correlation matrix of β and μ, and e represents the residual vector.
The molecular marker provided by the invention can be used for auxiliary selection and prediction of pig body weight.
The invention has the following beneficial effects:
the molecular marker screened by the invention can be applied to non-diagnosis-purpose genotype of the genes related to the pig weight or correlation analysis related to the pig weight, and provides a new molecular marker resource for the molecular marker-assisted selection of the pig weight. The invention can detect the genotype of the pig by adopting a gene chip technology in vitro, and is used for evaluating the weight of the pig with a non-diagnosis purpose.
[ description of the drawings ]
FIG. 1 is a schematic diagram of the general technical process of the present invention;
FIG. 2 is a Manhattan diagram of the whole genome association analysis of the present invention. Description of reference numerals: pig body weight was studied, and the black circles and arrows indicate molecular markers selected by the present invention, which are located on pig chromosome 14.
[ detailed description ] embodiments
In order to make the aforementioned objects, features and advantages of the present invention comprehensible, embodiments accompanied with figures are described in detail below. In the following description, numerous specific details are set forth in order to provide a thorough understanding of the present invention. This invention may, however, be embodied in many different forms and should not be construed as limited to the embodiments set forth herein, but rather should be construed as broadly as the present invention is capable of modification in various respects, all without departing from the spirit and scope of the present invention.
Example 1:
genotyping and detection
The method comprises the following steps: the re-sequencing data of 469 pigs containing 58 breeds, disclosed in the NCBI database (SRA, http:// www.ncbi.nlm.nih.gov/SRA /) and the European bioinformatics institute (EMBL-EBI, https:// www.ebi.ac.uk /), were collectively downloaded;
step two: the original data is converted into a fastq file by using SRATOOLKIT (V2.82), and then the fastq file is subjected to preliminary quality control by using Trimmomatic (V0.36) software. This step was followed by alignment of the remaining high quality reads to the porcine reference genome (version 11.1) using Burrows-Wheeler Aligner 0.7.17(BWA) software, and typing of the unique aligned sequences. In order to obtain high-quality mutation data, GATK (V4.0.3.0) software is used for quality control through a command of 'QUAL <30.0| | | QD <2.0| | FS >60.0| | MQ <40.0| | | SOR >4.0| | ReadPosRenkSum < -8.0', and genotype data which can be used for GWAS analysis is obtained.
Step three: genotyping data was quality checked, resulting in 404 individuals and 19198719 SNPs for genome wide association analysis (GWAS).
Example 2:
and (3) analyzing the association with the Duroc pig weight traits:
the main phenotype sources for the genotype and weight trait association analysis are that according to breed information corresponding to individuals in a group, the adult weight of each breed of pig is counted by consulting Chinese livestock and poultry genetic resource records (pig records), Wikipedia, foreign related pig breed websites, pig genetic resource related documents and the like, and the weight is taken as the phenotype, so that 404 individuals and 47 breeds are counted. The adult weight of the breed is divided into three categories according to the statistical result, namely 100kg below, 100-200kg above and 200kg above. Phenotypes are numbered 1, 2, 3 in sequence. And performing whole genome association analysis by using an MLM model in an MVP package under the R language by adopting a mixed linear model method.
The concrete model is as follows: y ═ X β + Z μ + e
Wherein y represents a phenotypic value of the individual;
beta represents a fixed effect including the main component;
μ represents obedience distribution
The random effect of (a);
g in the distribution represents an affinity matrix calculated from SNPs of corresponding individuals;
x and Z represent a correlation matrix of beta and mu;
e represents the residual vector.
The number of individuals with the marker genotype and the corresponding phenotype is shown in table 1, and the significant level of the whole genome association analysis is shown in table 2.
TABLE 1 weight classification of pigs and number of individuals in corresponding groups
TABLE 2 significance level of genome-wide association analysis in pigs
| Chromosome number | Position of | P- |
| 14 | 43416507 | 2.82E-12 |
Significant markers when the P-value of the marker is <0.05/19198719(Bonferroni correction)
As can be seen from Table 1, for individuals with genotype TT, the body weight is focused on the heavier category; for individuals with genotype GG, their body weight is focused on a lighter classification. In the whole genome association analysis adopting the MLM model, the rs321340075 marker reaches the significant level of the whole genome association analysis, which indicates that the marker is not only significantly associated with the weight traits of the pigs, but also the pigs may have heavier weight when the marker is mutated to T.
The sequence table SEQ ID NO 1 is a nucleotide sequence of 50bp respectively at the upstream and downstream of the molecular marker related to the Duroc pig weight trait screened by the invention, the sequence length is 101bp, an allelic gene mutation (T/G) exists at the 51bp position of the sequence, and the mutation causes the nucleotide sequence shown in the SEQ ID NO 1 to generate polymorphism.
Example 3:
according to the gene results obtained by the screening, the molecular genetic marker related to the total papilla of the pig is shown, and is located at the 43416507 th nucleic acid site of No. 14 chromosome of the pig, wherein the position is a T > G mutation, and corresponds to the 51 st nucleic acid site of the nucleic acid sequence table SEQ ID NO. 1.
Example 4:
the skilled person can easily design primers for amplifying the molecular marker or probes for identifying the molecular marker according to the present invention, and then use the primers or probes for detecting the molecular marker, for example, the molecular marker is obtained by PCR amplification, and the corresponding sequence is obtained by clone sequencing, or the Bsm-RFLP polymorphism is used for detection. Thus, the invention also includes primers for amplifying the molecular genetic marker or probes for identifying the molecular genetic marker, and kits containing the primers or probes.
Example 5:
the molecular genetic marker can be applied to assist pig breeding or auxiliary breeding work, and the specific method comprises the following steps: extracting genome DNA of a pig, designing a primer to amplify a gene fragment shown as a sequence table SEQ ID NO.1, and detecting that a 51 th site gene is T or G; judging whether the pig to be detected is TT type or GG type according to the locus genotype; selecting pigs of TT type or GG type according to breeding requirements for reseeding or mating; wherein, the weight of the pig with TT homozygous genotype is higher than that of the pig with GG homozygous genotype.
In conclusion, the method can simply, efficiently and accurately obtain the molecular genetic marker related to the pig weight, and can design a primer for amplifying the molecular marker and a probe for identifying the molecular marker according to the mutation; the method has the advantages that pigs with the weight of the pigs are quickly screened, and the accuracy and the efficiency of screening the molecular markers can be effectively improved by analyzing the pigs through a one-step whole genome association analysis method.
The above examples are merely illustrative of several embodiments of the present invention, and the description thereof is more specific and detailed, but not to be construed as limiting the scope of the invention. It should be noted that, for a person skilled in the art, several variations and modifications can be made without departing from the inventive concept, which falls within the scope of the present invention. Therefore, the protection scope of the present invention should be subject to the appended claims.
Sequence listing
<110> Guangxi Yangxiang GmbH
University of agriculture in china
<120> SNP molecular marker related to pig weight and application and acquisition method thereof
<160> 1
<170> SIPOSequenceListing 1.0
<210> 1
<211> 101
<212> DNA
<213> pig (Sus scrofa)
<220>
<221> misc_feature
<222> (51)..(51)
<223> n is t or g
<400> 1
gcatgggttg caattgcagc tcagatctga tccttggccc aggaatgcca natgctgcag 60
ggcgggcaaa aaaagagaaa aaaaaaattt cctagtcaga a 101
Claims (2)
1. The application of a molecular genetic marker in breeding or assisting in breeding high or low weight varieties or strains is characterized in that the molecular genetic marker is positioned at the 51 st nucleic acid site of a nucleic acid sequence table SEQ ID NO.1, and the basic group of the site is T or G;
judging whether the pig to be detected is TT type or GG type according to the locus genotype; selecting pigs of TT type or GG type according to breeding requirements for reseeding or mating; wherein, the weight of the pig with TT homozygous genotype is higher than that of the pig with GG homozygous genotype;
the pig is a Duroc pig.
2. A method for breeding or assisting in breeding pigs with heavier weights is characterized by comprising the following steps: extracting DNA of a pig individual, and detecting a 51 st nucleic acid site of a nucleic acid sequence table SEQ ID NO. 1; measuring the sequence of the locus as T or G, determining the genotype of the pig to be detected as TT type or GG type, and selecting the pig with TT type gene for further breeding; wherein, the weight of the pig with TT homozygous genotype is higher than that of the pig with GG homozygous genotype; the pig is a Duroc pig.
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| CN110512006A (en) * | 2019-08-01 | 2019-11-29 | 广西扬翔股份有限公司 | A kind of SNP marker relevant to bristles color character |
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| CN101389214A (en) * | 2004-10-22 | 2009-03-18 | 雷维维科公司 | Ungulates with genetically modified immune systems |
| WO2018102795A2 (en) * | 2016-12-02 | 2018-06-07 | University Of Southern California | Synthetic immune receptors and methods of use 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 |
| CN110195116A (en) * | 2019-06-27 | 2019-09-03 | 广西扬翔农牧有限责任公司 | One kind molecular genetic marker relevant to sperm motility of boars and its application and acquisition methods |
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