CN111118177A - SNP molecular marker related to swine sexual maturity character - Google Patents
SNP molecular marker related to swine sexual maturity character Download PDFInfo
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Abstract
The invention belongs to the technical field of pig molecular marker screening, and particularly relates to an SNP molecular marker related to the characters of a pig sexual maturity stage. By integrating the NCBI database and the re-sequencing data of 469 pigs of 58 breeds disclosed by the European bioinformatics research institute, comparing the reference genome sequence of the pigs to obtain genotyping data, and screening to obtain a molecular marker related to the sexual maturity of the pigs, wherein the nucleotide sequence of the marker is shown as SEQ ID NO:1, an A/C allelic mutation exists at the 51 st base of the sequence, and when the 51 st nucleotide of the sequence is C, the pig has longer sexual maturity.
Description
Technical Field
The invention belongs to the technical field of pig molecular marker preparation, and particularly relates to an SNP molecular marker related to the characters of a pig sexual maturity stage. The molecular marker can be used for auxiliary selection and prediction of the traits of the porcine sexual maturity.
Background
Pigs are an important economic animal in livestock production. Domestic pigs, one of the earliest domesticated animals in humans, originate in European wild boars (Sus scrofa), which are subsequently independently domesticated in Europe and Asia, respectively (Larson G, Dobney K, Albarella U, et al. world wide biology of world wide reales multiplexers of pig society [ J ] Science,2005,307(5715): 1618) 1621.). Due to the independent domestication process, the European pig species and the Asian pig species have well-differentiated germplasm characteristics, for example, the European pig species has higher lean meat percentage and larger body type, the Asian pig species has higher fat content, and has the advantages of high litter size and prematurity.
The sexual maturity is a process by which the animal reaches sexual maturity, which allows sexual reproduction. Studies have shown that sows with earlier sexual maturity are able to deliver more piglets with longer reproductive life, (Patterson J L, Beltrana E, Foxccroft G R. the effect of gilt at first and breedinggon third animals on body weight changes and long-term improvement performance [ J ]. Journal of Animal Science,2010,88(7): 2500-2513.). In the production process of pigs, the reproductive performance of the pigs is an important economic character, and great economic benefits can be brought by prolonging the reproductive life of sows. Therefore, exploring the relevant molecular markers for discovering the genetic mechanism of sexual maturity is helpful to better develop the breeding research of pigs.
Genome-wide association analysis (GWAS), a method of association analysis that has better and more statistically significant advantages than linkage analysis in association with complex traits, was first proposed by Risch in 1996 (Risch N, Merikangas K. The future of genetic students of complex Human diseases [ J ]. Science,1996,273(3):350-354.) as a powerful tool for exploring in The Genome-wide range genetic markers that identify The association between experimental populations and phenotypes of interest, has been widely used in various studies, including Human diseases and livestock important economic traits, etc. (Vischer P M, Brown M A, McCarthy M I, et al, five layers of AS discovery [ J.: journal of The animal, J. am. of The journal of The Human, 90-24, 24-2012, 7, 90-24.)
In recent years, the correlation between related genes and related genome has been reported about the research on the correlation analysis of the whole genome related to the porcine sexual maturity. The invention screens SNP molecular markers related to the sexual maturity stage by integrating the re-sequencing data of 469 pigs containing 58 breeds disclosed in NCBI database (SRA, http:// www.ncbi.nlm.nih.gov/SRA /) and European bioinformatics institute (EMBL-EBI, https:// www.ebi.ac.uk /), using MVP software and using MLM model (Zhang Z, Ersoz E, Lai C Q, et al.
The relevance of the SNP and the pig sexual maturity stage reaches a remarkable level, and a new genetic resource is provided for the research on the relevance of the pig sexual maturity stage.
Disclosure of Invention
The invention aims to perfect the development of molecular markers related to the traits of the pig sexual maturity, obtain SNP typing data by comparing pig re-sequencing data to a pig reference genome, and screen SNPs related to the pig sexual maturity by using whole genome analysis (GWAS).
The technical scheme of the invention is as follows:
the applicant obtains SNP typing data by integrating the re-sequencing data of 469 pigs of 58 breeds disclosed in NCBI database (SRA, http:// www.ncbi.nlm.nih.gov/SRA /) and European bioinformatics institute (EMBL-EBI, https:// www.ebi.ac.uk /), and comparing the pig re-sequencing data to a pig reference genome (genome version 11.1, Sscofa 11.1), and obtains a nucleotide sequence of about 50bp upstream and downstream of the SNP site with the accession number rs 341846, the nucleotide sequence of the fragment is shown in SEQ ID NO:1 (C at the 51 st base in SEQ ID NO:1 is a sequence after allele mutation), and the specific nucleotide sequence is:
CTGAACAGACCAATCAGTAGAAATGAAATTGAATATGCATTAAAAAAAAAR(A/C)CACTCTGTACAGAGTTAAGGACCAGATGGCTTCACAGATGAATTCGATCA，
the R at the 51 st base of the sequence is an allelic mutation of A51-C51, and the allelic mutation generates nucleotide polymorphism of the SEQ ID NO. 1 sequence. The molecular marker can be used as a molecular marker for detecting the characters related to the pig sexual maturity, and when the 51 st nucleotide on the sequence shown by SEQ ID NO. 1 is C, the molecular marker is favorable for the pig to have a longer sexual maturity.
The sequence can be developed to be used as a molecular marker for detecting the characters related to the porcine sexual maturity.
The applicant provides a method for screening SNP molecular markers related to the traits of the porcine sexual maturity, which comprises the following steps:
① integrating the re-sequencing data of 469 pigs of 58 breeds disclosed in NCBI database (SRA, http:// www.ncbi.nlm.nih.gov/SRA /) and European bioinformatics institute (EMBL-EBI, https:// www.ebi.ac.uk /), and aligning the pig re-sequencing data to a pig reference genome (genome version 11.1, Sscofa 11.1) to obtain SNP typing data;
② according to the breed information corresponding to the individual in the group, by consulting Chinese livestock genetic resource record (pig record), Wikipedia, foreign related pig breed websites, pig genetic resource related documents and the like, the characteristic sexual maturity stage of each breed is counted, and the sexual maturity stage is taken as the phenotype;
③ GWAS analysis is carried out by using MLM model in MVP software package under R statistical environment by adopting a method of mixed linear model, wherein, y is X β + Z mu + e, wherein, y represents individual table value, β represents fixed effect including main component (principal component), mu represents obedience distribution
X and Z represent the correlation matrix of β and μ, and e represents the residual vector (vectorrof residual errors).
The molecular marker screened by the invention can be applied to non-diagnosis-purpose correlation analysis related to the genotype of the genes related to the pig sexual maturity stage or the traits of the pig sexual maturity stage, and provides a new molecular marker resource for the molecular marker-assisted selection of the traits of the pig sexual maturity stage.
Compared with the prior art, the invention has the following beneficial effects:
the invention can detect the genotype of the pig by adopting a gene chip technology in vitro, the result can be used for evaluating the sexual maturity stage of the pig for the non-diagnosis purpose, and compared with the prior PCR-RFLP and other methods, the invention has the outstanding advantages of simplicity, rapidness, high sensitivity, good specificity and the like.
For a more detailed technical solution, refer to the detailed description.
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FIG. 1: the general technical process schematic diagram of the invention.
FIG. 2: is the nucleotide sequence of upstream and downstream 50bp of rs341848276 cloned by the invention and the nucleotide sequence of the molecular marker of the invention. Description of reference numerals: in FIG. 2, it is shown that an A/C allelic mutation exists at the 51 st base of the nucleotide sequence (the English letter "R" at 51bp is a mutation site).
FIG. 3: is a manhattan diagram of the present invention. Description of reference numerals: the characters of the porcine sexual maturity stage are researched, and the black circles and the arrows point to the markers which are the molecular markers screened by the invention and are positioned on the No. 15 chromosome of the pig.
Detailed Description
Description of sequence listing:
SEQ ID NO. 1 of the sequence table is the nucleotide sequence of the upstream and downstream 50bp fragment of clone rs341848276 of the invention. The fragment is the molecular marker screened by the invention. The fragment is 101bp in length, and R at the 51 base of the sequence is an A/C allelic mutation. This mutation results in polymorphism in the nucleotide sequence shown in SEQ ID NO. 1.
The sequence and whole genome correlation analysis results in the invention are based on the information of the 11.1 version of the pig genome.
Example 1: genotyping detection of genes
(1) 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;
(2) the raw data is converted into a fastq file using sratolkit (V2.8.2), and then the fastq file is preliminarily qualified using trimmatic (V0.36) software. This step was followed by alignment of the remaining high quality reads with the porcine reference genome (version 11.1) using Burrows-wheelerligner 0.7.17(BWA) software, and selection of the unique aligned sequences for typing. 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.
(3) Genotyping data was quality checked and finally 399 individuals and 19,487,140 SNPs were used for GWAS studies.
Example 2: application of rs341848276 molecular marker typing method in pig sexual maturity stage character association analysis
And (3) analyzing the association between the rs341848276 molecular marker and the sexual maturity stage trait:
the phenotype used for the correlation analysis of the genotype and the character of the sexual maturity period is mainly obtained by consulting the Chinese livestock and poultry genetic resource record (Pizhi) Wikipedia, foreign related pig variety websites, pig genetic resource related documents and the like according to variety information corresponding to individuals in a group, counting the characteristic sexual maturity period of each variety, taking the sexual maturity period as the phenotype, and totaling 399 individuals and 34 varieties. The specific maturation period of the variety is divided into three categories according to the statistical result, namely early maturation (sexual maturation is achieved in 1-3 months), medium maturation (sexual maturation is achieved in 4-6 months) and late maturation (sexual maturation is achieved in more than 6 months), and the categories are numbered as 1, 2 and 3 in sequence as digital phenotypes according to the categories.
The GWAS analysis is carried out by using an MLM model in an MVP software package under an R statistical environment by adopting a mixed linear model, wherein the specific model is that y is X β + Z mu + e, wherein y represents a table value of an individual, β represents a fixed effect including a principal component (principal component), and mu represents obedience distribution
X and Z represent correlation matrices of β and μ, e represents residual vectors (vector residual errors) the marker genotype and number of individuals with the corresponding phenotype are shown in table 1, and the genome-wide significance level is shown in table 2.
Table 1 rs341848276 polymorphisms and corresponding numbers of individuals within a population
Table 2 rs341848276 genome wide significance level
Table 2 illustrates: significant markers when the P-value of the marker P <0.05/19487140(Bonferroni correction)
As is clear from Table 1, the sexual maturity of individuals with genotype CC has been focused on a long classification (6 months or more). In the whole genome association analysis adopting the MLM model, the rs341848276 marker reaches a whole genome significant level, which shows that the marker is not only significantly related to the character of the sexual maturity stage of the pig, but also is beneficial to the pig to have a longer sexual maturity stage when the marker is mutated into C.
The main references:
[1]Larson G,Dobney K,Albarella U,et al.Worldwide phylogeography ofwild boar reveals multiple centers of pig domestication[J].Science,2005,307(5715):1618-1621.
[2]Patterson J L,Beltranena E,Foxcroft G R.The effect of gilt age atfirst estrus and breeding on third estrus on sow body weight changes andlong-term reproductive performance[J].Journal of Animal Science,2010,88(7):2500-2513.
[3]Risch N,Merikangas K.The future of genetic studies of complexhuman diseases.[J].Science,1996,273(3):350-354.
[4]Visscher P M,Brown M A,McCarthy M I,et al.Five years of GWASdiscovery[J].The American Journal of Human Genetics,2012,90(1):7-24.
[5]Zhang Z,Ersoz E,Lai C Q,et al.Mixed linear model approach adaptedfor genome-wide association studies[J].Nature genetics,2010,42(4):355。
SEQUENCE LISTING
<110> Huazhong agriculture university of Guangxi Yangxi Xiang Suo GmbH
<120> SNP molecular marker related to porcine sexual maturity traits
<130>
<141>2019-07-24
<160>1
<170>PatentIn version 3.1
<210>1
<211>101
<212>DNA
<213> pig (Sus scrofa)
<220>
<221>gene
<222>(1)..(101)
<223>
<220>
<221>mutation
<222>(51)..(51)
<223>
<400>1
ctgaacagac caatcagtag aaatgaaatt gaatatgcat taaaaaaaaa ccactctgta 60
cagagttaag gaccagatgg cttcacagat gaattcgatc a 101
Claims (3)
1. An SNP molecular marker related to the traits of the porcine sexual maturity, which is characterized in that the nucleotide sequence of the molecular marker is as follows:
CTGAACAGACCAATCAGTAGAAATGAAATTGAATATGCATTAAAAAAAAAR(A/C)CACTCTGTACAGAGTTAAGGACCAGATGGCTTCACAGATGAATTCGATCA，
the mutation, wherein R at base 51 of the above sequence is A or C, results in polymorphism of the sequence.
2. The SNP molecular marker related to the porcine sexual maturity trait of claim 1 wherein when SEQ ID NO:1 is C, the swine has longer sexual maturity period.
3. Use of the molecular marker of claim 1 in porcine sexual maturity trait marker assisted selection.
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| US20030215783A1 (en) * | 2002-01-18 | 2003-11-20 | Thurston Lisa M. | Genetic markers for semen viability |
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Non-Patent Citations (3)
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