CN115820875B - Molecular marker for evaluating area of porcine eye muscle and screening method and application thereof - Google Patents
Molecular marker for evaluating area of porcine eye muscle and screening method and application thereof Download PDFInfo
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Abstract
The invention relates to a molecular marker for evaluating the area of porcine eye muscle, a screening method and application thereof, and relates to the technical field of porcine genetic genes. The molecular marker is SNP molecular marker, the molecular marker is positioned at 30786798bp position of the chromosome 7 of the pig, 120345012bp position of the chromosome 7 of the pig, 56213488bp position of the chromosome 14 of the pig and/or 74418117bp position of the chromosome 5 of the pig. The molecular marker is used for evaluating the eye muscle area of pigs, further evaluating the lean meat percentage of pigs, and is used for breeding of breeding pigs, so that the eye muscle area of pigs can be effectively increased, the lean meat percentage of pigs is increased, the breeding molecular marker of pig ketone body shape is further perfected, and an effective means is provided for improving the pork quality and lean meat yield.
Description
Technical Field
The invention relates to the technical field of pig genetic genes, in particular to a molecular marker for evaluating the area of pig eye muscles, a screening method and application thereof.
Background
The pig raising country is a pig raising country and the pork consumption country, the pork is one of main animal protein sources in China, and the pork yield is closely related to the stability and the level of the domestic people's life. The growth characters such as lean meat percentage, daily gain, daily feed intake and the like are directly related to the meat and protein production performance of pigs, and the eye muscle area has high correlation with the lean meat percentage and is more convenient to measure than the lean meat percentage, so the eye muscle area becomes an important economic character in the current pig industry breeding.
The eye muscle area is obviously and positively correlated with the lean meat percentage, the lean meat percentage is calculated by slaughtering pigs, and the ratio of the lean meat to the carcass weight of the pigs is calculated, so that the measurement of the lean meat percentage is complex, the cost is high, and the method is not suitable for serving as a selection and retention index of conventional breeding. However, the determination of the eye muscle area can be obtained by measuring B-ultrasonic waves between the third and fourth ribs of the pig at a distance of 5cm from the dorsal midline. The eye muscle area can be used as a selection index for the lean meat percentage to be replaced to a great extent.
The eye muscle area is a higher genetic trait, a quantitative trait controlled by multiple genes. For such quantitative traits, multiple detection of candidate genes and QTLs associated with the trait contributes to the accuracy of genome selection. Most QTLs are identified using linkage disequilibrium methods, and the identified QTLs are difficult to use for genetic improvement in pigs.
Disclosure of Invention
Aiming at the problems, the invention provides a molecular marker for evaluating the area of the pig eye muscle, and the evaluation of the area of the pig eye muscle is carried out according to the molecular marker, so that the lean meat percentage of the pig is evaluated, the molecular marker is used for breeding a breeding pig, the area of the pig eye muscle can be effectively increased, the lean meat percentage of the pig is increased, the breeding molecular marker of the pig ketone body shape is further perfected, and an effective means is provided for improving the quality of the pork and the yield of the lean meat.
In order to achieve the above object, the present invention provides a molecular marker for assessing the area of porcine eye muscle, which is a SNP molecular marker located at 30786798bp position of porcine chromosome 7, 120345012bp position of porcine chromosome 7, 56213488bp position of porcine chromosome 14, and/or 74418117bp position of porcine chromosome 5.
In one embodiment, the molecular marker is located at 30786798bp of chromosome 7 of the pig, and when the genotype of the molecular marker is CC, the eye muscle area of the pig to be evaluated is indicated to be high;
the molecular marker is positioned at 120345012bp of the chromosome 7 of the pig, and when the genotype of the molecular marker is CC, the eye muscle area of the pig to be evaluated is indicated to be high;
the molecular marker is positioned at a 56213488bp position of a pig chromosome 14, and when the genotype of the molecular marker is CC, the high eye muscle area of the pig to be evaluated is indicated;
and/or the molecular marker is positioned at a 74418117bp position of a chromosome 5 of the pig, and when the genotype of the molecular marker is TT, the high eye muscle area of the pig to be evaluated is indicated.
The different genotypes of the molecular marker are obviously different in the aspect of the eye muscle area of the pig, wherein when the molecular marker is positioned at the 30786798bp position of the chromosome 7 of the pig, the genotype CC is obviously improved by 1.39 percent and 1.97 percent compared with the interocular muscle area of individuals of TC and TT Duroc boars, so that C in the marker is an allele which is favorable for obviously improving the eye muscle area; when the molecular marker is positioned at 120345012bp of a chromosome 7 of the pig, the genotype CC is obviously improved by 3.18% compared with TT, so that C in the marker is an allele which is beneficial to improving the eye muscle area; when the molecular marker is positioned at a 56213488bp position of a pig chromosome 14, the genotype CC is obviously improved by 2.46% compared with the inter-individual eye muscle area of a TT Duroc boar, so that C in the marker is more beneficial to T and improves the eye area; when the molecular marker is positioned at 74418117bp of the chromosome 5 of the pig, the genotype TT is improved by 1.59% and 3.07% compared with the interocular muscle area of individuals of CT and CC Duroc boars, so that the improvement of the interocular muscle area of T in the gene is more favorable for C.
The invention also provides a screening method of the molecular marker, which comprises the following steps:
collecting phenotype data: collecting phenotype data of the eye muscle area of the pig to be tested;
obtaining SNP molecular markers: sampling the pig to be detected, extracting DNA, and genotyping to obtain SNP molecular markers covering the whole genome; carrying out physical position update and quality control on the SNP molecular markers covering the whole genome;
screening SNP molecular markers: and combining phenotype data, performing GWAS analysis on the SNP molecular markers after quality control, analyzing the difference condition of the eye muscle areas of pigs with different genotype groups, and screening to obtain the SNP molecular markers for evaluating the eye muscle areas of the pigs.
With the development of sequencing technology in recent years, a large amount of acquisition of sequencing information is possible, whole genome association analysis (GWAS) is widely applied to animal breeding research, the development of chip sequencing technology facilitates the acquisition of high-density SNP information, the related research of the GWAS is more convenient, and the GWAS can effectively identify SNPs with remarkable correlation with characters. The analysis is carried out by using a FarmCPU model in rMVP software, and the model alternately uses a fixed effect and a random effect, so that the obvious SNP marker can be rapidly and accurately identified, and the analysis has promotion significance on the genetic improvement of the eye muscle area.
The invention also provides a detection kit for evaluating the lean meat percentage of pigs, which comprises a reagent for detecting the molecular marker.
The invention also provides a method for evaluating the lean meat percentage of the pig, which comprises the steps of obtaining the detection result of the molecular marker, and judging the eye muscle area of the pig according to the detection result so as to judge the lean meat percentage of the pig.
In one embodiment, the molecular marker is located at 30786798bp of chromosome 7 of the pig, and when the genotype of the molecular marker is CC, the eye muscle area of the pig is judged to be high, and the lean meat percentage of the pig is judged to be high;
the molecular marker is positioned at 120345012bp of the chromosome 7 of the pig, and when the genotype of the molecular marker is CC, the eye muscle area of the pig is judged to be high, and the lean meat percentage of the pig is high.
In one embodiment, the molecular marker is located at 56213488bp of chromosome 14 of the pig, and when the genotype of the molecular marker is CC, the eye muscle area of the pig is judged to be high, and the lean meat percentage of the pig is judged to be high.
In one embodiment, the molecular marker is located at 74418117bp of chromosome 5 of the pig, and when the genotype of the molecular marker is TT, the eye muscle area of the pig is judged to be high, and the lean meat percentage of the pig is judged to be high.
The invention also provides a pig breeding method, detection is carried out according to the method, the lean meat percentage of the pig is judged according to the genotype of the molecular marker, and the pig with high lean meat percentage is reserved; the molecular marker is positioned at 30786798bp position of the chromosome 7 of the pig, 120345012bp position of the chromosome 7 of the pig, 56213488bp position of the chromosome 14 of the pig or 74418117bp position of the chromosome 5 of the pig.
In one embodiment, the molecular marker is located at 30786798bp of chromosome 7 of the pig, and when the genotype of the molecular marker is CC, the eye muscle area of the pig is judged to be high, the lean meat percentage of the pig is high, and the pig is left;
the molecular marker is positioned at 120345012bp of the chromosome 7 of the pig, when the genotype of the molecular marker is CC, the eye muscle area of the pig is judged to be high, the lean meat percentage of the pig is high, and the pig is left for use;
the molecular marker is positioned at 56213488bp of the chromosome 14 of the pig, when the genotype of the molecular marker is CC, the eye muscle area of the pig is judged to be high, the lean meat percentage of the pig is high, and the pig is left for use;
the molecular marker is positioned at 74418117bp of the chromosome 5 of the pig, and when the genotype of the molecular marker is TT, the eye muscle area of the pig is judged to be high, the lean meat percentage of the pig is high, and the pig is left for use.
Compared with the prior art, the invention has the following beneficial effects:
according to the molecular marker for evaluating the pig eye muscle area, the screening method and the application thereof, the pig eye muscle area is evaluated according to the molecular marker, so that the pig lean meat percentage is evaluated, the molecular marker is used for breeding a breeding pig, the pig eye muscle area can be effectively improved, the pig lean meat percentage is improved, the pig ketone body-shaped breeding molecular marker is further perfected, and an effective means is provided for improving the pork quality and the lean meat yield.
Drawings
FIG. 1 is a Manhattan diagram of a marker screen in an embodiment.
Detailed Description
In order that the invention may be readily understood, a more complete description of the invention will be rendered by reference to the appended drawings. Preferred embodiments of the present invention are shown in the drawings. This invention may, however, be embodied in many different forms and should not be construed as limited to the embodiments set forth herein. Rather, these embodiments are provided so that this disclosure will be thorough and complete.
Unless defined otherwise, all technical and scientific terms used herein have the same meaning as commonly understood by one of ordinary skill in the art to which this invention belongs. The terminology used herein in the description of the invention is for the purpose of describing particular embodiments only and is not intended to be limiting of the invention. The term "and/or" as used herein includes any and all combinations of one or more of the associated listed items.
Definition:
SNP molecular marker: refers to the variation of a single nucleotide across the genome, resulting in a genetic marker.
The source is as follows:
GGP 50k SNP(GeneSeek，US)。
the reagents, materials and equipment used in the examples are all commercially available sources unless otherwise specified; the experimental methods are all routine experimental methods in the field unless specified.
Examples
1. Phenotype data is collected.
The study group of the invention is 2793 Duroc boars, all pigs are in pig farms of Guangxi Yangxiang Co., ltd. In 2014-2021, and the eye muscle area measurement part is 5cm away from the midline between the third rib and the fourth rib of the pig, and is measured by using a Mylab Touch Vet B super instrument at the weight of 100-135kg of the pigs. The measured data are corrected to 115kg body weight level by a KFNTs system, and 2783 Duroc boars remained for correlation analysis after quality control of the corrected data by mean value plus or minus 3 times of standard deviation.
2. Obtaining SNP molecular markers.
Collecting a pig ear tissue sample or blood sample, extracting total DNA, adopting GGP 50k SNP chip to genotype, and integrating multiple sequencing results to obtain 50697 SNP markers covering the whole genome. The physical location of all SNP markers was updated using NCBI genome alignment program (https:// www.ncbi.nlm.nih.gov /) according to the latest edition of porcine reference genome (Srcrofa 11.1). SNPs with unknown genomic positions and SNPs on sex chromosomes are not used for associationAnd (5) separating. For all SNP markers on autosomes, quality control was performed using Plink software, standard: the individual detection rate is more than or equal to 90 percent; SNP detection rate is more than or equal to 90%; the minimum allele frequency is more than or equal to 0.01; the Hardy-Winberg equilibrium p value is more than or equal to 10 -6 . Individuals lacking genotypes are filled by Beagle software (version 4.1), and quality control is carried out again after filling, wherein the quality control conditions are the same as the above. The 39428 SNP sites remaining after quality control were used for correlation analysis with the eye muscle area.
3. And (5) screening SNP molecular markers.
1. And (5) a statistical model.
The method of utilizing the multi-label correlation model uses field-year-season and column as fixed effects, uses the FarmCPU model of rMVP software package to carry out GWAS analysis under R statistical environment, and the research model is as follows:
Y n ＝T ni W i +P nj Q j +e n
wherein Y is n Representing the phenotype vector of the nth individual, T ni Is a fixed effect, comprising the first three major components of the genotype of field-year-season, field and i pseudoqtns and controlling the genetic background of the population; w (W) i Representing the corresponding effect; p (P) nj A j-th marker representing an nth subject; q (Q) j Representing the jth corresponding effect; e, e n Representing residual vectors, obeying normal distribution, e-N (0,I σ2e), σ e representing residual variance. The P value is 1 divided by the number of all SNP sites, i.e.: p=1/39428.
2. And (5) screening markers.
And drawing a Manhattan diagram by taking negative logarithmic conversion values of p values of all markers, and displaying and screening the most obvious SNP markers. And analyzing the difference of the eye muscle areas of Duroc boars of the populations with different genotypes by adopting analysis of variance (considering field-year-season, field and corresponding obvious SNP site effect in the model) and Duncan multiple comparison (R statistical analysis platform), wherein ASGA0032562, ASGA0036920, H3GA0040331 and ALGA0032929 are adopted.
The analysis results are shown in FIG. 1 and the following table.
TABLE 1 ASGA0032562 marking area of porcine eye muscle of different genotypes
TABLE 2 ASGA0036920 markers for porcine eye muscle areas of different genotypes
TABLE 3H 3GA0040331 marking porcine eye muscle areas of different genotypes
TABLE 4 ALGA0032929 marking areas of porcine eye muscles of different genotypes
The invention identifies a molecular marker for assessing the area of porcine eye muscle: ASGA0032562, ASGA0036920, H3GA0040331 or ALGA0032929, the panel marked a very significant difference in the area of porcine eye muscle of different genotypes.
ASGA0032562 marker was located at 30786798bp position of chromosome 7 in swine, which is a T > C mutation. The gene sequence of 200bp upstream and downstream of the SNP marker is as follows, wherein E is the locus of the SNP molecular marker:
5’-CTTGCCYTTTCTAGTGCACCTTTTCAGTATCTGCCAGAGTAACAGAGAAGGAAGAATT CCATCCTTCATTCAACAAATCATTTTTATTTATTTATTTGGCTGTSCCCACAGCATGTAAAAKTTCCAGCCAGGGATCAAACTCAAGCCATAGCAGTGACGCCAGATCTTTAACAGGGCCAGGGATYGAACCYGCATGGATG(SEQ ID NO:1)-E-TATTCGGGTCTACTAGCTACTGAGCC ATGACAGGAGCTCCTATTTTTTGCTTTTTAGGGCTATATCTGCAGCATATGGAAGTTCCCAGGCTAGGGGTCGAGTCAGAGCTGTAGCTGCCAGCCTACACCACAGCCACAGCAACACC AGATCAGAACTACATCTGTGACCTCCACCACTGCTCTCAGCAATGCTRGATCCTT-3’(SEQ ID NO:2)。
ASGA0036920 marker is located at 120345012bp of chromosome 7 in swine, which is a T > C mutation. The gene sequence of 200bp upstream and downstream of the SNP marker is as follows, wherein F is the locus of the SNP molecular marker:
5’-GTCCCCACAGCTGCACTGCCAGTCAGGGTTCTGCAGGCAGAGCYCRWAGGATGTATG CACACGGGTATATAAGGGGCTTTGTCCYAAGGAATTATTTCTCATGCCCATGGAGGTGGGCAAGGWGAGCTGATGTTTCCATTGRAATCAAAGGCAGGAGAAAGCCRATGTCCCAGCT CAAGGGCAGTCAGAMAGGGGGARCT(SEQ ID NO:3)-F-CCACTTACTCCAGGGAGGATGAGCCTTTGGTTTTACTCAGGCCCTCAACTGATTGGGTGAGGCCCACCCACCKGGGGACG GGCAATCTGCTTWYTTCTTAAAGGTTCATCTCACCCCATATATCCTCATAGGAMCCCCCC CCCCCSAGAATCATGCTGACCATATGTCTTGGACACCCCATGACCCAGCCAAACTGACAC -3’(SEQ ID NO:4)。
the H3GA0040331 marker is located at 56213488bp of chromosome 14 of pig, which is a C > T mutation. The gene sequence of 200bp upstream and downstream of the SNP marker is as follows, wherein L is the locus of the SNP molecular marker:
5’-YGGAATCCAAGTCATGTCTTTGACCTTACACCACAGCTCATGGCAATGCTGGATCCTT GACYCACTGAGCGAGRCCAGGGATTAAACCTGCATCCTCATGGATACTAKTYGGGTTTGTTACTGCYGAGCCACAGTGGGAAMTCCTCAAGCCCACTTTTAAGTCCCACGTTTCTGCC CTCTCGTAGGCTGCCTCTCGAAGA(SEQ ID NO:5)-L-CAGGTGGGAGGATGTGGGCCTTACGGAGGCGACTGGGAGCATGGGAGGAACAGATGGCACAGGTCTCTCTCCAGTACAT ACCAGTCACTACCTGGAAGCTAGCAGCTATGATGTAACYACCTTGTCCGGTGAAGGCTG CCTTTGCTCTGTGGGTGGGACYGCGATGCCGCCAGGCTGGGGAATCCCATTGGTGACAA CAC-3’(SEQ ID NO:6)。
the ALGA0032929 marker is located at the 74418117bp position of chromosome 5 in swine, which is the a > G mutation. The gene sequence of 200bp upstream and downstream of the SNP marker is as follows, wherein O is the locus of the SNP molecular marker:
5’-AGCTTGATTTTGTAATTTTTCTCCTTTATTAATKGCCTCTTTTTTTTTGGTAAGACTTGT ACTAAGAASTCATGATAAAAAGATGGTCCATGCCCTCGAGGAGCTTACATCTGATGTTACTCCTTGTCTTATTTTGATCCACCTAAATRAAATCCACACYGAAGGATTACAAACTCTAAG CCTAAAGCTGYGGTTTTTAA(SEQ ID NO:7)-O-TGGGAAAGATTTTGTGYCTAGGAGA TATTTGGTAAMACCTGGAGATATTTTTGGTTGTAACAATTGGAGGATGCTACTAGCATCTAGTGGGGAGAAACCAGARATGGTGCTAAACATCCTAAAATGCACAGGGCAGCTCTTCTC CCCTAAYSATRCAGAATTATCCAGCCTCAAAATCAAAACTTCTGAGGTTGAGAAAT-3’(SEQ ID NO:8)。
r, Y, M, K, S, W in the above sequence is a mixed base symbol, and has the following meanings:
r represents G or A, Y represents T/U or C, M represents A or C, K represents G or T/U, S represents G or C, W represents A or T/U.
ASGA0032562 marker genotype CC is obviously improved by 1.39% and 1.97% compared with the interocular muscle area of TC and TT Duroc boar individuals, so that C in the marker is an allele which is favorable for obviously improving the ocular muscle area; ASGA0036920 marker genotype CC is significantly increased by 3.18% compared to TT, so that C in this marker is an allele that contributes to increased ocular muscle area; the H3GA0040331 marker genotype CC is obviously improved by 2.46% compared with the inter-individual eye muscle area of the TT Duroc boar, so that C is more beneficial and improves the area of the eye volume compared with T in the marker; compared with CT and CC Duroc boar individuals, the ALGA0032929 marker genotype TT is improved by 1.59% and 3.07% respectively, so that the improvement of the eye muscle area is more favorable for the T in the gene relative to the C.
The detection marks ASGA0032562, ASGA0036920, H3GA0040331 and ALGA0032929 genotype assist breeding pigs, and the Duroc boars with the CC, CC and TT genotypes can be respectively selected to improve the eye muscle area, thereby being beneficial to improving the eye area of the pigs and further improving the lean meat percentage.
The technical features of the above-described embodiments may be arbitrarily combined, and all possible combinations of the technical features in the above-described embodiments are not described for brevity of description, however, as long as there is no contradiction between the combinations of the technical features, they should be considered as the scope of the description.
The above examples illustrate only a few embodiments of the invention, which are described in detail and are not to be construed as limiting the scope of the invention. It should be noted that it will be apparent to those skilled in the art that several variations and modifications can be made without departing from the spirit of the invention, which are all within the scope of the invention. Accordingly, the scope of protection of the present invention is to be determined by the appended claims.
Claims (4)
1. The application of a reagent for detecting a molecular marker in evaluating the area of porcine eye muscle is characterized in that the molecular marker is an SNP molecular marker, and the molecular marker is positioned at a 30786798bp position of a porcine 7 chromosome, a 120345012bp position of a porcine 7 chromosome, a 56213488bp position of a porcine 14 chromosome and/or a 74418117bp position of a porcine 5 chromosome;
the molecular marker is positioned at 30786798bp of the chromosome 7 of the pig, and when the genotype of the molecular marker is CC, the eye muscle area of the pig to be evaluated is indicated to be high;
the molecular marker is positioned at 120345012bp of the chromosome 7 of the pig, and when the genotype of the molecular marker is CC, the eye muscle area of the pig to be evaluated is indicated to be high;
the molecular marker is positioned at a 56213488bp position of a pig chromosome 14, and when the genotype of the molecular marker is CC, the high eye muscle area of the pig to be evaluated is indicated;
and/or the molecular marker is positioned at a 74418117bp position of a chromosome 5 of the pig, and when the genotype of the molecular marker is TT, the high eye muscle area of the pig to be evaluated is indicated.
2. Use of a reagent for detecting molecular markers according to claim 1 for preparing a detection kit for assessing the area of porcine eye muscle.
3. A method for evaluating the area of the eye muscle of a pig, comprising obtaining the detection result of the molecular marker of claim 1, and determining the area of the eye muscle of the pig based on the detection result;
the molecular marker is positioned at 30786798bp of the chromosome 7 of the pig, and when the genotype of the molecular marker is CC, the eye muscle area of the pig is judged to be high;
the molecular marker is positioned at 120345012bp of the chromosome 7 of the pig, and when the genotype of the molecular marker is CC, the eye muscle area of the pig is judged to be high;
the molecular marker is positioned at 56213488bp of the chromosome 14 of the pig, and when the genotype of the molecular marker is CC, the eye muscle area of the pig is judged to be high;
and the molecular marker is positioned at a 74418117bp position of the chromosome 5 of the pig, and when the genotype of the molecular marker is TT, the eye muscle area of the pig is judged to be high.
4. A pig breeding method, characterized in that the method according to claim 3 is used for detection, the eye muscle area of the pig is estimated according to the genotype of the molecular marker, and the pig with high eye muscle area is reserved; the molecular marker is positioned at 30786798bp position of the chromosome 7 of the pig, 120345012bp position of the chromosome 7 of the pig, 56213488bp position of the chromosome 14 of the pig or 74418117bp position of the chromosome 5 of the pig;
the molecular marker is positioned at 30786798bp of the chromosome 7 of the pig, and when the genotype of the molecular marker is CC, the eye muscle area of the pig is judged to be high, and the pig is reserved;
the molecular marker is positioned at 120345012bp of the chromosome 7 of the pig, and when the genotype of the molecular marker is CC, the eye muscle area of the pig is judged to be high, and the pig is reserved;
the molecular marker is positioned at 56213488bp of the chromosome 14 of the pig, and when the genotype of the molecular marker is CC, the eye muscle area of the pig is judged to be high, and the pig is reserved;
and when the genotype of the molecular marker is TT, judging that the eye muscle area of the pig is high, and reserving the pig.
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