CN116042849A - Genetic marker for assessing pig feed intake and screening method and application thereof - Google Patents
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Abstract
The invention relates to a genetic marker for assessing pig feed intake, a screening method and application thereof, and relates to the technical field of pig genetic genes. The genetic marker is an SNP molecular marker, and the SNP molecular marker is positioned at a 96632994bp position of a chromosome 4 of the pig. The genetic markers have extremely obvious difference in pig feed intake of different genotypes, and pigs with relatively high feed intake can be selected and remained by detecting the genetic markers, so that the breeding progress of the breeding pigs is accelerated, and a support is provided for comprehensive breeding of the breeding pigs.
Description
Technical Field
The invention relates to the technical field of pig genetic genes, in particular to a genetic marker for evaluating pig feed intake, a screening method and application thereof.
Background
With the vigorous development of domestic pig industry in recent years, the development of the breeding industry is limited by the cost of the feed, and the cost of the feed accounts for more than 60% of the total cost. Daily feed intake has important significance in different stages of pig growth. For weaned pigs, the feed intake is closely related to the health condition of pigs. The intestinal tracts are not yet developed completely, the piglet stress can be caused by the separation of the replacement environment and the sow, the feed intake is reduced, the malnutrition of the piglet can be caused, and the growth and development of the subsequent intestinal tracts of the piglet are seriously influenced. For growing pigs, the daily feed intake can be improved, the feed conversion rate can be improved, although the difference is not obvious, the daily feed intake is obvious, the daily weight gain of the pigs can be obviously improved, the higher the daily feed intake is, the more nutrient components are ingested by the pigs, and the positive influence is exerted on the daily weight gain, backfat thickness and eye muscle area increase of the pigs in the growing and fattening period. Therefore, the daily feed intake has a great relationship with the health condition, growth and development and feed cost of pigs, and is paid attention to in pig breeding industry for a long time.
Therefore, the mining and utilization of the novel genes related to daily feed intake has important significance for genetic breeding of pigs. The complex quantitative traits of the growth traits such as daily feed intake of pigs, which are controlled by multiple genes, have the advantages of strong purposefulness and result predictability by using the traditional QTL positioning method, but the number of the detectable QTL is limited, and complex alleles cannot be detected, the positioning analysis rate is low, and the like.
Disclosure of Invention
Aiming at the problems, the invention provides the genetic marker for evaluating the feed intake of pigs, which has extremely obvious difference in the feed intake of pigs with different genotypes, and pigs with relatively high feed intake can be selected and remained by detecting the genetic marker, so that the breeding progress of the breeding pigs is accelerated, and the support is provided for the comprehensive breeding of the breeding pigs.
In order to achieve the above object, the present invention provides a genetic marker for assessing the feed intake of pigs, which is a SNP molecular marker located at the 96632994bp position of chromosome 4 of pigs.
In one embodiment, when the genotype of the SNP molecular marker is GG, the high feeding rate of the pig to be evaluated is indicated.
In one embodiment, the food intake refers to daily food intake.
The invention also provides a gene sequence for assessing pig feed intake, which comprises the genetic marker loci of claim 1, wherein the gene sequence is as follows:
5'-ACTGACTTTCATTAGCGTCGCTCTTTCTCTTTCTCCAAGCCTCTGTCTCTCTTATGCGCGCACGCACACCCTCACATATACATATGTGAGTCTCCCTTATACTCTAACACTGAGTGTTTGTGGGGGCCTCAAGCCAGTTCTCTGTTAAGCTTATGGGATGAGAGGTGGTATTTTCCACCAATTTCCAAAACACATAGGTA (SEQ ID NO: 1) -E-TCACTATCCCCACTGGTCCATCTTTAGAAGGCATATGGCCCCGCTTCTTTTGCATGGCTCTCCTACCCTAAAGCTCCATGTGGCTCTTGAGGATGTTTTTTCCTTTTCAGGCTTTCCTTGGTCTTCATCTCACTCTCATTTCACTTGCATGAACGTGAACATGACGGTGAGGTTGTGGAGACGAGGGGTGTATATTGGAG-3' (SEQ ID NO: 2), wherein E is the site of the genetic marker.
The invention also provides a detection kit for assessing the feed intake of pigs, comprising reagents for detecting the genetic markers or comprising reagents for detecting the gene sequences.
The invention also provides a screening method of the genetic marker, which is characterized by comprising the following steps:
obtaining phenotype data: collecting phenotype data of feed intake of pigs to be tested;
obtaining a genetic marker: sampling the pig to be tested, extracting DNA, genotyping to obtain a genetic marker covering the whole genome; performing physical position updating and quality control on the genetic marker covering the whole genome;
screening genetic markers: and carrying out GWAS analysis on the genetic markers after quality control by combining the phenotype data, analyzing the difference situation of pig feed intake of different genotype groups, and screening to obtain the genetic markers for evaluating pig feed intake.
Based on the whole genome association analysis technique (GWAS) of the collection and analysis of high SNP data covering the whole genome and trait phenotype data of a large population, candidate genes controlling traits can be accurately located. Although there are some disadvantages, the gene has been widely used for candidate gene excavation of human complex diseases and positioning of important economic character key genes of livestock and poultry. The classical model of the GWAS is a Mixed Linear Model (MLM), single-label regression analysis is generally carried out on all labels one by one based on the software such as Plink, and then a significant threshold is set to screen significant sites. To further increase the efficiency of GWAS, new models and software are continually being proposed. The FarmCPU alternately uses a fixed effect and a random effect, so that more SNP loci can be rapidly positioned on the premise of ensuring accuracy. The patent performs whole genome association analysis on daily feed intake of Duroc boars based on a FarmCPU model of rMVP software to identify relevant obvious SNP loci.
The invention also provides a method for evaluating the feed intake of the pigs, which is characterized by comprising the steps of obtaining the detection result of the genetic marker and judging the feed intake of the pigs according to the detection result.
In one embodiment, the genetic marker is located at 96632994bp of chromosome 4 of the pig, and when the genotype of the genetic marker is GG, the pig is judged to have high feeding rate.
The genotype of the genetic marker is GG which is obviously improved by 19.7% compared with the daily feed intake among AA individuals, which indicates that the G allele obviously improves the daily feed intake.
The invention also provides a pig breeding method, detection is carried out according to the method, the feed intake of the pigs is judged according to the genotype of the genetic marker, and the pigs with high feed intake are reserved; the genetic marker is located at 96632994bp of the chromosome 4 of the pig.
In one embodiment, when the genotype of the genetic marker is GG, the pig is judged to have high feeding rate and is kept.
Through selecting and reserving GG homozygous pigs, daily feed intake can be effectively improved, and subsequent comprehensive breeding is facilitated.
Compared with the prior art, the invention has the following beneficial effects:
the genetic marker for evaluating the feed intake of pigs, the screening method and the application thereof have extremely obvious difference in the feed intake of pigs with different genotypes, and pigs with relatively high feed intake can be selected and kept by detecting the genetic marker, so that the breeding progress of the breeding pigs is accelerated, and the support is provided for the comprehensive breeding of the breeding pigs.
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.
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 obtained.
The study group of the invention is Duroc boars, all pigs are from pig farms of Guangxi Yangxiang Co Ltd, feed intake and other data are obtained through Rui Baole (Nedap) and Osbook (FIRE) automatic feeding measurement systems, and 60-115 kg stage data are extracted. The obtained raw data are subjected to strict quality control to obtain 624 duroque boars, and the 624 duroque boars are subjected to quality control with a mean value of +/-3 times of standard deviation and the rest 623 duroque boars are subjected to screening.
2. Obtaining the genetic marker.
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 association analysis. 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 loci remained after quality control are used for correlation analysis with daily feed intake.
3. Screening genetic 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:
Yn=TniWi+PnjQj+en
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), σ2e representing residual variance. P=2.72×10 -5 。
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. The obtained molecular marker INRA0015807 for influencing the daily feed intake of the boar is shown in figure 1, the INRA0015807 marker is positioned at 96632994bp of chromosome 4 of the boar, the position is a T/C mutation, and 200bp sequences at the upstream and downstream of the SNP molecular marker are as follows.
5'-ACTGACTTTCATTAGCGTCGCTCTTTCTCTTTCTCCAAGCCTCTGTCTCTCTTATGCGCGCACGCACACCCTCACATATACATATGTGAGTCTCCCTTATACTCTAACACTGAGTGTTTGTGGGGGCCTCAAGCCAGTTCTCTGTTAAGCTTATGGGATGAGAGGTGGTATTTTCCACCAATTTCCAAAACACATAGGTA (SEQ ID NO: 1) -E-TCACTATCCCCACTGGTCCATCTTTAGAAGGCATATGGCCCCGCTTCTTTTGCATGGCTCTCCTACCCTAAAGCTCCATGTGGCTCTTGAGGATGTTTTTTCCTTTTCAGGCTTTCCTTGGTCTTCATCTCACTCTCATTTCACTTGCATGAACGTGAACATGACGGTGAGGTTGTGGAGACGAGGGGTGTATATTGGAG-3' (SEQ ID NO: 2), wherein E is the site of the SNP molecular marker.
And analyzing the daily feed intake difference of the populations with different genotypes by adopting multi-factor analysis of variance and Duncan multiple comparison (based on an R statistical analysis platform) considering field year season, field effect and SNP locus effect.
The analysis results are shown in the following table, and the daily feed intake of the pigs with different genotypes of the markers is extremely obviously different.
TABLE 1INRA0015807 marker daily feed intake of different genotypes of breeding pigs
Analysis of results: compared with the daily feed intake among AA individuals, the INRA0015807 marker genotype GG is obviously improved by 19.7%, and the daily feed intake of G alleles is obviously improved; the pig breeding is assisted by detecting the INRA0015807 marker genotype, and the daily feed intake can be effectively improved by selecting and reserving GG homozygous pigs, so that the subsequent comprehensive breeding is facilitated.
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 (10)
1. A genetic marker for assessing pig feed intake, wherein the genetic marker is a SNP molecular marker located at 96632994bp of chromosome 4 of the pig.
2. The genetic marker of claim 1, wherein when the genotype of the SNP molecular marker is GG, the high intake of the pig to be evaluated is indicated.
3. The genetic marker of claim 2, wherein the feed intake is daily feed intake.
4. A gene sequence for assessing swine feed intake, comprising the genetic marker locus of claim 1, said gene sequence being as follows:
5'-ACTGACTTTCATTAGCGTCGCTCTTTCTCTTTCTCCAAGCCTCTGTCTCTCTTATGCGCGCACGCACACCCTCACATATACATATGTGAGTCTCCCTTATACTCTAACACTGAGTGTTTGTGGGGGCCTCAAGCCAGTTCTCTGTTAAGCTTATGGGATGAGAGGTGGTATTTTCCACCAATTTCCAAAACACATAGGTA (SEQ ID NO: 1) -E-TCACTATCCCCACTGGTCCATCTTTAGAAGGCATATGGCCCCGCTTCTTTTGCATGGCTCTCCTACCCTAAAGCTCCATGTGGCTCTTGAGGATGTTTTTTCCTTTTCAGGCTTTCCTTGGTCTTCATCTCACTCTCATTTCACTTGCATGAACGTGAACATGACGGTGAGGTTGTGGAGACGAGGGGTGTATATTGGAG-3' (SEQ ID NO: 2), wherein E is the site of the genetic marker.
5. A test kit for assessing swine feed intake comprising reagents for detecting a genetic marker according to any one of claims 1-3 or comprising reagents for detecting a gene sequence according to claim 4.
6. A method of screening for a genetic marker according to any one of claims 1 to 3, comprising the steps of:
obtaining phenotype data: collecting phenotype data of feed intake of pigs to be tested;
obtaining a genetic marker: sampling the pig to be tested, extracting DNA, genotyping to obtain a genetic marker covering the whole genome; performing physical position updating and quality control on the genetic marker covering the whole genome;
screening genetic markers: and carrying out GWAS analysis on the genetic markers after quality control by combining the phenotype data, analyzing the difference situation of pig feed intake of different genotype groups, and screening to obtain the genetic markers for evaluating pig feed intake.
7. A method for assessing the feed intake of a pig, the method comprising obtaining a result of the detection of the genetic marker of any one of claims 1 to 3 and determining the feed intake of the pig based on the result of the detection.
8. The method of claim 7, wherein the genetic marker is located at 96632994bp of chromosome 4 in the pig, and wherein the pig is judged to have high feeding when the genotype of the genetic marker is GG.
9. A method for breeding pigs, characterized in that the method according to any one of claims 7-8 is used for detection, the feed intake of pigs is judged according to the genotype of genetic markers, and pigs with high feed intake are left for use; the genetic marker is located at 96632994bp of the chromosome 4 of the pig.
10. The method according to claim 9, wherein if the genotype of the genetic marker is GG, the pig is judged to have high feeding rate and is kept.
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