CN108676897B - SNP marker influencing daily gain traits of pigs and application thereof - Google Patents
SNP marker influencing daily gain traits of pigs and application thereof Download PDFInfo
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Abstract
The invention belongs to the technical field of molecular biotechnology and molecular markers, and particularly relates to application of a pig SNP molecular marker in pig daily gain trait research and pig breeding. The pig SNP molecular marker locus is shown in SEQ ID NO.1, is positioned in the 321 st nucleic acid single base mutation of the sequence fragment and is named as: g15588826C > T. The SNP molecular marker corresponds to 15588826 th nucleotide site C > T mutation on the chromosome of the international pig reference genome 10.2 version 3. By optimizing the dominant allele of the SNP molecular marker, the genetic progress of the white-day weight gain character can be increased, the breeding time of the white-day weight gain character is reduced, and the economic benefit of breeding the breeding pigs is effectively improved.
Description
Technical Field
The invention belongs to the technical field of molecular biotechnology and molecular markers, and particularly relates to application of a pig SNP molecular marker in pig daily gain trait research and pig breeding.
Background
The daily gain character is an important index for evaluating the growth performance of the pigs, so the daily gain character is the key point in the research of genetic improvement of the breeding pigs. In recent centuries, the breeding goals of western pig breeds are often focused on increasing lean meat percentage and reducing backfat thickness, which improves the genetic progress of daily gain to a certain extent, but a more direct breeding method is also lacked. Traditional breeding methods have little effect on traits (such as daily gain) difficult to identify, and molecular Marker Assisted Selection (MAS) breaks this technical barrier. The method can be used for improving meat quality (such as intramuscular fat) and disease resistance (such as diarrhea) which are difficult to measure or measure in vivo for traits which are expensive (such as daily gain), and for breeding (such as litter size) which express late limiting traits in life activities. Since MAS is not easily affected by the environment, sex, and age, it is possible to perform early selection, and it is possible to achieve the purpose of shortening the generation interval and improving the seed selection efficiency (spring willow, etc., 2008). Therefore, the MAS technology can be used for improving the daily gain character of the breeding pigs, and the MAS technology has wide application prospect.
The big white pig is one of famous lean type pig species in the world. In the breeding system of modern pigs, Chinese cabbage is distinguished by the advantages of high reproductive capacity, good growth and fertility, strong adaptability and the like. The synthetic pig feed has excellent comprehensive performance, so that the synthetic pig feed can be used as a male parent or a female parent of a variety of synthetic line commercial pigs, and the application range is very wide. Therefore, the daily gain traits of the large white pigs are improved, and the fattening time of commercial pigs can be effectively shortened, so that the breeding cost is saved.
Disclosure of Invention
In order to overcome the defects and shortcomings of the prior art in the daily gain genetic breeding, the invention aims to provide the application of the pig SNP molecular marker in the research of the daily gain character of the pig and the breeding of the pig.
The purpose of the invention is realized by the following technical scheme:
application of pig SNP molecular marker in pig daily gain character research and pig breeding; the SNP locus of the pig SNP molecular marker corresponds to the C > T mutation at 15588826bp on the chromosome No. 3 of the international pig reference genome version 10.2; the SNP locus of the molecular marker is shown as SEQ ID NO.1, wherein M in the sequence is T or C, which causes different daily gain traits;
the pig is at least one of Chinese cabbage and a synthetic line thereof;
the primers for identifying the porcine SNP molecular markers are preferably PCR-F and PCR-R;
the upstream primer PCR-F: 5'-CAGGTAGGACACCTCCACT-3', respectively;
downstream primer PCR-R: 5'-TGACAGCAGCACTAAATGAC-3', respectively;
the pig daily gain character research preferably identifies the pig daily gain character by using the pig SNP molecular marker;
the pig daily gain character research preferably also comprises the step of regulating the daily gain of the pig by using the pig SNP molecular marker;
the breeding is preferably molecular marker assisted breeding;
a method for detecting daily gain traits of pigs comprises the following steps:
detecting whether the single nucleotide of the pig SNP molecular marker on the pig chromosome 3 is C or T;
the pig is at least one of Chinese cabbage and a synthetic line thereof;
a method of genetic improvement in pigs comprising the steps of:
determining the pig SNP molecular markers of the pigs in the pig core group, and making corresponding selection according to the pig SNP molecular markers: carrying out subculture breeding on the boars to select CT type and TT type individuals at 15588826bp on the chromosome No. 3 of the 10.2 version of the international pig reference genome, and eliminating CC type individuals at the point; increasing the frequency of the allele T of the locus generation by generation, thereby increasing the daily gain of the offspring pig;
the breeding pig is at least one of white rice and a synthetic line thereof;
compared with the prior art, the invention has the following advantages and effects:
(1) the invention researches and determines the molecular marker related to the daily gain, and the molecular marker is used for marker-assisted selection, so that the daily gain process of Chinese cabbage and a synthetic system thereof can be greatly increased.
(2) The invention provides a primer pair for identifying molecular markers influencing daily gain traits of pigs, and the molecular markers and the primer pair can establish a high-efficiency and accurate molecular marker assisted breeding technology and apply the molecular marker assisted breeding technology to genetic improvement of the daily gain traits of the pigs, so that the daily gain of the pigs is improved, further grain is saved, the production cost of enterprises is reduced, the profit of the enterprises is improved, and the core competitiveness is increased.
(3) According to the invention, by optimizing the dominant allele of the molecular marker, the genetic progress of the white-day weight gain character can be increased, and the breeding time of the white-day weight gain character is reduced, so that the economic benefit of breeding pigs is effectively improved, wherein by the molecular marker, CC type individuals are all bred into TT type individuals, the average daily gain of each pig can be increased by 88.7g, and 62.09t of pork can be increased in 70 days in a large-scale ten-thousand pig farm, so that the potential of providing income for the pig industry by excellent daily gain performance is huge.
Drawings
FIG. 1 is a graph of daily gain analysis of pigs of different genotypes.
FIG. 2 is a graph of a genome-wide association (GWAS) analysis of white pigs on chromosome 3 for the daily gain trait; wherein: the abscissa represents the chromosome number of the pig; the ordinate represents the-logP value.
Detailed Description
The present invention will be described in further detail with reference to examples and drawings, but the present invention is not limited thereto.
Example 1
In the examples, a total of 689 pure white seeds were used; wherein the Day age of the pig at a weight of 30Kg is determined by the OSBORNE system and recorded as Day1, and the Day age of the pig at a weight of 100Kg is recorded as Day 2. The formula for calculating the daily gain is as follows: 70/(Day2-Day 1). The experiment is carried out in a sand lake pig farm of Guangdong Wen food group, Inc., 10-12 pigs (each pig occupies 2 square meters) are raised in each fence freely for drinking water in a measuring stage, and daily ration is fed uniformly according to a uniform feeding standard.
(1) The extraction method of the big white pig ear sample tissue DNA refers to the phenol-chloroform labeling method for extracting the whole genome DNA. And (3) carrying out quality detection and concentration measurement on the DNA of the pure large white population by using a Nanodrop-ND1000 spectrophotometer. The ratio of A260/280 is 1.8-2.0, and the ratio of A260/230 is 1.7-1.9. Finally, the qualified DNA samples were uniformly diluted to 50 ng/L.
(2) Pig feedAnd (3) detecting the genotype of the genome 80K SNP: the GeneSeek Genomic Profile Portine 80KSNP typing platform adopts the instruction of Illumina Infinium and the standard flow to perform chip hybridization and result scanning. Finally, reading genotype data through genome studio software. Quality control of obtained genotype data by PLINK v1.07, and rejection rate<99.7%, the allele frequency (MAF)<0.01% or a deviation from Hardy-Weinberg Equilibrium (HWE) P of 10-6SNP marker of (1), exclusion of detection Rate<90%, individuals with a familial mendelian error rate higher than 0.1; the remaining 58991 SNP markers and 689 samples were quality controlled for subsequent data analysis.
(3) Genome-wide association (GWAS) analysis-GWAS analysis was performed using the GenABEL software package in R software, the model was y 1u + Xb + Sc + Za + α, where y is the measured phenotypic value and (average daily gain value), u is the overall mean, b is the gender and fixed effect value, c is the remaining micro-effect, c-N (0, б c2), α is the random additive genetic effect vector, and α -N (0, бα) (G is the molecular blood margin correlation matrix between individuals, бα is the additive genetic variance), E is the residual, X, S and Z are correlation matrices for fixed and random benefit, the field-yeary-season effect is included in the batch effect.a significant threshold was determined using Bonferroni method, the significant genomic level was divided by 0.05 by the effective SNP number, i.e. 0. 58991, the significant genomic level was found in the chromosome synthesis map 3-7, 3-8, the significant genomic level was found from the significant SNP number correlation results shown in fig. map 7-8, 3-8.
(4) Correlation analysis of different genotypes with daily gain phenotype: according to the table 1, the SNP locus g.15588826C > T of the molecular marker is extremely obviously related to the daily gain trait (P <0.001), which shows that the molecular marker obviously influences the daily gain trait of the pig, and the daily gain of the group can be improved by auxiliary selection of the SNP locus of the pig, so that the breeding process is accelerated. It can also be seen from table 1 and fig. 1 that type TT has a higher average daily gain than types CC and TC, indicating that homozygote CC is the most detrimental to average daily gain. The daily gain is an important index of growth traits, and high daily gain indicates that the growth performance of the pigs is good. Therefore, the growth performance of the pigs with CC genotype is the worst, and the breeding pigs with CC genotype need to be eliminated, and the breeding pigs with TT and TC genotype need to be kept during the breeding process so as to improve the frequency of the allele T at the position generation by generation.
Relevance of SNP site g.15588826C > T of molecular marker in table 1 and daily gain
Example 2
(1) The target fragment containing the target fragment of the SNP locus which is obviously related to the property of the white day weight gain is a nucleotide sequence of 695bp in a chromosome 3, and the upstream and downstream primers for sequence amplification are as follows:
the upstream primer PCR-F: 5'-CAGGTAGGACACCTCCACT-3', respectively;
downstream primer PCR-R: 5'-TGACAGCAGCACTAAATGAC-3' are provided.
(2) PCR amplification system and condition setting
A20 uL system was prepared in which 3.5. mu.L of the DNA sample, 0.6. mu.L of the forward primer, 0.6. mu.L of the reverse primer, PCR mix10mL, ddH2O5.3. mu.L, PCR conditions of 98 ℃ pre-denaturation for 2min, 98 ℃ denaturation for 10s, 56.5 ℃ annealing for 15s, 72 ℃ extension for 40s, 35 cycles total, and final extension for 72 ℃ for 10 min.
(3) DNA sequencing identification: the sequence sequencing is carried out in Shenzhen Hua Dagen science and technology Limited, and the gene fragment is used for detecting positive and negative reactions. The measured sequence was compared with the NCBI genomic sequence to obtain the mutation of the corresponding SNP site.
The sequencing results are shown below:
note: m marked in the sequence listing is a mutation site and is indicated by underlining (the mutation base is shown in parentheses, and is an allelic mutation), and the primer sequence is shown in bold from the beginning to the end of the sequence.
Example 3 SNP site g.15588826C > T Effect analysis of molecular marker
The invention provides the SNP marker which can obviously increase the daily gain of the white breeding pigs and the synthetic lines thereof, and the SNP marker is used for marker-assisted selection, so that the daily gain breeding process of the white breeding pigs and the synthetic lines thereof can be greatly increased. The CC type individuals of the molecular marker influencing the daily gain traits of the pigs are all bred into TT type individuals, so that the average daily gain of each pig can be increased by 88.7g, and 62.09t pork can be added in 70 days in a large-scale ten-thousand-pig farm, so that the potential of providing benefits for the pig industry by excellent daily gain performance is huge. In the SNP marker individual, the daily gain performance of the CC type individual and the TT type individual has obvious difference (P <0.01), and the aim of improving the economic benefit of the commercial pig can be finally realized by preferably selecting the dominant allele (T) of the SNP of the Chinese cabbage and the synthetic line thereof.
The above embodiments are preferred embodiments of the present invention, but the present invention is not limited to the above embodiments, and any other changes, modifications, substitutions, combinations, and simplifications which do not depart from the spirit and principle of the present invention should be construed as equivalents thereof, and all such changes, modifications, substitutions, combinations, and simplifications are intended to be included in the scope of the present invention.
SEQUENCE LISTING
<110> southern China university of agriculture
<120> SNP marker influencing daily gain traits of pigs and application thereof
<130>1
<160>3
<170>PatentIn version 3.5
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<211>695
<212>DNA
<213>Artificial Sequence
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<223> pig SNP molecular marker
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caggtaggac acctccactt ggctctccag ggactctccc aggtgggttg gtttgagtac 60
ctttgaaaca caatggctgg gttccaagac taagcatctc taaagagcca gttggaagtt 120
gtgttttttg actttgccac cagtcaccca gtgtcatgtc tactgcagtc acaattcaaa 180
ggaagccctg ggttcaagag gaggggacgt ggaccccact tctggctggg cagaataacc 240
ttacaaaaga gcatgtgggc gacatggctg cagagatttt gggaccatgt aatctacacg 300
tgggagactg ttcaacccac tctcccagct caggtggatt agccatcagc catccaaggg 360
cagagggcct gggactgcat ctgcagtctc tccctgctct gtttccctgt taactctgcc 420
atctctttga tggggcgtca ctgctgccac atctggtcct tgcaacctcg gtctggtctt 480
ccacccgaga aggaattgaa ttcagtccag cggccatttc cagagctgtg catgcaagga 540
caggagcgaa acattgcctc aggccctgtg cgggccgaga ggaaagggtg tctgcctgga 600
acgtgccgcg gtgagacgtg tgacaggtgt gcagctgacc gcaacacagg ccagatgtca 660
tttagtgctg ctgtcaggta gaagcaaagc attgg 695
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<211>19
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<223> primer PCR-F
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caggtaggac acctccact 19
<210>3
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<212>DNA
<213>Artificial Sequence
<220>
<223> primer PCR-R
<400>3
tgacagcagc actaaatgac 20
Claims (10)
1. The application of the pig SNP molecular marker in pig daily gain character research and pig breeding is characterized in that: the SNP locus of the pig SNP molecular marker corresponds to the 15588826bp C > T mutation on the chromosome of the international pig reference genome 10.2 version 3.
2. The application of the pig SNP molecular marker in pig daily gain trait research and pig breeding according to claim 1, wherein the pig SNP molecular marker comprises the following components in percentage by weight:
the pig is at least one of Chinese cabbage and a synthetic line thereof.
3. The application of the pig SNP molecular marker in pig daily gain trait research and pig breeding according to claim 1, wherein the pig SNP molecular marker comprises the following components in percentage by weight:
the primers used for identifying the porcine SNP molecular marker in claim 1 are PCR-F and PCR-R;
the upstream primer PCR-F: 5'-CAGGTAGGACACCTCCACT-3', respectively;
the downstream primer PCR-R': 5'-TGACAGCAGCACTAAATGAC-3' are provided.
4. The application of the pig SNP molecular marker in pig daily gain trait research and pig breeding according to claim 1, wherein the pig SNP molecular marker comprises the following components in percentage by weight:
the pig daily gain trait research is to identify the traits of the daily gain of pigs by using the pig SNP molecular markers in claim 1.
5. The application of the pig SNP molecular marker in pig daily gain trait research and pig breeding according to claim 4, wherein the pig SNP molecular marker comprises the following components in percentage by weight:
the pig daily gain trait research also comprises the step of regulating the daily gain of the pig by using the pig SNP molecular marker in claim 1.
6. The application of the pig SNP molecular marker in pig daily gain trait research and pig breeding according to claim 1, wherein the pig SNP molecular marker comprises the following components in percentage by weight:
the breeding is molecular marker assisted breeding.
7. A method for detecting the daily gain character of pigs is characterized by comprising the following steps:
detecting whether the single nucleotide of the porcine SNP molecular marker according to claim 1 on chromosome 3 of a pig is C or T.
8. The method for detecting the daily gain trait of pigs of claim 7, wherein:
the pig is at least one of Chinese cabbage and a synthetic line thereof.
9. A method of genetic improvement in pigs, comprising the steps of:
determining porcine SNP molecular markers according to claim 1 of the porcine in the porcine core group, and making corresponding selections according to the porcine SNP molecular markers: carrying out subculture breeding on the boars to select CT type and TT type individuals at 15588826bp on the chromosome No. 3 of the 10.2 version of the international pig reference genome, and eliminating CC type individuals at the point; so as to increase the frequency of the allele T of the locus generation by generation, thereby increasing the daily gain of the offspring pig.
10. The method of genetic improvement in swine according to claim 9, wherein:
the breeding pig is at least one of white rice and a synthetic line thereof.
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| CN201710427052.0A CN107177681A (en) | 2017-06-08 | 2017-06-08 | Application of the pig SNP marker in daily gain in pigs behavior study and/or pig breeding |
| CN2017104270520 | 2017-06-08 |
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| CN107267631A (en) * | 2017-07-18 | 2017-10-20 | 华南农业大学 | A kind of SNP marker for influenceing daily gain in pigs character and its application |
| CN107586854B (en) * | 2017-09-20 | 2019-01-11 | 温氏食品集团股份有限公司 | It is a kind of influence duroc waistline character molecular labeling and application |
| CN107868832B (en) * | 2017-11-14 | 2020-05-15 | 中国农业大学 | SNP molecular marker related to multiple economic traits of pig and application thereof |
| CN108913779B (en) * | 2018-06-14 | 2020-10-16 | 华南农业大学 | SNP marker influencing daily gain traits of pigs and application thereof |
| CN111154893A (en) * | 2020-02-14 | 2020-05-15 | 广西扬翔股份有限公司 | SNP (single nucleotide polymorphism) marker related to pig growth speed and application thereof |
| CN112458183B (en) * | 2020-11-30 | 2022-09-27 | 华南农业大学 | Copy number variation molecular marker on pig No. 3 chromosome and related to daily gain and weight and age on market of pig and application thereof |
| CN116287293A (en) * | 2023-02-13 | 2023-06-23 | 湖北省农业科学院畜牧兽医研究所 | Porcine SNP molecular marker and application thereof in swine litter size trait screening and/or swine breeding |
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| Publication number | Priority date | Publication date | Assignee | Title |
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| CN103898107A (en) * | 2014-04-17 | 2014-07-02 | 江西农业大学 | Major SNP (single nucleotide polymorphism) marker influencing growth traits of pigs and application thereof in genetic improvement of productivity of breeding pigs |
| CN105648077A (en) * | 2016-02-29 | 2016-06-08 | 华南农业大学 | Molecular marker affecting daily gain character of pigs and application of molecular marker |
| CN106636346A (en) * | 2016-11-07 | 2017-05-10 | 广西柯新源原种猪有限责任公司 | SNP molecular marker related to daily gain of Duroc and application thereof |
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| Publication number | Priority date | Publication date | Assignee | Title |
|---|---|---|---|---|
| CN103898107A (en) * | 2014-04-17 | 2014-07-02 | 江西农业大学 | Major SNP (single nucleotide polymorphism) marker influencing growth traits of pigs and application thereof in genetic improvement of productivity of breeding pigs |
| CN105648077A (en) * | 2016-02-29 | 2016-06-08 | 华南农业大学 | Molecular marker affecting daily gain character of pigs and application of molecular marker |
| CN106636346A (en) * | 2016-11-07 | 2017-05-10 | 广西柯新源原种猪有限责任公司 | SNP molecular marker related to daily gain of Duroc and application thereof |
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| Title |
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| 猪的全基因组水平SNP研究现状;陈慧勇;《生命科学》;20110430;第23卷(第4期);390-393 * |
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