CN106434909A - Molecular marker method for predicting and identifying duck growth and abdomen fat percentages and application - Google Patents

Molecular marker method for predicting and identifying duck growth and abdomen fat percentages and application Download PDF

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CN106434909A
CN106434909A CN201610835192.7A CN201610835192A CN106434909A CN 106434909 A CN106434909 A CN 106434909A CN 201610835192 A CN201610835192 A CN 201610835192A CN 106434909 A CN106434909 A CN 106434909A
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duck
frequency
growth
genotype
diplotype
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张汤杰
王聪
陈明亮
邢华
董轩
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Yangzhou University
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    • C12BIOCHEMISTRY; BEER; SPIRITS; WINE; VINEGAR; MICROBIOLOGY; ENZYMOLOGY; MUTATION OR GENETIC ENGINEERING
    • C12QMEASURING OR TESTING PROCESSES INVOLVING ENZYMES, NUCLEIC ACIDS OR MICROORGANISMS; COMPOSITIONS OR TEST PAPERS THEREFOR; PROCESSES OF PREPARING SUCH COMPOSITIONS; CONDITION-RESPONSIVE CONTROL IN MICROBIOLOGICAL OR ENZYMOLOGICAL PROCESSES
    • C12Q1/00Measuring or testing processes involving enzymes, nucleic acids or microorganisms; Compositions therefor; Processes of preparing such compositions
    • C12Q1/68Measuring or testing processes involving enzymes, nucleic acids or microorganisms; Compositions therefor; Processes of preparing such compositions involving nucleic acids
    • C12Q1/6876Nucleic acid products used in the analysis of nucleic acids, e.g. primers or probes
    • C12Q1/6888Nucleic acid products used in the analysis of nucleic acids, e.g. primers or probes for detection or identification of organisms
    • CCHEMISTRY; METALLURGY
    • C12BIOCHEMISTRY; BEER; SPIRITS; WINE; VINEGAR; MICROBIOLOGY; ENZYMOLOGY; MUTATION OR GENETIC ENGINEERING
    • C12QMEASURING OR TESTING PROCESSES INVOLVING ENZYMES, NUCLEIC ACIDS OR MICROORGANISMS; COMPOSITIONS OR TEST PAPERS THEREFOR; PROCESSES OF PREPARING SUCH COMPOSITIONS; CONDITION-RESPONSIVE CONTROL IN MICROBIOLOGICAL OR ENZYMOLOGICAL PROCESSES
    • C12Q2600/00Oligonucleotides characterized by their use
    • C12Q2600/124Animal traits, i.e. production traits, including athletic performance or the like
    • CCHEMISTRY; METALLURGY
    • C12BIOCHEMISTRY; BEER; SPIRITS; WINE; VINEGAR; MICROBIOLOGY; ENZYMOLOGY; MUTATION OR GENETIC ENGINEERING
    • C12QMEASURING OR TESTING PROCESSES INVOLVING ENZYMES, NUCLEIC ACIDS OR MICROORGANISMS; COMPOSITIONS OR TEST PAPERS THEREFOR; PROCESSES OF PREPARING SUCH COMPOSITIONS; CONDITION-RESPONSIVE CONTROL IN MICROBIOLOGICAL OR ENZYMOLOGICAL PROCESSES
    • C12Q2600/00Oligonucleotides characterized by their use
    • C12Q2600/156Polymorphic or mutational markers

Abstract

The invention provides a molecular marker method for predicting and identifying duck growth and abdomen fat percentages and application. A pair of primers are designed according to sequences of a duck VLDLR gene 5'UTR and a signal peptide coding region; duck genome DNA is subjected to PCR amplification through the primers, the amplification length is 374 bp, and sequencing is carried out after agarose gel electrophoresis detection. The polymorphisms, haplotypes and diplotypes of the VLDLR gene 5'UTR and the signal peptide coding region are judged according to the sequencing result, and the 8 haplotypes and the 15 diplotypes are established based on the 4 SNPs. The average weight of the diplotype H1H1 is highest, the abdomen fat percentage of the diplotype H5H7 is highest, and the abdomen fat percentage of the diplotype H1H1 is lowest. The diplotype H1H1 has a positive effect on the body weight, the diplotype H5H8 has a positive effect on the abdomen fat percentages, and the diplotype H1H1 and the diplotype H5H8 can be used as auxiliary molecular markers for selecting meat duck new varieties.

Description

A kind of molecule labelling method for indicating and identifying duck growth and abdominal fat and application
Technical field
The invention belongs to aquatic bird technical field of molecular biology is and in particular to one kind is used for indicating and identify duck growth and abdomen The molecule labelling method of fat rate, this molecule labelling method can be applicable to a duck duck new lines marker assisted selection breeding.
Background technology
China be in the world the most country of duck culturing it was reported that China's duck breeding stock accounts for world's duck livestock on hand total amount 60%, butcher the Liang Zhan world meat duck meat duck year and butcher the 75% about of total amount.Although its number of animals raised of meat duck is not as good as broiler chicken, alive Critical positions are still occupied, it is quite fast, especially in the development such as China, Southeast Asia that last decade carrys out development speed in boundary's poultry industry Country occupies an important position.Meat duck equally has prolificacy, expands numerous fast advantage with other poultry, and breeding is from originally originally Breed breeding develops into based on business mating system selective breeding, and the external meat duck breed system cultivated has the Cherry Village Duckss of Britain, Australia big Leah the high meat duck of Di, the maple leaf duck of the U.S., the extra large lattice meat duck of Denmark, beautiful good meat duck, France white star meat duck difficult to understand, kind duck and Osaka meat duck of Japan etc..China's meat duck breed improvement, genetic breeding work are started late, and the seed selection of scientific system is from previous generation Discipline is just paid attention to after the fifties and is carried out.Beijing duck seed selection at present reaches world-class levels.China's meat duck breeding choosing Educate the main method using conventional breeding method binding molecule breeding, DNA molecular is being aided with by closed population family breeding Labelling technique carries out selecting to cultivate the meat duck new lines with certain objective trait.Current dna molecular marking technique is lost in poultry The application passing in breeding is mainly reflected in analysis of genetic diversity, Germplasm Identification, affiliation research genetic map construction, QTL The aspect such as positioning and molecular mark.For meat duck objective trait new lines seed selection be concentrated mainly on the speed of growth, The aspects such as efficiency of feed utilization, carcass quality and reproductive performance.Speed of growth genetic force height and easily tolerance, therefore individual choice Effect is preferable.But if only focusing on the result that the speed of growth selects, while promoting meat duck fast-growth, fat easily occurs Deposition is excessive, reduces efficiency of feed utilization and affects carcass quality.The carcass quality main target of meat duck is to increase chest das Beinfleisch yield With reduction carcass lipid.Therefore reduce meat duck fat deposition, cultivating low fat lean meat strain has been important breeding content.With point The development of sub- biology techniques, people can control the key-gene of fat deposition or the molecular labeling chain with it by searching, Thus Seedling selection and indirect selections are implemented by molecular labeling.At present, although in the identification of duck fat deposition candidate gene and answering Had made some progress with aspect, but can really can be used for selecting low abdominal fat to carry out the very limited of breeding practice, therefore non- Often it is necessary to find candidate gene and the molecular labeling that effectively can affect duck fat deposition.
Very low density lipoprotein receptor (VLDLR) is a kind of protein of surface of cell membrane, is made up of 846 amino acid, It is the acceptor of multiple different ligands such as hdl particle containing ApoE.Very low density lipoprotein receptor has 5 functional domains: Ligand binding domains, EGF front body structure domain, domain containing glycosyl structure, membrane spaning domain and intracellular domain.It Mainly it is responsible for combining and interior shifting contains apolipoprotein, such as VLDL (VLDL), provide triglycerides to make to extrahepatic tissue For energy source.Many studies have shown that, the tissue that very low density lipoprotein receptor enlivens in fatty acid metabolism, such as heart, bone Rich content in flesh and adipose tissue, and can optionally combine with apo E, the lipoprotein rich in triglycerides. Peroxisome proliferation-activated receptors (PPAR α) are central node (central in fat deposition candidate gene Nodes), research display PPAR α can adjust the expression of VLDLR gene.Research about VLDLR mostly concentrates on people and mouse, grinds Study carefully and find that VLDLR is related to fat and body weight, the mutation of people's VLDLR gene also results in metabolism disorder of blood lipid, and dyslipidemia Closely related with atherosclerotic, belong to cardiovascular and cerebrovascular disease, therefore suffer from extensive concern and further investigation.
Content of the invention
It is an object of the invention to provide a kind of for indicate and identify duck growth and abdominal fat molecule labelling method and Application.The present invention, with Gaoyou duck conservation field pure strain duck as experimental subjects, detects VLDLR gene 5'UTR by PCR sequence measurement With the polymorphism of signal peptide coding region, and analyze different genotype and growth traits and the correlation of abdominal fat, new to finding Nucleotide polymorphism (SNPs) site and can affect growth and fat deposition effective Molecular Marker Information, the seed selection speed of growth Hurry up, meat duck that abdominal fat is low, the meat duck strain for cultivating high-quality lays the foundation.
The technical scheme realizing the object of the invention is:
A kind of molecule labelling method for indicating and identifying duck growth and abdominal fat, comprises the following steps:
With comprise VLDLR gene duck complete genome DNA to be measured as template, design primer, amplification length with Primer5.0 For 374bp, upstream and downstream primer sequence is:
Upstream 5 '-ATTACACTGCCAAATGACC-3 ';
Downstream 5 '-CGGGAACTGGGATTCTTC-3 ';
Product carries out purifying two-way sequencing, sequencing identification man duck VLDLR gene 5'UTR after agarose gel electrophoresis detection With signal peptide coding region polymorphism.To be associated between VLDLR gene haplotype combination and the speed of growth and abdominal fat analyze, Discovery can affect the speed of growth and effective Molecular Marker Information of abdominal fat, thus accessory molecule mark cultivates high-quality meat duck product System.
Further, described pcr amplification reaction system is 25 μ L, and response procedures are 94 DEG C of denaturations 10min, and then 35 are followed Ring (94 DEG C of denaturation 30S, 53.5 DEG C of annealing 30S, 72 DEG C of extension 30S), 72 DEG C of extension 10min, 4 DEG C of preservations.
Further, described purify two-way sequencing be using PCR reaction primer as sequencing primer, and PCR primer carry out pure Change sequencing, using the haplotype of PHASE software statistics SNP site, Haplotype frequencies and structure haplotype combination.
Sequencing result is compared with NCBI sequence (HQ446852.1), obtains 4 polymorphic sites and its parting feelings Condition:
In g.151 site, the frequency highest of GA genotype, it is that the frequency of 0.56, AA genotype is minimum, is 0.04, equipotential Gene frequency G>A;
In g.170 site, the frequency highest of CC genotype, it is that the frequency of 0.50, CT genotype is minimum, is 0.22, equipotential Gene frequency C>T;
In g.206 site, the frequency highest of AG genotype, it is that the frequency of 0.50, GG genotype is minimum, is 0.17, equipotential Gene frequency A>G;
In g.278-295 site, the frequency highest of DD type, it is that the frequency of 0.65, DB type is minimum, is 0.11, allele Frequency D>B.
Using PHASE2.0 software, haplotype, double type are constructed to 4 polymorphic sites.4 polymorphic sites construct altogether 8 kinds of haplotypes, respectively H1 (GTAB), H2 (ATAD), H3 (GTGD), H4 (GCAD), H5 (GCGD), H6 (ATGD), H7 (ACAD)、H8(ACGD).Wherein H8 (A-C-G-D) is main haplotype, and frequency is up to 29.81%, H3 (GTGD) and H7 (ACAD) Haplotype frequencies are minimum, are 0.96%.Construct 15 double types, H4H8 frequency highest based on 8 haplotypes, be 28.16%.In 15 double types, in addition to H1H1, H5H8, H2H8, H4H8, the frequency of remaining double type is below 5%, because This does not carry out correlation analysis.
The VLDLR gene molecule marker related to duck growth and fat of the present invention can apply to duck mark auxiliary In selection and use.
Compared with prior art, its remarkable advantage is the present invention:
(1) confirm that the polymorphism of VLDLR is relevant with growth and fat deposition with duck.
(2) by duck VLDLR gene 5'UTR and signal peptide coding region polymorphism and growth and being associated property of abdominal fat Analysis, lays a good foundation to cultivating high-quality meat duck strain.
Brief description
Fig. 1 is duck VLDLR gene 5'UTR and signal peptide coding region amplified fragments result.
Fig. 2 is the polymorphic site haplotype map of duck VLDLR gene 5'UTR and signal peptide coding region.
Specific embodiment
For a better understanding of the present invention, to illustrate technical scheme below by specific embodiment.
Embodiment 1
1 experiment material and method
1.1 animal used as test
Test is Gaoyou duck with duck, in the unified hatching of Gaoyou duck Breeding base, hatching, totally 267.According to a conventional method to examination Test duck and carry out feeding and management and immunity, ground is put down and supported to the 10th week, and feeding period has pond and space for activities.
1.2 growth performances measure
Respectively at 0,3,4,5,6,7,8,9,10 week old, first day morning empty stomach of every week old is weighed, the week of record Gaoyou duck Age body weight, in raising the 10th week, preserves after the blood sample anti-freezing of live body wing venous extraction Gaoyou duck, is slaughtered after measuring live body weight Kill, measure slaughter paramenter index.Slaughter determining is carried out according to national poultry breeding committee unified standard, measure entirely net thorax weight, Half net thorax and abdominal fat weight, and calculate abdominal fat.Abdominal fat=abdominal fat weight/(net thorax weight+abdominal fat weight entirely).
1.3DNA extracting
Extract genomic DNA with conventional phenol/chloroform extraction method.With micro ultraviolet spectrophotometry detect DNA concentration and Purity, its A260/A280 must be between 1.6~1.9.
1.4PCR amplification
According to the duck VLDLR gene order delivered in Genbank, design primer with Primer5.0, amplification length is 374bp, amplified fragments contain VLDLR gene 5 ' UTR and whole signal peptide region.
Upstream and downstream primer sequence is:
Upstream 5 '-ATTACACTGCCAAATGACC-3 '
Downstream 5 '-CGGGAACTGGGATTCTTC-3 '
Pcr amplification reaction system is 25 μ L, and response procedures are 94 DEG C of denaturations 10min, then 35 circulation (94 DEG C of denaturation 30S, 53.5 DEG C of annealing 30S, 72 DEG C of extension 30S), 72 DEG C of extension 10min, 4 DEG C of preservations.
1.5 sequencings and polymorphic detection
PCR primer detects after 1% agarose gel electrophoresis and Goldview dyeing in gel imaging instrument, by yield The PCR primer high, specificity is good is through sending Hua Da gene Co., Ltd to carry out purifying two-way sequencing;Combined using DNAMAN software and survey Sequence figure carries out polymorphism detection assay to sequencing result thus accurately determining SNPs.
1.6 statistical method
Calculate gene frequency, using Chi-square Test allele Hardy-Weinberg equilibrium balance.
Feature according to abdominal fat and for examination duck group, sets up linear regression model (LRM):Y=μ+G+e, wherein:Y is the survey of proterties Definite value;μ is colony's average;G is genotype effects;E is residual error immediately.
Using PHASE2.0 software, haplotype and double type are built and calculated the size of its frequency.
Using Popgen32, PIC_CALC software to genetic heterozygosity (He), effective number of allele (Ne) and polymorphic letter Breath content (PIC) is calculated.
Statistical analysis adopts SPSS15.0 software, the body weight of each genotype and abdominal fat average ± standard error to represent.
The linkage disequilibrium value in SNPs site is analyzed using SHEsis software and calculates r2.
2 results and analysis
2.1 amplification
Enter performing PCR amplification with designed primer pair Gaoyou duck genomic DNA, product is examined through 1% agarose gel electrophoresis Survey, a clearly band occurs between 500bp-250bp, consistent and not non-specific with expected clip size (374bp) Property amplification, result is shown in Fig. 1.
2.2 calculating gene frequencies
The genotype frequency of 4 polymorphic sites of VLDLR gene 5'UTR and signal peptide coding region and gene frequency are shown in Table 1.As can be seen from Table 1 in g.151 site, the frequency highest of GA genotype, gene frequency G>A;In g.170 site, The frequency highest of CC genotype, gene frequency C>T;In g.206 site, the frequency highest of AG genotype, allele frequency Rate A>G;In g.278-295 site, the frequency highest of DD type, gene frequency D>B.Genetic heterozygosity (He), effective equipotential Gene number (Ne) and polymorphism information content (PIC) are the important parameters reflecting Population genetics.As can be seen from Table 1, g.206 The He (genetic heterozygosity) in site and Ne (effective number of allele) highest, respectively 0.49 and 1.95, g.278-295 site He (genetic heterozygosity) and Ne (effective number of allele) is minimum, is 0.42 and 1.71;G.206 (polymorphism information contains the PIC in site Amount) highest, it is 0.37, g.278-295 site is minimum, be 0.33.Through Chi-square Test, except g.206 site meets Hardy- Weinberg genetic equilibrium state is outer (p > 0.05), and its excess-three site does not all meet Hardy-Weinberg genetic equilibrium shape State (p < 0.05).
Table 1 Gaoyou duck group VLDLR gene 5'UTR and signal peptide coding region gene frequency and balance check (n=267)
Representation in genotype frequency:Frequency/number (genotype);Representation in gene frequency:Equipotential base Because of frequency (allele)
2.3 haplotypes, double type build and its frequency
Using PHASE2.0 software, haplotype, double type are constructed to 4 polymorphic sites, and analyzes corresponding frequencies, knot Fruit is shown in Table 2 and table 3.4 polymorphic sites construct 8 kinds of haplotypes, respectively H1 (GTAB), H2 (ATAD), H3 (GTGD), H4 altogether (GCAD)、H5(GCGD)、H6(ATGD)、H7(ACAD)、H8(ACGD).Wherein H8 (A-C-G-D) is main haplotype, frequency Up to 29.81%, H3 (GTGD) and H7 (ACAD) Haplotype frequencies are minimum, are 0.96%.Construct 15 based on 8 haplotypes Individual double type, H4H8 frequency highest, is 28.16%.In 15 double types, in addition to H1H1, H5H8, H2H8, H4H8 remaining The frequency of double type is below 5%, does not carry out correlation analysis.
The haplotype of 24 pleomorphism sites of table and its frequency
The partly double type of 34 pleomorphism sites of table and its frequency
The analysis to growth performance and abdominal fat for the 2.4 double types
Table 4 lists part the related of the haplotype combination of notable or pole significant difference and growth traits and abdominal fat Property.
As seen from Table 4, in 0 to 5 week old, the body weight of each double type all no significant differences (P > 0.05);In 6 week old, The body weight highest of the double type of H1H1, the body weight of the double type of H2H8 is minimum, between the two significant difference (P < 0.05);In 7 to 10 weeks Age, the body weight highest of the double type of H1H1 pole are significantly higher than the double type of H2H8 (P < 0.01) and are significantly higher than the double type of H4H8 simultaneously (P < 0.05), and between the body weight of the double type of H2H8 and the double type of H4H8 no conspicuousness difference (P > 0.05).For butchering Rate, half net thorax rate and net thorax rate entirely, each double type there are no significant difference, and for abdominal fat, the abdominal fat of H5H8 type Rate pole is significantly higher than the double type of H1H1 and the double type of H2H8 (P < 0.01), is significantly higher than the double type of H4H8 (P < 0.05), H4H8 The abdominal fat of double type is significantly higher than the double type of H1H1 (P < 0.05), and between the double type of H1H1 and the double type of H2H8, difference does not show Write (P > 0.05).Least-square analysis result shows, the average weight highest of the double type of H1H1, and the double type of H2H8 is minimum; The abdominal fat highest of the double type of H5H8, the double type of H4H8 takes second place, and the double type of H1H1 is minimum.Double type H1H1 has positive work to body weight With the double type of H5H8 has positive acting to abdominal fat, can serve as selecting the accessory molecule mark of meat duck new lines.
The double type of 44 SNP site of table and the association analysis of growth traits and abdominal fat

Claims (5)

1. a kind of molecule labelling method for indicating and identifying duck growth and abdominal fat is it is characterised in that comprise the following steps:
With comprise VLDLR gene duck complete genome DNA to be measured as template, design primer with Primer5.0, amplification length is 374bp, upstream and downstream primer sequence is:
Upstream 5 '-ATTACACTGCCAAATGACC-3 ';
Downstream 5 '-CGGGAACTGGGATTCTTC-3 ';
Product carries out purifying two-way sequencing, sequencing identification duck VLDLR gene 5'UTR and signal after agarose gel electrophoresis detection Peptide-coding region polymorphism;
To being associated analysis between duck VLDLR gene haplotype combination and slaughter trait, discovery can affect the speed of growth and abdomen Effective Molecular Marker Information of fat rate, and then be used for cultivating high-quality meat duck new lines.
2. the molecule labelling method for detecting duck growth and abdominal fat according to claim 1 is it is characterised in that described Pcr amplification reaction system be 25 μ L, response procedures be 94 DEG C of denaturations 10min, then 35 circulation (94 DEG C of denaturation 30S, 53.5 DEG C annealing 30S, 72 DEG C extension 30S), 72 DEG C extension 10min, 4 DEG C preservation.
3. the molecule labelling method for detecting duck growth and abdominal fat according to claim 1 is it is characterised in that described Purifying two-way sequencing is using the primer of PCR reaction as sequencing primer, and PCR primer carries out purifying sequencing, using PHASE software The haplotype of statistics SNP site, Haplotype frequencies and structure haplotype combination.
4. the molecule labelling method for detecting duck growth and abdominal fat according to claim 1 is it is characterised in that described Duck VLDLR gene 5'UTR and this VLDLR gene of signal peptide coding region polymorphism result have 4 polymorphic sites:g.151、 g.170、g.206、g.278-295;
In g.151 site, the frequency highest of GA genotype, it is that the frequency of 0.56, AA genotype is minimum, is 0.04, allele Frequency G>A;
In g.170 site, the frequency highest of CC genotype, it is that the frequency of 0.50, CT genotype is minimum, is 0.22, allele Frequency C>T;
In g.206 site, the frequency highest of AG genotype, it is that the frequency of 0.50, GG genotype is minimum, is 0.17, allele Frequency A>G;
In g.278-295 site, the frequency highest of DD type, it is that the frequency of 0.65, DB type is minimum, is 0.11, gene frequency D >B.
5. in claim 1-4 arbitrary described molecule labelling method for detecting duck growth and abdominal fat in duck breeding process In be marked the application of assisted Selection.
CN201610835192.7A 2016-09-20 2016-09-20 Molecular marker method for predicting and identifying duck growth and abdomen fat percentages and application Pending CN106434909A (en)

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CN114703298A (en) * 2022-05-09 2022-07-05 安徽农业大学 Molecular marker for identifying duck feed utilization rate character based on neuropeptide gene NPY and method and application thereof

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CN108018359A (en) * 2017-12-15 2018-05-11 中国农业大学 A kind of molecular labeling and its application for being used to identify cherry valley duck
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Application publication date: 20170222