Summary of the invention
One of purpose of the present invention provides the relevant molecule marker of a kind of cock skin skin color.This molecule marker is positioned on the exon of cock skin skin color related gene B CDO2.Specifically, this molecule marker is arranged in the 259th A/G of bit base place base mutation of sequence shown in the SEQ ID NO:1.When this place's base was A, then cock skin skin color was a white, and when this place's base was G, then cock skin skin color was yellow.
The present invention based on the DNA full length sequence of cock skin skin color related gene B CDO2, seek the mutational site and the corresponding pleiomorphism detecting method that influence skin color on this gene, by the checking in a plurality of colonies, for chicken breeding provides a kind of molecular identification method about its skin color.Below be concrete technical scheme:
Dna sequence dna (reference sequences GeneBank accession number is NC 006111.2) with chicken BCDO2 gene is a template, this Gene Partial sequence of design primer amplification, and used primer is:
Forward primer: 5 '-TCCTCTGATTGCTTTACTGACTTG-3 ',
Reverse primer: 5 '-GGGAAGGAGGTATCATTGGAGA-3 '.
The sequence that obtains of increasing comprise the 6th complete exon and part the 5th intron, part the 6th intron, as described in sequence table SEQ ID NO:1, this sequence total length is 444bp.
The multisequencing compare of analysis of the present invention by the above-mentioned dna fragmentation that obtains being carried out (comprise pale skin chicken and yellow skin chicken) between chicken breed, the sequence of acquisition as shown in Figure 2.Comparison result is found a kind of molecule marker that the chicken marker assisted selection is used that can be used as, and this mark is relevant with the skin color of chicken, has the A/G sudden change at the 259th bit base place of this sequence, causes Sdu I-RFLP polymorphism.
Second purpose of the present invention provided the discrimination method of this molecule marker, is template with the dna sequence dna of chicken BCDO2 gene, selects following primer to increase:
Forward primer: 5 '-TCCTCTGATTGCTTTACTGACTTG-3 ',
Reverse primer: 5 '-GGGAAGGAGGTATCATTGGAGA-3 ';
The resulting product utilization Sdu of pcr amplification I restriction endonuclease is carried out endonuclease reaction, agarose gel electrophoresis detects enzyme and cuts product, if having only the band of a 444bp, then the dna double chain is the A base at this place, mutational site, be judged as the AA genotype, show as pale skin; If 2 bands that are respectively 263bp and 181bp are arranged, illustrate that then the dna double chain is the G base at this place, mutational site, be judged as the GG genotype, show as yellow skin; If 3 bands that are respectively 444bp, 263bp and 181bp are arranged, illustrate that then the dna double chain is the A base at this chain in place, mutational site, another chain is the G base, is judged as the AG genotype, because A allelotrope is dominance, shows as pale skin.
The 3rd purpose of the present invention provides the application of this molecule marker in the chicken molecular marker assisted selection, and particularly cock skin skin color is selected the application in the breeding.
By technical scheme provided by the present invention, can also be prepared into the identification reagent box of this molecule marker.
The invention has the beneficial effects as follows,, can know the genotype of this proterties of target chicken group skin color, thereby can have purpose that the chicken group is selected, improve the consistence of its offspring chicken group's skin and shin look by detection to above-mentioned A/G mutational site.In addition, detection method accuracy height used in the present invention, cost is low, efficient is high.
Embodiment
For making the present invention easier to understand,, further set forth the present invention below in conjunction with specific embodiment.Should be understood that these embodiment only to be used to the present invention is described and be not used in and limit the scope of the invention.
Embodiment 1: the foundation of cock skin skin color molecular detecting method
(1) primer:
Dna sequence dna (reference sequences GeneBank accession number is NC 006111.2) with chicken BCDO2 gene is a template, design a pair of primer YSD-F/YSD-R and clone the dna sequence dna (comprising the 6th complete exon and part the 5th intron, part the 6th intron) that obtains shown in sequence SEQ ID NO:1, this sequence total length is 444bp.Used primer sequence is respectively shown in SEQ ID NO:2 and SEQ ID NO:3, and is specific as follows:
YSD-F:5′-TCCTCTGATTGCTTTACTGACTTG-3′,
YSD-R:5′-GGGAAGGAGGTATCATTGGAGA-3′。
(2) pcr amplification condition:
Cumulative volume is to add dna profiling 1 μ L in the PCR reaction system of 25 μ L, each 1 μ L before and after 2 * PCR reaction mixture, the 12.5 μ L, 10mM primer, and Taq archaeal dna polymerase 0.625U, distilled water 8.25 μ L, the PCR reaction conditions is: 94 ℃ of pre-sex change 3min; 94 ℃ of sex change 30s, 56 ℃ of annealing 30s, 72 ℃ are extended 30s, totally 33 circulations; Last 72 ℃ are extended 10min, 4 ℃ of preservations.
(3) seek molecule marker:
Choose the blood DNA of 2 pale skin chickens and 2 yellow skin chickens and do template, carry out pcr amplification, the PCR product detects through 1.5% agarose gel electrophoresis, as shown in Figure 1.Fig. 1 is the partial dna sequence on the chicken BCDO2 gene, be used for seeking the segmental electrophoresis picture of molecule marker, clip size is 444bp (agarose gel concentration is 1.5%), wherein, the M swimming lane is a dna molecular amount standard (DL2000), B1, B2 represent pale skin chicken BCDO2 gene PCR amplified fragments, and H1, H2 represent yellow skin chicken BCDO2 gene PCR amplified fragments.The PCR product is reclaimed, clones, checks order the nucleotide sequence of its sequencing sequence shown in H1, H2, B1, B2 among Fig. 2.Find to exist 8 SNP of place by Cluster W comparison, the deletion mutantion of 1 place, at 259 places base mutation has taken place with pale skin chicken comparison discovery yellow skin chicken, sported G by A, the position of this mutational site on BCDO2 genome sequence (the GeneBank accession number is NC 006111.2) is 14253 places.Specifically see Fig. 2, Fig. 2 is the result that this fragment on the BCDO2 gene of 2 pale skin chickens and 2 yellow skin chickens is compared.B1, B2 represent the pale skin chicken among the figure, and H1, H2 represent the yellow skin chicken, and among the figure shown in the square frame is the A/G mutational site that this sequence exists at 259 bit base places, and the sequence shown in the underscore is the primer sequence that the present invention designs.Experiment concrete operations step is as follows:
1, the purifying of PCR product: under ultraviolet lamp, contain the segmental gel of purpose from the cutting-out of low melting-point agarose gel, put into 1.5mL Ependorff pipe, use PCR product purification test kit (available from Promega company) purified pcr product then, according to this test kit specification sheets operation.
2, ligation: the PCR product and the pMD18-T Vector (available from TaKaRa company) of purifying are connected, and the ligation cumulative volume is 10 μ L, connects damping fluid, 2.5 μ L comprising 2 * fast; Carrier (50ng), 0.5 μ L; Reclaim DNA, 7-8 μ L.Bullet is beaten and is mixed a little, connects more than the 1h or 4 ℃ of connections are spent the night in 16 ℃.
3, the preparation of competent cell: from 37 ℃ of incubators, cultivated on the fresh flat board of 16-20h the single colony inoculation of DH5 α of picking in 2mL LB, in 37 ℃ of shaking table shaking culture 3h, switching 1mL bacterium liquid is in the saline bottle that contains 300mL LB, continuation is at 37 ℃ of about 4h of shaking table shaking culture, treat that when OD600 reaches 0.3-0.4 saline bottle being put ice bath from the shaking table taking-up cools off 10-15min, then bacterium liquid is changed in the centrifuge tube in 4 ℃ 4, the centrifugal 10min of 000g is with collecting cell, centrifuge tube is inverted to abandon clean nutrient solution, is iced the CaCl of the 0.1mol/L of precooling with 10mL
2Resuspended precipitation, ice bath 30min repeats 4 ℃ 4, and the centrifugal 10min of 000g once ices the CaCl of the 0.1mol/L of precooling with 4ml
2Resuspended precipitation, it is standby to put 4 ℃ of preservations.
4, transform: in the 1.5mL centrifuge tube of sterilization, add 100 μ L competent cells, add on ice and connect product 5 μ L, with liquid-transfering gun piping and druming evenly, ice bath 30min; Centrifuge tube is placed 42 ℃ circulator bath (not vibrations), behind the heat shock 90s, rapid ice bath 2min; In centrifuge tube, add 400 μ L LB nutrient solutions again, bathe recovery 45-60min in 37 ℃ of shaking tables (200rpm/min) temperature; Centrifugal, remove the part supernatant liquor, the bacterium liquid of getting after 100 μ L recover is distributed on the flat board that contains Amp, smoothens; After treating that liquid fully absorbs, be inverted plate, in 37 ℃ of cultivations 14-16 hour, observation had or not bacterium colony to grow.
5, the evaluation of positive colony and order-checking: the bacterial plaque that picking transforms from flat board inserts the 1.5mL centrifuge tube that contains 400 μ L LB and in 37 ℃ of shaking table joltings and cultivates about about 8h.With this bacterium liquid is template, selects for use the universal primer M13 (Beijing Liuhe Huada Genomics Technology Co., Ltd provides) of former primer or order-checking to carry out pcr amplification (annealing temperature 58-60 ℃).Electrophoresis detection, the bacterium liquid of picking positive colony is sent to order-checking, and sequencing is finished by last Beijing Liuhe Huada Genomics Technology Co., Ltd.
In this side's of enforcement example, pcr amplification product is special PCR product (Fig. 1) through the demonstration of 1.5% agarose gel electrophoresis detected result, Fig. 1 is the partial dna sequence on the chicken BCDO2 gene among the embodiment 1, be used for seeking the segmental electrophoresis picture of molecule marker, clip size is 444bp (agarose gel concentration is 1.5%), wherein, the M swimming lane is a dna molecular amount standard (DL2000).With the recovery of PCR product, purifying rear clone, order-checking (comparison chart of measured sequence is seen Fig. 2), Fig. 2 uses the result that method of the present invention is compared to this fragment on the BCDO2 gene of 2 pale skin chickens and 2 yellow skin chickens, wherein B1, B2 represent pale skin chicken aligned sequences, H1, H2 represent yellow skin chicken aligned sequences, and square frame is depicted as the A/G mutational site that this sequence exists at 259 bit base places.The result shows that resulting dna sequence dna length is 444bp, comprises the 6th complete exon, and part the 5th intron and part the 6th intron sequences (shown in sequence table SEQ ID NO:1); Sequencing result shows at 259 places of this dna sequence dna and has the A/G base mutation.
(4) the PCR-RFLP detection method is set up:
The A/G base mutation at these fragment 259 places, just can be discerned by restriction endonuclease Sdu I, with above-mentioned PCR product 6 μ L, 10 * damping fluid, 1 μ L, restriction enzyme Sdu I 0.2 μ L (2U), adding distilled water mends to 10 μ L, with centrifugal behind the sample mixing, 37 ℃ of incubators are placed 6h, detect with 1.5% agarose gel electrophoresis, imaging system is observed enzyme and is cut the result, the record genotype.This gene mutation site is controlled by two allelotrope, and wherein A is the allelotrope that does not form restriction enzyme site, and G is the allelotrope that forms restriction enzyme site.These two allelotrope can be formed three kinds of genotype, wherein homozygous (the having only DNA band of 444bp during electrophoresis detection) that enzyme is cut for not taking place in the AA type, homozygous (the occurring two DNA bands of 263bp and 181bp during electrophoresis detection) that enzyme is cut for taking place in the GG type, AG is heterozygous (occurring three DNA bands of 444bp, 263bp and 181bp during electrophoresis detection), sees Fig. 3 for details.Fig. 3 is three kinds of genotype (AA, AG and the GG) electrophoretograms (agarose gel concentration is 1.5%) of the Sdu I-RFLP on the chicken BCDO2 gene extron 6 among the present invention, and the M swimming lane is a dna molecular amount standard (DL2000).
The detection and the application of embodiment 2:PCR-Sdu I-RFLP polymorphism distribution situation in each chicken strain
Having collected different shin looks and the skin-color chicken blood DNA of totally 3 strains in this example, is respectively B, Z, H totally 3 strains, and sample standard deviation is from Guangdong intelligence prestige agricultural science and technology company limited by shares.According to embodiment 1 described method above chicken kind has been carried out PCR-Sdu I-RFLP and detected, to verify the molecular diagnosis method of this kind of the present invention about cock skin skin color.Detected result is as shown in table 1.Table 1 is the distribution detected result of BCDO2 gene Sdu I-RFLP polymorphism in the chicken group.
Table 1
As shown in Table 1, the genotype of the individuality that is detected all conforms to its skin color, illustrates that method of the present invention is reliable, effective.
Molecule marker of the present invention can be applicable to cock skin skin color and selects in the breeding.As the Z Strains of Chickens that table 1 detected, its macroscopic features is that skin color is a white, the shin look is a black, and find that in our testing process some pale skin individualities are AG heterozygous genes type in its colony, if the stud mating of AG heterozygous genes type so, the GG genotype will occur in its offspring colony, show as yellow individuality, and yellow skin is the macroscopic features that does not meet this strain of Z.The individuality of this strain father, female Dai Zhongwei AG heterozygous genes type can be weeded out so use molecule marker of the present invention,, make colony's unanimity aspect this macroscopic features of skin color to guarantee not have among its offspring chicken group the appearance of yellow skin individuality.
Last institute should be noted that; above embodiment is only in order to illustrate technical scheme of the present invention but not limiting the scope of the invention; although the present invention has been done detailed description with reference to preferred embodiment; those of ordinary skill in the art is to be understood that; can make amendment or be equal to replacement technical scheme of the present invention, and not break away from the essence and the scope of technical solution of the present invention.
<120〉relevant molecule marker and discrimination method and the application of a kind of cock skin skin color