Summary of the invention
The present invention is intended at least to solve one of technical problem existed in prior art.For this reason, it is relevant to goat wool crimping proterties that one object of the present invention is to propose one, can be effective to the SNP marker of goat seed selection.
Wherein, it should be noted that, SNP (singlenucleotidepolymorphism, SNP, i.e. single nucleotide polymorphism) be the molecule genetic marker proposed by the human genome research centre scholar Lander of Massachusetts Institute Technology for 1996, mainly refer to the DNA sequence polymorphism caused by the variation of single core thuja acid in genomic level.The polymorphism that SNP shows only relates to the variation of single base, and performance has conversion, transversion, insertion and disappearance etc.
According to an aspect of the present invention, the invention provides the SNP marker that a kind of goat wool crimping proterties is relevant.According to embodiments of the invention, described SNP marker is base C or the T of goat No. 26 karyomit(e) 5119569 positions.
According to embodiments of the invention, described SNP marker is positioned at the square frame mark of nucleotide sequence shown in SEQIDNO:1:
TACTTGAGGCATAGATTGTAGATAACTTTTTTGAAAAAGTGTTTGCTCCTGTGAGAAAGTTAGACTGTTATCGTTAAAAATCAAATTCACAGTTGCGGTTCTTCTGTTTATTCAGGTAGAATTCAGGACTACTGAATTTACAAATTGATAACATTATGATTTATCCTTGAGCTGAAGAAATCAGTGATGTGTGAATAAAGGTTGCAAATGCTGATGAAGGCTTGTGTTGGTTATAGATTGAGTCTCAATAAAGTTTGGGTTTCTTTGCTTTCTGTTTTTTCTCCACTGCATTCAACATCAAGGTTTAACAAGGCAGTTTTCTTTTTACTTTTGGGTGGCAGGGCAGTGGTGGCTGGAAAGGGGAAATAAATTCTCATTCACCTTTAAAATTCACAACCCCATGGACTGCAGCATGCCAAGCCTTCCTGTCCATCACCAACTCCCAGAGATTATGCAGACTCATGTTCATCGAGTTAATGATGCCATCCAGCCACCTCATC
CACCTTTAGCATTCTTCAGATTGGAGTCTTATTAGACTTACATCTATGAGTGGGCCTTGATCTTGCCTCCTATTCTCTGAGCCACTCAAGACCTCATAAATTAAATTTTAAGTTCACTTGGATCAACAGAAACCCTATAAGTGAACTTACTGTCAGTACTAAACTGTCTAGATCCTTGTTTTCATTTAGTTTTTGACCTTCATACTTATTTTCTTCTTATCTTCTTGATATGTTTAGGAAAAATTATTAAGATCCTTTCAGTTCAGTCAGT(SEQIDNO:1)。
According to embodiments of the invention, in CC, CT genotype individuals of this SNP site, the individual proportion of broad wool is significantly higher than the individual proportion of the genotypic broad wool of TT.Thus, CC and the CT genotype of this SNP site can as the major criterion judging the straight frizzle proterties of goat.
Namely contriver finds, in CC, CT genotype individuals of this SNP site, the individual proportion pole of broad wool is significantly higher than the individual proportion (p=0.000) of the genotypic broad wool of TT.And then, show that CC and the CT genotype of this SNP site can as the major criterion judging the straight frizzle proterties of goat.And then, according to embodiments of the invention, by detecting the above-mentioned SNP of goat, effectively can predict its wool crimping proterties, particularly, as previously mentioned, in CC, CT genotype individuals of this SNP site, the individual proportion of broad wool is significantly higher than the individual proportion of the genotypic broad wool of TT.Thus when such as the genotype in described SNP marker site is CC and/or CT, then can predict that goat to be measured is very large may be individual for broad wool.Thus, contriver determines, the wool crimping proterties of SNP marker of the present invention and goat is closely related, and can be effective to the molecular mark of goat.And then Seedling selection (such as selecting broad wool goat individuality) can be carried out according to actual breeding demand to Goat Breeding material, effectively can improve efficiency and the accuracy of breeding further, improve the genetic level of Goat Reproduction colony, thus goat improved seeds can be selected accurately and efficiently.In addition, according to some embodiments of the present invention, utilize SNP marker of the present invention to carry out goat molecule marker-assisted breeding, there is early screening, save time, the advantage that with low cost, accuracy is high.
According to a further aspect in the invention, present invention also offers a kind of primer pair for detecting foregoing a kind of SNP marker of the present invention.According to embodiments of the invention, described primer pair comprises: have the nucleotide sequence shown in SEQIDNO:2-3, for detecting described SNP marker.
Particularly, the sequence of primer pair is as follows:
F:CAAGGTTTAACAAGGCAGTT(SEQIDNO:2)
R:CTGTTGATCCAAGTGAACTT(SEQIDNO:3)
According to embodiments of the invention, utilize primer pair of the present invention effectively can carry out pcr amplification to the fragment at the above-mentioned of the goat to be measured SNP marker place relevant to wool crimping proterties, and then by the detection that can effectively realize this SNP marker of checking order, determine the genotype in goat to be measured this kind of SNP marker site, and then effectively can predict the wool crimping proterties of goat to be measured.Particularly, in CC, CT genotype individuals of this SNP site, the individual proportion of broad wool is significantly higher than the individual proportion of the genotypic broad wool of TT.Thus, such as, when the genotype in described SNP marker site is CC and/or CT, then can predict goat to be measured most probably for broad wool is individual.Thus, for detecting the primer pair of foregoing SNP marker of the present invention, the molecular mark of goat can be effective to, and then can assist and realize short period of time, low cost, high accuracy ground seed selection goat improved seeds in early days.
According to another aspect of the invention, present invention also offers a kind of test kit for detecting foregoing SNP marker.According to embodiments of the invention, this test kit comprises: the foregoing primer pair for detecting SNP marker of the present invention.Namely the primer pair with the nucleotide sequence shown in SEQIDNO:2-3 is comprised in test kit of the present invention.According to embodiments of the invention, utilize the primer pair comprised in test kit of the present invention, effectively can realize the polymorphic detection to the above-mentioned of the goat to be measured SNP marker relevant to wool crimping proterties, determine the genotype in this SNP marker site of goat to be measured, and then effectively can predict the wool crimping proterties of goat to be measured.Particularly, in CC, CT genotype individuals of this SNP site, the individual proportion of broad wool is significantly higher than the individual proportion of the genotypic broad wool of TT.Thus when such as the genotype in described SNP marker site is CC and (or) CT, then can predict that goat to be measured is very large may be individual for broad wool.Thus, the test kit for detecting foregoing SNP marker of the present invention of the present invention, can be effective to the molecular mark of goat, and then can assist and realize short period of time, low cost, high accuracy ground seed selection goat improved seeds in early days.
In accordance with a further aspect of the present invention, present invention also offers foregoing SNP marker of the present invention, primer pair or test kit, the purposes in goat seed selection.As previously mentioned, by the reagent that can be used in detecting the SNP marker relevant to goat wool crimping proterties of the present invention such as aforesaid primer pair or comprise the test kit etc. of this primer pair, effectively can detect the genotype of the above-mentioned SNP marker determining goat to be measured, and then effectively can predict the wool crimping proterties of goat to be measured based on the genotype obtained, thus effectively can assist goat seed selection.
And then, according to a further aspect in the invention, present invention also offers a kind of method detecting goat wool crimping proterties.According to embodiments of the invention, the method, by carrying out the detection of foregoing SNP marker to goat to be measured, predicts the wool crimping proterties of described goat to be measured.Particularly, can by the reagent that can be used in detecting the SNP marker relevant to goat wool crimping proterties of the present invention such as aforesaid primer pair or comprise the test kit etc. of this primer pair, pcr amplification, order-checking are carried out to goat to be measured, to detect the genotype determining the above-mentioned SNP marker of goat to be measured, and then effectively can predict the wool crimping proterties of goat to be measured based on the genotype obtained.Wherein, as previously mentioned, in CC, CT genotype individuals of this SNP site, the individual proportion of broad wool is significantly higher than the individual proportion of the genotypic broad wool of TT.Thus, such as, when the genotype in described SNP marker site is CC and (or) CT, then can predict goat to be measured most probably for broad wool is individual.Thus, the method of detection goat wool crimping proterties of the present invention, goat wool crimping proterties can be detected fast, efficiently and accurately, and then the molecular mark of goat can be effective to, thus can assist and realize short period of time, low cost, high accuracy ground seed selection goat improved seeds in early days.
In addition, the method for detection goat wool crimping proterties according to the above embodiment of the present invention can also have following additional technical characteristic:
According to embodiments of the invention, the method for goat to be measured being carried out to SNP marker detection is not particularly limited.Order-checking, single strand conformation polymorphism polymerase chain reaction (PCRsinglestrandconformationpolymorphism, PCR-SSCP), the technology such as restriction fragment length polymorphism polymerase chain reaction (PCR-restrictionfragmentlengthpolymorphism, PCR-RFLP) and flight time mass spectrum all can realize the detection of SNP.Wherein, order-checking is that a kind of accuracy is the highest, handiness strong, the detection technique that flux is large, sense cycle is short.Only need at the both sides of SNP site design pair of primers, the product of amplification 400-700bp, then can the genotype of direct-detection SNP site by order-checking.Thus, the present invention adopts the method for order-checking to carry out SNP marker detection.According to concrete examples more of the present invention, by carrying out the detection of SNP marker noted earlier to goat to be measured, predict the wool crimping proterties of described goat to be measured, comprise further: the genomic dna extracting goat to be measured; Utilize foregoing primer pair, the genomic dna of described goat to be measured is carried out pcr amplification, to obtain pcr amplification product; Described pcr amplification product is checked order, to obtain sequencing result; Based on described sequencing result, determine the genotype of the described SNP marker of described goat to be measured; And the genotype of described SNP marker based on described goat to be measured, predict the wool crimping proterties of described goat to be measured.Thereby, it is possible to effectively improve the efficiency detecting goat wool crimping proterties.
According to embodiments of the invention, the method extracting the genomic dna of goat to be measured is not particularly limited, and any known genome DNA extracting method or test kit can be adopted to carry out.According to concrete examples more of the present invention, adopt the genomic dna of conventional phenol-chloroform method extracting goat to be measured.Thereby, it is possible to effectively obtain the genomic dna that quality is good, purity is high, be convenient to subsequent step and carry out.
According to embodiments of the invention, the condition that the genomic dna of described goat to be measured carries out pcr amplification is not particularly limited.According to concrete examples more of the present invention, the amplification system of this pcr amplification is counted with 20 μ l: the template DNA 2 μ l of 25-50ng/ μ l, the each 0.3 μ l of primer shown in SEQIDNO:2-3 of 10pmol/ μ l, the dNTPmix0.5 μ l of 10mmol/L, the Taq DNA polymerase 0.2 μ l of 5U/ μ l, 10 × PCR reaction buffer 2 μ l, surplus is distilled water; The reaction conditions of this pcr amplification is: 94 DEG C 5 minutes; 94 DEG C 30 seconds, 56 DEG C 30 seconds, 72 DEG C 30 seconds, 35 circulations; 72 DEG C 5 minutes.The fragment at SNP marker place of the present invention thereby, it is possible to increase fast, efficiently and accurately, obtains target amplification product, is convenient to the carrying out of subsequent step.
According to embodiments of the invention, the method that described pcr amplification product checks order is not particularly limited, as long as the sequence of the fragment at pcr amplification product and SNP marker place effectively can be obtained.According to concrete examples more of the present invention, can adopt be selected from HISEQ2000, SOLiD, 454 and at least one of single-molecule sequencing method described pcr amplification product is checked order.Thereby, it is possible to high-throughput, obtain sequencing result fast, efficiently and accurately.
According to embodiments of the invention, based on sequencing result, by comparison goat with reference to genome sequence, effectively can determine that the SNP marker of goat to be measured is CC, TT or CT.
According to embodiments of the invention, in CC, CT genotype individuals of this SNP site, the individual proportion pole of broad wool is significantly higher than the individual proportion (p=0.000) of the genotypic broad wool of TT.Thus, based on the genotype of this SNP marker of the goat to be measured determined, the wool crimping proterties of goat to be measured can be predicted accurately and effectively.Particularly, such as, when the genotype in described SNP marker site is CC and (or) CT, then can predict that goat to be measured is very large may be individual for broad wool.And then method of the present invention can be effective to the molecular mark of goat, thus can assist and realize short period of time, low cost, high accuracy ground seed selection goat improved seeds in early days.
It should be noted that, the SNP marker relevant to goat wool crimping of the present invention and apply tool and have the following advantages:
(1) SNP marker provided by the invention is not by the restriction such as age, sex of goat, can be used for the early stage seed selection of goat, significantly can promote the breeding process of goat;
(2) method of goat SNP site of the present invention is detected, accurately and reliably, easy to operate;
(3) the detecting, for the marker assisted selection of goat wool crimping proterties provides scientific basis of goat SNP site of the present invention.
Additional aspect of the present invention and advantage will part provide in the following description, and part will become obvious from the following description, or be recognized by practice of the present invention.
The acquisition of the SNP marker that embodiment 1 is relevant to goat wool crimping
Contriver excavates Grey Goats wool crimping correlated inheritance mark by RAD-seq and whole-genome association (GWAS), utilizes these marks can improve the accuracy of wool crimping character determination.Concrete steps are as follows:
1, the collection of Grey Goats blood sample and the extraction of DNA
1) 457 parts of blood samples all pick up from Shandong Yong Wang herding Development Co., Ltd Grey Goats, and wool crimping proterties statistics is as table 1.
2) genomic dna adopts phenol-chloroform method to extract.
Table 1 Grey Goats wool crimping proterties statistics
Proterties |
Broad wool |
Frizzle |
Add up to |
Number of individuals |
431 |
26 |
457 |
2, RAD-seq library construction
Library constructing method is with reference to (RapidSNPDiscoveryandGeneticMappingUsingSequencedRADMarke rs), specific as follows:
1) carry out enzyme with TaqI to genome to cut, connect P1 joint (containing barcode);
2) interrupt at random, connect P2 joint;
3) by the sequence with P1 and P2 joint while of PCR screening;
4) fragment choosing 400bp-700bp checks order, and wherein, each sample mean obtains the data of 1.2G, the average order-checking degree of depth 15 ×.
3, whole-genome association
Adopt Plink software to carry out whole-genome association (GWAS), filter out from 140,000 SNP 1 with the SNP of the close significant correlation of goat straight frizzle proterties, specifying information is as Fig. 1 and table 2.
Fig. 1 shows the Manhattan figure in this SNP marker site.As shown in Figure 1, X-coordinate is chromosome numbers, and ordinate zou is association analysis-logP value, and dotted line is the significant threshold line (6.6) of genomic level 5%, and the Color pair of single nucleotide polymorphism mark should specific karyomit(e).
The Statistical information of this SNP site of table 2
Karyomit(e) |
Position
a |
Allelotrope
b |
Minimum gene frequency |
P
c |
Chr26 |
5119569 |
C/T |
0.037 |
3.10×10
-10 |
Note: the SNP flanking sequence that a. RAD-seq obtains carries out BLAST, is located at (CaprahircusCHIR_1.0) in genome.
B. there are 51 idiotype disappearances in this site.C. in association analysis by the P value that χ2-test,chi-square test obtains.
Shown by the whole-genome association result shown in Fig. 1, table 2 and Statistical information: this SNP site and significant correlation (p=3.10 × 10, goat straight frizzle proterties pole
-10).And then, show that SNP site is judge that goat wool directly rolls up relevant SNP marker.
4, the statistics of SNP site genotype and wool crimping number of individuals
The genotype of 457 parts of Grey Goats these SNP site individual and phenotype Statistical information as table 3, and have carried out t inspection to different genotype broad wool probability of occurrence, and result shows significant difference (p < 0.05).
The information of this SNP site genotype of table 3 and individual wool crimping
Statistical information shown in table 3 shows: in CC, CT genotype individuals of this SNP site, the individual proportion pole of broad wool is significantly higher than the individual proportion (p=0.000) of the genotypic broad wool of TT.And then, show that CC and the CT genotype of this SNP site can as the major criterion judging the straight frizzle proterties of goat.
The sequence verification of the SNP marker that embodiment 2 is relevant to goat wool crimping
2.1 extract the genomic dna in Grey Goats blood sample to be measured
Grey Goats blood sample to be measured is from Shandong Han Longyang industry limited-liability company Grey Goats, and random selecting 5 parts, according to the DNA extraction method extracting genomic dna described in embodiment 1.
2.2 amplifications are containing the nucleotide fragments of SNP site
With the genomic dna in the aforementioned Grey Goats blood sample each to be measured extracting acquisition for template, utilize forward primer F:CAAGGTTTAACAAGGCAGTT (SEQIDNO:2) and reverse primer R:CTGTTGATCCAAGTGAACTT (SEQIDNO:3), amplify the nucleotide fragments at SNP place to be measured.The amplification system of this pcr amplification is counted with 20 μ l: the template DNA 2 μ l of 25-50ng/ μ l, the each 0.3 μ l of primer shown in SEQIDNO:2-3 of 10pmol/ μ l, the dNTPmix0.5 μ l of 10mmol/L, the Taq DNA polymerase 0.2 μ l of 5U/ μ l, 10 × PCR reaction buffer 2 μ l, surplus is distilled water; The reaction conditions of this pcr amplification is: 94 DEG C 5 minutes; 94 DEG C 30 seconds, 56 DEG C 30 seconds, 72 DEG C 30 seconds, 35 circulations; 72 DEG C 5 minutes.
2.3 order-checkings identify SNP site genotype
The PCR primer obtained in abovementioned steps is first after the agarose gel electrophoresis of 1.5% detects, result is (see Fig. 2 after single specificity band, as shown in Figure 2, left side is electrophoresis result figure, target fragment is 270bp, right side is corresponding Marker figure), more unidirectional order-checking is carried out on ABI3730 sequenator, identify the genotype at 501bp place (i.e. SNP marker of the present invention) in SEQIDNO:1 sequence.Wherein, the genotypic order-checking peak figure of CC and CT two kinds is respectively as shown in Fig. 3 a, 3b.Wherein, as shown in Figure 3, during order-checking, have employed reverse primer sequences, so the sequence recorded is reverse complementary sequence.
In the description of this specification sheets, specific features, structure, material or feature that the description of reference term " embodiment ", " some embodiments ", " example ", " concrete example " or " some examples " etc. means to describe in conjunction with this embodiment or example are contained at least one embodiment of the present invention or example.In this manual, identical embodiment or example are not necessarily referred to the schematic representation of above-mentioned term.And the specific features of description, structure, material or feature can combine in an appropriate manner in any one or more embodiment or example.
Although illustrate and describe embodiments of the invention, those having ordinary skill in the art will appreciate that: can carry out multiple change, amendment, replacement and modification to these embodiments when not departing from principle of the present invention and aim, scope of the present invention is by claim and equivalents thereof.