CN109355400B - Method for identifying genes related to content of glycogen of crassostrea gigas and SNP (Single nucleotide polymorphism) marker and screening high glycogen individuals - Google Patents
Method for identifying genes related to content of glycogen of crassostrea gigas and SNP (Single nucleotide polymorphism) marker and screening high glycogen individuals Download PDFInfo
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Abstract
The invention relates to a gene and a primer related to the glycogen content of crassostrea gigas and a method for screening individuals with high glycogen content. Glycogen content-related gene: protein phosphatase 1 regulatory subunit 3B (glycogen targeting subunit). The gene promoter region has 3 SNP-PPR1, PPR2 and PPR3 which are obviously related, and meanwhile, the glycogen content of an individual with 3 dominant genotypes is obviously improved by more than 10 percent compared with an individual with a disadvantaged genotype combination. Subsequently, parent oysters with dominant genotype combinations can be screened by the method and used for oyster breeding. The invention provides an SNP marker obviously related to the glycogen content of crassostrea gigas and potential application thereof, and has the advantages that the genotype identification can be carried out on parent scallops before offspring seed breeding, and the glycogen content of offspring is increased. The reliability of the SNP marker obtained by the research result is higher, the population adaptation range is wider, and the effect is more stable.
Description
Technical Field
The invention belongs to the field of molecular biology and genetic breeding, and relates to an SNP identification method related to the glycogen content of crassostrea gigas and potential application.
Background
Oysters are important cultured shellfishes, the annual output of the oysters in China is more than 400 ten thousand tons, and accounts for more than 80% of the output of the oysters in the world, wherein the crassostrea gigas is a main cultured variety in the northern area. Although the yield of oysters is high, the overall quality of oysters produced in China is poor, the sales price is about 1/3 of the international market, and the occupancy rate of the international high-end market is low. The quality and properties of oyster mainly include body size, fullness and glycogen content. Especially, glycogen content greatly contributes to the milky color and luster and fullness of the oysters in the non-reproductive period. Therefore, the genetic improvement on the oyster quality traits, particularly the glycogen content is a reliable way for improving the oyster quality and competitiveness in China.
The glycogen content of oyster is characterized by seasonal variation, high content in autumn and winter, and gradually reduced by supplying energy for gonad development in spring and summer. And the content difference among different tissues is large, and the content of the gonad, the lip valve and the mantle is the highest. The heritability of the glycogen content traits belongs to a high level, which indicates that the glycogen content traits are genetically controlled, and the glycogen content difference among oyster individuals is large, so that the breeding of the glycogen content is necessary and feasible. Meanwhile, the glycogen content is a slaughter trait, and the glycogen content can be measured only after oysters are killed, so that the glycogen content breeding by the traditional breeding means is severely restricted. Since the glycogen content and growth traits, which can be measured in vivo, have a very weak correlation, indirect breeding by growth traits is also not feasible, and therefore, molecular breeding is essential.
The oyster transcriptome and whole genome re-sequencing develops tens of millions of Single Nucleotide Polymorphism (SNP) sites, and the sites lay a foundation for molecular marker assisted breeding. Among them, candidate gene association analysis and whole genome association analysis are the main analysis methods. With the completion of the whole genome sequencing of the crassostrea gigas and the acquisition of a high-density genetic linkage map, the whole genome association analysis becomes possible. The subject group obtained a large number of SNP markers by re-sequencing 427 individual whole genomes, and performed whole genome association analysis of nutritional quality traits such as glycogen. The results show that there is a cluster of significant sites that are significantly associated with glycogen content (P)<10-6). A gene, protein phosphatase 1 regulatory subunit 3B, which has a function of glycogen regulating metabolism in mammals, is screened by scanning a genome region of 100kb upstream and downstream of the significant site. After gene cloning, 3 extremely significant SNP sites are found in the gene region through site fine positioning.
Based on the result of the whole genome association analysis of the glycogen content of crassostrea gigas, the invention obtains the major SNP sites and key genes which affect the glycogen content, screens 3 SNP markers which are extremely obviously related to the glycogen content, develops the optimal combination and is used for predicting the glycogen content. Compared with the SNP locus developed in the past, the locus is obtained by whole genome association analysis, is precisely positioned by the locus, has higher reliability and wider application range, is easier to be verified in a group, and is used for molecular breeding.
Disclosure of Invention
The invention aims to provide an SNP marker related to the glycogen content of crassostrea gigas, and provides reference for molecular marker-assisted selective breeding of crassostrea gigas.
In order to achieve the aim, the technical scheme of the invention is an SNP marker related to the content of crassostrea gigas glycogen, 3 significant mutations (located at 436,202,115 bases upstream of a transcription initiation site respectively) are located in a protein phosphatase 1 glycogen targeting subunit promoter region, and the mutation types are T/C and are named as PPR1, PPR2 and PPR 3.
The nucleotide sequence of 500bp of the upstream and downstream of the target PPR1 site obtained by whole genome re-sequencing is shown in SEQ ID NO.1, and the 501 th, 735 th and 822 th sites are PPR1, PPR2 and PPR3 respectively.
Genotype and phenotype data of each individual are detected in a whole genome association analysis population, and the association analysis prediction is carried out on the genotype and the glycogen content to obtain that PPR1, PPR2, PPR3 and the glycogen content of the crassostrea gigas are obviously related (P)<10-6) Can be used for marker-assisted selective breeding of crassostrea gigas. The method for detecting the SNP marker related to the glycogen content trait of the crassostrea gigas comprises the screening steps of:
a) collecting and homogenizing experimental materials: 427 ostrea gigas wild individual female parents are collected, 427 half sib families are constructed with one male parent in Jiaonan, and the homogeneous culture is carried out.
b) Determination of glycogen content: glycogen content determination is carried out on crassostrea gigas individuals of different families by using a kit (anthrone colorimetry), and the female parent phenotype value is represented by 30 offspring mean values.
c) Genotyping: and (3) carrying out whole genome re-sequencing on 427 oyster female parents by adopting a second-generation sequencing technology platform, screening SNP sites and carrying out individual typing to obtain effective SNP sites for association analysis.
d) Correlation analysis: fusion of linear models using GAPIT softwareGenome association analysis is carried out to obtain protein phosphatase 1 glycogen targeting subunit which is obviously associated with characters, and 3 extremely obvious SNP sites (p) in the gene region<10-6). Whole genome association analysis Manhattan plots are shown in FIG. 2. Subsequently, SNP-PPR1, PPR2 and PPR3 located in protein phosphatase 1 glycogen targeting subunit promoter regions are selected as candidate SNP sites of the item.
The invention identifies a string of SNP signals which are positioned on the chromosome of the crassostrea gigas and are obviously related to glycogen content through genome-wide association analysis, and the interval is positioned to a gene related to glycogen content: protein phosphatase 1 regulatory subunit 3B (glycogen targeting subunit). The gene promoter region has 3 significantly related SNP-PPR1, PPR2 and PPR3 (respectively located at 436,202,115 bases upstream of the transcription initiation site), and corresponding detection methods are developed, and the results show that the SNP sites can be simply and rapidly detected by the method, and the significance of the sites is verified in a wild independent population. Meanwhile, the glycogen content of the individual with 3 dominant genotypes is obviously improved by more than 10 percent compared with the glycogen content of the individual with the combination of the disadvantaged genotypes. Subsequently, parent oysters with dominant genotype combinations can be screened by the method and used for oyster breeding. The nucleotide sequence of 500bp upstream and downstream of the crassostrea gigas PPR1 is shown in SEQ ID No.1, and PPR2 and PPR3 are contained in the interval.
The potential application of the SNP marker obviously related to the glycogen content of the crassostrea gigas has the advantages that the genotype identification can be carried out on parent scallops before the breeding of offspring seeds, and the glycogen content of offspring is increased. The reliability of the SNP marker obtained by the research result is higher, the population adaptation range is wider, and the effect is more stable.
The invention has the advantages that:
the method is used for predicting the glycogen content of the individual through the method for detecting the individual genotype, sampling can be carried out before seedling breeding through a nondestructive sampling technology in breeding, a target genotype combination individual is selected as a parent, and molecular marker-assisted selective breeding is carried out. Overcomes the characteristic that the slaughter traits are difficult to select and breed, and ensures the operation to be simple and easy.
Drawings
FIG. 1 is a diagram of the peaks of the three genotypes of the PPR1, PPR2 and PPR3 sites contained in the above. Respectively located at 501 st, 735 th and 822 th bits of the sequence table 1;
FIG. 2 is a Manhattan plot of the whole genome correlation analysis of the glycogen content of crassostrea gigas.
Detailed Description
The characteristic length of the information sequence of SEQ ID NO.1 in the sequence table (1): 1001bp, 500bp respectively upstream and downstream of PPR1 site.
The characteristic length of the information sequence of SEQ ID NO.1 in the sequence table (1): 1001bp
Type (2): nucleic acids
Chain type: single strand
Topological structure: line shape
Molecular type: DNA
The source is as follows: concha Ostreae
Description of the sequence:
example 1
a) Collecting a sample: 288 individuals of a wild population of the Jiaonan contemporaneous hatching are collected and divided into monomers to be cultured in an isopycnic scallop cage, in the next 2 months, oysters are dissected when reaching the commodity specification and having high and stable glycogen content, adductor muscle and residual tissues are taken, quick frozen by liquid nitrogen and stored at-80 ℃ for later use. "
b) Glycogen content determination
The remaining tissue was freeze-dried for 48 hours, ground to a fine powder using a tissue grinder, and glycogen content was measured using a near-infrared spectroscopy model.
c) Extraction of DNA: total DNA per individual was extracted from adductor muscle using the sodium laurate method
1) Preparing a sodium laurate buffer solution: 5.844g of NaCl and 10g of sodium laurate were accurately weighed and placed in a 1000mL beaker, 100mL of Tris-HCl (1M), 40mL of EDTA (0.5M) and 800mL of dH2O were added, the pH was adjusted to 8.0 with hydrochloric acid, the volume was adjusted to 1000mL, and the mixture was sterilized and stored at room temperature.
2) 1.5ml of sterilized centrifuge tube was added with 200. mu.l of sodium laurate extraction buffer, 5-20mg of oyster adductor muscle tissue was taken, and the tissue was homogenized with a grinding bar. Then 500. mu.l of sodium laurate extraction buffer were added.
3) Add 700. mu.l phenol: chloroform: isopentanol (volume ratio 25:24:1) was repeatedly and slowly shaken until the upper layer was cloudy.
4) After centrifugation at 12000rpm for 15min twice at 4 ℃ the supernatant was immediately removed and 400. mu.l of the supernatant carefully pipetted into a new 1.5ml centrifuge tube.
5) Add 280 μ l (0.7 x 400 μ l) -20 ℃ pre-cooled isopropanol; the centrifuge tube was placed in a-20 ℃ freezer for 30 minutes. And slowly inverting for 6 times to separate out white flocculent precipitate, and turning upside down to one direction to prevent the precipitate from dispersing.
6)12000 turns, centrifugates for 10 minutes at 4 ℃, the bottom of the tube appears precipitation, sucks up the supernatant.
7) Add 500. mu.l of pre-cooled 70% strength by volume ethanol to the centrifuge tube, wash the pellet with repeated shaking, centrifuge at 12000rpm for 10 minutes at 4 ℃, discard the supernatant and repeat twice.
8) The pellet was spun 12000 times, centrifuged briefly at 4 ℃ for 8 seconds to wash out the residual ethanol, and the residual ethanol was air-dried in a clean bench.
9) After the precipitate was cleared, 80. mu.l of TE buffer (pH8.0) was added and the mixture was flicked and dissolved at 65 ℃ in a metal bath.
10) Mu.l of RNase (0.1mg/ml) was added thereto, and the RNA was digested in a water bath at 37 ℃ for 30 minutes to obtain a DNA solution. At-20 ℃ for use.
d) SNP site genotyping was performed using the SNaPshot (multiplex single base extension SNP typing technique):
adopting three specific primer sequences to carry out typing detection on three SNP sites respectively;
1) peripheral amplification is performed using specific primers. The reaction system is as follows;
the primer sequence is as follows:
a forward primer F: 5'-AGTTCGAATCTCACTGGGGCC-3'
Reverse primer R: 5'-CCGGCATTTCCACTGACTGA-3'
The reaction procedure for PCR amplification was:
2) and (3) preparing template DNA. To 15. mu.l of the PCR product were added 5U SAP (shrimp alkaline phosphatase) and 2U ExoI (exonuclease I) and mixed by shaking and incubated at 37 ℃ for 1 hour and then at 75 ℃ for 15 minutes to inactivate SAP and ExoI.
3)SNaPshot PCR
Template: the PCR product was used as a template for the SNaPshot PCR, and after purification of the product, 3. mu.l of each individual was mixed and subjected to detection of one site, and the three sites were performed in three times.
SNaPshot PCR：
The specific primer sequences are respectively as follows:
PPR1:5’-TTTTTTTTTTTTTTTTTTCGCGCATGCGATACATATTTTA-3’，
PPR2:5’-TTTTTTTTTTTTTTTTCATCTATTATGATATTTTTA-3’；
PPR3:5’-TTTTTTTTTTTTGCACAAAAGTAATTGGGCCTTATAGTTGTTTA-3’
4) purification of the SNaPshot PCR product
Adding 1U SAP into 10 μ l of the above SNaPshot PCR product, shaking, mixing, keeping the temperature at 37 deg.C for 1 hr, keeping the temperature at 75 deg.C for 15min to inactivate enzyme, and keeping at 4 deg.C for 24 hr or-20 deg.C for a long period.
5) Capillary electrophoresis.
Preparing an electrophoresis sample: the SNaPshot product was first diluted 20-fold:
electrophoresis conditions:
denaturation at 95 deg.C for 5min, and rapidly cooling with ice for 4 min. The prepared samples were subjected to capillary electrophoresis using a 3730xL DNA analyzer and the signals were collected. Environmental conditions: laboratory temperature: 18-25 ℃; capillary length: 50 cm; temperature of the heating furnace: 60 ℃; operating voltage: 15 kV. Results the results of the experiment were analyzed using GeneMapper V4.0 to determine the genotype for each individual at three sites.
e) Correlation analysis: glycogen content data and genotype data were imported into SPSS22.0 software and correlation analysis was performed by linear regression. The results show that the SNP sites PPR1, PPR2 and PPR3 are all significantly related to the glycogen content (P < 0.001). The glycogen content of 288 individuals is obtained through statistics, the PPR1 site TT > TC > CC, the PPR2 site TT > TC > CC, the PPR3 site CC > TC > TT, and the specific content information is shown in Table 1. The content of dominant genotype combination individuals at three sites is obviously higher than that of disadvantaged genotype combination individuals, wherein only two dominant genotype combinations (TT + TT + CC, TT + TC + CC) have 3 or more individuals in the population, and the specific information is shown in Table 2.
Table 1: 288 individuals glycogen content and genotyping analyses.
Glycogen content is the average value of individuals of each genotype, wherein glycogen content is the dry weight proportion thereof.
Table 2: combining three sites (sequentially corresponding to SNP sites PPR1, PPR2 and PPR3) with advantageous genotypes to obtain glycogen content
Sequence listing
<110> oceanographic institute of Chinese academy of sciences
<120> method for identifying genes related to glycogen content of crassostrea gigas and SNP markers and screening high glycogen individuals
<160> 1
<170> SIPOSequenceListing 1.0
<210> 1
<211> 1001
<212> DNA
<213> Crassostrea gigas (Crassostra gigas)
<400> 1
caagggatgt gtgtgtgttg gagggggggg gggtagattt gaggttagtc ggcggtactt 60
aatttacaga gtaattaaag ataaagagct agaaatgtag aaattgacct gacatgtagt 120
tacaaatgta catgtatata ctacaatgac gtactataat tatatttaac gatacggccg 180
gtacatgcgc ggattttcat taagtgactt ttaggtggta tgggacacct ccatagtgtg 240
gcgtacttcc gatcgaaata aacaataaaa tcaagcattt aataatttta caaacttttt 300
cttctacaaa actttggact aatagcgtag cgcaatgggt tgaagcgtta accacgaatc 360
tttaagttat gagttcgaat ctcactgggg cttttatagt ttttaccttt cccaaacatt 420
tcgaaacatt tttggccaaa tattgtaaaa tttgaaagaa aaaaaacccc gatagtttcg 480
cgcatgcgat acatatttta caaggactga aaatatgttc agattgttcc attttagagg 540
atacatatac atttaagttt cgattaaaaa tggcttaaca ccccaccaaa atccgcaaaa 600
tagaatgtaa aaaaagaaat cgtgtacctt tctaattgca ttttttacaa ttagttttcc 660
acattatttt actcgtaata cttatttttt ttacgaggta aacatatttt tgttcatcta 720
ttatgatatt tttacacata catgtaccta cattcatgga ataaggaaat tatttgacct 780
tcatcttatg cacaaaagta attgggcctt atagttgttt attttttaaa ccaccttagc 840
aatggaatgc tgcattcatt ctgttctttc ctgcaatttt gttcaacaac aatgtataaa 900
tagacacgtc acgtagactc gacgctcagt cagtggaaat gccgggtcag ctgtttacag 960
tcgtctgcaa ggtaaggaat tatatacccg tacatgtttg t 1001
Claims (4)
1. The gene related to the glycogen content of the crassostrea gigas is characterized in that: shown as a base sequence in a sequence table SEQ ID No. 1;
comprises three SNP gene loci PPR1, PPR2 and PPR3, the mutation types of the three SNP gene loci are T/C types and are respectively positioned at the 501 th site, the 735 th site and the 822 th site of SEQ ID No. 1;
the glycogen content of the individual is PPR1 site TT > TC > CC, PPR2 site TT > TC > CC, PPR3 site CC > TC > TT.
2. An SNP marker specific primer related to the glycogen content of crassostrea gigas is characterized in that: comprises one, two or three of the following single-base extension primer gene sequences;
the single base extension primer is:
PPR1：5’- TTTTTTTTTTTTTTTTTTCGCGCATGCGATACATATTTTA-3’ ；
PPR2: 5’-TTTTTTTTTTTTTTTTCATCTATTATGATATTTT TA-3’ ；
PPR3: 5’-TTTTTTTTTTTTGCACAAAAGTAATTGGGCCTTATA GTTGTTTA-3’。
3. an SNP marker identification method for screening individuals with high glycogen content of crassostrea gigas is characterized in that:
the mutation types of the two are T/C types and are respectively positioned at the 501 th site, the 735 th site and the 822 th site of the sequence table 1;
obtaining an SNP marker through whole genome association analysis, wherein the SNP marker comprises three SNP marker gene loci PPR1, PPR2 and PPR3, and is located in a glycogen targeting subunit promoter region of the crassostrea gigas chromosome, and the genotypes of the three SNP marker gene loci are all T/C; three sites have two basic forms of T and C, the genotype identification of the SNP marker site is carried out on the parent shellfish before seedling breeding, the glycogen content of an individual is shown in the specification, wherein the PPR1 site TT > TC > CC, the PPR2 site TT > TC > CC, and the PPR3 site CC > TC > TT;
by screening parent scallops of genotypes with high glycogen content corresponding to one, two or three sites of the three sites, the glycogen content of the offspring population is improved,
the method comprises the following steps:
1) extraction of DNA: total DNA per individual was extracted from adductor muscle using the sodium laurate method
2) Adopting three specific primer sequences to carry out typing detection on three SNP sites respectively;
a. carrying out peripheral amplification by using a specific primer; the primer sequence is as follows:
a forward primer F: 5'-AGTTCGAATCTCACTGGGGCC-3'
Reverse primer R: 5'-CCGGCATTTCCACTGACTGA-3'
The reaction procedure for PCR amplification was:
B. preparation of template DNA: adding 5U of SAP and 2U of ExoI into 15 mul of PCR product, shaking, uniformly mixing, preserving heat for 1 hour at 37 ℃, and then preserving heat for 15 minutes at 75 ℃ to inactivate the SAP and the ExoI;
c. SNaPshot PCR: taking a PCR product as a template of the SNaPshot PCR, and respectively detecting sites after purifying the product;
the specific primer sequences are respectively as follows:
PPR1:5’- TTTTTTTTTTTTTTTTTTCGCGCATGCGATACATATTTTA-3’，
PPR2: 5’-TTTTTTTTTTTTTTTTCATCTATTATGATATTTT TA-3’ ；
PPR3: 5’-TTTTTTTTTTTTGCACAAAAGTAATTGGGCCTTATA GTTGTTTA-3’
d. purification of SNaPshot PCR product:
adding SAP into the SNaPshot PCR product, shaking and uniformly mixing, preserving heat at 37 ℃ for 1 hour, and preserving heat at 75 ℃ for 15min to inactivate enzyme;
3) capillary electrophoresis: judging different genotypes of the three sites of each individual respectively;
the glycogen content of an individual, PPR1 site TT > TC > CC, PPR2 site TT > TC > CC, PPR3 site CC > TC > TT; the content of dominant genotype combination individuals of the three loci is obviously higher than that of the disadvantaged genotype combination individuals.
4. The method of claim 3, further comprising: meanwhile, glycogen content of 3 dominant genotype individuals is higher than that of a disadvantaged genotype, combined individuals are remarkably improved, parent scallops combined with the dominant genotypes are screened by the method and used for breeding oysters, wherein 3 dominant genotypes are provided, 3 sites of the dominant genotypes comprise PPR1 site TT, PPR2 site TT and PPR3 site CC which are all optimal bases corresponding to high glycogen content, and 3 sites of the disadvantaged genotype comprise PPR1 site, PPR2 site CC and PPR3 site TT corresponding to low glycogen content.
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