CN110747282B

CN110747282B - Low-salt-resistant molecular marker C22 of portunus trituberculatus and application thereof

Info

Publication number: CN110747282B
Application number: CN201911213455.0A
Authority: CN
Inventors: 吕建建; 张文; 金玲; 刘萍; 李健
Original assignee: Yellow Sea Fisheries Research Institute Chinese Academy of Fishery Sciences
Current assignee: Yellow Sea Fisheries Research Institute Chinese Academy of Fishery Sciences
Priority date: 2019-12-02
Filing date: 2019-12-02
Publication date: 2021-06-08
Anticipated expiration: 2039-12-02
Also published as: CN110747282A

Abstract

The invention provides a low-salt-resistant molecular marker C22 of portunus trituberculatus and application thereof. The nucleotide sequence of the molecular marker C22 is shown as SEQ ID No.1, and the nucleotide sequence of the primer pair for detecting the molecular marker C22 is shown as SEQ ID No.2 and SEQ ID No. 3. The molecular marker C22 is an SNP marker, and the low-salt tolerance genotype of the molecular marker is a CC genotype. The molecular marker C22 provided by the invention can not be limited by the growth stage of the portunus trituberculatus, is used for accelerating the breeding process of the portunus trituberculatus and quickly breeding the crab species with the excellent low-salt resistance, is beneficial to the healthy culture and sustainable development of the portunus trituberculatus, and has wide application prospect.

Description

Low-salt-resistant molecular marker C22 of portunus trituberculatus and application thereof

Technical Field

The invention belongs to the technical field of DNA molecular markers, and particularly relates to a low-salt-resistant molecular marker C22 of portunus trituberculatus and application thereof.

Background

Portunus trituberculatus (Portugulus trituberculatus) belongs to Crustacea, decapod, Paralithodes, and Paralithodes, commonly called Portunus trituberculatus, and is an important large-scale marine economic crab in China. The swimming crabs are delicious in meat quality and rich in nutrition, enjoy full names at home and abroad, and are deeply loved by consumers. The adaptive salinity of the portunus trituberculatus is 20-35, however, as the portunus trituberculatus is mainly cultured in an outdoor pond or a beach purse net, the salinity of culture water is often suddenly reduced under the influence of factors such as heavy rain, the ingestion rate, the metamorphosis rate and the survival rate of young crabs are obviously reduced, and the normal molting and growth of adult crabs are also influenced. Therefore, the low-salt resistance is one of important breeding traits of the portunus trituberculatus, and has important significance for improving the culture rate and promoting the culture and popularization of the portunus trituberculatus in low-salt sea areas. However, the low-salt-resistant character has an obvious low heritability characteristic, the inheritance of the traditional breeding method is slowly progressed, an advanced molecular marker-assisted breeding technology is urgently needed to accelerate the breeding process, and the identification and innovative application of the low-salt-resistant molecular marker are necessary preconditions and ways for developing molecular marker-assisted breeding.

The molecular marker is a genetic marker based on nucleotide sequence variation of genetic materials among individuals, and is a direct reflection of DNA level genetic polymorphism. The molecular marker has remarkable advantages: most molecular markers are co-dominant, and selection of recessive characters is very convenient; the genome variation is extremely abundant, and the number of molecular markers is almost unlimited; the DNA of different tissues at different stages of biological development can be used for marking analysis; the molecular marker is simple and rapid to detect. At present, the research on the development of low-salt-resistant molecular markers of the portunus trituberculatus is less, and the industry lacks markers applicable to molecular marker-assisted breeding. Therefore, the development of the low-salt-resistant molecular marker has important significance for the healthy culture and breeding of the blue crabs.

Disclosure of Invention

The invention provides a low-salt-resistant molecular marker C22 of portunus trituberculatus and application thereof, the invention utilizes the methods of polymorphic site filtration, comparison analysis and PCR sequencing of sequencing data to obtain SNP and InDel markers, and a new low-salt-resistant molecular marker C22 of portunus trituberculatus is finally obtained through the gradual screening and verification of the markers, and the molecular marker is favorable for screening the low-salt-resistant character of the portunus trituberculatus.

In order to realize the purpose of the invention, the invention adopts the following technical scheme to realize:

the invention provides a low-salt-resistant molecular marker C22 of Portunus trituberculatus, and the nucleotide sequence of the molecular marker C22 is shown in SEQ ID No. 1.

Further, the molecular marker C22 is an SNP marker.

Further, the low salt tolerance genotype of the molecular marker C22 is CC genotype.

The invention also provides a primer pair for detecting the molecular marker C22 as claimed in claim 1, wherein the nucleotide sequence of the forward primer in the primers is shown as SEQ ID No.2, and the nucleotide sequence of the reverse primer is shown as SEQ ID No. 3.

The invention also provides application of the molecular marker C22 in screening low-salt tolerant varieties of blue crabs.

The invention also provides application of the molecular marker C22 in genetic diversity analysis, germplasm identification and genetic map construction of the blue crab.

Compared with the prior art, the invention has the following advantages and beneficial effects:

1. the low-salt-tolerant molecular marker C22 of the portunus trituberculatus provided by the invention can not be limited by the growth stage of the portunus trituberculatus, and can be used for breeding early-stage crab seedlings of the portunus trituberculatus, so that the breeding process of the portunus trituberculatus is obviously accelerated, and the crab seeds with excellent low-salt-tolerant characters are rapidly bred.

2. The molecular marker C22 provided by the invention is used for detecting the low-salt-resistant character of the portunus trituberculatus, the method is accurate and reliable, the operation is simple, the character meeting the requirements can be effectively and quickly screened, early breeding is assisted, the low-salt-resistant portunus trituberculatus variety is bred in a short time and at low cost, the number of the portunus trituberculatus with excellent quality is increased, the ingestion rate, the metamorphosis rate and the breeding rate of the portunus trituberculatus juvenile crabs are improved, the yield of the portunus trituberculatus is further improved, the healthy breeding of the portunus trituberculatus is promoted, and the method has wide application prospect and is suitable for being popularized in.

Drawings

FIG. 1 shows the result of gel electrophoresis of mixed template PCR products according to the present invention.

FIG. 2 shows the difference between the two groups of corresponding positions of the sensitive population mixed template and the resistant population mixed template according to the present invention.

FIG. 3 is the result of gel electrophoresis band of the product of PCR amplification with two sets of primers with obvious position difference corresponding to the screened sensitive population mixed template and the screened resistant population mixed template.

Detailed Description

The technical solution of the present invention will be described in further detail with reference to specific examples.

The blue crabs used in the invention are all from the experimental base of Changyi Haifeng aquatic products Limited company of yellow sea aquatic product research institute of Chinese academy of aquatic science, healthy and active blue crabs are randomly obtained from a pond by a trawl fishing method, are temporarily placed in a net basket and are paved with a layer of waterweeds to prevent crab fighting, and finally 300 blue crabs with the weight of 35 g and 3g are obtained and are placed in 4 culture ponds (500cm multiplied by 300cm multiplied by 150cm) for temporary culture for 7d, the water temperature is kept at 22 soil and 1 ℃, water is added to 20cm, the salinity is 33 per thousand, the pH value is 8.2 +/-0.5, oxygen is continuously supplied, fresh seawater is replaced at 8 o 'clock each day, fresh trash fish is fed at 5 o' clock in the afternoon, and the feeding amount is about 1/3 of the total weight of the crabs. And 7d, selecting the portunids with better vitality and shape for subsequent experiments.

During formal experiments, crabs with vigorous activity and perfect body surfaces are placed in 4 cement pools, 50 crabs in each pool are used, the salinity of seawater is firstly regulated to 11ppt by fresh water, the pH of a water body is 7.9, 0.5 of soil, the water temperature is kept at 22, 1 and 1 ℃, and the water depth is 20 cm. Feeding fresh trash fish at 5 pm with 1/4 of crab weight to ensure no bait residue on the bottom of the pond and influence water quality. The death time and number of crabs are recorded every 3h in the first 48h, 1/4 seawater is discharged after 48h, and fresh water is added to adjust the salinity to 8ppt again, wherein the pH of the water body is 7.7 +/-0.5, and the water temperature is kept at 22-soil 1 ℃. The death time and number were continuously recorded every 3h, and the experiment was stopped until the number of surviving crabs in 4 pools was 20. The first 20 individuals who died were low salt sensitive (0 h), the last 20 individuals who survived were low salt tolerant (72 h), and muscle tissue was dissected out in a cryovial and stored in liquid nitrogen.

Example 1

Screening of candidate molecular markers with low salt tolerance

1. Sequencing data filtering and alignment

DNA extraction is carried out by adopting a kit of the whole gold company and by utilizing the principle that silica gel membrane centrifugal columns specifically adsorb DNA. First, approximately 30mg of a tissue sample was put into a 1.5ml sterile enzyme centrifuge tube, 200. mu.l of lysine Buffer 8(LB8) and 20. mu.l of RNaseA (10mg/m1) were added, the mixture was incubated at room temperature for about 10 seconds with shaking for 2min, 20. mu.l of protease K (20mg/m1) was added, the mixture was mixed well with shaking, incubated at 55 ℃ until the mixture was completely lysed, Binding Buffer 8(BB8) was added in a volume 1.5 times the volume of the mixture, the mixture was added to a centrifugal column, centrifuged at 12000rpm in a high-speed low-temperature refrigerated centrifuge (model Eppendorf 5804R) for 30 seconds, and the waste liquid was discarded. Then 500. mu.l of Clean Buffer 8(CB8) was added, centrifuged at 12000rpm for 30s, the waste liquid was discarded (repeated), 500. mu.l of Wash Buffer 8(WB8) was added, centrifuged at 12000rpm for 30s, the waste liquid was discarded (repeated), and the mixture was left to stand at 12000rpm for 2min to completely remove the remaining WB 8. The column was placed in a clean centrifuge tube, 50. mu.l of Elution Buffer (EB) was added to the center of the column, and the column was allowed to stand at room temperature for 2min, centrifuged at 12000rpm for 1min, and the DNA was eluted. DNA purity and integrity was analyzed by agarose gel electrophoresis; the purity of the DNA (OD260/280 ratio) was measured by Nanodrop, and the DNA concentration was precisely quantified by Qubit.

DNA samples qualified in the test are equivalently mixed into two mixing pools which are named as a low-salt sensitive DNA mixing pool (SG) and a low-salt tolerant DNA mixing pool (TG) respectively. Randomly breaking a mixed DNA sample into fragments with the length of 350bp by a Covaris crusher, constructing a Library by adopting a TruSeq Library Construction Kit, and completing the preparation of the whole Library by the steps of end repair, ployA tail addition, sequencing joint addition, purification, PCR amplification and the like of the DNA fragments. The constructed library was sequenced by illumina hiseq PE 150. And filtering Raw reads obtained by sequencing to obtain Clean reads for subsequent analysis, wherein the sequencing data result is shown in table 1.

TABLE 1 summary of sequencing data quality

The filtered effective data are compared by Burrows-Wheeler alignment tool (BWA) software, and the comparison result is subjected to SAMTOOLS to remove duplication. The comparison result shows that the comparison rate of all samples is more than 85%, the average sequencing depth is more than 25X, and the method can be used for subsequent analysis.

2. Marker detection and annotation

SNP and InDel are detected by a UnifiedGentyper module in Genome analysis toolkit 3.8(GATK) software, with SNP filtration parameters set as: MQ is less than 40, QD is less than 4, FS is more than 60; the InDel filtration parameters were set to QD < 4, FS > 200, and the total number of SNPs and InDel markers obtained was 369,229.

3. SNP and InDel frequency difference analysis

And respectively analyzing and calculating SNP-index and InDel-index of two groups of individuals at each site, and filtering polymorphic sites, wherein the filtering standard is as follows:

(1) the SNP/InDel-index frequencies in the two groups of individuals are less than 0.3;

(2) the sites of SNP/InDel deletion in one individual were filtered out.

And simultaneously calculating the frequency difference distribution of SNP and InDel, wherein the directions are as follows: and (delta) (index) is index (low salt tolerance character) -index (low salt sensitivity character), sites with the delta index smaller than 0.3 are filtered, 100 SNPs and 95 InDel which are different among groups are finally obtained, the SNPs and the InDel are all low salt tolerance related candidate molecular markers, and the statistics of the results of the candidate SNPs and the InDel are shown in Table 2.

TABLE 2 SNPs and InDel detection and annotation statistics

4. Marker screening

And screening candidate SNP and InDel markers, and selecting a site with All-index close to 0 in the individual or selecting a site with All-index close to 1 in the individual as a preferential selection site for next verification. The screening criteria were as follows:

(1) according to the annotation information of SNP loci, on the basis of sorting from high to low according to delta index, loci of synonymous, non-synonymous mutation or upstream and downstream regions are preferentially selected;

(2) according to the annotation information of InDel sites, sites with more than 5 inserted or deleted bases are preferentially selected on the basis of the order from high to low according to Delta index.

Finally, the markers with large frequency difference before and after low salt stress are screened out, and 39 SNP markers and 37 InDel markers are screened out in total.

Second, verification of low-salt-resistant related molecular marker

The method for sequencing the PCR products is adopted to verify the low-salt-resistance related candidate molecular markers in SG and TG populations:

(1) firstly, designing primers on flanking sequences of marker sites, wherein at least one primer is more than 70bp away from the marker sites;

(2) carrying out PCR amplification by using the designed primers and SG and TG mixed DNA materials as templates respectively, sequencing the PCR products successfully amplified, and selecting the primer far away from the marking site as a sequencing primer;

(3) analyzing the sequencing peak map by using ContigExpress software, selecting two groups of SG and TG with relatively large difference marks in the sequencing peak maps at corresponding positions, and continuing to perform PCR amplification and sequencing analysis on the individual DNA template;

(4) the genotype of each individual was counted from the sequencing results and analyzed by SPSS software whether the markers were associated with low salt tolerance.

The specific operation steps are as follows:

1. PCR amplification

The PCR system of the invention is as follows: template 1. mu.l, forward primer (10. mu.M) 0.2. mu.l, reverse primer (10. mu.M) 0.2. mu.l, Buffer 1. mu.l, dNTPs 0.8. mu.l, HiFi 0.2. mu.l, ddH₂O 6.6μl。

After the sample is added according to the system, PCR amplification is carried out according to the following reaction conditions: pre-denaturation at 94 deg.C for 2-5 min; denaturation at 94 ℃ for 30s, annealing at 56 ℃ for 30s, extension at 72 ℃ for 1-2kb/min, repeating for 35 cycles; finally, extending the temperature of 72 ℃ for 5-10 min; storing at 4 ℃.

2. Electrophoretic detection

Preparing 1% electrophoresis gel by agarose, mixing agarose and TAE in a certain proportion, heating the mixture in a microwave oven until the mixture is dissolved into colorless transparent liquid, pouring the colorless transparent liquid into a gel-making mould, inserting a comb, standing for 20min for solidification, then pulling out the comb, putting the agarose gel into a horizontal electrophoresis tank, arranging a sample application hole at a negative electrode, taking 0.5% TAE as a buffer solution, selecting Genegeen as a nucleic acid coloring agent, sucking 3ul of PCR products of a mixed template out of a sample hole by a liquid-transferring gun, adjusting voltage and current to 120V and 60mA respectively, setting the time to be 30min for carrying out gel electrophoresis, stopping when a dyeing zone strip reaches 2/3, observing and photographing and recording by a gel imaging system after the electrophoresis is finished, selecting a bright sample with a single strip, sending the sample to a producer for DNA sequencing, carrying out data image analysis on a returned sequencing result, selecting two groups of the markers with obvious sequencing difference at corresponding positions for carrying out individual PCR amplification, the amplification products were also subjected to gel electrophoresis and the PCR products were sequenced.

3. Statistical analysis

Selecting a band (shown in figure 1) meeting the requirement according to the position and the brightness of the gel electrophoresis band of the mixed template PCR product, and selecting 11 pairs of SNP primers and 12 pairs of InDel primers to carry out sequencing analysis continuously.

Analyzing the sequenced peak map by using contigeexpress software, selecting a primer (shown in figure 2) with obvious position difference corresponding to the sequenced peak map of the mixed template of the sensitive and tolerant groups, continuously using the primer to perform PCR amplification by taking an individual as a template, keeping the amplification condition unchanged, then selecting a strip with the consistent size and brightness, sending the strip to be sequenced (shown in figure 3), re-amplifying the strip with poor amplification effect for complementing, and selecting 10 SNP markers and 5 InDel marker primers for continuous sequencing analysis.

And observing the returned individual sequencing result by using contig software, introducing the genotype information into SPSS software, calculating a P value by using a chi-square test method, selecting primers with the P value less than 0.05, and finally verifying 2 SNP markers in total.

As shown in table 3, it can be seen that the genotype CC accounts for 50% or more of 72h (susceptible population) in C22_1599467 (C22 for short), and the genotype TT accounts for 50% or more of 0h (sensitive population), and the data P of the genotype TT is significantly different from 0.019, and thus the genotype CC is considered to be a low-salt-tolerant genotype at this site. The nucleotide sequence of the C22 molecular marker is shown as SEQ ID No.1, the length is 601bp, wherein the amplification primers for developing the molecular marker are shown as SEQ ID No.2 and SEQ ID No.3 (Table 4).

TABLE 3 genotype results for the C22 molecular marker

TABLE 4 amplification primers for molecular markers

The molecular marker C22 obtained by the invention can be used for assisting in breeding low-salt-resistant varieties of portunus trituberculatus, and the application steps are simply as follows: extracting DNA of a portunus trituberculatus test sample and using the DNA as a template, carrying out PCR amplification by using amplification primers C22-F and C22-R of a molecular marker C22, sequencing the PCR product, and selecting the test sample as a parent for cultivating a low-salt-resistant variety of the portunus trituberculatus if the genotype of C22 in the sequencing result is CC. In addition, the molecular marker C22 can be used for analyzing the genetic diversity of the blue crab, identifying the germplasm and constructing the genetic map of the blue crab.

The above examples are only intended to illustrate the technical solution of the present invention, but not to limit it; although the present invention has been described in detail with reference to the foregoing embodiments, it will be apparent to those skilled in the art that various changes may be made and equivalents may be substituted for elements thereof; and such modifications or substitutions do not depart from the spirit and scope of the corresponding technical solutions.

Sequence listing

<110> research institute for aquatic products in yellow sea of China institute for aquatic science

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Claims

1. The low-salt-resistant molecular marker C22 of the portunus trituberculatus is characterized in that the nucleotide sequence of the molecular marker C22 is shown as SEQ ID No.1, wherein the 301 th base is C or T.

2. The use of the molecular marker C22 of claim 1 in screening low-salt resistant varieties of Portunus trituberculatus.