CN108546773B - Primer of SSR molecular marker for identifying flower color characters of red flower strawberries and application - Google Patents

Primer of SSR molecular marker for identifying flower color characters of red flower strawberries and application Download PDF

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CN108546773B
CN108546773B CN201810519506.1A CN201810519506A CN108546773B CN 108546773 B CN108546773 B CN 108546773B CN 201810519506 A CN201810519506 A CN 201810519506A CN 108546773 B CN108546773 B CN 108546773B
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雷家军
薛莉
丁言
代汉萍
宋雨桐
郑洋
毕晓颖
张莹莹
曲娜
关婧竹
赫嵩
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Abstract

The invention discloses a primer of SSR molecular markers for identifying flower color characters of red flower strawberries and application thereof, wherein the number of the primer of the SSR molecular markers is 4, and the primer is UgRFsr57622, UgRFsr94149, UgRFsr40142 and UgRFsr 54608; the invention obtains the specificity mark capable of marking the red flower (red, dark pink, pink and light pink) of the red line of the filial generation of the red strawberry. The method can conveniently and effectively distinguish white flowers from other colors in the period of the red flower strawberry seedlings, and greatly shortens the breeding period of the red flower strawberry.

Description

Primer of SSR molecular marker for identifying flower color characters of red flower strawberries and application
Technical Field
The invention belongs to the field of molecular biology, and particularly relates to a molecular marker for identifying flower color traits of red flower strawberries.
Background
Strawberry plants all bloom white flowers, and safflower strawberries (Pink-flowered strawberries) are intergeneric hybrids (Fragaria x Potentilla), and are novel perennial herbaceous flowers with both ornamental and edible properties (Mabberley, 2002). The safflower strawberry is popular with people due to the fact that the safflower strawberry has beautiful flower colors and edible fruits, has great market potential and economic value, and the price of the safflower strawberry is far higher than that of a common white strawberry cultivar (Bentvelsen and Bouw, 2006). At present, the breeding of new varieties of the red flower strawberries still depends on the traditional cross breeding method, the breeding period is long, at least 2-3 years are needed from cross to normal flowering and fructification of seedlings, and the colors of filial generations are obviously separated.
Disclosure of Invention
The technical problem to be solved by the invention is as follows: how to provide a method for rapidly identifying the flower color characters of filial generations of red flower strawberries.
The technical scheme of the invention is as follows: the SSR molecular marker primers for identifying the flower color traits of the red flower strawberries comprise 4 primers, namely UgRFsr57622, UgRFsr94149, UgRFsr40142 and UgRFsr 54608; wherein, the upstream nucleotide sequence of UgRFsr57622 is shown in SEQ ID No.1, and the downstream nucleotide sequence is shown in SEQ ID No. 2; the upstream nucleotide sequence of UgRFsr94149 is shown as SEQ ID No.3, and the downstream nucleotide sequence is shown as SEQ ID No. 4; the upstream nucleotide sequence of UgRFsr40142 is shown in SEQ ID No.5, and the downstream nucleotide sequence is shown in SEQ ID No. 6; the upstream nucleotide sequence of UgRFsr54608 is shown in SEQ ID No.7, and the downstream nucleotide sequence is shown in SEQ ID No. 8.
A kit for identifying the flower color traits of strawberry, which contains one or more of UgRFsr57622, UgRFsr94149, UgRFsr40142 or UgRFsr54608 primers.
The application of primers UgRFsr57622, UgRFsr94149, UgRFsr40142 or UgRFsr54608 of SSR molecular markers for identifying the flower color traits of red flower strawberries in identification of the flower color traits of strawberries.
The method for identifying the flower color characters of the red flower strawberry comprises the following steps:
(1) using UgRFsr57622, UgRFsr94149, UgRFsr40142 or UgRFsr54608 as primers, and performing PCR amplification by using strawberry DNA to be identified as a template;
(2) and (3) carrying out electrophoresis detection on the PCR amplification product: if the amplification product of the primer UgRFsr57622 simultaneously obtains products of 127bp and 165bp, the strawberry to be identified is the red flower strawberry; if the amplification product of the primer UgRFsr94149 obtains a 265bp product, the strawberry to be identified is a safflower strawberry; if the amplification product of the primer UgRFsr40142 obtains a 276bp product, the strawberry to be identified is a safflower strawberry; if the amplification product of the primer UgRFsr54608 obtains a product of 250bp, the strawberry to be identified is the red flower strawberry.
Compared with the prior art, the invention has the following beneficial effects:
the invention obtains the specificity mark capable of marking the red flower (red, dark pink, pink and light pink) of the red line of the filial generation of the red strawberry. The method can conveniently and effectively distinguish the white flowers from other colors in the seedling period, and greatly shortens the breeding period of the safflower strawberries.
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FIG. 1 schematic representation of transcriptome sequencing to SSR marker development;
fig. 2 is an agarose gel electrophoresis format in which a is an electrophoresis image of an amplification product of UgRFsr57622, b is an electrophoresis image of an amplification product of UgRFsr94149, c is an electrophoresis image of an amplification product of UgRFsr40142, and d is an electrophoresis image of an amplification product of UgRFsr 54608.
Detailed Description
Developing a specific SSR molecular marker related to the flower color characters of the red flower strawberry based on transcriptome sequencing, and specifically comprising the following steps:
safflower strawberry transcriptome sequencing
Selecting petals of all red flower-opened seedlings (6 plants) and white flower seedlings (6 plants) in the full-bloom period in filial generations of a safflower strawberry princess multiplied by Pink beautiful woman, and carrying out transcriptome sequencing. Petal total RNA is extracted by a CTAB method, and eukaryotic mRNA is enriched by magnetic beads with oligo (dT). Fragmenting buffer is added to break mRNA into short segments, the cracked short segments are used as templates, hexabasic random primers (random hexamers) are used for synthesizing a first cDNA chain, then buffer solution, dNTPs, RNase H and DNA polymerase I are added to synthesize a second cDNA chain, and AMPure XP beads are used for purifying double-stranded cDNA. The purified double-stranded cDNA is firstly added with A tail, the tail end is repaired and connected with a sequencing joint, and then AMPure XP beads are used for segment size selection and PCR amplification. And continuously purifying the PCR product by using AMPure XP beads to obtain a final sequencing library which is respectively named as PH _ R1, PH _ R2, PH _ W1 and PH _ W2. The constructed sequencing library was sequenced with Illumina HiSeqTM2500 to obtain 91835 non-redundant unigenes.
Second, SSR primer development
Based on 91835 unigenes obtained by sequencing a safflower strawberry transcriptome, 12077 unigenes containing SSR repeated primitives are found by using MISA software, the repeated primitives of the SSR are randomly selected to be SSR sequences with mononucleotide repetition times being more than or equal to 10, dinucleotide repetition times being more than or equal to 6, and trinucleotide repetition times being more than or equal to 5, and 105 SSR primers are designed by using software Primer 5.0. The principle of primer design is as follows: firstly, SSR sites do not exist in the primer; secondly, matching to obtain primers of the total Unigenes, wherein no more than three mismatches are at the 5 'end and no more than one mismatch is at the 3' end; keeping the only matched primers and discarding the multiple matched primers; fourthly, the length of the primer is 18-24 bp; the length of the PCR amplified fragment is 100-500 bp; sixthly, the SSR Finder verifies SSR (http:// www.fresnostate.edu/length /), and selects a both-hit primer.
Third, DNA extraction
The method comprises the following steps of (1) extracting the safflower strawberry genome DNA by a CTAB (cetyl triethyl ammonium bromide) method:
performing primer screening on hybrid progeny seedlings of Pingguo and Pingguojia people;
and selecting materials from filial generations of the Pingguo multiplied by Hanni, the beautiful woman multiplied by Hanni and the Pingguo multiplied by the beautiful woman to verify the molecular marker. The flower color of the filial generation can be divided into 5 kinds of flower colors: white, light pink, dark pink and red. And respectively taking fresh tender leaves of all filial generations as test materials.
(1) Preparing a DNA extraction buffer solution: 2% CTAB (PVP), lM Tris-HCl,0.5M EDTA (pH 8.0),5M NaCl and l0mg/mL of the enzyme RNAase.
(2) The safflower strawberry material is respectively treated as follows:
A. extraction: preheating 600 mu L CTAB +12 mu L beta-mercaptoethanol extract in a 65 ℃ water bath; rapidly grinding 1/3-volume fresh tender leaves in liquid nitrogen, transferring the powdery material into a 1.5mL centrifuge tube, adding preheated extracting solution 612. mu.L, keeping the temperature at 65 ℃ for 30min, taking out every other L0min, turning upside down and mixing uniformly;
B. extraction: an equal volume of 612. mu.L chloroform was added: isoamyl alcohol (24:1), mixing uniformly, centrifuging at 4 ℃ at 10000rpm/min for L0min, taking 500 mu L of supernatant, transferring into a new centrifuge tube, adding 500 mu L of chloroform/isoamyl alcohol (24:1) with the same volume, mixing uniformly, centrifuging at 10000rpm/min for L0min, extracting 250 mu L again, and putting into a new centrifuge tube with 1.5 mL; and (3) settling: adding 2 times volume of precooled absolute ethyl alcohol (-20 deg.C), turning upside down, mixing, placing in a refrigerator at-80 deg.C, settling for 20min, taking out, centrifuging at 10000rpm/min for 10min, and discarding the solution;
C. cleaning: after 350. mu.L of TE was added to dissolve (most of) the supernatant, the mixture was centrifuged at 10000rpm/min for 10min, 300. mu.L of the supernatant was taken out and put in 1.5mL of RNAase, and then 1. mu.L of RNAase was added in a 37 ℃ water bath for 45 min. The mixture was cooled to room temperature, 1/10 volumes (30. mu.L) of 3M NaAc and 2 volumes of absolute ethanol (660. mu.L) were added, and the mixture was allowed to stand at-70 ℃ for 30min by inversion. Taking out, centrifuging at 10000rpm/min for 10min, discarding the supernatant, adding 500 μ L70% anhydrous ethanol, washing at 8000rpm/min, and centrifuging for 3 min. Discarding the supernatant, adding 500 μ L70% anhydrous alcohol, cleaning with 8000rmp/min, and centrifuging for 3 min;
D. and (3) draining: pouring out ethanol, sucking the attached liquid as much as possible by using a liquid transfer gun, and putting the liquid on an ultraclean workbench for drying. Dissolving: after adding 45. mu.L of TE to dissolve the DNA, the DNA was stored by instantaneous centrifugation at-20 ℃.
E. And D, detecting the concentration of the DNA sample obtained in the step D by using an ultraviolet spectrophotometry method, and detecting the integrity of the DNA by using 1% agarose gel electrophoresis.
Fourth, genic-SSR primer screening
And selecting a combination (Pingyou multiplied by Pingyou) for transcriptome sequencing and filial generations of different colors for screening 105 pairs of SSR primers. PCR amplification with thermocycling (Veriti)TM96-well Thermal), 20. mu.L of PCR amplification reaction system: 2 XEs Taq Master Mix 10. mu.L (CWBIO, China; 2 XEs Taq Master Mix contains Es Taq DNA Polymerase,3Mm MgCl2And dNTP 400. mu. M), 10 ng. mu.L-1DNA 0.5μL,10μmol·L-1The upstream and downstream primers were each 0.8. mu.L, and the remainder was made up to 20. mu.L with sterile distilled water. PCR amplification procedure: pre-denaturation at 94 ℃ for 1 min; denaturation at 94 ℃ for 1min, annealing at optimal Tm for 2min, extension at 72 ℃ for 2min, 35 cycles; extension at 72 ℃ for 7 min. And (3) product detection: after the PCR product is electrophoretically separated on 8 percent polyacrylamide gel, the PCR product is observed and photographed after being dyed and developed, and the result is recorded, namely red and white4 pairs of primer pairs capable of amplifying bands with clear polymorphism for each flower color are used for the next step of verifying the specific primers of flower color characters.
Fifth, verifying specific genic-SSR primer
According to the results of the four analysis steps, the specificity of the primer is verified by the PCR reaction system and conditions in 3% (W/V) agarose gel by taking safflower, white flower, dark pink, pink and light pink in the offspring of different hybridization combinations as DNA templates.
The red flower phenotype can be observed visually after the plants bloom in the filial generation of the red strawberry. Therefore, the development of the trail-specific marker is helpful for the selection of the seedling stage and accelerates the breeding process of the new variety of the red flower strawberry. The 4 trap-specific marker markers obtained in this study, UgRFsr57622 (shown in SEQ ID No.1 and SEQ ID No. 2), UgRFsr94149 (shown in SEQ ID No.3 and SEQ ID No. 4), UgRFsr40142 (shown in SEQ ID No.5 and SEQ ID No. 6), and UgRFsr54608 (shown in SEQ ID No.7 and SEQ ID No. 8), were verified by electrophoresis on 3% agarose gel, and only UgRFsr57622 amplified to form a band in the white flower type, and the second bands in other flower type plants were significantly amplified (a in FIG. 2); the UgRFsr94149 and UgRFsr40142 primer pairs amplified a single band (b and c in FIG. 2) in the phenotype of colored flowers (red, dark pink, pink and light pink), while the UgRFsr54608 primer pair amplified not only one band but also a secondary band (d in FIG. 2) in the phenotype of colored flowers, and the 3 primers did not express no amplified band in all the phenotypes of white flowers.
To further determine the polymorphism of the microsatellite sequence, 4 primer codominant isolates were recovered and sequenced after TA cloning. The result shows that the sequence is consistent with the original sequence, and the developed 4 pairs of SSR character specific markers have high specificity.
Table 14 specific primer sequences cosegregating with flower color characters of strawberry
Figure BDA0001674467040000041
Figure BDA0001674467040000051
The above-mentioned embodiments only express the specific embodiments of the present application, and the description thereof is more specific and detailed, but not construed as limiting the scope of the present application. It should be noted that, for those skilled in the art, without departing from the technical idea of the present application, several changes and modifications can be made, which are all within the protection scope of the present application.
Sequence listing
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Claims (5)

1. The primers of the SSR molecular markers for identifying the flower color traits of the filial generations of the red flower strawberry are characterized by comprising 4 primers, namely UgRFsr57622, UgRFsr94149, UgRFsr40142 and UgRFsr 54608; wherein, the upstream nucleotide sequence of UgRFsr57622 is shown in SEQ ID No.1, and the downstream nucleotide sequence is shown in SEQ ID No. 2; the upstream nucleotide sequence of UgRFsr94149 is shown as SEQ ID No.3, and the downstream nucleotide sequence is shown as SEQ ID No. 4; the upstream nucleotide sequence of UgRFsr40142 is shown in SEQ ID No.5, and the downstream nucleotide sequence is shown in SEQ ID No. 6; the upstream nucleotide sequence of UgRFsr54608 is shown in SEQ ID No.7, and the downstream nucleotide sequence is shown in SEQ ID No. 8.
2. A kit for identifying a floral character of a progeny of a safflower strawberry cross, comprising a mixture of one or more of the UgRFsr57622, UgRFsr94149, UgRFsr40142 or UgRFsr54608 primers of claim 1.
3. The application of the SSR molecular marker primer for identifying the flower color traits of the filial generations of red flower strawberries in the identification of the flower color traits of the strawberries, which is disclosed by claim 1; the hybrid generation of the safflower strawberry is the filial generation of 'Pink princess x Pink woman', 'Pink princess x Hani', 'Qiao Jia xHani' or 'Pink princess x Qiao Jia'.
4. The method for identifying the flower color characters of the filial generation of the red flower strawberry is characterized by comprising the following steps of:
(1) performing PCR amplification using UgRFsr57622, UgRFsr94149, UgRFsr40142 or UgRFsr54608 described in claim 1 as primers and strawberry DNA as a hybrid progeny to be identified as "Pinggu princess XPing", "Pinggu princess XHani", "pretty woman XHani" or "Pinggu princess Xpretty woman";
(2) and (3) carrying out electrophoresis detection on the PCR amplification product: if the amplification product of the primer UgRFsr57622 simultaneously obtains products of 127bp and 165bp, the strawberry to be identified is the red flower strawberry; if the amplification product of the primer UgRFsr94149 obtains a 265bp product, the strawberry to be identified is a safflower strawberry; if the amplification product of the primer UgRFsr40142 obtains a 276bp product, the strawberry to be identified is a safflower strawberry; if the amplification product of the primer UgRFsr54608 obtains a product of 250bp, the strawberry to be identified is the red flower strawberry.
5. The method for identifying the flower color trait of the progeny of a safflower strawberry hybrid according to claim 4, wherein a PCR amplification reaction system is 20 μ L: 2 XEs Taq Master Mix 10. mu.L, 10 ng. mu.L-1DNA0.5μL,10μmol·L-1The upstream primer and the downstream primer are respectively 0.8 mu L, and the rest is supplemented to 20 mu L by sterile distilled water; PCR amplification procedure: pre-denaturation at 94 ℃ for 1 min; denaturation at 94 ℃ for 1min, annealing at 58 ℃ for 2min, extension at 72 ℃ for 2min, and 35 cycles; extension at 72 ℃ for 7 min.
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