CN107177691B - SNP marker and its detection method for assisted Selection cotton excellent parent genetic background - Google Patents

SNP marker and its detection method for assisted Selection cotton excellent parent genetic background Download PDF

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CN107177691B
CN107177691B CN201710577285.9A CN201710577285A CN107177691B CN 107177691 B CN107177691 B CN 107177691B CN 201710577285 A CN201710577285 A CN 201710577285A CN 107177691 B CN107177691 B CN 107177691B
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genetic background
cotton
assisted selection
snp
excellent parent
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CN107177691A (en
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李威
杨代刚
孙宽
周晓箭
马雄风
裴小雨
刘艳改
张飞
贺昆仑
王振玉
张文生
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Institute of Cotton Research of Chinese Academy of Agricultural Sciences
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Abstract

The present invention relates to strong advantage hybrid cotton excellent parent detection fields, in particular to are used for the SNP marker and its detection method of assisted Selection cotton excellent parent genetic background.It is following any one or more of: the CC of 4947923 positions bp on TT, D11 chromosome of 30704984 positions bp on TT, D05 chromosome of 35924124 positions bp on AA, D03 chromosome of 81174157 positions bp on GG, A12 chromosome of 1824659 positions bp on A06 chromosome for the SNP marker of assisted Selection cotton excellent parent genetic background.The SNP marker provided by the invention, analyzes to obtain by high-flux sequence, is identified that the method is simple and quick using HRM technology, and qualification result is reliable and stable, increases substantially the efficiency of selection and accuracy of genetic background, the significant cultivation age limit for shortening excellent parent.

Description

SNP marker and its detection for assisted Selection cotton excellent parent genetic background Method
Technical field
The present invention relates to strong advantage hybrid cotton excellent parent detection fields, in particular to for assisted Selection cotton The SNP marker and its detection method of excellent parent genetic background.
Background technique
Hybrid vigour is a kind of generally existing phenomenon of nature.From Shull be put forward for the first time the concept of " hybrid vigour " with Come, scientists from all over the world are successively studied and inquired into crop heterosis.Now, hybrid vigour obtains on many crops Extensive utilization is arrived, heterosis utilization is one of the core technology that yield is increased substantially in Crop Genetic Breeding.
Cotton is a kind of significant industrial crops.It was verified that persistently formulating and promoting strong advantage cotton crossbreed It is one of to increase substantially output of cotton, improve fiber quality and enhance the main path of cotton variety adaptability.Strong advantage is miscellaneous The key for handing over cotton new varieties to be bred as is to cultivate the excellent parent that coordinate force is high, Comprehensive Traits are good.But in recent years due to breeding Technology and methods innovate the reasons such as deficiency, and excellent parent is cultivated and improvement is increasingly difficult to, and lead to the kind that Heterosis is strong It is fewer and fewer.The study found that excellent parent has excellent genetic background, can be continued by the technologies such as hybridizing and being returned Improvement, can derive a series of new excellent parent, and then efficient cultivate a series of strong advantage hybrid cotton varieties.But It is, due to that can only identify at present using cumbersome field character observation, to select the genetic background of excellent parent in improved, process Low efficiency, breeding year limit for length, time-consuming, and character is affected by environment larger, be easy to cause misjudgment, so as to cause Cultivate failure.
In view of this, the present invention is specifically proposed.
Summary of the invention
The first object of the present invention is to provide the SNP marker for assisted Selection cotton excellent parent genetic background, be somebody's turn to do Label is analyzed to obtain by high-flux sequence, provides basis to stablize effectively identification cotton excellent parent.
The second object of the present invention is to provide drawing for the SNP marker for assisted Selection cotton excellent parent genetic background Object pair, the primer pair are obtained by screening after high-flux sequence analysis, design, and high specificity can be stablized and effectively identify cotton Excellent parent.
The third object of the present invention is to provide the examination of the SNP marker for assisted Selection cotton excellent parent genetic background Agent box, the kit provide convenience for the identification of cotton excellent parent.
The fourth object of the present invention is to provide the inspection of the SNP marker for assisted Selection cotton excellent parent genetic background Survey method, this method are identified that the method is simple and quick by molecular level, and qualification result is reliable and stable.
In order to realize above-mentioned purpose of the invention, the following technical scheme is adopted:
For the SNP marker of assisted Selection cotton excellent parent genetic background, the SNP marker is any one of following It is or a variety of: AA, D03 dyeing of the position 81174157bp on GG, A12 chromosome of the position 1824659bp on A06 chromosome On TT, D11 chromosome of the position 30704984bp on TT, D05 chromosome of the position 35924124bp on body The CC of the position 4947923bp.
Provided by the present invention for the SNP marker of assisted Selection cotton excellent parent genetic background, pass through high-flux sequence Analysis obtains, and provides basis to stablize effectively auxiliary identification cotton excellent parent.
It should be noted that SNP refers to single base mutation, refer to a site, and GG, AA, TT, CC in the present invention are indicated The a certain site of two homologues indicates that the site is homozygous site;This five sites i.e. in the present invention are homozygosis Site.
The present invention also provides the primer pairs of the SNP marker for assisted Selection cotton excellent parent genetic background, including Following primer pair is any one or more of;
The upstream and downstream nucleic acid sequence of Gh_A06G0169_SNP primer pair as shown in SEQ ID No.1 and SEQ ID No.2, The upstream and downstream nucleic acid sequence of Gh_A12G1857_SNP primer pair is as shown in SEQ ID No.3 and SEQ ID No.4, Gh_ The upstream and downstream nucleic acid sequence of D03G1074_SNP primer pair is as shown in SEQ ID No.5 and SEQ ID No.6, Gh_D05G2790_ The upstream and downstream nucleic acid sequence of SNP primer pair is as shown in SEQ ID No.7 and SEQ ID No.8, Gh_D11G0580_SNP primer pair Upstream and downstream nucleic acid sequence as shown in SEQ ID No.9 and SEQ IDNo.10.
The present invention is derivative multiple in the excellent parents breeding pedigrees such as strong advantage hybrid cotton nakamise 63 by analyzing Excellent parent material genome weight sequencing data, develops for the excellent parents genetic background such as assisted Selection nakamise 63 SNP marker can increase substantially the efficiency of selection and accuracy of genetic background, the significant cultivation age limit for shortening excellent parent.
Provided by the present invention for the primer pair of the SNP marker of assisted Selection cotton excellent parent genetic background, Ke Yiwei Any one in above-mentioned primer pair, or any two kinds, three kinds any, any four, or for all, certainly, mirror The primer used when determining is more, then qualification result is more definite.
Further, the cotton excellent parent include the anti-cotton in Hubei Province No. 9, in 309,9053, in 9018,1638.
The present invention also provides the kits of the SNP marker for assisted Selection cotton excellent parent genetic background, contain Above-mentioned primer pair.I.e. in the kit, any one in above-mentioned primer pair can be contained, or any two kind, times Meaning three kinds, any four, or for all.
The kit be for assisted Selection cotton excellent parent genetic background SNP marker carry out convenience is provided.
The present invention also provides the detection methods of the SNP marker for assisted Selection cotton excellent parent genetic background, adopt With above-mentioned primer pair, the detection of molecular level is carried out to the genome of cotton to be detected.
Above-mentioned primer pair at this is any one or more of above-mentioned primer pair.
Further, the detection of the molecular level are as follows: the genome of kind to be detected is first subjected to PCR amplification, then Carry out HRM detection.
Further, annealing temperature used in the PCR amplification is 59 ± 1 DEG C.The annealing temperature, the product expanded High specificity, miscellaneous band are few.PCR amplification program is using conventional program.
Such as PCR amplification program are as follows: 94-95 DEG C initial denaturation 3-5 minutes;94 DEG C are denaturalized 30 seconds;60 DEG C are annealed 30 seconds;72 DEG C are prolonged It stretches 30 seconds;35-45 circulation;72 DEG C extension 5-10 minutes;4 DEG C of product preservations.
Further, PCR reaction system used in the PCR amplification is 10-25 μ L, preferably 20 μ l.Such as PCR of the present invention Amplification PCR reaction system used can be 10 μ L, 15 μ L, 20 μ L, 25 μ L etc..
If PCR reaction system is 20 μ L, specific ingredient is as follows:
10 μ l Master Mix, 5 μ l 10 μ g/mL DNA, each 0.5 μ l, 1.6-2.4 μ lMgCl of upstream and downstream primer2, add PCR-grade H2O is supplied to 20 μ l.
The volume of other reaction systems, each ingredient are expanded or shunk accordingly or are added i.e. according to conventional system It can.
Further, the content of the template DNA in the PCR reaction system is not less than 5ng, preferably 5-30ng.Such as this The content for inventing the template DNA in PCR reaction system can be 5ng, 10ng, 20ng, 25ng, 30ng etc..
Further, the recurring number of the PCR amplification is 30-45, preferably 35-45.Such as the circulation of PCR amplification of the present invention Number can be 30,35,38,40,42,45 etc..
Amplify sample DNA by certain PCR amplification, melts test convenient for subsequent high-resolution.
Further, extraction material used in the genome of cotton to be detected is the kernel of cotton to be detected.It is by the cotton The seed decladding of floral material obtains.
Compared with prior art, the invention has the benefit that
(1) it provided by the present invention for the SNP marker of assisted Selection cotton excellent parent genetic background, is measured by high pass Sequence is analyzed to obtain, and provides basis to stablize effectively identification cotton excellent parent.
(2) provided by the present invention for the primer pair of the SNP marker of assisted Selection cotton excellent parent genetic background, pass through It screens and obtains after high-flux sequence analysis, design, high specificity can stablize effectively identification cotton excellent parent.
It (3) is cotton provided by the present invention for the kit of the SNP marker of assisted Selection cotton excellent parent genetic background The identification of flower excellent parent provides convenience.
It (4), should provided by the present invention for the detection method of the SNP marker of assisted Selection cotton excellent parent genetic background Method is identified that the method is simple and quick by molecular level, and qualification result is reliable and stable, increases substantially the choosing of genetic background Efficiency and accuracy are selected, the significant cultivation age limit for shortening excellent parent.
Detailed description of the invention
In order to more clearly explain the embodiment of the invention or the technical proposal in the existing technology, to embodiment or will show below There is attached drawing needed in technical description to be briefly described.
Fig. 1 is the breeding family tree of the excellent parent provided in the embodiment of the present invention 1;
Fig. 2 is the initial data scatter plot that 5 excellent parents provided in the embodiment of the present invention 2 are sequenced;
Fig. 3 is the valid data scatter plot that 5 excellent parents provided in the embodiment of the present invention 2 are sequenced;
Fig. 4 is that the 5 excellent parent sequencing datas provided in the embodiment of the present invention 2 are compared to the ratio on reference genome Scatter plot;
Fig. 5 is that the 5 excellent parent sequencing datas provided in the embodiment of the present invention 2 are compared to the covering on reference genome Depth scatter plot;
Fig. 6 is the SNP site ratio pie chart detected in 5 excellent parents provided in the embodiment of the present invention 2;
Fig. 7 be in the embodiment of the present invention 35 excellent parents providing and TM-1 with Gh_A06G0169_SNP primer pair into Capable HRM curve graph;
Fig. 8 be in the embodiment of the present invention 35 excellent parents providing and TM-1 with Gh_A12G1857_SNP primer pair into Capable HRM curve graph;
Fig. 9 be in the embodiment of the present invention 35 excellent parents providing and TM-1 with Gh_D03G1074_SNP primer pair into Capable HRM curve graph;
Figure 10 be in the embodiment of the present invention 35 excellent parents providing and TM-1 with Gh_D05G2790_SNP primer pair into Capable HRM curve graph;
Figure 11 be in the embodiment of the present invention 35 excellent parents providing and TM-1 with Gh_D11G0580_SNP primer pair into Capable HRM curve graph.
Specific embodiment
Embodiment of the present invention is described in detail below in conjunction with embodiment, but those skilled in the art will Understand, the following example is merely to illustrate the present invention, and is not construed as limiting the scope of the invention.It is not specified in embodiment specific Condition person carries out according to conventional conditions or manufacturer's recommended conditions.Reagents or instruments used without specified manufacturer is The conventional products that can be obtained by commercially available purchase.
Embodiment 1
The breeding pedigree of the strong advantage hybrid cotton varieties of the series such as nakamise 63
E Kangmian 9 (primary number: chaste tree 55173) is derived from [Hubei Province chaste tree No. 1 × (middle 7263+MO-3)], in 1999 and 2001 Year is successively authorized by Hubei and two province of Hunan, (Yangtze river basin cotton region) is authorized by national within 2001, in Yangtze river basin cotton region Show stable high yield (knot bell is strong and uniform, ginning outturn is high), high-quality, mostly anti-(anti-blight, resistance to verticillium wilt, anti-cotten aphid etc.).With E Kangmian 9 establish excellent parent breeding pedigree using the methods of systematic breeding or crossbreeding for basic breeding material, 309 in persistently having formulated, 9053, in a series of excellent parents such as 9018 and 1638, bell weight, bell number, ginning outturn and son are referred to etc. and produced Amount correlated traits has carried out different degrees of improvement respectively, and inherits the genetic background of the anti-cotton in Hubei Province No. 9.Further by matching Cross combination is set, these excellent parents cultivate nakamise 62, nakamise 63, nakamise 65, nakamise 66 respectively as female parent With the strong advantage hybrid cotton varieties of the equal series of nakamise 71, pass through country or provincial authorization respectively.Specific breeding pedigree is such as Shown in Fig. 1.
Embodiment 2
The strong advantage hybrid cotton varieties genetic background evaluation of the series such as nakamise 63
1, the genome of excellent parent resurveys sequence
Filter out the anti-cotton in Hubei Province No. 9, in 309,9053, in the same pedigree sources such as 9018 and 1638 5 excellent parents, In Plant cotton material in illumination box takes cotton seedling young leaflet tablet, extracts genomic DNA, broken using Covaris ultrasonic wave DNA Broken instrument is broken into 350bp segment at random, constructs sequencing DNA using TruSeq Library Construction Kit kit Library carries out the sequencing of double each 150bp in end by 4000 microarray dataset of IlluminaHiSeq.9053 (nakamise 63 is maternal) Plan output 150G data (sequencing covering gene group depth is 60 ×), other materials respectively plan output 75G data, and (sequencing is covered Gai gene group depth is 30 ×).Finally, 9053 (nakamise 63 is maternal) obtain 180.25G initial data (Raw data), such as scheme Shown in 2;After removing belt lacing and low-quality data, the valid data (Clean data) of 179.58G are obtained;Other materials obtain 75.11~94.25G initial data is obtained, as shown in Figure 2;After removing belt lacing and low-quality data, 74.93 are obtained~ The valid data of 93.92G, concrete outcome are as shown in Figure 3.
It is classified as with the genome sequence of issued upland cotton Genetic standard line (TM-1) with reference to genome, it is soft using BWA Sequencing is obtained data (Clean data) and compared onto reference genome by part, the results showed that 5 material sequencings obtain data ratio To the ratio on genome, more than 99% (Fig. 4), 9053 (nakamise 63 is maternal) genome overburden depths reach 59.9 times, Other materials are minimum also to reach 30 times or more (Fig. 5), illustrates the genome weight sequencing data substantially full base of covering material Because of group, and covering multiple is relatively high, is able to carry out the evaluation of full-length genome genetic background.
2, the genetic background evaluation of excellent parent
It is to detect 1,395,011 altogether in 5 excellent parents using SAMtools software with reference to genome with TM-1 The site single nucleotide polymorphism (Single Nucleotide Polymorphic, SNP).Wherein, 816,096 excellent at 5 There is polymorphism, 578,915 do not have polymorphism between 5 excellent parents, and Zhan always detects the big of SNP site number in parent About 41% (Fig. 6) illustrates that 5 excellent parents have similar genetic background.
Embodiment 3
It is applied to the SNP marker of excellent parent genetic background selection based on HRM technological development
High-resolution melting curve (High Resolution Melting, HRM) technology is the detection list risen in recent years The tool of nucleotide polymorphisms.It passes through real-time monitoring temperature-rise period double center chain DNA fluorescent dye and polymerase chain reaction The case where (Polymerase Chain Reaction, PCR) product combines, to determine whether there are SNP.Fluorescent dye not with Single stranded DNA reacts, but fluorescence can occur in conjunction with double-stranded DNA.During PCR, with the raising of Double stranded DNA concentration, Fluorescence constantly enhances, and as temperature increases in high-resolution fusion processes, it is single-stranded, fluorescent dye that DNA untwists from double-strand It is constantly released to which fluorescence intensity weakens.Since different bases stability is different in fusion processes, therefore the speed of unwinding is different, So the variation according to fluorescence intensity can effectively distinguish different SNP sites.
1, DNA is extracted
Take the anti-cotton in Hubei Province No. 9, in 309,9053, in the seed of 9018 and 1638 etc. 5 excellent parents and TM-1, use SDS method (rectifying violent etc., 2010) extracts genomic DNA, and specific extraction step is as described below:
(1) cotton seed kind skin shell is peelled off, and guarantees the integrality of kernel as far as possible.
(2) it is placed in the 2mL centrifuge tube for being put into steel ball, is crushed on tissue grinder instrument.
(3) 800 μ L SDS extracting solution (constituents: 1%SDS, 0.01mol/L EDTA, 0.705mol/L are added NaCl, 0.05mol/L Tris, 0.5% sorbierite, 1%PVP, 1% beta -mercaptoethanol), after whirlpool is abundant, 65 DEG C of water-baths 30min, interval 10min or so jog are primary.
(4) isometric 800 μ L phenol: chloroform: isoamyl alcohol (25:24:1) is added, mixes to not stratified, 12000r/min centrifugation 10min。
(5) supernatant is taken, 1 μ L RNase A (10mg/mL), 37 DEG C of water-bath 30min is added.
(6) it repeats to extract primary rear centrifuging and taking supernatant, 0.7 times of volume isopropanol is added, slowly mixes to the agglomerating analysis of DNA Out, it is stored at room temperature 30min.
(7) 70% ethanol washing DNA are precipitated 2 times, and dehydrated alcohol washs 1 time.
(8) it is inverted and dries, 200 μ L ddH are added2The abundant dissolving DNA of O, it is spare.
2, the design of HRM primer
According to sequencing analysis as a result, it is random to pick out 20 sequencing depth higher, and the SNP site on gene (table 1) utilizes primer3.0 software Design primers (table 2).
The information for 20 SNP sites that table 1 is selected
The primer that table 2 designs
3, polymorphism is verified
HRM test uses Light480High Resolution Melting Master kit, it is first First there are Light480 high-resolution pass through real-time PCR in the case where melting dyestuff and amplify sample DNA.DNA After amplification, high-resolution is carried out immediately and melts test, finally uses Light480 genescan softwares are analyzed To determine sequence variations.All tests are in LightIt carries out on 480 analyzers, is reacted using 20 μ l PCR System: 10 μ l Master Mix, 5 μ l 10 μ g/mL DNA, each 0.5 μ l, 1.6-2.4 μ lMgCl of upstream and downstream primer2, add PCR- grade H2O is supplied to 20 μ l.At 60 DEG C, other parameters setting uses HRM default parameters for annealing temperature setting during PCR.
Concrete outcome is as shown in Fig. 7-Figure 11.
The present invention has rule of thumb randomly selected that 20 sequencing depth are higher, and the SNP site design on these genes Primer, further using the anti-cotton in Hubei Province No. 9, in 309,9053, in 9018 and 1638 etc. 5 excellent parents and TM-1 as material Material detects the efficiency that this 20 SNP sites identify cotton excellent parent genetic background by HRM technology, the results showed that 5 primers Excellent parent and TM-1 can be accurately distinguished, and excellent parent is gathered for one kind, so this 5 primers can be used for assisted Selection The genetic background of excellent parent.
Embodiment 4
Respectively to the anti-cotton in Hubei Province to be detected No. 9, in 309,9053, in 9018 and 1638 each 50 cotton plants of filial generation cotton Flower seed, the genome of sample to be tested is extracted using the DNA extraction method in embodiment 3.
Gh_A06G0169_SNP primer pair, Gh_A12G1857_SNP primer pair, Gh_D03G1074_SNP is respectively adopted to draw The object mode same as Example 3 to, Gh_D05G2790_SNP primer pair, Gh_D11G0580_SNP primer pair carries out HRM inspection It surveys, obtained result is as follows:
The filial generation that E Kangmian 9: 20 and TM-1 without significant difference, 30 are excellent parent;
In 309 filial generation: 20 and TM-1 without significant difference, 30 are excellent parent;
9053 filial generation: 19 and TM-1 without significant difference, 31 are excellent parent;
In 9018 filial generation: 25 and TM-1 without significant difference, 25 are excellent parent;
1638 filial generation: 28 and TM-1 without significant difference, 22 are excellent parent.
The filial generation of each material respectively randomly chooses 5 non-excellent parents and 5 excellent parents carry out the sight of field character Identification is examined, is as a result consistent with the result of above-mentioned detection.
The primer pair of identification cotton excellent parent provided by the invention, is detected by HRM, if result and excellent parent are poly- For one kind, then sample to be tested has the genetic background of strong advantage hybrid cotton excellent parent, can continue to cultivate, this method is substantially Degree improves the efficiency of selection and accuracy of genetic background, the significant cultivation age limit for shortening excellent parent.
Although illustrate and describing the present invention with specific embodiment, it will be appreciated that without departing substantially from of the invention Many other change and modification can be made in the case where spirit and scope.It is, therefore, intended that in the following claims Including belonging to all such changes and modifications in the scope of the invention.
<110>the Chinese Academy of Agriculture Science and Technologys Cotton Research Institute
<120>SNP marker and its detection method of assisted Selection cotton excellent parent genetic background are used for
<160> 10
<170> PatentIn version 3.3
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Claims (10)

1. the primer pair of the SNP marker for assisted Selection cotton excellent parent genetic background, which is characterized in that draw including following Object is to any one or more of;
The upstream and downstream nucleic acid sequence of Gh_A06G0169_SNP primer pair is as shown in SEQ ID No.1 and SEQID No.2, Gh_ The upstream and downstream nucleic acid sequence of A12G1857_SNP primer pair is as shown in SEQ ID No.3 and SEQ ID No.4, Gh_D03G1074_ The upstream and downstream nucleic acid sequence of SNP primer pair as shown in SEQID No.5 and SEQID No.6, Gh_D05G2790_SNP primer pair Upstream and downstream nucleic acid sequence is as shown in SEQ ID No.7 and SEQ ID No.8, the upstream and downstream core of Gh_D11G0580_SNP primer pair Acid sequence is as shown in SEQID No.9 and SEQ ID No.10.
2. the primer pair of the SNP marker according to claim 1 for assisted Selection cotton excellent parent genetic background, Be characterized in that, the cotton excellent parent include the anti-cotton in Hubei Province No. 9, in 309,9053, in 9018,1638.
3. the kit of the SNP marker for assisted Selection cotton excellent parent genetic background, which is characterized in that wanted containing having the right Seek primer pair described in 1.
4. the detection method of the SNP marker for assisted Selection cotton excellent parent genetic background, which is characterized in that use right It is required that primer pair described in 1, the detection of molecular level is carried out to the genome of cotton to be detected.
5. the detection method of the SNP marker according to claim 4 for assisted Selection cotton excellent parent genetic background, It is characterized in that, the detection of the molecular level are as follows: the genome of kind to be detected is first carried out PCR amplification, then carries out HRM Detection.
6. the detection method of the SNP marker according to claim 5 for assisted Selection cotton excellent parent genetic background, It is characterized in that, annealing temperature used in the PCR amplification is 59 ± 1 DEG C.
7. the detection method of the SNP marker according to claim 5 for assisted Selection cotton excellent parent genetic background, It is characterized in that, PCR reaction system used in the PCR amplification is 10-25 μ L.
8. the detection method of the SNP marker according to claim 7 for assisted Selection cotton excellent parent genetic background, It is characterized in that, the content of the template DNA in the PCR reaction system is not less than 5ng.
9. the detection method of the SNP marker according to claim 8 for assisted Selection cotton excellent parent genetic background, It is characterized in that, the recurring number of the PCR amplification is 30-45.
10. according to the described in any item SNP markers for assisted Selection cotton excellent parent genetic background of claim 4-9 Detection method, which is characterized in that extraction material used in the genome of cotton to be detected is the kernel of cotton to be detected.
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