CN106011135A - SSR mark related to stem diameter of ramie and application of SSR mark - Google Patents
SSR mark related to stem diameter of ramie and application of SSR mark Download PDFInfo
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Abstract
The invention discloses an SSR mark related to the stem diameter of ramie, comprising an SSR mark RAM290. The invention also discloses application of the SSR mark related to the stem diameter of ramie in culture of new species of ramie. The invention also discloses application of the SSR mark related to the stem diameter of ramie in stabilization or improvement of the yield of ramie. The SSR mark provided by the invention is related to the stem diameter of ramie, and the stem diameter is directly related to the yield of ramie. The invention lays a foundation for screening of elite germplasm, localization and cloning of genes as well as auxiliary breeding of molecular marks in the future. The SSR mark disclosed by the invention can be applied to molecular breeding of ramie and improvement of the yield of ramie. The SSR mark has important significance for breeding and production of ramie at the present stage in China. Meanwhile, the invention also provides a beneficial reference for molecular mark breeding.
Description
Technical field
The present invention relates to a kind of SSR marker slightly associated with Boehmeria stem and application thereof.
Background technology
Boehmeria (BoehmerianiveaL.Gaud), is again " China's grass ", originates from China, many for Urticaceae Section of Genus Boehmeria
Year life perennial root herbaceous plant, is natural textile raw material with Chinese characteristics.At present, Boehmeria is that the second largest fiber of China is made
Thing.Although Boehmeria yield there has been bigger raising before comparing, but improve fiber production and be still the important goal of Breeding of Ramie.Make
The yield traits of thing is extremely complex quantitative trait, is a series of growth and development processes and environment in the whole life cycle of crop
The end product of interaction, generally by controlled by multiple genes.Ramee yield forming key element includes that plant height, stem be thick, skin depth, fibre percentage
With sub-character such as plant division power.Research shows, these character are quantitative traits, and its heredity is by minor-polygene control, by tradition
It is limited that breeding technique carries out genetic improvement efficiency.
Find destination number linkage of characters molecular marker, by molecular marker assisted selection, can be effectively improved quantitative
The genetic improvement process of shape.Modern breeding is necessary to utilize Genetic Diversity platform, and combines up-to-date genome-based technologies
Find new gene or allele, for the improvement of character.Utilize DNA molecular marker technology and QTL (quantitative
Trait loci) QTL of Boehmeria Correlated Yield Characters reports less by drawing method, the linkage molecule labelling of report only has 33
Individual, limit molecular marker utilization in breeding.Pass based on linkage disequilibrium (Linkage disequilibrium, LD)
It is the effective ways excavating neomorph that connection analyzes (Association analysis).Association analysis is with natural population for grinding
Study carefully object, between the gene (site) remained after long-term restructuring based on linkage disequilibrium, by many for objective trait phenotype
Sample combines analysis with the polymorphism of gene (or marker site), can go out and tool closely related with phenotypic variation by Direct Identification
There are gene loci or the marker site of specific function.
Summary of the invention
It is an object of the invention to solve at least the above and/or defect, and at least will be described later excellent is provided
Point.
It is a still further object of the present invention to provide a kind of SSR marker slightly associated with Boehmeria stem, educate solving Boehmeria molecule
The problem that in kind, linkage molecule labelling is few.
A further object of the present invention is to provide the SSR marker slightly associated with Boehmeria stem use in cultivating New Ramie Variety
On the way.
The present invention separately has a purpose to be to provide the SSR marker that slightly associates with Boehmeria stem stable or improve in Boehmeria yield
Purposes.
To this end, the technical scheme that the present invention provides is:
A kind of SSR marker slightly associated with Boehmeria stem, including SSR marker RAM290.
Preferably, in the described SSR marker slightly associated with Boehmeria stem, also include SSR marker RAM109, RAM131 and
RAM156。
Preferably, in the described SSR marker slightly associated with Boehmeria stem, SSR marker RAM39 is also included.
Preferably, in the described SSR marker slightly associated with Boehmeria stem, described SSR marker RAM290 and Boehmeria head season
Fiber crops, two seasons numb and three seasons fiber crops stem are slightly associated.
Preferably, in the described SSR marker slightly associated with Boehmeria stem, described SSR marker RAM109, RAM131 and
RAM156 is slightly associated with the stem of Boehmeria head season fiber crops and two seasons fiber crops.
Preferably, in the described SSR marker slightly associated with Boehmeria stem, described SSR marker RAM39 and two seasons of Boehmeria
The stem of fiber crops and three seasons fiber crops is slightly associated.
Preferably, in the described SSR marker slightly associated with Boehmeria stem, described SSR marker RAM39 also with the head of Boehmeria
Season, numb and two seasons fiber crops plant division number was associated.
The described SSR marker slightly associated with Boehmeria stem purposes in cultivating New Ramie Variety.
The described SSR marker slightly associated with Boehmeria stem is being stablized or is being improved the purposes in Boehmeria yield.
The present invention at least includes following beneficial effect:
Compared with traditional Q TL localization method, the natural population that GWAS uses genetic background abundant is material, it is not necessary to Hua Duo
Year builds specific segregating population, has mapping positioning precision height, the energy all associated bit of scan control objective trait simultaneously
The advantage of point.
The SSR marker that the present invention provides is the most relevant to the stem of Boehmeria, and stem is the most directly related with the yield of Boehmeria, for from now on
Screening elite germplasm, gene mapping and cloning and molecular mark lay the first stone, and the SSR marker of the present invention can be used
In the molecular breeding and raising Boehmeria yield of Boehmeria.Breeding and production for present stage China Boehmeria are significant.
Meanwhile, the present invention also provides useful reference for molecular mark.
Part is embodied by the further advantage of the present invention, target and feature by description below, and part also will be by this
Invention research and practice and be understood by the person skilled in the art.
Accompanying drawing explanation
Fig. 1 is the schematic diagram that in one of them embodiment of the present invention, △ K value changes with subgroup number.
Fig. 2 is the cladogram of 107 parts of germ plasm resources of the present invention.
Note: in figure, each branch is a sample.0.05 genetic distance representing the sample room in regular length.
Fig. 3 is SSR marker linkage strength r in the present invention2A part for cartogram.
Detailed description of the invention
The present invention is described in further detail below in conjunction with the accompanying drawings, to make those skilled in the art with reference to description literary composition
Word can be implemented according to this.
Should be appreciated that used herein such as " have ", " comprising " and " including " term do not allot one or many
Other element individual or the existence of a combination thereof or interpolation.
The present invention, with 107 parts of Boehmeria natural populations as material, utilizes 95 pairs of SSR molecular marker with polymorphism, analyzes
Genetic diversity, group structure etc.;And the character such as, plant height, plant division power thick to its stem carry out 1 year 3 environment repetitive identified and
The character such as skin depth, fibre percentage carries out 1 year 2 environment repetitive identified, and is associated its above character and molecular marker point
Analysis, excavates relative SSR site, and the QTL for Boehmeria yield traits positions and the research such as improvement provides scientific basis.
The present invention provides a kind of SSR marker slightly associated with Boehmeria stem, including SSR marker RAM290.
In one of them embodiment of the present invention, as preferably, in the described SSR marker slightly associated with Boehmeria stem,
Also include SSR marker RAM109, RAM131 and RAM156.
In one of them embodiment of the present invention, as preferably, in the described SSR marker slightly associated with Boehmeria stem,
Also include SSR marker RAM39.
In one of them embodiment of the present invention, as preferably, described SSR marker RAM290 and Boehmeria head season fiber crops, two
Season, numb and three seasons fiber crops stem was slightly associated.
In one of them embodiment of the present invention, as preferably, described SSR marker RAM109, RAM131 and RAM156
Slightly it is associated with the stem of Boehmeria head season fiber crops and two seasons fiber crops.
In one of them embodiment of the present invention, as preferably, described SSR marker RAM39 and Boehmeria two seasons fiber crops and
Three seasons fiber crops stem be slightly associated.
In one of them embodiment of the present invention, as preferably, described SSR marker RAM39 is also numb with the head season of Boehmeria
The plant division number numb with two seasons is associated.
The present invention also provides for the described SSR marker slightly associated with Boehmeria stem purposes in cultivating New Ramie Variety.
The present invention also provides for the described SSR marker slightly associated with Boehmeria stem and is stablizing or improving the use in Boehmeria yield
On the way.
1 materials and methods
1.1 material to be tested
(it is shown in Table 1) as research material with 107 parts of Boehmeria core authors.
1.2 field tests and character investigation
In late April, 2014 is in the cutting seedling of Wangcheng, Changsha Experimental Base 107 parts of Ramie Germplasms resources of plantation.Line-spacing
1m, spacing in the rows 60cm, single file district, often row 4 strain (pocket).Randomized block design, twice repetition.In June, 2015, August, October adjusts respectively
Look into season fiber crops, two seasons fiber crops, three seasons fiber crops plant height, the character such as stem is thick, skin depth, fibre percentage, plant division power.The most each community investigation 15
The plant height of strain, stem are thick, skin depth, fibre percentage;Investigate the plant division power of 4 pocket fiber crops.Investigation method is with reference to " Ramie Germplasms resource description specification
And data standard ".
1.3SSR molecular marker analysis
CTAB plant genome DNA rapid extraction test kit is utilized to extract DNA.Pure with 1% agarose gel electrophoresis detection
Degree and concentration.Method with reference to Chen etc. carries out SSR-PCR.PCR primer alkene acyl ammonia gel vertical electrophoresis detects, and silver staining is examined
Survey polymorphism, Taking Pictures recording band.
1 107 parts of Ramie Germplasms resources of table
1.4 statistical method
Utilize normal distribution situation and the correlation analysis of SPSS software statistics phenotypic character;Utilize software Popgene1.32
(version 1.31) calculates Shannon diversity indices, observation number of alleles (Na), effective number of allele (Ne), sees
Survey heterozygosity (Ho) and expectation heterozygosity (He);Based on each sample in the genotype in each SSR site, K-means is utilized to cluster
Algorithm, it is thus achieved that the cladogram between various matter;Utilize STRUCTURE2.2 software, the monoid differentiated a species from another according to mathematical model, and
Calculate Q-value (i.e. its genome mutation of i-th material comes from the probability of kth colony) corresponding to material (Wang Yanmin etc., 2008;
Wang Xicheng etc., 2010), the false positive of association analysis is eliminated as covariance, accurate to ensure the analysis result of species population structure
Truly have effect.Utilize the variance component of Popgene computed in software LD;Use the MLM program of TASSEL software, with the K matrix obtained
With colony Q-value matrix as covariance, significance level P < 0.05 time, by molecular data respectively with multiple number of contexts
Shape data carry out the logistic regression rate inspection of Q+K+MLM mixed linear model.
2 results and analysis
2.1 phenotypic character normal distribution-test and correlation analysiss
As can be seen from Table 1, plant height, stem thick head season fiber crops are the highest, three season fiber crops minimum;Head season fiber crops and two season fiber crops all meet normal state
Distribution, three season fiber crops do not meet normal distribution.Strain number head season, fiber crops were minimum, three season fiber crops the highest;Head season fiber crops, two season fiber crops all do not meet normal state
Distribution, and three season fiber crops meet normal distribution.Skin depth and fibre percentage are contrary trend.Skin depth two season fiber crops are numb more than three seasons, but go out
Fiber crops rate two season fiber crops are numb less than three seasons;And skin depth two season fiber crops are all in normal distribution, and fibre percentage two season fiber crops all do not meet normal distribution.
Table 1 normal distribution detection table
Table 2 yield traits correlation coefficient
As can be seen from Table 2, plant height and stem is thick, the notable positive correlation of skin depth, negative correlation notable with fibre percentage;Stem is thick and skin depth
Notable negative correlation.Stem thick with strain number head season fiber crops, two season fiber crops all show extremely significantly negative correlation.
2.2 analysis of genetic diversity
Utilizing 95 pairs of SSR polymorphism primers to expand 107 parts of Boehmeria Core Germplasms, coamplification goes out 255 polymorphisms
Band.Each site number of alleles average out to 2.6559, is distributed between 2~5;Gene diversity average out to 0.5211, point
Cloth is between 0.2276~0.7258;Expect heterozygosity minimum 0, the highest by 0.90;Observe heterozygosity minimum 0.05, the highest by 1.00.
3 95 pairs of SSR primer information of table
2.3 group structure analyses
Utilize the group structure of STRUCTURE 2.2 software analysis material to be tested.Analyze the group structure of 107 samples.
The number (K value) that hives off of 107 samples of hypothesis is 2-17 respectively, clusters, determines, according to the position of Δ K peak value, the number that hives off,
Result shows, as K=2, Δ K is maximum (Fig. 1), shows that material to be tested exists a certain degree of group structure, can be divided into 2
Subgroup.
2.4 relationship cluster analyses
Cladogram is used for representing the evolutionary relationship between species, according to the distance of the sibship between different kind organism, each
Class biology is placed on paniculate tree-shaped chart, represents biological evolution course and sibship concisely.Based on each
Sample, in the genotype in each SSR site, utilizes K-means clustering algorithm, it is thus achieved that the cladogram between each sample.Entering from sample room
Change tree upper it can be seen that each sample is broadly divided into two big classes (Fig. 2).Wherein the first kind comprises 87 kinds, and Equations of The Second Kind comprises 20
Individual kind.
2.5 linkage disequilibrium value
In a certain colony, on different seats, the frequency of certain two site heredity simultaneously is apparently higher than intended random frequency
Phenomenon, claim linkage disequilibrium (linkage disequilibrium).Carry out linkage disequilibrium value, it is possible to obtain species
Minimum genetic element.This research, with SSR site as object, utilizes TASSEL software 95 pleomorphism sites to carry out colony even
Lock imbalance is analyzed, and obtains the distribution situation (Fig. 3) of linkage disequilibrium in genome.Test obtains the 4465 of 95 labellings altogether
Individual combination, as P, < when 0.05,210 Sites Combination are in LD, account for the 4.70% of total Sites Combination number;When P < when 0.01,41
Sites Combination is in LD, accounts for the 0.92% of total Sites Combination number;By R2Scope, R2> 0.01 Sites Combination have 2795, account for
The 62.6% of total Sites Combination number;R2> 0.05 Sites Combination have 1206, account for the 27% of total Sites Combination number;R2> 0.1 position
Point combination has 491, accounts for the 11% of total Sites Combination number.In a word, 107 material linkage disequilibrium levels that this institute uses
The lowest, it is suitable for whole-genome association strategy and carries out just positioning.
2.6SSR site and the association analysis of Boehmeria yield traits
For avoiding the existence of group structure and sibship to affect the accuracy of association analysis, Tassel 3.0 is soft in application
Part, using the Q-value of each for Core Germplasms individuality and Kinship value as covariant, carries out plant height phenotypic variation to mark based on MLM model
The regression analysis of note variation, seeks the connective marker of Correlated Yield Characters QTL, and adds up the phenotypic variation explanation rate in each site.
Result shows, head season fiber crops, two seasons fiber crops, three season fiber crops 7,13,5 plant heights association molecular marker (p detected respectively
<0.05).Wherein simultaneously detected in two environment have 6.Head season fiber crops and two season fiber crops in can be detected simultaneously
It is marked with RAM144, RAM123;Head season fiber crops and three seasons fiber crops unmarked be detected simultaneously.Two seasons fiber crops and three season fiber crops in permissible
Be detected simultaneously is marked with RAM598, RAM156, RAM130.RAM144, RAM130 be phenotypic variation solution in two environment
Release rate all more than 10%.
Head season fiber crops, two seasons fiber crops, three season fiber crops 6,3,9 plant division numbers association molecular marker (p < 0.05) detected respectively.
Wherein can be detected simultaneously in two environment is marked with 2.RAM147 two seasons fiber crops and three season fiber crops in examined simultaneously
Measure, and RAM39 head season fiber crops and two season fiber crops in be detected simultaneously.RAM147 phenotypic variation explanation rate in two environment is equal
More than 15%.
Head season fiber crops, two seasons fiber crops, three season fiber crops detect respectively 12,8,5 stems slightly associate molecular marker (p < 0.05). its
Middle RAM290 molecular marker is detected in three environment entirely, and 4 association molecular markers are detected simultaneously by two environment.
Head season fiber crops and two season fiber crops in can be detected simultaneously be marked with RAM109, RAM156, RAM131;Numb and three seasons in head season
Fiber crops are unmarked to be detected simultaneously.Two seasons fiber crops and three season fiber crops in can be detected simultaneously be marked with RAM39.Detected
To molecular marker in, have 2 (RAM290 and RAM109) molecular markers phenotypic variation explanation rate in two environment all to exceed
15%.
Two seasons fiber crops, three season fiber crops 13,8 skin depths association molecular marker (p < 0.05) detected respectively.Wherein, at two rings
Be simultaneously detected in border is marked with 3, respectively RAM200, RAM108 and RAM141.Wherein, RAM200 and RAM141 exists
In two environment, phenotypic variation explanation rate is all more than 10%.
Two seasons fiber crops, three season fiber crops 5,8 fibre percentages association molecular marker (p < 0.05) detected respectively.Wherein, at two
Simultaneously detected in environment it is marked with 3, respectively RAM144, RAM179 and RAM181.Phenotypic variation explanation rate is at 0.06-
Between 0.37.Wherein RAM144 phenotypic variation explanation rate is up to 15%-37%.
In the multiple constant rate of production correlated traits SSR marker detected, wherein 3 molecular markers simultaneously with 2 character
Relevant.Wherein RAM144 and plant height, fibre percentage are relevant;RAM156 and plant height, stem are the most relevant;RAM39 phase thick with plant division number and stem
Close.
More than 4 constant rate of production correlated traits association SSR marker of table
Discuss
Utilize traditional Q TL drawing method to carry out Boehmeria character QTL location and have a lot of deficiency.Firstly, since segregating population is only
Relating to two specific parent materials, (Boehmeria is heterozygote, at most may be used therefore to pertain only to two allele of same gene seat
Relate to 4 allele), the QTL of location is not likely to be excellent allele (Magnus et al.2008);Secondly, build group
Body is wasted time and energy.Boehmeria builds colony and can position with QTL from starting to hybridize to colony, needs 3 years if All going well.Separately
Outward, due to the restriction of Boehmeria hybridization pollination technology, building process external source pollen contamination is serious, it is thus achieved that the true filial generation of Boehmeria
Difficulty.Discriminating to true and false cenospecies is exactly a very time-consuming laborious job, and colony more serious (Zou of inclined segregation ratio built
From levying, 2012).Therefore, the present invention utilizes natural population as analyzing colony, and the heredity that not only can make full use of germ plasm resource is many
Sample and excellent allele, and avoid the deficiency building colony.
Group structure is the key factor affecting association analysis result, and the mixing of subgroup makes the LD intensity of whole colony increase
By force, spurious correlation is easily caused.The hereditary constitution of Different Crop is different.Such as, Fructus Persicae can be divided into 7 subgroups;Semen avenae nudae is then divided into 4
Individual subgroup.The different natural population of same crop the most also can show different group structures.Research on Semen sojae atricolor confirms
This point.Forefathers report few about the population genetic variations of Boehmeria, and Liu Chenchen thinks that 104 parts of Ramie Germplasms resources can be divided into
2 big monoids.This research also leads to the same conclusion.Therefore, Ramie Germplasms resource being divided into 2 big monoids is the puppet reducing Boehmeria
Association is laid a good foundation.
Linkage disequilibrium is the premise of association analysis.Self pollination crop LD level is higher, and cross pollinated plant LD water
Flat relatively low.Boehmeria, as cross pollinated plant, also shows relatively low LD level, identical with the conclusion of forefathers.Due to LD water
Flat relatively low, carrying out whole-genome association needs more molecular marker.And the molecular marker of this institute only has 95,
Therefore, this research has only been by the whole-genome association in rough meaning, the simply coarse positioning on definite meaning.Cause
This, in order to obtain more reliably as a result, it is desirable to expand number of labels further.
The yield traits QTL that Liu reports Boehmeria by the method for linkage analysis positions, detect altogether 9 stable
QTL.This research is found that altogether 19 stable molecule labellings relevant to yield traits.Wherein, plant height 6, plant division number 2,
Thick 5 of stem, skin depth 3, fibre percentage 3.Compared for the result of Liu, do not find to overlap with its any one molecular marker.At this
In 19 stable molecular markers, the molecular marker RAM290 the most relevant to stem is all detected in three environment, and heredity
Contribution rate, between 8.32%-23.42%, is a molecular marker that can be used for molecular breeding.
In 19 the stable molecule labellings detected, be all season fiber crops and two seasons fiber crops or two seasons fiber crops and three season fiber crops simultaneously
Detect.It is not detected by a season numb simultaneous molecular marker numb with three seasons.It is perennial crop that reason is probably Boehmeria, head
Season fiber crops and two seasons fiber crops and two seasons fiber crops and three season fiber crops physiological age close, be therefore easier to excavate total molecular marker.Also
The gene expression of hint Boehmeria yield traits is relevant with physiological age, and relative to annual crop, its yield traits QTL positions more
Complicated.
In the present invention, the correlation analysis result of phenotypic character shows, plant height and stem is thick, the notable positive correlation of skin depth, and goes out fiber crops
The notable negative correlation of rate;Plant division number and stem slightly notable negative correlation.Meanwhile, association analysis result also indicates that, RAM144 and plant height, goes out fiber crops
Rate is correlated with;RAM156 and plant height, stem are the most relevant;RAM39 is the most relevant to plant division number and stem.The QTL positioning result table of various crop
Bright, the distribution of QTL cluster is the most common because of multiple-effect with one.Phenotype of the present invention and molecular results all imply and may deposit near these labellings
At the different genes relevant to 2 character, or there may be the gene simultaneously controlling 2 character.More than research is
Carry out molecular breeding to provide convenience.
Module number described herein and treatment scale are used to the explanation of the simplification present invention.Molecule mark to the present invention
The application of note, modifications and variations will be readily apparent to persons skilled in the art.
As it has been described above, according to the present invention, because it is found that the SSR marker being slightly associated with Boehmeria stem, therefore have point
Carry out the guidance of Breeding of Ramie in sub-level, also the yield improving or stablizing Boehmeria is proposed technical guidance.
Although embodiment of the present invention are disclosed as above, but it is not restricted in description and embodiment listed
Using, it can be applied to various applicable the field of the invention completely, for those skilled in the art, and can be easily
Realizing other amendment, therefore under the general concept limited without departing substantially from claim and equivalency range, the present invention does not limit
In specific details with shown here as the legend with description.
Claims (9)
1. the SSR marker slightly associated with Boehmeria stem, including SSR marker RAM290.
2. the SSR marker slightly associated with Boehmeria stem as claimed in claim 1, it is characterised in that also include SSR marker
RAM109, RAM131 and RAM156.
3. the SSR marker slightly associated with Boehmeria stem as claimed in claim 1, it is characterised in that also include SSR marker RAM39.
4. the SSR marker slightly associated with Boehmeria stem as claimed in claim 1, it is characterised in that described SSR marker RAM290 and
Boehmeria head season is numb, two seasons are numb and the stem of three seasons fiber crops is slightly associated.
5. the SSR marker slightly associated with Boehmeria stem as claimed in claim 2, it is characterised in that described SSR marker RAM109,
RAM131 and RAM156 is slightly associated with the stem of Boehmeria head season fiber crops and two seasons fiber crops.
6. the SSR marker slightly associated with Boehmeria stem as claimed in claim 3, it is characterised in that described SSR marker RAM39 and
Two seasons of Boehmeria, numb and three seasons fiber crops stem was slightly associated.
7. the SSR marker slightly associated with Boehmeria stem as claimed in claim 3, it is characterised in that described SSR marker RAM39 is also
Numb with the head season of Boehmeria and two seasons fiber crops plant division numbers are associated.
8. the purposes in cultivating New Ramie Variety of the SSR marker slightly associated with Boehmeria stem described in claim 1.
9. the SSR marker slightly associated with Boehmeria stem as claimed in claim 1 is being stablized or is being improved the purposes in Boehmeria yield.
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CN104212897A (en) * | 2014-09-05 | 2014-12-17 | 中国农业科学院麻类研究所 | Method for large-scale development of ramie genome SSR (simple sequence repeat) markers and primers developed by method |
CN105018477A (en) * | 2015-07-09 | 2015-11-04 | 中国农业科学院麻类研究所 | Major quantitative trait locus for controlling fiber fineness of ramie, method and application thereof |
CN105018479A (en) * | 2015-07-09 | 2015-11-04 | 中国农业科学院麻类研究所 | Molecular marker tightly linked to fiber strength of ramie, obtaining method and application thereof |
CN105018478A (en) * | 2015-07-09 | 2015-11-04 | 中国农业科学院麻类研究所 | Molecular marker tightly linked to fiber fineness of ramie, obtaining method and application thereof |
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