CN106801105A - The SSR marker being associated with ramee fineness and application - Google Patents

The SSR marker being associated with ramee fineness and application Download PDF

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CN106801105A
CN106801105A CN201710155866.3A CN201710155866A CN106801105A CN 106801105 A CN106801105 A CN 106801105A CN 201710155866 A CN201710155866 A CN 201710155866A CN 106801105 A CN106801105 A CN 106801105A
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ramie
fineness
ramee
ssr
ssr marker
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陈晓蓉
高海军
晏文武
陈健萍
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INST OF AGRICULTURAL SCIENCES YICHUN CITY JIANGXI PROV
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Abstract

The present invention provides a kind of SSR marker being associated with ramee fineness and application, including SSR marker R74, R51, the R90 being associated with ramee fineness.A kind of SSR marker being associated with ramee fineness, it is characterized in that the ramee fineness of SSR marker R51, R74, R90 and ramie head season fiber crops, two seasons fiber crops and three seasons fiber crops is associated;Application of the associated SSR marker of the ramee fineness in New Ramie Variety is cultivated;Application of the SSR marker being associated with ramee fineness in the New Ramie Variety for cultivating ramee fineness high.SSR marker of the invention can be used in the molecular breeding and raising ramie yield of ramie, and the breeding and production for China ramie are significant.Meanwhile, the present invention is also for molecular mark provides beneficial reference.

Description

The SSR marker being associated with ramee fineness and application
Technical field:
The present invention relates to the associated SSR marker of the ramie of agricultural production and application, and in particular to a kind of and ramee The associated SSR marker of fineness and application.
Background technology:
Ramie is natural textile raw material with Chinese characteristics.Ramee has pulling force strong, full of elasticity, water-fast wet, heat hardiness Greatly, the characteristic such as rich insulating properties.And ramee moisture absorption dissipates wet fast, and good permeability can be widely used in as excellent textile raw material Clothing making, adornment and fabrics for industrial use etc..In addition, ramie can also be planted as forage crop.In south China, Due to summer high temperature high humidity, the north such as clover herbage growth potentiality are limited.The annidation of ramie is strong, not only can normally give birth to It is long, moreover it is possible to obtain biological yield higher;It is nutritious rich in multivitamin and amino acid and Leaf Protein Content is high, can be with Compared favourably with clover.There is result of study to show, ramie Leaf Protein Content and yield are above hybridizing napier grass and English ryegrass Deng southern Dominant Species of Forage Grass.Therefore, ramie removes and makees beyond the region of objective existence as traditional fibrous raw material, and it is used as the new of south China area at present Type albumen Forage Germplasm Resources have been widely recognized, and middle feeding ramie, Hunan have been bred as in the prior art and have raised the series of products such as ramie.It is in Fowl, livestock, aquaculture aspect, have good development prospect as feed or fine dual-purpose crop of raising.
Fibre fineness is to evaluate the critical index of ramee grade, fiber quality and weaving value.Due to fibre Dimension fineness and yield are negatively correlated, and its yield component of fineness kind high is integrally relatively low.Existing ramee variety fiber quality is difficult to Meet weaving branch high, the requirement of thin thin product, main cause is a lack of fineness high, the kind of more than 2500.Protein content It is the important Nutrient Quality Traits of many crops.Research shows that protein content is a quantitative character for complexity, by polygenes Control.For ramie, leaf protein or to be leaf protein content be important forage nutritive quality index.There is research table It is bright, Leaf Protein Content significant difference between different ramee varieties, the low too late content of content it is high 50%, and in continuous variability. Therefore, how the actual requirement that fibre fineness kind high is Breeding of Ramie is cultivated, is ramie industrial economy development bottleneck system Important breakthrough about, is also key point that ramie resources advantage is changed into economic advantages.
Conventional breeding method is to carry out seed selection to the Main Agronomic Characters of crop by phenotype and breeding man experience, its Efficiency is low, and the cycle is long;And genotype selection and the molecule ancillary technique of efficiently and accurately are based on, open the new side of crop breeding To.Molecular marking technique is used for the assisted Selection of crop Main Agronomic Characters or identification is substantially shorter breeding time and carries High selection efficiency.Molecular labeling is concentrated mainly on molecular markers development on ramie(Chen et al.2011; Liu et al. 2013;Chen et al.2015), the analysis of genetic diversity of germ plasm resource(Take off rain into etc., 2002;Guo An equalitys, 2003; Liu et al. 2008;Luan et al. 2015b), molecular identity card build(Wang Xiaofei etc., 2010;Luan et al. 2015a), genetic linkage mapses build(Zou Zizheng, 2012;Luan Mingbao etc., 2013;Liu et al. 2014)And QTL positioning (Liu et al. 2014).Chen et al.(2015)Developing 52 by transcript profile may be related to fiber quality SSR molecular marker.But also rarely have report to the research for being currently undertaken by excavating fibre fineness and leaf protein content molecular labeling Road.
Modern breeding is necessary using Genetic Diversity platform, and finds new base with reference to newest genome-based technologies Cause or allele, for the improvement of proterties.Using destination number linkage of characters molecular labeling, aid in selecting by molecular labeling Select, genetics of quantitative characters improvement process can be effectively improved.Association analysis (Association analysis) is in plant number A kind of newer analysis method applied in amount behavior study and plant breeding.It identifies certain a group based on linkage disequilibrium Internal relation between proterties and genetic marker or candidate gene.Colony compares with restructuring, and its remarkable advantage is high flux, i.e., Can effectively detect that the proterties of the substantial amounts of Germplasms with different genetic backgrounds controls gene in full-length genome scope Site or region;In addition to high flux, it is material that GWAS uses the abundant natural population of genetic background, it is not necessary to when spending for many years Between build specific segregating population, with mapping positioning precision it is high, can reach monogenic level.Current full-length genome association Analysis has been successfully applied to the important crops such as corn, paddy rice, arabidopsis, rape, barley.
How to come using the natural population of ramie is material, using the SSR molecular marker with polymorphism, analyzes its heredity Diversity, group structure etc.;Analysis is associated to its fibre fineness and SSR molecular marker simultaneously, is developed and is excavated and its phase The SSR sites of pass, so that for the researchs such as the QTL positioning of ramee fineness proterties and its improvement provide scientific basis;And apply In New Ramie Variety breeding aspect.
The content of the invention:
The present invention provides a kind of SSR marker be associated with ramee fineness and application, its be utilize up to a hundred parts ramie oneself Right colony is material, using some SSR molecular markers of polymorphism, analyzes ramie genetic diversity and group structure, so that Analysis is associated to its fibre fineness and SSR molecular marker, and is applied to the breed improvement of ramie.
One of the object of the invention is to provide a kind of SSR marker being associated with ramee fineness, including with ramee fineness Associated SSR marker R74.
A kind of described SSR marker being associated with ramee fineness, it preferably also includes and ramee fineness Associated SSR marker R51, R90.
A kind of SSR marker being associated with ramee fineness of the present invention, its be preferably the SSR marker R51, The ramee fineness of R74, R90 and ramie head season fiber crops, two seasons fiber crops and three seasons fiber crops is associated.
It is another object of the present invention to the associated SSR marker of the ramee fineness in New Ramie Variety is cultivated Using.
It is preferred that the described SSR marker being associated with ramee fineness is cultivating the ramie new product of ramee fineness high Application in kind.
Application of the present invention, it is with several pieces ramie natural population as material, using 95 couple with polymorphism SSR molecular marker, is analyzed ramie genetic diversity, group structure;And ramee fineness and SSR molecular marker are carried out Association analysis, and then determine the SSR site related to ramie, and to the QTL positioning and ramee variety of ramee fineness proterties Improved.
Beneficial effects of the present invention:Compared with traditional QTL localization methods, the natural population that GWAS is enriched using genetic background Be material, it is not necessary to spend many years to build specific segregating population, with mapping positioning precision it is high, can scan control mesh simultaneously The advantage in all association sites of mark proterties.
The SSR marker that the present invention is provided is associated with ramee fineness, and cultivates the fibre fineness quality with ramie high It is directly associated, is that screening elite germplasm, the molecular mark of the assignment of genes gene mapping lay the first stone from now on, SSR of the invention Mark can be used in the molecular breeding and raising ramie yield of ramie.Breeding and production for China ramie have important meaning Justice.Meanwhile, the present invention is also for molecular mark provides beneficial reference.
Further advantage of the invention, target and feature embody part by following explanation, and part will also be by this The research and practice of invention and be understood by the person skilled in the art.
Brief description of the drawings:
Fig. 1 is the schematic diagram of variation tendency of the CV values with K values in one of embodiment of the invention;
Fig. 2 is 107 parts of chadograms of germ plasm resource of the invention;
Note:Each branch is a sample in figure;0.05 genetic distance for representing the sample room in regular length;
Fig. 3, is the affiliation association analysis result figure in natural population of the invention between individuality,
Illustrate, the affiliation in figure is weighed with kinship similarity factors, as a result find to show, 67.704% material two-by-two Kinship values between material between 0 to 0.05, illustrate affiliation between the 107 Ramie Germplasms resources that utilize of the present invention compared with Far, with genetic diversity higher.
Specific embodiment:With reference to embodiment, the present invention is further detailed explanation.
Embodiment 1:
It with 107 parts of ramie natural populations is material that the embodiment of the present invention is, using 95 pairs of SSR molecular markers with polymorphism, Analyze its genetic diversity, group structure etc.;And analysis is associated to its fibre fineness and SSR molecular marker, excavate and fibre The related SSR sites of dimension fineness, are that QTL positioning and its improvement of ramee fineness proterties etc. provide scientific basis.
The present invention provides a kind of SSR marker being associated with ramee fineness, including is associated with ramee fineness SSR marker R74.
It preferably also includes SSR marker R51, R90 being associated with ramee fineness.
A kind of SSR marker being associated with ramee fineness of the present invention, its be preferably the SSR marker R51, The ramee fineness of R74, R90 and ramie head season fiber crops, two seasons fiber crops and three seasons fiber crops is associated.
Ramee fineness of the present invention and the associated SSR marker of Leaf Protein Content are in New Ramie Variety is cultivated Using.
It is preferred that the described SSR marker being associated with ramee fineness and Leaf Protein Content is thin in cultivation ramee high Application in the New Ramie Variety of degree.
Application of the present invention, it is with several pieces ramie natural population as material, using 95 couple with polymorphism SSR molecular marker, is analyzed ramie genetic diversity, group structure;And ramee fineness and SSR molecular marker are carried out Association analysis, and then determine the SSR site related to ramie, and to the QTL positioning and ramee variety of ramee fineness proterties Improved.Specific method is as follows.
1st, materials and methods
Material to be tested, is research material with 107 parts of ramie core authors.
Fibre fineness is determined and statistical analysis,
In October, 2014 (2014 three fiber crops), in August, 2015(2015 two fiber crops), in October, 2015(2015 three fiber crops)In maturation Phase harvests ramie, investigates its fibre fineness proterties.
In September, 2014(2014 three fiber crops), in May, 2015(2015 year fiber crops)With in July, 2015(2015 two fiber crops), Vigorous period, each cell takes 5 plants of leaves on top, is finished 30 minutes at 105 DEG C, and then 70 DEG C of drying are crushed to constant weight 60 mesh sieves are crossed, crude protein content is determined using kjeldahl determination;Using SPSS softwares, to 107 parts of fibre finenesses of germ plasm resource and Blade crude protein content carries out statistics descriptive analysis.
SSR molecular marker is analyzed
DNA is extracted using CTAB plant genome DNA rapid extractions kit.With 1% agarose gel electrophoresis detect purity with it is dense Degree.95 pairs of SSR polymorphism primers in laboratory are entered with performing PCR amplification with reference to the method for Chen etc..PCR primer alkene acyl ammonia gel hangs down Straight electrophoresis polyacrylamide gel electrophoresis detection amplified production, silver staining detection polymorphism, Taking Pictures recording band;With numeral 1 and 0 point Not Biao Shi material to be tested electrophoretic band with or without, sample missing be designated as 2, counted with Excel, and according to corresponding software lattice Formula is changed.
Genetic diversity and cluster analysis
Using powerMark3.25, analyze its maximum gene frequency, genotype number, number of alleles, gene diversity, Heterozygosity and polymorphism information content (PIC value);According to NJ clustering procedures, its dendrogram is built.
Group structure is analyzed
By admixturer softwares, 107 group structures of sample are analyzed.107 point group's numbers of sample are assumed respectively(K values) It is 1-10, is clustered, point group's number is determined according to CV values;Corresponding K values when CV values are minimum, as divide group number.
Genetic relationship
Between this research and utilization 95 calculates 107 parts of Ramie Germplasms resource materials two-by-two to molecular labeling, using software SPAGeDi Kinship similarity factors.In the result that computing is obtained, the affiliation similarity factor of promising negative value be disposed as zero, so All of affiliation coefficient correlation is multiplied by 2 afterwards, association analysis is applied to.
Association analysis
Using the general linear model of TASSLE softwares(General linear model, GLM)With it is mixed Linear model(Mixed linear model, MLM), by group structure analyze obtained by Q values and affiliation K As covariant, the association analysis with proterties is marked.
2. result and analysis
Fibre fineness and blade crude protein content phenotypic analysis, table 1
Illustrate, analysis of genetic diversity
107 portions of ramies are expanded using the 95 pairs of SSR polymorphism primers for filtering out, coamplification goes out 252 polymorphic bandses. The polymorphism information content PIC of each primer sites(The polymorphic sex index of Simpson)Average out to 0.447969;Each site equipotential base Factor average out to 2.642105, expects that average value is 2.185957;Heterozygosity average out to 0.319365 is observed in each site, is expected Average value is 0.519303;Gene diversity average out to 0.522578;Genotypic diversity(Shannon-wiener diversity refers to Number)Average out to 0.82431;MAF average out to 0.325672.
Group structure is analyzed
The group structure of test material is supplied using admixture software analysis, it is assumed that 107 point group's numbers of sample(K values) It is 1-10, is clustered, point group's number is determined according to CV values.CV values are shown in Fig. 1 with the variation tendency of K values.Result shows, works as colony Its cross validation error value is 0.87987 during number K=1, and now error amount is minimum, shows that material to be tested group structure is simple, can be straight Connect and be divided into a subgroup.
Genetic relationship
As shown in figure 3, the affiliation in natural population between individuality is a key factor for influenceing association analysis result, it is this Affiliation can be weighed with kinship similarity factors.Analysis result find show, 67.704% storeroom two-by-two Kinship values show that affiliation between the 107 Ramie Germplasms resources of this research and utilization farther out, has between 0 to 0.05 Genetic diversity higher.
Relationship clustering relationships are analyzed
As shown in Fig. 2 chadogram is used for representing the evolutionary relationship between species, according to the remote of the affiliation between different kind organism Closely, different kind organism is placed on paniculate tree-shaped chart, concisely represents biological evolution course and affiliation.Base In each germ plasm resource in the genotype in each SSR sites, NJ clusters are carried out using powermarker, between obtaining each germ plasm resource Chadogram.As can be seen that 107 parts of germ plasm resources are broadly divided into two major classes from the chadogram between germ plasm resource.Wherein first Class includes 87 kinds, and Equations of The Second Kind includes 20 kinds.
SSR sites and the association analysis of ramee fineness
The accuracy of association analysis is influenceed for the presence for avoiding group structure and affiliation, using the softwares of Tassel 3.0, will Each individual Q values of Core Germplasms and Kinship values carry out fibre fineness as covariant based on GLM models and MLM models Regression analysis of the phenotypic variation to mark variation, seeks the connective marker of correlated traits, and count the phenotypic variation solution in each site Release rate.
Result shows that head season is numb in based on GLM model analysis, two seasons are numb, three seasons fiber crops detect 1,8,4 respectively Fibre fineness associates molecular labeling(p<0.05).What is be detected simultaneously by two environment has 3, and wherein R74 molecular labelings exist It is detected entirely in three environment.Two seasons fiber crops and three seasons fiber crops in the mark that can be detected simultaneously have, R74, R90. R51, R74 in two environment phenotypic variation explanation rate more than 10%.
Head season is numb in based on MLM model analysis, two seasons are numb, three seasons fiber crops detect 1,5,4 fibre finenesses respectively Association molecular labeling(p<0.05);The mark being detected simultaneously in two environment has individual, and wherein R74 molecular labelings are three It is detected entirely in individual environment.Two seasons fiber crops and three seasons fiber crops in the mark that can be detected simultaneously have, R74.R51、R74 Phenotypic variation explanation rate is more than 10% in two environment.
The molecular labeling site that MLM model inspections are arrived, is detected in GLM models.Under MLM models, for fibre For dimension fineness, relative molecular labeling site is detected under 3 kinds of environment 1;Detected under 2 kinds of environment Molecular labeling site have 1;Remaining 5 molecular labeling site is only detected under a kind of environment.Illustrate ramee Although be present the QTL of effect stabilization in fineness, but significantly affected by genotype by environment interaction.
Table 2
3. discuss
Ramie proterties QTL is carried out using traditional QTL drawing methods be positioned with many deficiencies.Firstly, since segregating population is only related to Two specific parent materials, therefore pertain only to two allele of same gene seat(Ramie is heterozygote, at most be can relate to 4 allele), the QTL of positioning may not be excellent allele(Magnus et al. 2008);Secondly, build colony Waste time and energy.Ramie builds a colony from starting to hybridize to colony and can be positioned with QTL, and 3 years are needed if All going well.Separately Outward, due to the limitation of ramie hybridization pollination technology, building process external source pollen contamination is serious, obtains the true filial generation of ramie It is difficult.Discriminating to true and false cenospecies is exactly a very time-consuming laborious job, and the inclined segregation ratio of colony for building is more serious.Cause This, this research and utilization natural population can not only make full use of the genetic diversity of germ plasm resource and excellent etc. as analysis colony Position gene, and avoid the deficiency for building colony.
Success or not of the appropriate choice relation of test group material to association analysis.Because phenotypic character is easily subject to ring The influence of border factor, the phenotypic character of germplasm often occurs inconsistent, the similar blastogenesis pass of phenotypic character with genetic background It is far, the colony that 107 parts of germplasm construct association analysis is selected in this experiment, accomplishes that group structure is simple as far as possible, and contain Relatively enrich Genetic variability.Group structure is the key factor for influenceing association analysis result, and the mixing of subgroup makes whole colony LD intensity enhancings, easily cause spurious correlation.The different natural population of same crop can also show different group structures sometimes. Population genetic variations report of the forefathers on ramie is few, has scholar to think that 104 parts of Ramie Germplasms resources can be divided into 2 major classes Group.107 parts of Ramie Germplasms resources in the present invention are divided for 1 big monoid, and Ramie Germplasms resource is divided into 1 big monoid will be examined Consider the spurious correlation of its ramie being likely to result in.
Linkage disequilibrium is the premise of association analysis.Self pollination crop LD levels are higher, and cross pollinated plant LD water It is flat relatively low.Ramie also shows relatively low LD levels as cross pollinated plant, and the conclusion with forefathers is consistent.Due to LD water Flat relatively low, carrying out whole-genome association needs more molecular labeling.And the molecular labeling used by the present invention only has 95, Therefore, this research is to have carried out the whole-genome association in rough meaning, simply the coarse positioning on definite meaning.Cause This, in order to obtain more reliably as a result, it is desirable to further expand number of labels.
Group structure analysis is the basis of association mapping.Because the presence of cluster structure can be by the LD in site so that whole The linkage disequilibrium intensity of individual colony increases, and linkage disequilibrium state is between causing non-linkage site, therefore by mathematical modulo Influence of the treatment of type to eliminate group structure turns into the necessary process of current association analysis.This research employs GLM moulds simultaneously Type and MLM carry out the association analysis of flax phenotypic character, can correct the false positive results caused by cluster structure, for improving Analytical precision is significant.The present invention is found that altogether 5 stable molecule marks related to quality trait.Wherein, Fibre fineness 3, crude protein content 2.In this 5 molecular labelings of stabilization, the molecular labeling R74 related to fibre fineness It is detected in three environment, and genetic contribution is reached between 11.29%-14.23%, is one and be can be used for molecular breeding Molecular labeling.Other 4 molecular labelings are detected in 2 environment, and value is still needed and further verify.This hair Bright finding has individual in two models with the mark that fibre fineness is all associated jointly, is respectively R51, R74, with crude protein content That related is R43.The two are associated in contribution degree in two models more than 10%.
The present invention is associated analysis to material using SSR molecular marker;It is domestic at present to use SSR molecular marker to ramie Germplasm carries out the also less of genetic diversity Journal of Sex Research.The present invention is expanded using 95 primer pairs, 107 parts of ramie core germplasms materials Increase and 255 sites, the average PIC values of all sites are 0.4480, and average diversity indices is 0.5226, ramie SSR marker Polymorphism be more or less the same with the polymorphic sex index of phenotypic character, speculate reason be probably the present invention analysis 107 parts of ramie kinds Matter is natural population, although morphologically showing abundant diversity, genetic background is still more complicated.
The present invention utilizes molecular labeling R51 and R74, quick detection has been carried out to the kind in Germplasm Resources, according to it Genotype, the success prediction fibre fineness height situation of kind, table 3 below be 4 genotype and fibre fineness of kind just Situation.
Table 3
Kind R51 R74 Fibre fineness
208 BB AA It is high
515 AA BB It is low
1276 AA BB It is low
1455 BB AA It is high
Illustrate, amplifying BB genotype, R74 using R51 amplifies AA genotype, and fibre fineness is high, more than 2200;Utilize R51 amplifies AA genotype, R74 and amplifies BB genotype, then fibre fineness is low, less than 1200.
Those skilled in the art are not departing from essence of the invention and spirit, can have various deformation scheme to realize this hair It is bright, preferably feasible embodiment of the invention is the foregoing is only, not thereby limit to interest field of the invention, all utilizations The equivalent structure change that description of the invention and accompanying drawing content are made, is both contained within interest field of the invention.

Claims (6)

1. a kind of SSR marker being associated with ramee fineness, including the SSR marker R74 being associated with ramee fineness.
2. a kind of SSR marker being associated with ramee fineness according to claim 1, it is characterized in that also including and ramie Associated SSR marker R51, R90 of flaxen fiber fineness.
3. a kind of SSR marker being associated with ramee fineness according to claim 1, it is characterized in that the SSR is marked The ramee fineness of note R51, R74, R90 and ramie head season fiber crops, two seasons fiber crops and three seasons fiber crops is associated.
4. application of the associated SSR marker of ramee fineness as claimed in claim 1 in New Ramie Variety is cultivated.
5. the SSR marker being associated with ramee fineness as claimed in claim 1 is cultivating the ramie of ramee fineness high Application in numb new varieties.
6. the application according to claim 4 or 5, it is characterized in that with several pieces ramie natural population as material, using having 95 pairs of SSR molecular markers of polymorphism, are analyzed ramie genetic diversity, group structure;And to ramee fineness and SSR Molecular labeling is associated analysis, and then determines the SSR site related to ramie, and fixed to the QTL of ramee fineness proterties Position and ramee variety are improved.
CN201710155866.3A 2017-03-16 2017-03-16 The SSR marker being associated with ramee fineness and application Pending CN106801105A (en)

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Cited By (3)

* Cited by examiner, † Cited by third party
Publication number Priority date Publication date Assignee Title
CN107586879A (en) * 2017-10-30 2018-01-16 中国农业科学院麻类研究所 A kind of primer pair group, kit, method and application for being used to detect flax SSR molecular marker
CN111607659A (en) * 2020-06-02 2020-09-01 中国农业科学院麻类研究所 SNP molecular marker associated with hemicellulose content of ramie and application thereof
CN112251530A (en) * 2020-10-23 2021-01-22 江西省宜春市农业科学研究所(江西省麻类科学研究所) SSR (simple sequence repeat) marker associated with ramie fiber fineness and application thereof

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Application publication date: 20170606