CN106011261A - Ramie-yield-trait-associated SSR (simple sequence repeat) markers and application thereof - Google Patents
Ramie-yield-trait-associated SSR (simple sequence repeat) markers and application thereof Download PDFInfo
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Abstract
The invention discloses ramie-yield-trait-associated SSR (simple sequence repeat) markers which comprise SSR markers RAM200, RAM108 and RAM141. The invention also discloses application of the ramie-yield-trait-associated SSR markers in cultivating ramie new species. The invention also discloses application of the ramie-yield-trait-associated SSR markers in stabilizing or enhancing ramie yield. The SSR markers disclosed by the invention are associated with the ramie stem diameter, and the stem diameter is directly associated with the ramie yield. The SSR markers lay a foundation for high-quality germplasm screening, gene localization and cloning, and molecular marker assisted breeding in future. The SSR markers can be used in ramie molecular breeding and ramie yield enhancement. The SSR markers have important meanings for ramie breeding and production in China in the present stage. Meanwhile, the invention provides beneficial references for molecular marker breeding.
Description
Technical field
The present invention relates to a kind of SSR marker associated with Boehmeria yield traits 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 associated with Boehmeria yield traits, divide solving Boehmeria
The problem that in sub-breeding, linkage molecule labelling is few.
A further object of the present invention is to provide the SSR marker associated with Boehmeria yield traits in cultivating New Ramie Variety
Purposes.
The present invention separately has a purpose to be to provide the SSR marker associated with Boehmeria yield traits at stable or raising Boehmeria product
Purposes in amount.
To this end, the technical scheme that the present invention provides is:
A kind of SSR marker associated with Boehmeria yield traits, including SSR marker RAM200, RAM108 and RAM141.
Preferably, in the described SSR marker associated with Boehmeria yield traits, also include SSR marker RAM144,
RAM179 and RAM181.
Preferably, in the described SSR marker associated with Boehmeria yield traits, described SSR marker RAM200, RAM108
It is associated with the skin depth character of RAM141 with Boehmeria two season fiber crops and three seasons fiber crops.
Preferably, in the described SSR marker associated with Boehmeria yield traits, described SSR marker RAM144, RAM179
It is associated with the fibre percentage character of RAM181 with Boehmeria two season fiber crops and three seasons fiber crops.
Preferably, in the described SSR marker associated with Boehmeria yield traits, described SSR marker RAM144 also with ramie
The plant height character that the head season fiber crops of fiber crops are numb with two seasons is associated.
The described SSR marker associated with Boehmeria yield traits purposes in cultivating New Ramie Variety.
The described SSR marker associated with Boehmeria yield traits 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 present invention provide SSR marker directly related with the yield of Boehmeria, for screen from now on elite germplasm, gene mapping and
Clone and molecular mark lay the first stone, and the SSR marker of the present invention can be used in molecular breeding and the raising of Boehmeria
In Boehmeria yield.Breeding and production for present stage China Boehmeria are significant.Meanwhile, the present invention is also molecular marker
Assistant breeding provides useful reference.
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 its character such as fibre percentage and skin depth is carried out 1 year 3 environment repetitive identified and skin
The character such as thickness, fibre percentage carry out 1 year 2 environment repetitive identified, and are associated its above character and molecular marker analyzing,
Excavating relative SSR site, 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 associated with Boehmeria yield traits, including SSR marker RAM200, RAM108 and
RAM141。
In one of them embodiment of the present invention, as preferably, the described SSR marker associated with Boehmeria yield traits
In, also include SSR marker RAM144, RAM179 and RAM181.
In one of them embodiment of the present invention, as preferably, the described SSR marker associated with Boehmeria yield traits
In, described SSR marker RAM200, RAM108 and RAM141 are associated with the skin depth character of Boehmeria two season fiber crops and three seasons fiber crops.
In one of them embodiment of the present invention, as preferably, the described SSR marker associated with Boehmeria yield traits
In, described SSR marker RAM144, RAM179 and RAM181 are associated with the fibre percentage character of Boehmeria two season fiber crops and three seasons fiber crops.
In one of them embodiment of the present invention, as preferably, the described SSR marker associated with Boehmeria yield traits
In, also numb with the head season of Boehmeria and two seasons fiber crops the plant height character of described SSR marker RAM144 is associated.
The present invention also provides for the described SSR marker associated with Boehmeria yield traits use in cultivating New Ramie Variety
On the way.
The present invention also provides for the described SSR marker associated with Boehmeria yield traits and is stablizing or improving in Boehmeria yield
Purposes.
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 skin depth, the character such as fibre percentage.The skin depth of 15 strains, fibre percentage are investigated in the most each community.
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.With reference to Chen etc.[6]Method carry out SSR-PCR.PCR primer alkene acyl ammonia gel vertical electrophoresis detects, silver staining
Detection 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, skin depth and fibre percentage are contrary trend.Skin depth two season fiber crops are numb more than three seasons, but fibre percentage
Two season fiber crops less than three seasons fiber crops；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
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.
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 RAM144 and plant height, fibre percentage are relevant.
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.Compared for the result of Liu, do not find to overlap with its any one molecular marker.
In 6 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, correlation analysis result and the association analysis result of phenotypic character show, RAM144 and plant height, fibre percentage
Relevant.The QTL positioning result of various crop shows, the distribution of QTL cluster is the most common because of multiple-effect with one.Phenotype of the present invention and molecule
Result all implies and there may be the different genes relevant to 2 character near these labellings, or there may be and control 2 simultaneously
One gene of individual character.More than research is provided convenience for carrying out molecular breeding.
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 associated with Boehmeria yield traits, therefore have
Carry out the guidance of Breeding of Ramie on a molecular scale, 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 (7)
1. the SSR marker associated with Boehmeria yield traits, including SSR marker RAM200, RAM108 and RAM141.
2. the SSR marker associated with Boehmeria yield traits as claimed in claim 1, it is characterised in that also include SSR marker
RAM144, RAM179 and RAM181.
3. the SSR marker associated with Boehmeria yield traits as claimed in claim 1, it is characterised in that described SSR marker
RAM200, RAM108 and RAM141 are associated with the skin depth character of Boehmeria two season fiber crops and three seasons fiber crops.
4. the SSR marker associated with Boehmeria yield traits as claimed in claim 2, it is characterised in that described SSR marker
RAM144, RAM179 and RAM181 are associated with the fibre percentage character of Boehmeria two season fiber crops and three seasons fiber crops.
5. the SSR marker associated with Boehmeria yield traits as claimed in claim 2, it is characterised in that described SSR marker
RAM144 is also numb with the head season of Boehmeria and two seasons fiber crops, and plant height character is associated.
6. the purposes in cultivating New Ramie Variety of the SSR marker associated with Boehmeria yield traits described in claim 1.
7. the SSR marker associated with Boehmeria yield traits as claimed in claim 1 is being stablized or is being improved the use in Boehmeria yield
On the way.
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Cited By (2)
| Publication number | Priority date | Publication date | Assignee | Title |
|---|---|---|---|---|
| CN106801105A (en) * | 2017-03-16 | 2017-06-06 | 江西省宜春市农业科学研究所 | The SSR marker being associated with ramee fineness and application |
| CN113388693A (en) * | 2021-06-23 | 2021-09-14 | 中国农业科学院麻类研究所 | QTL (quantitative trait loci) for controlling ramie bark thickness character as well as obtaining method and application thereof |
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| 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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| Publication number | Priority date | Publication date | Assignee | Title |
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| 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 |
Non-Patent Citations (2)
| Title |
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| TOUMING LIU ET AL.: "QTL mapping for fiber yield-related traits by constructing the first genetic linkage map in ramie (Boehmeria nivea L. Gaud)", 《MOLECULAR BREEDING》 * |
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Cited By (2)
| Publication number | Priority date | Publication date | Assignee | Title |
|---|---|---|---|---|
| CN106801105A (en) * | 2017-03-16 | 2017-06-06 | 江西省宜春市农业科学研究所 | The SSR marker being associated with ramee fineness and application |
| CN113388693A (en) * | 2021-06-23 | 2021-09-14 | 中国农业科学院麻类研究所 | QTL (quantitative trait loci) for controlling ramie bark thickness character as well as obtaining method and application thereof |
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