CN106803026A - A kind of utilization SSR marker information improves the method that forest tree genetic assesses accuracy - Google Patents
A kind of utilization SSR marker information improves the method that forest tree genetic assesses accuracy Download PDFInfo
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Abstract
The method that forest tree genetic assesses accuracy is improved the invention discloses a kind of utilization SSR marker information.The method carries out forest tree genetic assessment using the G matrix that SSR marker builds, the all individual ground diameters of clone seedling to be detected are determined first forms phenotypic data, and extract all clonal DNA, expanded with 134 pairs of SSR markers, amplification is recorded as 0/1 SSR marker data, then the genetic identity between clone is calculated, its inverse matrix is calculated as clonal G matrix；Phenotypic data is analyzed, with reference to the G matrix that S4 builds, environmental error and genetic variance is estimated, is calculated according to repeatability formula and is tried to achieve repeatability estimate.The method of the present invention can accurately improve the effect of forest tree genetic assessment, and without relying on the information of traditional pedigree, not limited by genetic stocks Pedigree information, and limitation of the test material without seeds and pilot forest type, application prospect is good.
Description
Technical field
The invention belongs to Forest Tree Genetic Breeding technical field.More particularly, to one kind woods is improved using SSR marker information
The method of wooden genetic evaluation accuracy.
Background technology
Woody energy is needed by field comparison test and property determination, is planted with estimating various genetic parameters and evaluating
Source, family, individual plant or clonal performance meet the high quality tree species of production of forestry demand to cultivate.For by certain mating
Design the filial generation for obtaining, it is possible to use Pedigree information estimates more genetic parameters (Lin Yuanzhen and Chen Xiao by individual body Model
Sun, R and ASReml-R statistical analysis study courses, Beijing：China Forestry Publishing House, 2014).But for provenance test or asexual
System determines, and Pedigree information is often unintelligible, even pedigree clearly progeny test, due to the molecule affiliation that pedigree is provided
Matrix information than relatively limited, so as to the accuracy for causing forest tree genetic to be assessed is not high enough, so influence high quality tree species seed selection can
By property.Therefore, it is necessary to find a kind of method for improving forest tree genetic assessment accuracy.
Compared with other molecular marking techniques, there is SSR marker easy detection, codominant inheritance, reproducible, quantity to enrich
High with polymorphism and the advantages of spread all over whole gene group, be used widely (Schlotterer C in plant genetic research
2004.The evolution of molecular markers just amatter of fashion.Nat Rev
Genet,5:63~69).But, it is various that SSR marker was used for plant genetic map construction, comparative map, blastogenesis in the past
Property evaluate and Relationship iden- tification research (Lin Yuanzhen, Guo Hai, Liu Chunxin, Liu Tianyi, Huang Shaowei, Chen Xiaoyang .EST-SSR mark
Remember the development and application Plant Physiology Communications in xylophyta, 2009,45 (12):1221-1225).At present, there are no
The report of accuracy is assessed using SSR marker information raising forest tree genetic, a kind of dividing for accurate raising forest tree genetic assessment is invented
Analysis method is extremely urgent.
The content of the invention
The technical problem to be solved in the present invention is when overcoming the existing experimental design to carry out genetic evaluation, it is impossible to provide pedigree
Information or Pedigree information than it is relatively limited when, it is impossible to accurately estimate genetic variance, and then can not accurately estimate forest tree genetic parameter
Problem, there is provided a kind of utilization SSR marker information improves the method that forest tree genetic assesses accuracy, the G built using SSR marker
Matrix carries out forest tree genetic assessment, and no matter accurate forest tree genetic assessment is identified for fine-variety breeding or breeding, all weighed very much
Will.
The method that forest tree genetic assesses accuracy is improved it is an object of the invention to provide a kind of utilization SSR marker information.
Above-mentioned purpose of the present invention is achieved through the following technical solutions：
One group can improve the SSR marker that forest tree genetic assesses accuracy, including 134 pairs of SSR markers, its upstream and downstream primer
Sequence is successively respectively as shown in SEQ ID NO.1~268.
The SSR marker improve forest tree genetic assessment accuracy in terms of application, also protection scope of the present invention it
It is interior.
A kind of utilization SSR marker information improves the method that forest tree genetic assesses accuracy, is the G built using SSR marker
Matrix carries out forest tree genetic assessment.
Specifically, the utilization SSR marker information improves the method that forest tree genetic assesses accuracy, i.e., using SSR marker
The method that the G matrix of structure carries out forest tree genetic assessment, comprises the following steps：
S1：The all individual ground diameters of several (such as 11 or so) clone Potted orchards to be detected are determined, Phenotype Number is formed
According to；
S2：All clonal DNA are extracted, is expanded with 134 pairs of SSR markers, amplification is recorded as 0/1
SSR marker data；
S3：According to SSR marker data, the genetic identity between clone is calculated；
S4：According to the genetic identity coefficient between clone, its inverse matrix is calculated, as clonal G matrix；
S5：Phenotypic data is analyzed, with reference to the G matrix that S4 builds, environmental error and genetic variance is estimated, analysis is public
Formula is：
Y=Xb+Zu+e
Wherein, y represents the measured value of clone individuality ground diameter, and b represents fixed effect value, and u represents stochastic effects value, e generations
Table residual error effect；
S6：Calculated according to repeatability formula and seek repeatability estimate, the repeatability formula is：
Rep=Vc/Vp
Wherein rep represents repeatability, and Vc is clone genetic variance, and Vp is phenotypic variance.
Preferably, in step S5, test data is analyzed using ASReml-R softwares, in combination with the G that S4 builds
Matrix, so as to estimate genetic variance and environmental error.
Preferably, in step S3, SSR marker data are analyzed using NTsys softwares, so that between calculating clone
Genetic identity.
Preferably, in step S1, the clone to be detected is Eucalyptus clone.
Preferably, the clone seedling to be detected is 5 monthly age of Eucalyptus clone Potted orchard.
Preferably, in step S1, clone of participating in the experiment totally 11,10 Potted orchards of each clone.
In addition, in step S2, described SSR marker information is 0/1 form.
In step S2,134 pairs of SSR markers are 134 pairs of SSR primers, and downstream primer sequence is successively respectively such as thereon
Shown in SEQ ID NO.1~268.
More specifically preferably, above-mentioned utilization SSR marker information improves the method that forest tree genetic assesses accuracy, including as follows
Step：
(1) test material described in is 5 months Potted orchards of Eucalyptus clone, clone of participating in the experiment totally 11, each clone
10 Potted orchards；
(2) whole Potted orchards are carried out with the measurement of ground diameter, the measured value of each individual ground diameter is obtained；
(3) all clonal genomic DNAs are extracted, is expanded by 134 pairs of SSR primers, selected clear, repeatable
Band statistics, data-entry-form：There is band to be designated as 1,0 is designated as without band, set up SSR marker data matrix；
(4) to SSR marker data matrix, the genetic identity coefficient between clone is calculated by NTsys 2.10e softwares
Matrix；
(5) to genetic identity coefficient matrix, by the genetic identity between R-3.2.1 softwares calculating clone against square
Battle array, as clonal G matrix；
(6) genetic variance is accurately estimated using ASReml-R softwares:
Y=Xb+Zu+e
Wherein y represents the measured value of clone individuality ground diameter, and b represents fixed effect value, and u represents stochastic effects value, and e is represented
Residual error effect；
(7) calculated further according to repeatability formula and try to achieve repeatability estimate：
Rep=Vc/Vp
Wherein rep represents repeatability, VcIt is genetic variance, VpIt is phenotypic variance.
The invention has the advantages that：
The method of the present invention compared to the traditional analysis by experimental design, the information without relying on traditional pedigree,
Do not limited by genetic stocks Pedigree information, and the present invention has no the specific limit of seeds and pilot forest type for test material
System, therefore other seeds and provenance test woods, progeny test forost and clonal test woods are all not only restricted to this, by the present invention
The effect of forest tree genetic assessment can accurately be improved.
Brief description of the drawings
Fig. 1 is the genetic identity between 11 Eucalyptus clones, illustrates the clone based on genetic identity coefficient and gathers
Class figure.
Specific embodiment
The present invention, but embodiment are further illustrated below in conjunction with Figure of description and specific embodiment not to the present invention
Limit in any form.Unless stated otherwise, reagent, the method and apparatus that the present invention is used are for the art is routinely tried
Agent, method and apparatus.
Unless stated otherwise, following examples agents useful for same and material are purchased in market.
The method of the present invention goes for any existing experimental design, is opened using the G matrix of SSR marker information architecture
Exhibition forest tree genetic evaluation work, can be particularly suitable for the unsharp pilot forest of pedigree for proterties such as growth, material, resistances.Can
Assessed with the forest tree genetic for meeting any growth phase.
The method of the present invention is further described below.
Embodiment 1
The accurate appraisal procedure of forest tree genetic of the invention, including the collection of family individual data items, SSR marker data structure, mould
Type is set up and data analysis step；It is specific as follows：
First, clone individual data items collection
All potted plant individualities are all carried out with the measurement of ground diameter, corresponding ground diameter data are then input into according to clone number.
2nd, the structure of SSR marker data
SSR marker data are the polymorphism data collection that clone is expanded to different SSR markers, for calculating clone between
Genetic identity.Specific construction method：All clonal DNA must be extracted, 134 pairs of amplifications of SSR marker are sequentially completed.There is band
1 is designated as, 0 is designated as without band, set up SSR marker data matrix, the heredity calculated by NTsys 2.10e softwares between clone is consistent
Property coefficient matrix, and draw the dendrogram between clone.Finally further counted according to genetic identity matrix with R-3.2.1 softwares
Calculate without its inverse matrix, as clonal G matrix.
Wherein, 134 pairs of SSR markers are 134 pairs of SSR primers, and downstream primer sequence is successively respectively such as SEQ thereon
Shown in ID NO.1~268.
The title and its sequence of specific 134 pairs of SSR markers are as shown in the table：
3rd, model is set up
In order to realize the object of the invention, the solution of the present invention is provided with 2 kinds of analysis models and compares：
Model 1, contains ground diameter measured value y, population mean μ (fixed effect), clone Clone (stochastic effects) and residual
Difference e.
Model 2, contains ground diameter measured value y, population mean μ (fixed effect), clone Clone (stochastic effects) and residual
Difference e；Difference with model 1 is, the G matrix that the random clone effect of model 2 is built using SSR marker matrix, and model 1
Be unit matrix I.
4th, data analysis
From accompanying drawing 1, with genetic identity coefficient 0.45 as boundary, it is seen that 11 clones are divided into 3 classes：No. 12, No. 20
It is a class to gather, a No. 22 independent classes, and it is a class that other 8 are gathered.Result based on SSR marker shows do not have not between clone
There is relation.
Based on above-mentioned specific different models, point difference component and a repeatability are estimated respectively using ASReml-R softwares, accurately
Estimation genetic variance：
Y=Xb+Zu+e
Wherein y represents the measured value of clone individuality ground diameter, and b represents fixed effect value μ, and it is asexual that u represents stochastic effects value
It is Clone, e represents residual error effect.
Calculated further according to repeatability formula and try to achieve repeatability estimate：
Rep=Vc/Vp
Wherein rep represents repeatability, VcIt is genetic variance, VpIt is phenotypic variance.
5th, result
Concrete outcome is shown in Table 1.
For model 1, clone genetic variance Vc is 1.93, and residual error Ve is 1.13, and the repeatability h2 of estimation is 0.63.It is right
In model 2, clone genetic variance Va is 5.86, and residual error Ve is 1.06, and the repeatability h2 of estimation is 0.85.Compare with model 1,
Residual error is not changed in substantially, but clone genetic variance increases by 202%, and repeatability also increases 34%, it is seen that model 2 compares model
The result of 1 fitting is more preferable.
The model genetic parameter estimation value of table 1
| Model | Vc | Ve | rep | rep.se | UVc | Urep |
| Model 1 | 1.93 | 1.13 | 0.63 | 0.09 | -- | -- |
| Model 2 | 5.86 | 1.06 | 0.85 | 0.06 | 202% | 34% |
Note：Vc is clone genetic variance, and Ve is error, and rep is repeatability, and rep.se is repeatability error, and UVc is something lost
Variance increment rate is passed, Urep is repeatability increment rate.
Understood based on above-mentioned analysis, model 2, i.e., be optimal models using the model of SSR marker information architecture G matrix, i.e.,
Optimized analysis model of the invention.By best model, the genetic affinity between genetic stocks, and then accurate estimation heredity can be specified
Error, and other genetic parameters are further accurately estimated, then reach the accurate purpose for improving forest tree genetic assessment.
Obviously, the above embodiment of the present invention is only intended to clearly illustrate example of the present invention, and is not right
The restriction of embodiments of the present invention.For those of ordinary skill in the field, may be used also on the basis of the above description
To make other changes in different forms.There is no need and unable to be exhaustive to all of implementation method.It is all this
Any modification, equivalent and improvement made within the spirit and principle of invention etc., should be included in the claims in the present invention
Protection domain within.
SEQUENCE LISTING
<110>Agricultural University Of South China
<120>A kind of utilization SSR marker information improves the method that forest tree genetic assesses accuracy
<130>
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<170> PatentIn version 3.3
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cgctcagggc tagagagaga 20
<210> 84
<211> 20
<212> DNA
<213>SSR marker S420 reverse primers
<400> 84
cttttgcatg gccttcattt 20
<210> 85
<211> 20
<212> DNA
<213>SSR marker S425 forward primers
<400> 85
agaacccgta gtagtcggca 20
<210> 86
<211> 20
<212> DNA
<213>SSR marker S425 reverse primers
<400> 86
gataaccacc cctctccctc 20
<210> 87
<211> 20
<212> DNA
<213>SSR marker S430 forward primers
<400> 87
ggtttcgtga tttaagcgga 20
<210> 88
<211> 20
<212> DNA
<213>SSR marker S430 reverse primers
<400> 88
tattcggaca aatggcttcc 20
<210> 89
<211> 21
<212> DNA
<213>SSR marker S431 forward primers
<400> 89
caatggtcat gagttgattc g 21
<210> 90
<211> 20
<212> DNA
<213>SSR marker S431 reverse primers
<400> 90
gctcataatg ggcatcacac 20
<210> 91
<211> 20
<212> DNA
<213>SSR marker S432 forward primers
<400> 91
tccctactca ttgccaggac 20
<210> 92
<211> 20
<212> DNA
<213>SSR marker S432 reverse primers
<400> 92
aagcacaagc tctctctgcc 20
<210> 93
<211> 20
<212> DNA
<213>SSR marker S501 forward primers
<400> 93
tcactcccca tgatgtcaaa 20
<210> 94
<211> 20
<212> DNA
<213>SSR marker S501 reverse primers
<400> 94
gcgctgacgt catatttcaa 20
<210> 95
<211> 20
<212> DNA
<213>SSR marker S505 forward primers
<400> 95
catcgaataa tttgcaccga 20
<210> 96
<211> 21
<212> DNA
<213>SSR marker S505 reverse primers
<400> 96
ccaagttttt ggtgaagatg g 21
<210> 97
<211> 19
<212> DNA
<213>SSR marker S510 forward primers
<400> 97
acaccatcac ggggaattt 19
<210> 98
<211> 20
<212> DNA
<213>SSR marker S510 reverse primers
<400> 98
tgtttcacaa agagcgcaac 20
<210> 99
<211> 20
<212> DNA
<213>SSR marker S511 forward primers
<400> 99
ctggtctcca aggtccagag 20
<210> 100
<211> 19
<212> DNA
<213>SSR marker S511 reverse primers
<400> 100
gaggcggaga tcgagtacc 19
<210> 101
<211> 20
<212> DNA
<213>SSR marker S512 forward primers
<400> 101
catcatgagg cttttgagca 20
<210> 102
<211> 21
<212> DNA
<213>SSR marker S512 reverse primers
<400> 102
tcatcctctc cctctctctc c 21
<210> 103
<211> 20
<212> DNA
<213>SSR marker S513 forward primers
<400> 103
tgggtcgtca cactagacca 20
<210> 104
<211> 20
<212> DNA
<213>SSR marker S513 reverse primers
<400> 104
atcggattgt tgtttctgcc 20
<210> 105
<211> 20
<212> DNA
<213>SSR marker S514 forward primers
<400> 105
gatgagatgg agaaggaccg 20
<210> 106
<211> 20
<212> DNA
<213>SSR marker S514 reverse primers
<400> 106
cattgtgcga agaccagaaa 20
<210> 107
<211> 20
<212> DNA
<213>SSR marker S516 forward primers
<400> 107
tggatcgttg ctctcacaag 20
<210> 108
<211> 20
<212> DNA
<213>SSR marker S516 reverse primers
<400> 108
gctttggcga gcatttattt 20
<210> 109
<211> 20
<212> DNA
<213>SSR marker S524 forward primers
<400> 109
cgaaattgca accttttgct 20
<210> 110
<211> 20
<212> DNA
<213>SSR marker S524 reverse primers
<400> 110
gggaggattc tcacccaagt 20
<210> 111
<211> 20
<212> DNA
<213>SSR marker S526 forward primers
<400> 111
aagacaacct tgccatcagg 20
<210> 112
<211> 21
<212> DNA
<213>SSR marker S526 reverse primers
<400> 112
tcgcttaatg tgtgtgctct g 21
<210> 113
<211> 20
<212> DNA
<213>SSR marker S605 forward primers
<400> 113
ccacagcgga aggaaaataa 20
<210> 114
<211> 20
<212> DNA
<213>SSR marker S605 reverse primers
<400> 114
gggggtagaa gaggatcgag 20
<210> 115
<211> 20
<212> DNA
<213>SSR marker S610 forward primers
<400> 115
ggtgaggtca ctagcccttg 20
<210> 116
<211> 20
<212> DNA
<213>SSR marker S610 reverse primers
<400> 116
tttttccttt cttcctcccc 20
<210> 117
<211> 20
<212> DNA
<213>SSR marker S611 forward primers
<400> 117
atccagcaat cgaccaactc 20
<210> 118
<211> 20
<212> DNA
<213>SSR marker S611 reverse primers
<400> 118
ctttttcaat gggcacgtct 20
<210> 119
<211> 20
<212> DNA
<213>SSR marker S615 forward primers
<400> 119
agggcgctca tcttagtgtg 20
<210> 120
<211> 20
<212> DNA
<213>SSR marker S615 reverse primers
<400> 120
acgtagttgc cacaacacca 20
<210> 121
<211> 20
<212> DNA
<213>SSR marker S616 forward primers
<400> 121
tttttcggaa ccaaaactgg 20
<210> 122
<211> 20
<212> DNA
<213>SSR marker S616 reverse primers
<400> 122
atgtcgttga gtggaggagg 20
<210> 123
<211> 20
<212> DNA
<213>SSR marker S618 forward primers
<400> 123
aacattggcc aaaaatctcg 20
<210> 124
<211> 20
<212> DNA
<213>SSR marker S618 reverse primers
<400> 124
tggccttaga attccgctta 20
<210> 125
<211> 20
<212> DNA
<213>SSR marker S619 forward primers
<400> 125
ctgagatgga gcggtaggag 20
<210> 126
<211> 20
<212> DNA
<213>SSR marker S619 reverse primers
<400> 126
tcgcttaagc acatttggtg 20
<210> 127
<211> 20
<212> DNA
<213>SSR marker S621 forward primers
<400> 127
cgaaactcac gacttgttcg 20
<210> 128
<211> 20
<212> DNA
<213>SSR marker S621 reverse primers
<400> 128
ccgttctccc ctctctctct 20
<210> 129
<211> 19
<212> DNA
<213>SSR marker S626 forward primers
<400> 129
ctctccgaga aggaggagg 19
<210> 130
<211> 20
<212> DNA
<213>SSR marker S626 reverse primers
<400> 130
tgagtgaaac aatggcgttc 20
<210> 131
<211> 20
<212> DNA
<213>SSR marker S629 forward primers
<400> 131
tcgttgacca tgcatttgat 20
<210> 132
<211> 20
<212> DNA
<213>SSR marker S629 reverse primers
<400> 132
atgatacgcc aaacaaaggg 20
<210> 133
<211> 20
<212> DNA
<213>SSR marker S630 forward primers
<400> 133
cccaatagct ctccgattca 20
<210> 134
<211> 20
<212> DNA
<213>SSR marker S630 reverse primers
<400> 134
acgatctcca atcaaccgac 20
<210> 135
<211> 20
<212> DNA
<213>SSR marker S631 forward primers
<400> 135
tgattcggga atattttggc 20
<210> 136
<211> 20
<212> DNA
<213>SSR marker S631 reverse primers
<400> 136
tggtgaccat ccaggcttat 20
<210> 137
<211> 20
<212> DNA
<213>SSR marker S632 forward primers
<400> 137
cctcgatccc catttgtaag 20
<210> 138
<211> 20
<212> DNA
<213>SSR marker S632 reverse primers
<400> 138
ctgatgagga atttgcatgg 20
<210> 139
<211> 20
<212> DNA
<213>SSR marker S633 forward primers
<400> 139
tctccacctt ccactgctct 20
<210> 140
<211> 20
<212> DNA
<213>SSR marker S633 reverse primers
<400> 140
ggccgagtgg tgaattctaa 20
<210> 141
<211> 20
<212> DNA
<213>SSR marker S701 forward primers
<400> 141
tgcgagtgga tctgtgaaac 20
<210> 142
<211> 20
<212> DNA
<213>SSR marker S701 reverse primers
<400> 142
tggatgaaca aacacggaaa 20
<210> 143
<211> 20
<212> DNA
<213>SSR marker S703 forward primers
<400> 143
aagagaccga agctggttga 20
<210> 144
<211> 20
<212> DNA
<213>SSR marker S703 reverse primers
<400> 144
gcagctgctt ctcttctgct 20
<210> 145
<211> 20
<212> DNA
<213>SSR marker S709 forward primers
<400> 145
attgatgcag gggcaaaata 20
<210> 146
<211> 21
<212> DNA
<213>SSR marker S709 reverse primers
<400> 146
tcatttgact tctggcactg a 21
<210> 147
<211> 20
<212> DNA
<213>SSR marker S713 forward primers
<400> 147
cgactttcag tgcaaaacga 20
<210> 148
<211> 21
<212> DNA
<213>SSR marker S713 reverse primers
<400> 148
tgactcagca agtaaacgca a 21
<210> 149
<211> 20
<212> DNA
<213>SSR marker S714 forward primers
<400> 149
tacgtgtgcg cgacttctac 20
<210> 150
<211> 20
<212> DNA
<213>SSR marker S714 reverse primers
<400> 150
cgcattagtg gttggtgatg 20
<210> 151
<211> 20
<212> DNA
<213>SSR marker S715 forward primers
<400> 151
agctggaccg tcttcttcaa 20
<210> 152
<211> 20
<212> DNA
<213>SSR marker S715 reverse primers
<400> 152
gcattggaga aggaattgga 20
<210> 153
<211> 20
<212> DNA
<213>SSR marker S719 forward primers
<400> 153
gccggcatga aactaaacat 20
<210> 154
<211> 20
<212> DNA
<213>SSR marker S719 reverse primers
<400> 154
atccgagaga gaaagagggg 20
<210> 155
<211> 20
<212> DNA
<213>SSR marker S720 forward primers
<400> 155
agatatgttg ggtcccctcc 20
<210> 156
<211> 20
<212> DNA
<213>SSR marker S720 reverse primers
<400> 156
caccaccaga aaacaaaggg 20
<210> 157
<211> 20
<212> DNA
<213>SSR marker S721 forward primers
<400> 157
tgtcccatca gcaaaatcaa 20
<210> 158
<211> 20
<212> DNA
<213>SSR marker S721 reverse primers
<400> 158
gggatttagc ggcactcata 20
<210> 159
<211> 20
<212> DNA
<213>SSR marker S722 forward primers
<400> 159
agctggaccg tcttcttcaa 20
<210> 160
<211> 20
<212> DNA
<213>SSR marker S722 reverse primers
<400> 160
gcattggaga aggaattgga 20
<210> 161
<211> 20
<212> DNA
<213>SSR marker S801 forward primers
<400> 161
accaaattca gtggacccag 20
<210> 162
<211> 20
<212> DNA
<213>SSR marker S801 reverse primers
<400> 162
aaaggggact gcaaaggaat 20
<210> 163
<211> 20
<212> DNA
<213>SSR marker S804 forward primers
<400> 163
ccttgtggag tcacggatct 20
<210> 164
<211> 20
<212> DNA
<213>SSR marker S804 reverse primers
<400> 164
gttagcaatt cgatcgggaa 20
<210> 165
<211> 20
<212> DNA
<213>SSR marker S808 forward primers
<400> 165
aaaatatacg gagcccgctt 20
<210> 166
<211> 20
<212> DNA
<213>SSR marker S808 reverse primers
<400> 166
cttgacggcc accattatct 20
<210> 167
<211> 20
<212> DNA
<213>SSR marker S809 forward primers
<400> 167
cattcttggc aagcaggttt 20
<210> 168
<211> 20
<212> DNA
<213>SSR marker S809 reverse primers
<400> 168
tcctatccaa cgcatcatca 20
<210> 169
<211> 20
<212> DNA
<213>SSR marker S810 forward primers
<400> 169
cattcttggc aagcaggttt 20
<210> 170
<211> 20
<212> DNA
<213>SSR marker S810 reverse primers
<400> 170
tcctatccaa cgcatcatca 20
<210> 171
<211> 20
<212> DNA
<213>SSR marker S812 forward primers
<400> 171
tccatcattg ttgagccaaa 20
<210> 172
<211> 20
<212> DNA
<213>SSR marker S812 reverse primers
<400> 172
ccttgttctc ccctcacaaa 20
<210> 173
<211> 20
<212> DNA
<213>SSR marker S815 forward primers
<400> 173
cttatagctc gcgccttttg 20
<210> 174
<211> 20
<212> DNA
<213>SSR marker S815 reverse primers
<400> 174
tagcaattcg atcgggaatc 20
<210> 175
<211> 20
<212> DNA
<213>SSR marker S816 forward primers
<400> 175
ccacaaacat tgcgattcaa 20
<210> 176
<211> 20
<212> DNA
<213>SSR marker S816 reverse primers
<400> 176
gccgtgcaga gagagagaga 20
<210> 177
<211> 21
<212> DNA
<213>SSR marker S819 forward primers
<400> 177
tgtgttcaaa tcaaagtgcc a 21
<210> 178
<211> 20
<212> DNA
<213>SSR marker S819 reverse primers
<400> 178
ttgccttaac ccaaggaatg 20
<210> 179
<211> 20
<212> DNA
<213>SSR marker S820 forward primers
<400> 179
tgtgacatga tgcccacata 20
<210> 180
<211> 20
<212> DNA
<213>SSR marker S820 reverse primers
<400> 180
gaagggatgc attggaagaa 20
<210> 181
<211> 20
<212> DNA
<213>SSR marker S825 forward primers
<400> 181
aaaatttggc ctttgtcacg 20
<210> 182
<211> 20
<212> DNA
<213>SSR marker S825 reverse primers
<400> 182
tgagagagag aagtggggga 20
<210> 183
<211> 20
<212> DNA
<213>SSR marker S827 forward primers
<400> 183
aagccgagga aaaagaaacg 20
<210> 184
<211> 20
<212> DNA
<213>SSR marker S827 reverse primers
<400> 184
cctttggatc tgctggagag 20
<210> 185
<211> 20
<212> DNA
<213>SSR marker S828 forward primers
<400> 185
aagtccagcc tttgcagtgt 20
<210> 186
<211> 20
<212> DNA
<213>SSR marker S828 reverse primers
<400> 186
tggctatgaa aatggcacaa 20
<210> 187
<211> 20
<212> DNA
<213>SSR marker S901 forward primers
<400> 187
atgatgatgg taatggcggt 20
<210> 188
<211> 20
<212> DNA
<213>SSR marker S901 reverse primers
<400> 188
aggcttatga tatcgtggcg 20
<210> 189
<211> 20
<212> DNA
<213>SSR marker S902 forward primers
<400> 189
ccatggtgaa atgtgatgga 20
<210> 190
<211> 20
<212> DNA
<213>SSR marker S902 reverse primers
<400> 190
gtcttgtggg catcgttctt 20
<210> 191
<211> 19
<212> DNA
<213>SSR marker S905 forward primers
<400> 191
cgacttcggt gctgaagaa 19
<210> 192
<211> 20
<212> DNA
<213>SSR marker S905 reverse primers
<400> 192
actctctcac caccaccacc 20
<210> 193
<211> 20
<212> DNA
<213>SSR marker S906 forward primers
<400> 193
tctccctcta caccgaccac 20
<210> 194
<211> 20
<212> DNA
<213>SSR marker S906 reverse primers
<400> 194
gtcttgatgc aacccctgat 20
<210> 195
<211> 20
<212> DNA
<213>SSR marker S907 forward primers
<400> 195
atcaggggtt gcatcaagac 20
<210> 196
<211> 20
<212> DNA
<213>SSR marker S907 reverse primers
<400> 196
gtgtacaccg ggacttgctt 20
<210> 197
<211> 20
<212> DNA
<213>SSR marker S911 forward primers
<400> 197
cgttcttcac caaaaacggt 20
<210> 198
<211> 20
<212> DNA
<213>SSR marker S911 reverse primers
<400> 198
tcacccactc ctccattttc 20
<210> 199
<211> 20
<212> DNA
<213>SSR marker S914 forward primers
<400> 199
ggagtccgat accagaacga 20
<210> 200
<211> 20
<212> DNA
<213>SSR marker S914 reverse primers
<400> 200
gagaagtgca ggattggagc 20
<210> 201
<211> 20
<212> DNA
<213>SSR marker S922 forward primers
<400> 201
acatgaacgc acaccaattc 20
<210> 202
<211> 20
<212> DNA
<213>SSR marker S922 reverse primers
<400> 202
agcgagccaa aggaaactct 20
<210> 203
<211> 20
<212> DNA
<213>SSR marker S925 forward primers
<400> 203
atcggtgagc gtgagcttat 20
<210> 204
<211> 21
<212> DNA
<213>SSR marker S925 reverse primers
<400> 204
caaatcctca cttcctcctc t 21
<210> 205
<211> 20
<212> DNA
<213>SSR marker S1006 forward primers
<400> 205
tgtttgtgcc tcatcagctc 20
<210> 206
<211> 20
<212> DNA
<213>SSR marker S1006 reverse primers
<400> 206
cggacatttg tacccgaaga 20
<210> 207
<211> 20
<212> DNA
<213>SSR marker S1007 forward primers
<400> 207
cgtctctgac cacgaattga 20
<210> 208
<211> 20
<212> DNA
<213>SSR marker S1007 reverse primers
<400> 208
acttgctacc cacttgccac 20
<210> 209
<211> 20
<212> DNA
<213>SSR marker S1018 forward primers
<400> 209
cttcattggc ctctgaggag 20
<210> 210
<211> 20
<212> DNA
<213>SSR marker S1018 reverse primers
<400> 210
ccataggtgg agccaggtaa 20
<210> 211
<211> 20
<212> DNA
<213>SSR marker S1021 forward primers
<400> 211
aaacgaaaac ctcgaggaca 20
<210> 212
<211> 20
<212> DNA
<213>SSR marker S1021 reverse primers
<400> 212
ctggcaatga tttcgtgttg 20
<210> 213
<211> 20
<212> DNA
<213>SSR marker S1022 forward primers
<400> 213
caacacgaaa tcattgccag 20
<210> 214
<211> 20
<212> DNA
<213>SSR marker S1022 reverse primers
<400> 214
cgctattgca agcaacaaaa 20
<210> 215
<211> 20
<212> DNA
<213>SSR marker S1024 forward primers
<400> 215
gggcattgtc cagagctaaa 20
<210> 216
<211> 20
<212> DNA
<213>SSR marker S1024 reverse primers
<400> 216
gtttagctgg agccttggag 20
<210> 217
<211> 20
<212> DNA
<213>SSR marker S1025 forward primers
<400> 217
cctaagcctc gcatcaaatc 20
<210> 218
<211> 20
<212> DNA
<213>SSR marker S1025 reverse primers
<400> 218
cttgccgaag acgacaaaat 20
<210> 219
<211> 20
<212> DNA
<213>SSR marker S1107 forward primers
<400> 219
ttggtgtcgc aggaattgta 20
<210> 220
<211> 20
<212> DNA
<213>SSR marker S1107 reverse primers
<400> 220
aaatcggttc caagtcaacg 20
<210> 221
<211> 20
<212> DNA
<213>SSR marker S1109 forward primers
<400> 221
gtcgttgact tggaaccgat 20
<210> 222
<211> 20
<212> DNA
<213>SSR marker S1109 reverse primers
<400> 222
ccattcgcca acttgcttat 20
<210> 223
<211> 20
<212> DNA
<213>SSR marker S1114 forward primers
<400> 223
tttcatgggg tactcttgcc 20
<210> 224
<211> 20
<212> DNA
<213>SSR marker S1114 reverse primers
<400> 224
agagagaaag ggggagatgg 20
<210> 225
<211> 20
<212> DNA
<213>SSR marker S1115 forward primers
<400> 225
ttttcgtttt tgtgtgctgc 20
<210> 226
<211> 20
<212> DNA
<213>SSR marker S1115 reverse primers
<400> 226
actaccgctc aagatcgcac 20
<210> 227
<211> 20
<212> DNA
<213>SSR marker S1119 forward primers
<400> 227
cctctcgttt cttgccgtag 20
<210> 228
<211> 20
<212> DNA
<213>SSR marker S1119 reverse primers
<400> 228
aaggaaggaa ggagaaccga 20
<210> 229
<211> 20
<212> DNA
<213>SSR marker S1121
<400> 229
ctctctctca ttcgtcgcct 20
<210> 230
<211> 20
<212> DNA
<213>SSR marker S1121 reverse primers
<400> 230
gctaaggcgg accttcttct 20
<210> 231
<211> 20
<212> DNA
<213>SSR marker S1122 forward primers
<400> 231
cctctcgttt cttgccgtag 20
<210> 232
<211> 20
<212> DNA
<213>SSR marker S1122 reverse primers
<400> 232
aaggaaggaa ggagaaccga 20
<210> 233
<211> 20
<212> DNA
<213>SSR marker S1123 forward primers
<400> 233
tcgctacctt ctctccctcc 20
<210> 234
<211> 20
<212> DNA
<213>SSR marker S1123 reverse primers
<400> 234
tcttcttcgt cagctcctgc 20
<210> 235
<211> 20
<212> DNA
<213>SSR marker S1125 forward primers
<400> 235
gcaggagctg acgaagaaga 20
<210> 236
<211> 20
<212> DNA
<213>SSR marker S1125 reverse primers
<400> 236
tacgtacacg aacagcgagc 20
<210> 237
<211> 17
<212> DNA
<213>SSR marker S1126 forward primers
<400> 237
caatgcctgc gcagaag 17
<210> 238
<211> 20
<212> DNA
<213>SSR marker S1126 reverse primers
<400> 238
aagaagagga gctaaggcgg 20
<210> 239
<211> 20
<212> DNA
<213>SSR marker S1129 forward primers
<400> 239
tccagtccag gtcatcacaa 20
<210> 240
<211> 20
<212> DNA
<213>SSR marker S1129 reverse primers
<400> 240
gagtgggctt gtggagtagc 20
<210> 241
<211> 20
<212> DNA
<213>SSR marker S1203 forward primers
<400> 241
tggtggtttg gttttcgttt 20
<210> 242
<211> 20
<212> DNA
<213>SSR marker S1203 reverse primers
<400> 242
gaacattact tgggggtcca 20
<210> 243
<211> 20
<212> DNA
<213>SSR marker S1206 forward primers
<400> 243
gatgacggcg acccttatta 20
<210> 244
<211> 20
<212> DNA
<213>SSR marker S1206 reverse primers
<400> 244
ggagagagag aagctggcaa 20
<210> 245
<211> 20
<212> DNA
<213>SSR marker S1207 forward primers
<400> 245
ctgagagttc cgagtcggtc 20
<210> 246
<211> 20
<212> DNA
<213>SSR marker S1207 reverse primers
<400> 246
atgccttttt ggacgctatg 20
<210> 247
<211> 20
<212> DNA
<213>SSR marker S1209 forward primers
<400> 247
gctttgtcca tataacgggc 20
<210> 248
<211> 20
<212> DNA
<213>SSR marker S1209 reverse primers
<400> 248
tgaacttggc acaaagcaag 20
<210> 249
<211> 20
<212> DNA
<213>SSR marker S1215 forward primers
<400> 249
gcaaaatcga gctaattgcg 20
<210> 250
<211> 20
<212> DNA
<213>SSR marker S1215 reverse primers
<400> 250
ccgctagggt ttccttttct 20
<210> 251
<211> 20
<212> DNA
<213>SSR marker S1216 forward primers
<400> 251
tgtatcatag caatggcgga 20
<210> 252
<211> 20
<212> DNA
<213>SSR marker S1216 reverse primers
<400> 252
gccctccatc ctttcttttc 20
<210> 253
<211> 20
<212> DNA
<213>SSR marker S1219 forward primers
<400> 253
tgtaaaaatg cgaatgcacc 20
<210> 254
<211> 20
<212> DNA
<213>SSR marker S1219 reverse primers
<400> 254
tgggctatta cccaatgagg 20
<210> 255
<211> 20
<212> DNA
<213>SSR marker S1221 forward primers
<400> 255
tgcccttgag aagaggaaga 20
<210> 256
<211> 20
<212> DNA
<213>SSR marker S1221 reverse primers
<400> 256
aaaacacgtg gctctttgct 20
<210> 257
<211> 19
<212> DNA
<213>SSR marker S1223 forward primers
<400> 257
acattctcgg gaggattgg 19
<210> 258
<211> 20
<212> DNA
<213>SSR marker S1223 reverse primers
<400> 258
tctttcactg ctgcaagagc 20
<210> 259
<211> 20
<212> DNA
<213>SSR marker S1228 forward primers
<400> 259
tttcatccat gtagggcaca 20
<210> 260
<211> 20
<212> DNA
<213>SSR marker S1228 reverse primers
<400> 260
ttggcacaaa gaaagaagca 20
<210> 261
<211> 20
<212> DNA
<213>SSR marker S1230 forward primers
<400> 261
ctgcaaatgg tcaatccctt 20
<210> 262
<211> 20
<212> DNA
<213>SSR marker S1230 reverse primers
<400> 262
tgatgcacat acatgccaaa 20
<210> 263
<211> 20
<212> DNA
<213>SSR marker S1232 forward primers
<400> 263
aattggacaa gtggcaaagg 20
<210> 264
<211> 20
<212> DNA
<213>SSR marker S1232 reverse primers
<400> 264
tccacttgcc tctaggatgg 20
<210> 265
<211> 20
<212> DNA
<213>SSR marker S1236 forward primers
<400> 265
tcgtgctagc aatctcatgg 20
<210> 266
<211> 20
<212> DNA
<213>SSR marker S1236 reverse primers
<400> 266
acaacggttg ctaatcgtcc 20
<210> 267
<211> 20
<212> DNA
<213>SSR marker S1237 forward primers
<400> 267
gatcgaggga cgattagcaa 20
<210> 268
<211> 20
<212> DNA
<213>SSR marker S1237 reverse primers
<400> 268
gcatacatgc ccaaagtgaa 20
Claims (9)
1. one group can improve the SSR marker that forest tree genetic assesses accuracy, it is characterised in that including 134 pairs of SSR markers, its
Upstream and downstream primer sequence is successively respectively as shown in SEQ ID NO.1~268.
2. application of the SSR marker described in claim 1 in terms of forest tree genetic assessment accuracy is improved.
3. a kind of utilization SSR marker information improves the method that forest tree genetic assesses accuracy, it is characterised in that marked using SSR
Remember that the G matrix for building carries out forest tree genetic assessment.
4. method according to claim 3, it is characterised in that comprise the following steps：
S1：The all individual ground diameters of several clone seedlings to be detected are determined, phenotypic data is formed；
S2：All clonal DNA are extracted, is expanded with 134 pairs of SSR markers, amplification is recorded as 0/1 SSR marks
Numeration evidence；
S3：According to SSR marker data, the genetic identity between clone is calculated；
S4：According to the genetic identity coefficient between clone, its inverse matrix is calculated, as clonal G matrix；
S5：Phenotypic data is analyzed, with reference to the G matrix that S4 builds, environmental error and genetic variance, analytical formula is estimated
For：
y=Xb+Zu+e
Wherein, y represents the measured value of clone individuality ground diameter, and b represents fixed effect value, and u represents stochastic effects value, and e represents residual
Difference effect, e includes measurement error；
S6：Calculated according to repeatability formula and try to achieve repeatability estimate, the repeatability formula is：
rep=Vc/Vp
Wherein rep represents repeatability, and Vc is clone genetic variance, and Vp is phenotypic variance.
5. method according to claim 4, it is characterised in that in step S5, using ASReml-R softwares to test data
It is analyzed, in combination with the G matrix that S4 builds, so as to estimate genetic variance and environmental error.
6. method according to claim 4, it is characterised in that in step S3, using NTsys softwares to SSR marker data
It is analyzed, so that the genetic identity between calculating clone.
7. method according to claim 4, it is characterised in that in step S1, the clone to be detected is that eucalyptus is asexual
System.
8. method according to claim 4, it is characterised in that in step S2,134 couples of SSR marks are 134 pairs
SSR primers, downstream primer sequence is successively respectively as shown in SEQ ID NO.1~268 thereon.
9. method according to claim 4, it is characterised in that comprise the following steps：
（1）Described test material is 5 months Potted orchards of Eucalyptus clone, clone of participating in the experiment totally 11, each clone 10
Potted orchard；
（2）Whole Potted orchards are carried out with the measurement of ground diameter, the measured value of each individual ground diameter is obtained；
（3）All clonal genomic DNAs are extracted, is expanded by 134 pairs of SSR primers, clear, the repeatable bar of selection
Band statistics, data-entry-form：There is band to be designated as 1,0 is designated as without band, set up SSR marker data matrix；
（4）To SSR marker data matrix, the genetic identity coefficient matrix between clone is calculated by NTsys 2.10e softwares；
（5）To genetic identity coefficient matrix, the genetic identity inverse matrix between clone is calculated by R-3.2.1 softwares, made
It is clonal G matrix；
（6）Genetic variance is accurately estimated using ASReml-R softwares:
y=Xb+Zu+e
Wherein y represents the measured value of clone individuality ground diameter, and b represents fixed effect value, and u represents stochastic effects value, and e represents residual error
Effect；
（7）Calculated further according to repeatability formula and try to achieve repeatability estimate：
rep=Vc/Vp
WhereinrepRepresent repeatability, VcIt is genetic variance, VpIt is phenotypic variance.
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|---|---|---|---|---|
| CN101617047A (en) * | 2007-01-12 | 2009-12-30 | 卡纳维亚利斯有限公司 | The fingerprinting system that is used for the saccharum complex group based on little satellite |
| CN102226178A (en) * | 2011-05-13 | 2011-10-26 | 华南农业大学 | Method for developing SSR (simple sequence repeats) marker at high throughput from forest genome |
| CN103911372A (en) * | 2014-03-03 | 2014-07-09 | 江汉大学 | Cowpea chloroplast SSR molecule labeled polymorphic primers and screening method thereof, and method for identifying genetic relationship of cowpeas |
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2016
- 2016-12-29 CN CN201611245837.8A patent/CN106803026B/en active Active
Patent Citations (3)
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| CN101617047A (en) * | 2007-01-12 | 2009-12-30 | 卡纳维亚利斯有限公司 | The fingerprinting system that is used for the saccharum complex group based on little satellite |
| CN102226178A (en) * | 2011-05-13 | 2011-10-26 | 华南农业大学 | Method for developing SSR (simple sequence repeats) marker at high throughput from forest genome |
| CN103911372A (en) * | 2014-03-03 | 2014-07-09 | 江汉大学 | Cowpea chloroplast SSR molecule labeled polymorphic primers and screening method thereof, and method for identifying genetic relationship of cowpeas |
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