CN107577920A - Utilize the method and apparatus of form mark structure Bermuda grass Core Germplasms - Google Patents
Utilize the method and apparatus of form mark structure Bermuda grass Core Germplasms Download PDFInfo
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Abstract
The invention discloses a kind of method and apparatus that Bermuda grass Core Germplasms are built using morphological markers, methods described includes：The original germplasm of Bermuda grass of the embodiment of the present invention is test material, 11 morphological characters are determined by morphological markers, from the optimal strategy of 5 levels screening structure Bermuda grass Core Germplasms of 7 kinds of Entire samples ratios, 3 kinds of sampling methods, 5 kinds of clustering methods, 3 kinds of genetic distances and 3 kinds of Sampling proportion within group, so as to build Core Germplasms.Using the embodiment of the present invention, constructed Bermuda grass Core Germplasms can effectively retain the phenotypic genetic diversity, phenotypic character correlation and colony's phenotypic genetic structure of original germplasm, can be as the representative sample of overall resource.
Description
Technical field
The present invention relates to field of computer technology, more particularly to a kind of side that Bermuda grass Core Germplasms are built using form mark
Method and device.
Background technology
The C4 types perennial herb that Bermuda grass (Cynodon Richard) belongs to grass family india lovegrass subfamily speedwell race is planted
Thing, is one of three big warm season turf of the world, and a kind of good forage (Harlan, 1969).Cynodon plant is divided into 9
10 mutation of kind (Taliaferro, 1995).Most of Bermuda grass originates from African Territories, is mainly distributed on the torrid zone of warm and moist
Or subtropical zone, also have part Bermuda grass be distributed in Temperate Region in China (Rochecouste, 1962；Wofford and
Baltensperger,1985；Harlan,1970).Wherein common bermudagrass (C.var.dactylon) belongs to cosmopolitan,
Horizontal distribution scope is 53 ° of N~45 ° S；In vertical distribution, can be grown in b.s.l. can also be grown in height above sea level 4000m's
On the Himalayas.There is 2 kind of 1 mutation in China, is common bermudagrass (C.dactylon) and curved fringe Bermuda grass respectively
(C.radiatus) 2 kinds, and 1 mutation (Flora of of honeysuckle Bermuda grass (C.dactylon var.biflorus)
(China Editorial Committee,2006).Collection of the domestic and foreign scholars in Bermuda grass germ plasm resource, genetic diversity
Evaluation etc. obtained certain progress (Wang et al., 2009；Wu et al.,2004；Wu et al.,2006；
Tiwari et al.,2016；Zheng et al., 2017), these researchs are established for structures of the Core Germplasms of Bermuda grass introduces a collection
Good basis is determined.
The structure research of Core Germplasms at present be concentrated mainly on crops or garden crop (Li et al., 2002；Martí
nez,et al.,2017；Ortiz et al., 1998), research is fewer in terms of straw or like vegetable.Core has been built in nearly 20 years
The herbage of germplasm mainly includes English ryegrass (Lolium perenne), perennial clover (Medicago sativa), one
Year raw clover (annual Medicago), ovum leaf beggarweed (Desmodium ovalifolium) and pigeonpea (Cajanus
Cajan) etc. (Charmet and Balfourier, 1995；Basigalup et al.,1995；Diwan et al.,1995；
Reddy et al.,2005；Bhattacharjee et al.,2007).Research in terms of Bermuda grass Core Germplasms structure compared with
Few, Anderson (2005) constructs the Bermuda grass core kind for including 169 parts of materials using the phenotypic data of 598 parts of Bermuda grass
Matter.Jewell etc. (2011) has carried out EST-SSR amplifications to the DNA of 690 parts of Australian Bermuda grass germplasm, the SSR that will be obtained
Geographic origin information, chromosome G banding and the morphological data of data combination Bermuda grass are with the method that hierarchical cluster samples from original species
The core material that 13% has been extracted in matter constructs Australian Bermuda grass Core Germplasms.Zheng Yiqi is using phenotypic data
831 parts of Bermuda grass construct the primary core collection (Zheng et al., 2014) comprising 208 parts of materials.
Tropical Crop Variety Resource Institute of Chinese Academy of Tropical Agricultural Sciences have collected substantial amounts of Bermuda grass introduces a collection in recent years,
Collected representative resource has been ground from form, molecule, resistance, Turf characteristic, feeding value etc. at present
Study carefully (Huang et al., 2013；Huang et al., 2014), system research and something lost of the abundant germ plasm resource for Bermuda grass
Pass breeding work and provide substantial amounts of material, however, so numerous resource to preserve, evaluation, identification and tired using bringing
Difficulty, how faster, more effectively study, using existing germ plasm resource, be breeding service for accelerating to excavate excellent resource
It is particularly important.Therefore, carry out the structure research of Bermuda grass Core Germplasms, for Germplasm enhancement and effective Sustainable use with
And the tool such as breed improvement, breeding of new variety is of great significance and application prospect.
The content of the invention
A kind of method and apparatus that Bermuda grass Core Germplasms are built using form mark that the embodiment of the present invention proposes, it is constructed
Into Bermuda grass Core Germplasms can effectively retain the phenotypic genetic diversity, phenotypic character correlation and colony of original germplasm
Phenotypic genetic structure, can be as the representative sample of overall resource.
In a first aspect, the embodiment of the present invention provides a kind of method that Bermuda grass Core Germplasms are built using morphological markers, bag
Include：
According to morphological markers, the character of Bermuda grass in Bermuda grass test material is determined, obtains the table of the original germplasm of Bermuda grass
Type data；
The substrategy included in sampling method, Entire samples ratio, clustering method and genetic distance is subjected to combination of two,
The strategy being combined into carries out the selection of germplasm to the original germplasm, obtains Bermuda grass Core Germplasms subset；
The phenotypic data for the germplasm for being included each Core Germplasms subset according to evaluating and the phenotype of original germplasm
Data are analyzed, from the sampling method, the Entire samples ratio, the clustering method and the genetic distance
Select corresponding optimal substrategy；
The substrategy that Sampling proportion within group the includes substrategy optimal with four types selected is combined,
The strategy being combined into carries out the selection of germplasm to each group of the original germplasm after packet, and will according to the evaluating
The phenotypic data of the phenotypic data and original germplasm of the selected germplasm got is analyzed, and filters out Sampling proportion within group
Optimal substrategy；
According to the optimal substrategy of five types selected, the selection of germplasm is carried out from the original germplasm, is built into
Bermuda grass Core Germplasms.
Preferably, the substrategy of the sampling method includes repeatedly clustering preferential sampling method, the repeatedly sampling of cluster degree of variation
Method and do not cluster completely random method；
The substrategy of the Entire samples ratio includes 5%, 10%, 15%, 20%, 25%, 30% and 35%；
The substrategy of the clustering method includes knearest neighbour method, longest distance method, intermediate distance method, does not weight class and be averaged
Method and sum of squares of deviations method；
The substrategy of the genetic distance includes Euclidean distance, mahalanobis distance and principal component distance.
Preferably, the substrategy of the Sampling proportion within group includes simple ratio, square root ratio and logarithmic scale.
Preferably, the optimal substrategy of five types selected is：The sampling method is preferential for repeatedly cluster
Sampling method, the Entire samples ratio are 20%, and for the clustering method not weight the class method of average, the genetic distance is geneva
Distance, and the Sampling proportion within group is square according to ratio.
Preferably, the evaluating includes average percent difference, variance percent difference, extreme difference coincidence rate and variation
Index variation rate.
Further, the method being grouped to the original germplasm is：
The original germplasm is divided into by corresponding group class according to botany classification；
The original germplasm in each group of class is divided according to geographic origin, completes the packet to the original germplasm.
Second aspect, the embodiment of the present invention also provide a kind of device that Bermuda grass Core Germplasms are built using morphological markers,
Including：
Phenotypic data determines module, for according to morphological markers, determining the character of Bermuda grass in Bermuda grass test material, obtaining
Obtain the phenotypic data of the original germplasm of Bermuda grass；
Core Germplasms Subset Module, for will be included in sampling method, Entire samples ratio, clustering method and genetic distance
Substrategy carry out combination of two, the strategy being combined into carries out the selection of germplasm to the original germplasm, obtains Bermuda grass core
Germplasm subset；
First strategy chooses module, for the phenotype for the germplasm for being included each Core Germplasms subset according to evaluating
Data and the phenotypic data of original germplasm are analyzed, from the sampling method, the Entire samples ratio, the cluster
Corresponding optimal substrategy is selected in method and the genetic distance；
Second slightly chooses module, for the substrategy that includes Sampling proportion within group with four types selected most
Excellent substrategy is combined, and the strategy being combined into carries out the selection of germplasm to each group of the original germplasm after packet,
And the phenotypic data of the phenotypic data and original germplasm of the selected germplasm got is analyzed according to the evaluating,
Filter out the optimal substrategy of Sampling proportion within group；
Core Germplasms build module, for the optimal substrategy according to five types selected, from the original germplasm
The selection of germplasm is carried out, is built into Bermuda grass Core Germplasms.
The substrategy of preferably described sampling method includes repeatedly clustering preferential sampling method, repeatedly cluster degree of variation sampling method
Completely random method is not clustered；
The substrategy of the Entire samples ratio includes 5%, 10%, 15%, 20%, 25%, 30% and 35%；
The substrategy of the clustering method includes knearest neighbour method, longest distance method, intermediate distance method, does not weight class and be averaged
Method and sum of squares of deviations method；
The substrategy of the genetic distance includes Euclidean distance, mahalanobis distance and principal component distance.
The substrategy of the Sampling proportion within group includes simple ratio, square root ratio and logarithmic scale.
The evaluating includes average percent difference, variance percent difference, extreme difference coincidence rate and the coefficient of variation and become
Rate.
Preferably, the optimal substrategy of five types selected is：The sampling method is preferential for repeatedly cluster
Sampling method, the Entire samples ratio are 20%, and for the clustering method not weight the class method of average, the genetic distance is geneva
Distance, and the Sampling proportion within group is square according to ratio.
Further, the device that Bermuda grass Core Germplasms are built using morphological markers is also included for described original
The germplasm grouping module that germplasm is grouped, the germplasm grouping module include：
Special grouped element is planted, for the original germplasm to be divided into corresponding group class according to botany classification；
Geographic origin grouped element, for being divided the original germplasm in each group of class according to geographic origin, complete
Packet to the original germplasm.
Implement the embodiment of the present invention, have the advantages that：
The method and apparatus provided in an embodiment of the present invention that Bermuda grass Core Germplasms are built using form mark, according to form mark
Note, the character of Bermuda grass in Bermuda grass test material is determined, obtain the phenotypic data of the original germplasm of Bermuda grass；By sampling method,
The substrategy included in Entire samples ratio, clustering method and genetic distance carries out combination of two, and the strategy being combined into is to described
Original germplasm carries out the selection of germplasm, obtains Bermuda grass Core Germplasms subset；And then according to evaluation ginseng to Bermuda grass Core Germplasms
Subset is analyzed, from the sampling method, the Entire samples ratio, the clustering method and the genetic distance
Select corresponding optimal substrategy；And the substrategy included with Sampling proportion within group is combined, the strategy being combined into is to dividing
Each group of original germplasm after group carries out the selection of germplasm, and filters out Sampling proportion within group according to the evaluating
Optimal substrategy；So select and sampled in the sampling method come, Entire samples ratio, clustering method, genetic distance and group
Ratio is optimal strategy, and the table of original germplasm can be effectively retained by the constructed Bermuda grass Core Germplasms of the optimal strategy
Type genetic diversity, phenotypic character correlation and colony's phenotypic genetic structure, can be as the representative sample of overall resource.
Brief description of the drawings
Fig. 1, it is one embodiment of the method provided by the invention that Bermuda grass Core Germplasms are built using morphological markers
Schematic flow sheet；
Fig. 2 is the something lost of the germplasm and original germplasm in the core subset provided in an embodiment of the present invention according to step S3 structures
Pass the evaluation analysis table figure of comparison in difference；
Fig. 3 is that the present invention provides the number that different Sampling proportion within group are drawn into Core Germplasms in the group of each original germplasm
Scale trrellis diagram；
Fig. 4 is the evaluating pair of the core subset of provided by the invention 10% and 20% Entire samples ratio combination structure
Compare tabular drawing；
Fig. 5 is the Core Germplasms and original germplasm character matter that the method for structure Core Germplasms provided by the present invention is built into
Between correlation analysis tabular drawing；
Fig. 6 is between the Core Germplasms that the method for structure Core Germplasms provided by the present invention is built into and original germplasm
The characteristic value of principal component analysis and accumulation contribution rate tabular drawing；
Fig. 7 a be the first principal component of Core Germplasms that the method for structure Core Germplasms provided by the present invention is built into and
The two-dimentional scatter diagram of Second principal component,；
Fig. 7 b are the first principal component of original germplasm provided by the invention and the two-dimentional scatter diagram of Second principal component,；
Fig. 8 is the knot of one embodiment of the device provided by the invention that Bermuda grass Core Germplasms are built using morphological markers
Structure schematic diagram.
Embodiment
Below in conjunction with the accompanying drawing in the embodiment of the present invention, the technical scheme in the embodiment of the present invention is carried out clear, complete
Site preparation describes, it is clear that described embodiment is only part of the embodiment of the present invention, rather than whole embodiments.It is based on
Embodiment in the present invention, those of ordinary skill in the art are obtained every other under the premise of creative work is not made
Embodiment, belong to the scope of protection of the invention.
It is that one of the method provided by the invention that Bermuda grass Core Germplasms are built using morphological markers is implemented referring to Fig. 1
The schematic flow sheet of example；The embodiment of the present invention provides a kind of method that Bermuda grass Core Germplasms are built using morphological markers, including
Step S1 to step S5：
S1, according to morphological markers, the character of Bermuda grass in Bermuda grass test material is determined, obtains the original germplasm of Bermuda grass
Phenotypic data.
Bermuda grass test material used in the embodiment of the present invention is Chinese Academy of Tropical Agricultural Sciences's tropical crops variety source
Grass cultivation research department of research institute was in 2006~2014 years 537 parts of wild dog teeth gathered from domestic and international 22 country variants and area
Root, including 476 parts of common bermudagrass, 59 parts of curved fringe Bermuda grass, 1 part of honeysuckle Bermuda grass, 1 part of African Bermuda grass.Utilize form mark
Note carries out property determination to above-mentioned test material, determines 11 characters, wherein quantitative character 7, qualitative character 4 altogether.Quantity
Character has that upright branches and leaves length, vertical branch leaf width, branches and leaves length of crawling, stolon leaf width, stolon stem is thick, stolon internode length, grass
Layer height, replication 15 times, averages.The measure project of qualitative character includes：Leaf hair, Ye Zi, leaf color and stem color.
It should be noted that it is a kind of traditional and important of Core Germplasms structure based on morphological markers structure Core Germplasms
Method, but because morphological markers are easily influenceed by external environment, so being difficult to represent based on the Core Germplasms that morphological markers obtain
The genetic diversity of original germ plasm resource, using the method for molecular labeling, substantial amounts of heredity letter can be obtained within a short period of time
Breath, and the affiliation that can reflect well between germ plasm resource individual in population, but due to molecular labeling experiment expense compared with
Height, and the initial population of germ plasm resource is typically in large scale, thus be difficult that Markers for Detection is carried out one by one to each sample.Cause
This, only fully integrates structure Core Germplasms by phenotypic markers and molecular labeling etc., could represent heredity to greatest extent
Diversity, improve representativeness, the validity of Core Germplasms.
S2, the substrategy included in sampling method, Entire samples ratio, clustering method and genetic distance is subjected to group two-by-two
Close, the strategy being combined into carries out the selection of germplasm to the original germplasm, obtains Bermuda grass Core Germplasms subset.
Preferably, the substrategy of the sampling method includes repeatedly clustering preferential sampling method, the repeatedly sampling of cluster degree of variation
Method and do not cluster completely random method；The substrategy of the Entire samples ratio includes 5%, 10%, 15%, 20%, 25%, 30%
With 35%；The substrategy of the clustering method includes knearest neighbour method, longest distance method, intermediate distance method, does not weight class and be averaged
Method and sum of squares of deviations method；The substrategy of the genetic distance includes Euclidean distance, mahalanobis distance and principal component distance.Will sampling
The tactful each substrategy of method, Entire samples ratio, clustering method and genetic distance this 4 carries out complete combination two-by-two, group
Selection of the strategy of synthesis to progress germplasm in the population of the original germplasm, constructs 315 parts of Bermuda grass core subsets altogether, and
Core subset is evaluated in subsequent step S3, therefrom filters out optimal sampling method, Entire samples ratio, cluster side
The substrategy of method and genetic distance.
S3, the phenotypic data for the germplasm for being included each Core Germplasms subset according to evaluating and the table of original germplasm
Type data are analyzed, from the sampling method, the Entire samples ratio, the clustering method and the genetic distance
In select corresponding optimal substrategy.
It should be noted that above-mentioned 315 parts of core subsets of the phenotypic data structure based on original germplasm, in order to evaluate core
Whether the Core Germplasms that center is concentrated save the phenotypic genetic diversity of original germplasm, and the embodiment of the present invention have selected equal value difference
4 different percentage, variance percent difference, extreme difference coincidence rate and the coefficient of variation rate of change evaluatings are evaluated it, core
Heart germplasm only has sufficient average percent difference less than 20% and extreme difference coincidence rate is only effectively at least above 80%, and equal value difference
Different percentage is smaller, and variance percent difference, extreme difference coincidence rate and coefficient of variation rate of change are more big more to represent original species
The genetic diversity of matter, so can therefrom filter out optimal sampling method, Entire samples ratio, clustering method and heredity away from
From substrategy.
For a core subset, carry out evaluating specific calculating process using above-mentioned evaluating be：
Average percent difference MD calculation formula is MD=(St/ n) × 100%；
Variance percent difference VD calculation formula is VD=(SF/ n) × 100%；
Extreme difference coincidence rate CR calculation formula is
Coefficient of variation rate of change VR calculation formula are
Wherein, i represents i-th of character；N is character sum；StIt is that the Core Germplasms of the core subset and original germplasm enter
Row t examines the character number of hourly value significant difference；SFWhen being that the Core Germplasms of the core subset carry out F inspections with original germplasm
The character number of variance significant difference；RC(i)It is the extreme difference of i-th of character of colony of the core subset；RI(i)Represent original germplasm
Population in i-th of character extreme difference；CVC(i)Represent the coefficient of variation of i-th of character of the Core Germplasms of the core subset；
CVI(i)Represent the coefficient of variation of i-th of character of population of original germplasm.
As shown in Fig. 2 Fig. 2 is germplasm and original in the core subset provided in an embodiment of the present invention according to step S3 structures
The evaluation analysis table figure that the hereditary difference of beginning germplasm compares.
Screening for sampling method, it is specially：Met using average percent difference, variance percent difference, extreme difference
4 parameters of rate and coefficient of variation rate of change are evaluated the core subset of 3 kinds of sampling method structures respectively, can by calculating
To draw result as shown in Figure 2, the core subset for as a result representing repeatedly to cluster preferential sampling method structure is except mean range meets
Rate and repeatedly cluster degree of variation sampling method are all outside 100%, and other 3 each parameters are substantially better than repeatedly cluster degree of variation sampling method
Completely random method is not clustered, therefore optimal sampling method is repeatedly to cluster preferential sampling method.
Screening for genetic distance, it is specially：Met using average percent difference, variance percent difference, extreme difference
4 parameters of rate and coefficient of variation rate of change are evaluated the core subset of 3 kinds of genetic distance structures respectively, by the way that core is sub
The germplasm of concentration calculates compared with the germplasm in original germplasm, it can be deduced that result as shown in Figure 2, as a result represents three
Difference is not notable on 4 evaluatings, and average mean percent difference scope is 2.86~4.16%；Average variance difference
Percent ranges are 65.32~65.58%；Mean range coincidence rate value is all 100%；Average coefficient of variation rate of change value model
It is 136.35~157.76% to enclose, thus, it is believed that any one in three kinds of genetic distances of selection, the embodiment of the present invention
It is preferred that geneva genetic distance is the substrategy of optimal genetic distance.
Screened for clustering method, be specially：Utilize average percent difference, variance percent difference, extreme difference coincidence rate
The core subset built respectively to 5 kinds of clustering methods with 4 parameters of coefficient of variation rate of change is evaluated, by the way that core is sub
The germplasm of concentration calculates compared with the germplasm in original germplasm, it can be deduced that result as described in Figure 2, as a result represents,
In above-mentioned core subset, the minimum value of average mean percent difference is 0.87%, maximum 4.33%；Average variance difference
The span of percentage is 62.34~68.83%；Mean range coincidence rate is all 100%；Average coefficient of variation rate of change
Scope is 135.21%~160.08%.5 kinds of clustering methods difference on 4 evaluatings is not notable.So selection is any
A kind of clustering method structure Core Germplasms can, the embodiment of the present invention evaluates 4 of each clustering method by weighted calculation
Evaluating, it is optimal clustering method not weight the class method of average preferably.
For Entire samples ratio preliminary screening, with 5%, 10%, 15%, 20%, 25%, 30% and 35% etc. 7 kind not
Very big difference be present in the core subset of same Entire samples ratio structure Bermuda grass, the evaluating of each core subset.To 4
Evaluating carries out comprehensive analysis, and discovery 5%, 10% is all optimal in 4 evaluatings, and difference is not notable；10%th,
15% and 20% on 3 evaluatings in addition to average coefficient of variation rate of change difference not significantly, population parameter value is slightly poor
In 5%；25% population parameter value is 4 poor but better than 30% and 35% earlier above；30% and 35% population parameter value is worst and poor
It is different not notable.In summary, what Entire samples ratio was optimal is 5% and 10%, next to that 15% and 20%, worst is 30%
With 35%.In theory, 5% or 10% should be chosen and be used as Entire samples ratio, but the two Entire samples ratios are ground similar
Study carefully middle fortune to be used less, and 15% and 20% is little with their differences, and therefore, the embodiment of the present invention preferably 10% and 20% is stayed
Standby Entire samples ratio is done, takes the selection of ratio further to be screened in calculating in ensuing group.
S4, the substrategy that Sampling proportion within group the is included substrategy optimal with four types selected carry out group
Close, the strategy being combined into carries out the selection of germplasm to each group of the original germplasm after packet, and is joined according to the evaluation
The phenotypic data of the phenotypic data and original germplasm of the selected germplasm got is analyzed number, filters out sampling rate in group
The optimal substrategy of example.
Sampling proportion within group is set as 3 kinds of simple ratio, square root ratio and logarithmic scale, and Entire samples ratio is set as
10% and 20% 2 kinds of grade, Entire samples ratio and Sampling proportion within group are combined into 6 kinds of modes and screened, calculated with this 6 kinds
The core material quantity that mode extracts from each group is (as shown in figure 3, Fig. 3, which is the present invention, provides different Sampling proportion within group each
The quantity tabular drawing of Core Germplasms is drawn into the group of original germplasm).From the figure 3, it may be seen that the dog included in the 9th, 10 and 11 group
Root of the tooth material only has 4,1 and 1 parts respectively.In order to ensure that Core Germplasms can retain the special material in original germplasm, taken in 3 kinds of groups
Only have square root ratio all to extract core material from this 3 groups in sample ratio, therefore select square root ratio.
Wherein, as shown in figure 3, the whole population of the original germplasm provided in an embodiment of the present invention provided step S1 is carried out
The method of packet is：First, the original germplasm is divided into by corresponding group class according to botany classification.Such as：The present invention is implemented
The test material that example provides is 537 parts of Native Bermudagrass, and 537 parts of Native Bermudagrass materials are divided into common dog by special credit class is planted
Root of the tooth (C.dactylon), curved fringe Bermuda grass (C.radiatus), honeysuckle Bermuda grass (C.dactylon var.biflorus) and
African 4 big groups of Bermuda grass (C.transuaalensis).Then, the original germplasm in each group of class is carried out according to geographic origin
Division, completes the packet to the original germplasm, can provide the example above 4 big groups are divided into 11 groups, thus will be original
Germplasm has been divided into 11 groups.
It is relatively more overall to take 10% and 20% structure and core on the basis of selection square root ratio is as Sampling proportion within group
The evaluating of center collection.Fig. 4 is the core subset of provided by the invention 10% and 20% Entire samples ratio combination structure
Evaluating contrasts tabular drawing, and as shown in Figure 4, both are equal on average percent difference；In variance percent difference and pole
On poor coincidence rate, 20% both greater than 10%；And on coefficient of variation rate of change, 10% is larger.It follows that 20% is slightly better than
10%, therefore select 20% to be used as optimal sampling ratio.
In summary, the strategy of the phenotypic data structure Bermuda grass Core Germplasms based on original germplasm has been filtered out, that is, has been taken
Quadrat method selection repeatedly clusters preferential sampling method, and Entire samples ratio selection 20%, Sampling proportion within group selects square root ratio,
Genetic distance selects mahalanobis distance, and clustering method selection does not weight the class method of average.
S5, according to the optimal substrategy of five types selected, the selection of germplasm, structure are carried out from the original germplasm
Into Bermuda grass Core Germplasms.
Using it is above-mentioned filter out " sampling method selection repeatedly clusters preferential sampling method, Entire samples ratio selection 20%,
Sampling proportion within group selects square root ratio, genetic distance selection mahalanobis distance, and clustering method selection does not weight the class method of average "
Phenotypic data (537 portion dogs of the optimal Core Germplasms construction strategy (the optimal substrategy of i.e. above-mentioned five type) to original germplasm
The phenotypic data of root of the tooth germplasm) analyzed, germplasm is therefrom chosen, is built into the core kind being made up of 108 parts of Bermuda grass germplasm
Matter.
It should be noted that step S5 builds the detailed process of Core Germplasms, the population of original germplasm is actually based on
On the basis of using it is above-mentioned select the optimal Core Germplasms construction strategy come for the continuous sample drawn of Sampling Strategy mistake with can be with
The genetic redundancy of original germplasm colony is farthest rejected, and the variation of Core Germplasms and former population genetic diversity can be made
Recoverable amount reach maximization.First, the process of Core Germplasms is built, first with 20% in the population of ungrouped original germplasm
Entire samples ratio completely random sample out corresponding germplasm, be then grouped, it is complete with the Sampling proportion within group of square root ratio
Full grab sample selects corresponding germplasm.Then, it is unevenly distributed due to the genetic diversity of resource, it is random performing
The different Core Germplasms of Diversity structure will be obtained by carrying out cluster sampling again after sampling, cluster sampling method can from heredity away from
From a certain proportion of sample is rejected in nearer material, so as to reduce the genetic redundancy of original seed matter and keep the heredity of original seed matter
Structure, the clustering method selection of the embodiment of the present invention do not weight the class method of average.And then press genetic distance again after cluster
(mahalanobis distance) is sampled, and is finally completed the structure of Core Germplasms.
The method and apparatus provided in an embodiment of the present invention that Bermuda grass Core Germplasms are built using form mark, according to form mark
Note, the character of Bermuda grass in Bermuda grass test material is determined, obtain the phenotypic data of the original germplasm of Bermuda grass；By sampling method,
The substrategy included in Entire samples ratio, clustering method and genetic distance carries out combination of two, and the strategy being combined into is to described
Original germplasm carries out the selection of germplasm, obtains Bermuda grass Core Germplasms subset；And then according to evaluation ginseng to Bermuda grass Core Germplasms
Subset is analyzed, from the sampling method, the Entire samples ratio, the clustering method and the genetic distance
Select corresponding optimal substrategy；And the substrategy included with Sampling proportion within group is combined, the strategy being combined into is to dividing
Each group of original germplasm after group carries out the selection of germplasm, and filters out Sampling proportion within group according to the evaluating
Optimal substrategy；So select and sampled in the sampling method come, Entire samples ratio, clustering method, genetic distance and group
Ratio is optimal strategy, and the table of original germplasm can be effectively retained by the constructed Bermuda grass Core Germplasms of the optimal strategy
Type genetic diversity, phenotypic character correlation and colony's phenotypic genetic structure, can be as the representative sample of overall resource.
The property correlation among traits of germplasm is the intrinsic characteristic of a species, is to exist to associate in inhereditary material in species
External manifestation.Sampling should not change the correlation between the intrinsic character of this species, therefore an excellent Core Germplasms should
Keep the characters correlation of original germplasm.Because phenotype Core Germplasms are fewer than the germplasm materials quantity of initial population, both are freely
Spend it is different, so the size for comparing coefficient correlation is nonsensical,
Whether only need to compare in initial population in significantly correlated character is also in notable phase in phenotype Core Germplasms
Pass.The constructed core of the methods of structure Core Germplasms to being provided according to above-described embodiment respectively of the embodiment of the present invention
The correlation analysis based on 11 phenotypic characters has been carried out between germplasm and original germplasm, has found structure provided in an embodiment of the present invention
The Core Germplasms that the method for Core Germplasms can be built can keep the character of original germplasm more than 85% related.
It will be illustrated below with test material provided in an embodiment of the present invention (phenotypic data of 537 parts of Native Bermudagrass)
Prove description：
Correlation analysis between the Core Germplasms and original germplasm character matter that are built into the embodiment of the present invention, referring specifically to
Fig. 5, Fig. 5 are between the Core Germplasms that the method for structure Core Germplasms provided by the present invention is built into and original germplasm character matter
Correlation analysis tabular drawing, original germplasm and Core Germplasms have 11 phenotypes, in the phenotypic data of original germplasm, 28 pairs of tables
Type character is in extremely significantly correlated, and 4 pairs of phenotypic characters are in significantly correlated；And there are 24 pairs of characters to be in the phenotypic data of Core Germplasms
Extremely significantly correlated, 4 pairs of characters are in significantly correlated.85% or so characters correlation obtains in phenotype Core Germplasms in original germplasm
Holding is arrived.Original species can be kept so as to demonstrate the Core Germplasms being built into by construction method provided in an embodiment of the present invention
85% or so characters correlation in matter.
One qualified Core Germplasms not only will as often as possible preserve the genetic diversity of original germplasm, also keep as far as possible
The population genetic variations of original germplasm.Principal component analysis is that multivariable, multi objective are converted into less variable, less index by one kind
Data analysis technique, be widely used in biodiversity research, including Core Germplasms structure.According to germplasm materials
1st, the 2 dimension scatter diagrams that the score in the 2nd principal component is drawn can approx reflect distribution situation of the germplasm materials in colony, can
Intuitively to reflect the genetic structure of colony.Distance in scatter diagram between germplasm materials reflects their genetic similarty,
Distance is nearer, and similarity is higher, and distance is more remote, and distinctiveness ratio is bigger；And the 1st, contribution rate of 2 principal components is bigger, reflecting to get over
Accurately.The principal component 2 of original germplasm and Core Germplasms is tieed up into distribution map to be contrasted, can intuitively reflect Core Germplasms to original
The representativeness of beginning germplasm.The embodiment of the present invention has carried out principal component analysis to original germplasm and Core Germplasms, and depicts them
The 2 dimension distribution maps based on the 1st, the 2nd principal component.It was found that Core Germplasms 2 dimension distribution maps have with original germplasm similar in geometry
Profile and characteristic distributions, it can largely keep the population genetic variations of original germplasm.
In order to further examine the Core Germplasms being built into by construction method provided in an embodiment of the present invention to original species
The representativeness of matter, the embodiment of the present invention has carried out principal component analysis to the phenotypic data of Liang Ge colonies respectively, as shown in fig. 6, Fig. 6
It is that principal component between the Core Germplasms that are built into of method of structure Core Germplasms provided by the present invention and original germplasm is analysed
Characteristic value and accumulation contribution rate tabular drawing；It will be appreciated from fig. 6 that more than 1 being standard with characteristic value, 4 principal components are have chosen.Core kind
Matter and original germplasm in the characteristic value of each principal component, ratio and are accumulated in contribution rate all relatively, and first three principal component
Characteristic value it is more slightly higher than original germplasm.Two-dimentional scatter diagram is drawn according to score of the germplasm materials in the first and second principal components
(Fig. 7 a and Fig. 7 b, wherein, the transverse axis in two figures is the first principal component of germplasm, and the longitudinal axis is Second principal component).From Fig. 7 a and figure
7b can be seen that the geometry of Core Germplasms principal component two-dimensional distribution, feature and original germplasm are closely similar, both kinds
The all main integrated distribution of material is in the left of scatter diagram, and there is fragmentary distribution lower section in figure, illustrates that Core Germplasms are protected well
The genetic structure of initial population is held.
Referring to Fig. 8, Fig. 8 is a reality of the device provided by the invention that Bermuda grass Core Germplasms are built using morphological markers
Apply the structural representation of example.
Second aspect, the embodiment of the present invention also provide a kind of device that Bermuda grass Core Germplasms are built using morphological markers,
Including：
Phenotypic data determines module 10, for according to morphological markers, determining the character of Bermuda grass in Bermuda grass test material,
Obtain the phenotypic data of the original germplasm of Bermuda grass；
Core Germplasms Subset Module 20, for will be wrapped in sampling method, Entire samples ratio, clustering method and genetic distance
The substrategy contained carries out combination of two, and the strategy being combined into carries out the selection of germplasm to the original germplasm, obtains Bermuda grass core
Heart germplasm subset；
First strategy chooses module 30, for the table for the germplasm for being included each Core Germplasms subset according to evaluating
Type data and the phenotypic data of original germplasm are analyzed, from the sampling method, Entire samples ratio, described poly-
Corresponding optimal substrategy is selected in class method and the genetic distance；
Second slightly chooses module 40, for substrategy and four types selected for including Sampling proportion within group
Optimal substrategy is combined, and the strategy being combined into carries out the choosing of germplasm to each group of the original germplasm after packet
Take, and carried out the phenotypic data of the phenotypic data of the selected germplasm got and original germplasm to score according to the evaluating
Analysis, filter out the optimal substrategy of Sampling proportion within group；
Core Germplasms build module 50, for the optimal substrategy according to five types selected, from the original species
Matter carries out the selection of germplasm, is built into Bermuda grass Core Germplasms.
The substrategy of preferably described sampling method includes repeatedly clustering preferential sampling method, repeatedly cluster degree of variation sampling method
Completely random method is not clustered；
The substrategy of the Entire samples ratio includes 5%, 10%, 15%, 20%, 25%, 30% and 35%；
The substrategy of the clustering method includes knearest neighbour method, longest distance method, intermediate distance method, does not weight class and be averaged
Method and sum of squares of deviations method；
The substrategy of the genetic distance includes Euclidean distance, mahalanobis distance and principal component distance.
The substrategy of the Sampling proportion within group includes simple ratio, square root ratio and logarithmic scale.
The evaluating includes average percent difference, variance percent difference, extreme difference coincidence rate and the coefficient of variation and become
Rate.
Preferably, the optimal substrategy of five types selected is：The sampling method is preferential for repeatedly cluster
Sampling method, the Entire samples ratio are 20%, and for the clustering method not weight the class method of average, the genetic distance is geneva
Distance, and the Sampling proportion within group is square according to ratio.
Further, the device that Bermuda grass Core Germplasms are built using morphological markers is also included for described original
The germplasm grouping module that germplasm is grouped, the germplasm grouping module 60 include：
Special grouped element is planted, for the original germplasm to be divided into corresponding group class according to botany classification；
Geographic origin grouped element, for being divided the original germplasm in each group of class according to geographic origin, complete
Packet to the original germplasm.
Further, the embodiment of the present invention also provides a kind of computer-readable recording medium, wherein a plurality of instruction is stored with,
The utilization morphological markers structure dog tooth that any embodiment of first aspect provides is realized in the instruction when being executed by processor
The method of root Core Germplasms.
Further, the embodiment of the present invention also provides a kind of terminal device, including storage device, processor and is stored in
In the storage device and a plurality of instruction that can run on the processor, wherein, when being instructed described in the computing device
Realize the method that Bermuda grass Core Germplasms are built using morphological markers that any embodiment of first aspect provides.
Implement the embodiment of the present invention, have the advantages that：
Device, the computer-readable storage medium provided in an embodiment of the present invention that Bermuda grass Core Germplasms are built using form mark
Matter and terminal device, according to morphological markers, the character of Bermuda grass in Bermuda grass test material is determined, obtains the original germplasm of Bermuda grass
Phenotypic data；The substrategy included in sampling method, Entire samples ratio, clustering method and genetic distance is subjected to group two-by-two
Close, the strategy being combined into carries out the selection of germplasm to the original germplasm, obtains Bermuda grass Core Germplasms subset；And then according to commenting
Bermuda grass Core Germplasms subset is analyzed valency ginseng, from the sampling method, the Entire samples ratio, the cluster
Corresponding optimal substrategy is selected in method and the genetic distance；And the substrategy included with Sampling proportion within group carries out group
Close, the strategy being combined into carries out the selection of germplasm to each group of the original germplasm after packet, and is joined according to the evaluation
Number sieve selects the optimal substrategy of Sampling proportion within group；So select the sampling method come, Entire samples ratio, cluster side
Method, genetic distance and Sampling proportion within group are optimal strategy, can by the constructed Bermuda grass Core Germplasms of the optimal strategy
Effectively retain the phenotypic genetic diversity, phenotypic character correlation and colony's phenotypic genetic structure of original germplasm, can conduct
The representative sample of overall resource.
One of ordinary skill in the art will appreciate that realize all or part of flow in above-described embodiment method, being can be with
The hardware of correlation is instructed to complete by computer program, described program can be stored in a computer read/write memory medium
In, the program is upon execution, it may include such as the flow of the embodiment of above-mentioned each method.Wherein, described storage medium can be magnetic
Dish, CD, read-only memory (Read-Only Memory, ROM) or random access memory (Random Access
Memory, RAM) etc..
Described above is the preferred embodiment of the present invention, it is noted that for those skilled in the art
For, under the premise without departing from the principles of the invention, some improvements and modifications can also be made, these improvements and modifications are also considered as
Protection scope of the present invention.
Claims (10)
- A kind of 1. method that Bermuda grass Core Germplasms are built using morphological markers, it is characterised in that including：According to morphological markers, the character of Bermuda grass in Bermuda grass test material is determined, obtains the Phenotype Number of the original germplasm of Bermuda grass According to；The substrategy included in sampling method, Entire samples ratio, clustering method and genetic distance is subjected to combination of two, combination Into strategy the selection of germplasm is carried out to the original germplasm, obtain Bermuda grass Core Germplasms subset；The phenotypic data for the germplasm for being included each Core Germplasms subset according to evaluating and the phenotypic data of original germplasm It is analyzed, is chosen from the sampling method, the Entire samples ratio, the clustering method and the genetic distance Go out corresponding optimal substrategy；The substrategy that Sampling proportion within group the includes substrategy optimal with four types selected is combined, combined Into strategy carry out the selection of germplasm to each group of the original germplasm after packet, and according to the evaluating will selected by The phenotypic data of the phenotypic data for the germplasm got and original germplasm is analyzed, and filters out the optimal of Sampling proportion within group Substrategy；According to the optimal substrategy of five types selected, the selection of germplasm is carried out from the original germplasm, is built into dog tooth Root Core Germplasms.
- 2. the method for morphological markers structure Bermuda grass Core Germplasms is utilized as claimed in claim 1, it is characterised in thatThe substrategy of the sampling method includes repeatedly clustering preferential sampling method, repeatedly cluster degree of variation sampling method and not clustered Full randomized；The substrategy of the Entire samples ratio includes 5%, 10%, 15%, 20%, 25%, 30% and 35%；The substrategy of the clustering method include knearest neighbour method, longest distance method, intermediate distance method, do not weight the class method of average and Sum of squares of deviations method；The substrategy of the genetic distance includes Euclidean distance, mahalanobis distance and principal component distance.
- 3. the method for morphological markers structure Bermuda grass Core Germplasms is utilized as claimed in claim 2, it is characterised in that described group The substrategy of interior sampling ratio includes simple ratio, square root ratio and logarithmic scale.
- 4. the method for morphological markers structure Bermuda grass Core Germplasms is utilized as claimed in claim 3, it is characterised in that the choosing The optimal substrategy of five types taken out is：The sampling method is repeatedly to cluster preferential sampling method, the overall sampling rate Example is 20%, and for the clustering method not weight the class method of average, the genetic distance is to be sampled in mahalanobis distance, and described group Ratio is square according to ratio.
- 5. the method for morphological markers structure Bermuda grass Core Germplasms is utilized as claimed in claim 1, it is characterised in that institute's commentary Valency parameter includes average percent difference, variance percent difference, extreme difference coincidence rate and coefficient of variation rate of change.
- 6. the method for morphological markers structure Bermuda grass Core Germplasms is utilized as claimed in claim 1, it is characterised in that to described The method that original germplasm is grouped is：The original germplasm is divided into by corresponding group class according to botany classification；The original germplasm in each group of class is divided according to geographic origin, completes the packet to the original germplasm.
- A kind of 7. device that Bermuda grass Core Germplasms are built using morphological markers, it is characterised in that including：Phenotypic data determines module, for according to morphological markers, determining the character of Bermuda grass in Bermuda grass test material, obtaining dog The phenotypic data of the original germplasm of root of the tooth；Core Germplasms Subset Module, for the son that will be included in sampling method, Entire samples ratio, clustering method and genetic distance Strategy carries out combination of two, and the strategy being combined into carries out the selection of germplasm to the original germplasm, obtains Bermuda grass Core Germplasms Subset；First strategy chooses module, for the phenotypic data for the germplasm for being included each Core Germplasms subset according to evaluating It is analyzed with the phenotypic data of original germplasm, from the sampling method, the Entire samples ratio, the clustering method With corresponding optimal substrategy is selected in the genetic distance；Second slightly chooses module, optimal for the substrategy for including Sampling proportion within group and four types selected Substrategy is combined, and the strategy being combined into carries out the selection of germplasm, and root to each group of the original germplasm after packet The phenotypic data of the phenotypic data and original germplasm of the selected germplasm got is analyzed according to the evaluating, screened Go out the optimal substrategy of Sampling proportion within group；Core Germplasms build module, for the optimal substrategy according to five types selected, are carried out from the original germplasm The selection of germplasm, it is built into Bermuda grass Core Germplasms.
- 8. the device of morphological markers structure Bermuda grass Core Germplasms is utilized as claimed in claim 7, it is characterised in thatThe substrategy of the sampling method includes repeatedly clustering preferential sampling method, repeatedly cluster degree of variation sampling method and not clustered Full randomized；The substrategy of the Entire samples ratio includes 5%, 10%, 15%, 20%, 25%, 30% and 35%；The substrategy of the clustering method include knearest neighbour method, longest distance method, intermediate distance method, do not weight the class method of average and Sum of squares of deviations method；The substrategy of the genetic distance includes Euclidean distance, mahalanobis distance and principal component distance.The substrategy of the Sampling proportion within group includes simple ratio, square root ratio and logarithmic scale.The evaluating includes average percent difference, variance percent difference, extreme difference coincidence rate and coefficient of variation rate of change.
- 9. the device of morphological markers structure Bermuda grass Core Germplasms is utilized as claimed in claim 8, it is characterised in that the choosing The optimal substrategy of five types taken out is：The sampling method is repeatedly to cluster preferential sampling method, the overall sampling rate Example is 20%, and for the clustering method not weight the class method of average, the genetic distance is to be sampled in mahalanobis distance, and described group Ratio is square according to ratio.
- 10. the device of morphological markers structure Bermuda grass Core Germplasms is utilized as claimed in claim 1, it is characterised in that also wrap The germplasm grouping module for being grouped to the original germplasm is included, the germplasm grouping module includes：Special grouped element is planted, for the original germplasm to be divided into corresponding group class according to botany classification；Geographic origin grouped element, for being divided the original germplasm in each group of class according to geographic origin, complete to institute State the packet of original germplasm.
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