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CN109616159A - A phenotypic distance-based screening method for soybean specificity testing similar varieties - Google Patents

A phenotypic distance-based screening method for soybean specificity testing similar varieties Download PDF

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Publication number
CN109616159A
CN109616159A CN201811462618.4A CN201811462618A CN109616159A CN 109616159 A CN109616159 A CN 109616159A CN 201811462618 A CN201811462618 A CN 201811462618A CN 109616159 A CN109616159 A CN 109616159A
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Prior art keywords
phenotype
varieties
distance
soybean
phenotypic
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Inventor
张晗
李汝玉
段丽丽
王晖
孙加梅
郑永胜
王玮
王穆穆
王雪梅
李华
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Institute of Biotechnology of Fujian Academy of Agricultural Science
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Institute of Biotechnology of Fujian Academy of Agricultural Science
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Abstract

本发明公开了一种基于表型距离的大豆特异性测试近似品种筛选方法。该方法根据各个表型性状的表达状态观测值受环境条件影响的程度和人员观测偏差的大小,对各个表达状态的代码差值设置不同的权重(如表1),所有表型性状上的权重相加得出两品种间的表型距离;将大量表型距离与品种间差异的明显程度进行比较,确定一个表型距离阈值:计算申请品种与每个已知品种的表型距离,表型距离小于阈值的已知品种作为申请品种的近似品种。采用这种方法,较好排除了人员观测偏差、互作和数据录入错误和对近似品种筛选的影响,提高了近似品种筛选的严谨性;该方法还便于田间试验时将最近似的品种与申请品种相邻种植,提高了特异性测试的针对性。

The invention discloses a soybean specificity test approximate variety screening method based on phenotypic distance. This method sets different weights for the code differences of each expression state according to the degree to which the observed value of the expression state of each phenotypic trait is affected by environmental conditions and the magnitude of the deviation of personnel observations (see Table 1). The weights on all phenotypic traits Add the phenotypic distance between the two varieties; compare a large number of phenotypic distances with the obvious degree of differences between varieties, and determine a phenotypic distance threshold: calculate the phenotypic distance between the applied variety and each known variety, and the phenotype The known varieties whose distance is less than the threshold are regarded as the approximate varieties of the applied varieties. By adopting this method, personnel observation bias, interaction and data entry errors and the influence on the screening of similar varieties are better excluded, and the rigor of screening of similar varieties is improved; this method is also convenient for comparing the most similar varieties with application Varieties are planted next to each other, improving the pertinence of specific tests.

Description

A kind of soybean specific test approximation method for screening varieties based on phenotype distance
Technical field
The present invention relates to a kind of soybean specific test approximation method for screening varieties based on phenotype distance, it is new to belong to plant Kind test (or DUS test) technical field.
Background technique
Specificity, consistency and stability are the basic demands to plant variety, are that new variety of plant obtains kind power guarantor The precondition of shield, staple crops kind variety certification and the registration of non-principal variety of crops.Specificity refers to application kind All before the applying date known belong to or kind of the same race should be clearly distinguishable from.Have specificity for one kind of identification, needs Prove that the kind is different from other any kinds of known similar crop on phenotypic character.Kind known to chief crop is often It is ten hundreds of, by the kind (" application kind ") of each application DUS test compared with these known kinds carry out field planting, It is infeasible in practice.For this reason, it may be necessary to which those, which are not needed plantation, relatively can determine and apply by some Filtering systems The visibly different kind of kind phenotypic character excludes, and only planting those and not passing through field comparative test then not can determine that and application product Whether kind has the kind (i.e. approximate kind) of obvious phenotypic difference.It is tested by field planting, compares application kind and approximate product Kind whether there is notable difference, show whether application kind has the conclusion of specificity accordingly.Therefore, the selection of approximate kind is The key link of specific test.
Although kind is large number of known to chief crop, for most of known kinds, the especially product of breeding morning Kind, because the reasons such as yielding ability have been unable to meet current production needs, can not considered in approximate screening varieties.Approximate kind Screening generally have by comparing application kind and still the known kind (such as the kind being bred as nearly ten years) of application potential Trait expression state carries out.If can determine a known kind and apply kind expression status difference be big enough in Notable difference is inherently shown when field planting between the two, then can be excluded the known kind, remaining kind is as close Like kind.For quantitative character and false qualitative character (expression status in the consecutive variations region of especially false qualitative character), Following characteristics can be presented because of the influence of environmental condition and human factor in expression status observation: (1) same by environmental influence The same character of a kind, when different year and different regions are planted, expression status observation (expression status code) meeting Certain fluctuation occurs;(2) different trait expressions degree affected by environment is different, show as expression status degree of fluctuation because Character and it is different.(3) different testers are easy to produce deviation to the observed result of trait expression state.The size of deviation, with property Shape and personnel have relationship.How to determine approximate screening varieties index, is the difficult point of approximate screening varieties.A kind of way is basis The expression way of character, trait expression are influenced degree of fluctuation by environment degree and are influenced size by human error, by applying for product Kind screens approximate kind: for false qualitative character and quantitative character, using therewith compared with each expression status of known kind Differ the expression status range of 1-3 code.It is very high for the accuracy requirement of data using above-mentioned way.In practice, exist Individual character expression status data it is excessive or due to data inputting due to being influenced to deviate normal value by personnel's observed deviation Mistake, or due to the interaction (under rare occasion) of character and environmental condition, will lead to should be as the known product of approximate kind Kind fails screening and comes in, and causes the omission of approximate kind, directly affects the accuracy of specific test.In addition, to each kind Screening conditions be configured, process is cumbersome, and screening efficiency is lower.
Applicant develops the approximate method for screening varieties in a kind of soybean specific test based on phenotypic character before (application number of invention patent 201610061379.6).This method is the approximate method for screening varieties based on single phenotypic character, is Degree of fluctuation is influenced by environment degree according to the expression way of character, trait expression and is influenced size by human error, for Shen Please kind each false qualitative character and quantitative character, it is known that kind is using the expression status model for differing 1-3 code therewith It encloses, through application kind compared with each expression status of known kind, screens approximate kind.Applicant sends out in follow-up study Existing, this method has still had following deficiency, needs further to improve: (1) poor fault tolerance, very to the accuracy requirements of data It is high.In practice, there is the data of individual character expression status due to by personnel's observed deviation influenced deviate normal value it is excessive, Or due to data inputting mistake, or due to the interaction (under rare occasion) of character and environmental condition, will lead to should be as close Fail to screen like the known kind of kind, causes the omission of approximate kind.(2) this method is sieved based on the difference of single character Approximate kind is selected, interracial difference cannot be added up, be selected into less approximate kind;(3) selected approximation cannot be shown The degree of approximation of kind and application kind is not easy to design field specific test test.
Summary of the invention
Aiming at the problem that the above-mentioned approximate method for screening varieties based on single character is easy to cause omission approximation kind, this hair It is bright to provide a kind of soybean specific test approximation method for screening varieties based on phenotype distance.This method is directed to kind dissimilarity Shape expression status observation is observed this different feature of influence degree by environment and personnel, between application kind and known kind Selected phenotype trait expression state code difference gives certain weight, by application kind and known kind in one group of character Weight is added, and obtains interracial phenotype distance.The size of weight depends on the trait expression State Viewpoint measured value by environment and people The size of member observation influence degree and code difference.Trait expression is more stable, observed deviation is smaller, and weight is bigger;Code difference Bigger, weight is bigger.By, there are the statistics of a large amount of test article inter-species phenotype distances of notable difference, finding out one to character The safe distance of approximate screening varieties, guarantee be higher than the safe distance kind there are apparent differences.Screening approximate kind When, using the safe distance as the threshold value of approximate screening varieties: the known kind higher than the distance exists obviously with approximate kind Difference, do not need to plant;Less than the known kind of the distance as the plantation adjacent with application kind progress field of approximate kind And Evaluation on specificity.In this way, personnel's observed deviation, interaction and data inputting mistake and pairing approximation product are preferably eliminated The influence of kind screening, improves the preciseness of approximate screening varieties.
The technical scheme is that a kind of soybean specific test approximation method for screening varieties based on phenotype distance, It is characterized in that
(1) weight of each soybean phenotypic character code difference is set
The phenotypic character number of the current still soybean varieties (such as the kind being bred as nearly ten years) with application potential of acquisition According to (the high character of Variety identification power in DUS Testing Guideline, two growth cycles of each kind general test), to the table of acquisition Type trait data is arranged, and soybean varieties phenotype trait data library is established;It is observed according to the expression status of each phenotypic character Value is by the degree of environmental influence and the size of personnel's observed deviation, to all expression status of each soybean phenotypic character (such as code is 1-9 to code difference, and difference 0,1,2 ... 8) is arranged different weights, obtains data as shown in Table 1, is inputted Soybean varieties phenotype trait data library;
For qualitative character, when code difference is more than or equal to 1, weight 4-6, for quantitative character and false qualitative character, It is poor to different codes according to trait expression State Viewpoint measured value by the degree of environmental influence and the size of personnel's observed deviation Value, gives different weights.
The weight of 1 soybean difference DUS test character expression status difference of table
Note: 1.QN: quantitative character, PQ: false qualitative character;QL: qualitative character
2. "-" indicates do not have (weight of corresponding respective code difference)
(2) setting of phenotype distance threshold
To the phenotypic character expression status code difference of pairs of soybean varieties, weight is assigned by the method for step (1), is owned Weight addition on phenotypic character obtains two interracial phenotype distances;By the obvious journey of a large amount of phenotype distances and Differences Degree is compared, and obtains relationship between the two, determines a phenotype distance threshold on this basis: when phenotype distance between kind When greater than the threshold value, difference compares it is obvious that not needing field planting between kind;And by phenotype distance threshold input database System.
The present invention after years of research and found that, suitable phenotype distance threshold be 2, i.e., when between kind phenotype distance >=2 when, product Difference is apparent between kind;It is determined as approximate kind when two interracial phenotype distance < 2.
(3) approximate screening varieties
The approximate screening varieties software based on phenotype distance is developed in soybean varieties phenotype trait data library based on foundation. The phenotype trait data of application kind to be measured is inputted into soybean varieties phenotype trait data library, which can be according to step Suddenly the method for (2) calculates the phenotype distance of application kind to be measured and each known kind, and is compared with phenotype distance threshold Compared with phenotype distance is less than approximate kind of the known kind of threshold value as the application kind to be measured.
Method of the invention is different with influence degree of the personnel to various trait expression status observation according to environmental condition This feature gives a weight, the sum of all differences character weight is used as product between calculating kind to the difference of code kind The phenotype distance of inter-species.By the comparative analysis between phenotype distance and difference obvious degree a large amount of true kinds, one is determined The phenotype distance threshold of safety when guaranty inter-species phenotype distance is higher than the threshold value, certainly exists apparent difference between kind. When carrying out approximate screening varieties, lower than the kind of the phenotype distance threshold as approximate kind.Method of the invention has following excellent Point: (1) fault-tolerance is strong, and preciseness is good.Even if individual character expression status observations are (observed deviation, individual due to artificial origin Error in data) or kind and environment interaction, deviate normal value, approximate kind, the i.e. fault-tolerance of this method will not be omitted more By force, the preciseness of approximate screening varieties is improved.(2) with strong points.This method by Database Systems calculate application kind with The phenotype distance of approximate kind, convenient for, by the plantation adjacent with application kind of closest kind, being improved special when field trial Property test specific aim;(3) high-efficient.Using this method, do not need to be separately provided according to the expression status of application kind each The expression status range of character shortens the approximate screening varieties time.
Detailed description of the invention
Fig. 1 is soybean application kind 2014-0698A (the approximate screening varieties result of peaceful 17) in mountain.
Specific embodiment
Embodiment 1: kind phenotype trait data library known to soybean is established
2004 to 2017, applicant carried out DUS survey to more than 700 part of Huang-Huai-Hai time soybean application kind altogether Examination.Two growth cycles of each kind general test acquire number to all 31 characters in Testing Guideline in each period According to acquisition phenotype trait data more than 20,000 is a altogether.To the phenotype trait data of acquisition, according to test character expression way, data class Type is arranged.On this basis, Main Characters of Soybean Cultivars In The Huang-huai-hai Valley phenotype trait data library is established, stores 550 altogether The DUS test character data of kind.The screening of this example approximation kind relies on above-mentioned phenotype trait data library to carry out.
According to the expression status observation of each phenotypic character by the degree and personnel's observed deviation of environmental influence Size, to all expression status code differences of selected soybean phenotypic character, (such as code is 1-9, and difference 0,1,2 ... 8) Different weights is set, and the weight of each character is arranged as shown in table 2.1-23.2, is further arranged based on the table To one group of statistical data (table 1), above-mentioned phenotype trait data library is inputted.
1 hypocotyl of character: anthocyanin colour developing;
Trait expression mode: QL;
Stability grade: 1.
2.1 expression status of table and code
Expression status Nothing Have
Code 1 2
2.2 code difference of table and weight
Code difference 0 1
Weight 0 6
2 hypocotyl of character: anthocyanin colored intensity;
Trait expression mode: QN;
Stability grade: 4 (generally 4 codes of fluctuation).
3.1 expression status of table and code
3.2 code difference of table and weight
Code difference 0 1 2 3 4 5 6 7 8
Weight 0 0 0 1 2 3 4 5 6
3 stem of character: fine hair color;
Trait expression mode: QL;
Stability grade: 2.
4.1 expression status of table and code
Expression status Grey Brown
Code 1 2
4.2 code difference of table and weight
Code difference 0 1
Weight 0 4
4 stem of character: density of pubescent;
Trait expression mode: QN;
Stability grade: 4 (generally 4 codes of fluctuation).
5.1 expression status of table and code
5.2 code difference of table and weight
Code difference 0 1 2 3 4 5 6 7 8
Weight 0 0 0 1 2 3 4 5 6
5 compound leaf of character: leaflet shape;
Trait expression mode: PQ;
Stability grade: 2 (generally 2 codes of fluctuation).
6.1 expression status of table and code
Expression status Lanceolar Triangle Point is oval Circle is oval
Code 1 2 3 4
6.2 code difference of table and weight
Code difference 0 1 2 3
Weight 0 0 2 4
6 compound leaf of character: leaflet quantity;
Trait expression mode: QN;
Stability grade: 3 (generally 3 codes of fluctuation).
7.1 expression status of table and code
Expression status Three leaflets Five leaflets More leaflets
Code 1 2 3
7.2 code difference of table and weight
Code difference 0 1 2
Weight 0 1 4
7 blade of character: green intensity;
Trait expression mode: QN;
Stability grade * *: 4 (generally 4 codes of fluctuation).
8.1 expression status of table and code
8.2 code difference of table and weight
Code difference 0 1 2 3 4 5 6 7 8
Weight 0 0 0 1 2 3 4 5 6
8 florescence of character;
Trait expression mode: QN;
Stability grade: 4 (generally 3-4 codes of fluctuation).
9.1 expression status of table and code
9.2 code difference of table and weight
Code difference 0 1 2 3 4 5 6 7 8
Weight 0 0 0 1 2 3 4 5 6
The flower of character 9: corolla color;
Trait expression mode: QL;
Stability grade: 1.
101 expression status of table and code
Expression status White Purple
Code 1 2
10.2 code difference of table and weight
Code difference 0 1
Weight 0 6
12 plant of character: height;
Trait expression mode: QN;
Stability grade: 3 (generally 3 codes of fluctuation).
11.1 expression status of table and code
11.2 code difference of table and weight
13 plant of character: pod bearing habit;
Trait expression mode: PQ;
Stability grade * *: 2.
12.1 expression status of table and code
Expression status It is limited It is sub- limited Infinitely
Code 1 2 3
12.2 code difference of table and weight
Code difference 0 1 2
Weight 0 1 4
15 maturity period of character;
Trait expression mode: QN;
Stability grade: 3 (generally 3 codes of fluctuation).
13.1 expression status of table and code
13.2 code difference of table and weight
Code difference 0 1 2 3 4 5 6 7 8
Weight 0 0 0 1 2 3 4 5 6
16 stem of character: joint number amount;
Trait expression mode: QN;
Stability grade: 3 (generally 3 codes of fluctuation).
14.1 expression status of table and code
14.2 code difference of table and weight
Code difference 0 1 2 3 4 5 6 7 8
Weight 0 0 0 1 2 3 4 5 6
18 plant of character: fallen leaves property;
Trait expression mode: QN;
Stability grade: 2.
15.1 expression status of table and code
Expression status It does not fall leaves Half falls leaves Fallen leaves
Code 1 2 3
15.2 code difference of table and weight
Code difference 0 1 2
Weight 0 0 2
19 plant of character: pod quantity;
Trait expression mode: QN;
Stability grade: 4 (can up to 4 codes).
16.1 expression status of table and code
16.2 code difference of table and weight
Code difference 0 1 2 3 4 5 6 7 8
Weight 0 0 0 1 2 3 4 5 6
21 pod of character: bending degree;
Trait expression mode: PQ;
Stability grade: 2 (generally 2 codes of fluctuation).
17.1 expression status of table and code
17.2 code difference of table and weight
Code difference 0 1 2 3
Weight 0 0 2 4
23 pod of character: color;
Trait expression mode: PQ;
Stability grade: 2 (generally 2 codes of fluctuation).
18.1 expression status of table and code
18.2 code difference of table and weight
Code difference 0 1 2 3 4
Weight 0 0 1 2 3
Character 24:* 100-grain weight;
Trait expression mode: QN;
Stability grade: 3 (generally 3 codes of fluctuation).
19.1 expression status of table and code
19.2 code difference of table and weight
Code difference 0 1 2 3 4 5 6 7 8
Weight 0 0 0 1 2 3 4 5 6
Character 26: seed: kernel seed coat colour quantity;
Trait expression mode: QL;
Stability grade: 1.
20.1 expression status of table and code
Expression status It is monochromatic It is double-colored
Code 1 2
20.2 code difference of table and weight
Code difference 0 1
Weight 0 6
Character 27: it is only applicable to monochromatic kind of skin kind: seed: kernel seed coat colour;
Trait expression mode: PQ;
Stability grade: 2 (generally 2 codes of fluctuation).
21.1 expression status of table and code
21.2 code difference of table and weight
Code difference 0 1 2 3 4 5 6
Weight 0 0 4 4 4 4 4
Character 29:* is only applicable to monochromatic kind of skin kind: seed: Cotyledon color;
Trait expression mode: PQ;
Stability grade: 2 (generally 2 codes of fluctuation).
22.1 expression status of table and code
Expression status Yellow Yellow green Green
Code 1 2 3
22.2 code difference of table and weight
Code difference 0 1 2
Weight 0 0 4
Character 30: hilum: color;
Trait expression mode: PQ;
Stability grade: 2 (generally 2 codes of fluctuation).
23.1 expression status of table and code
23.2 code difference of table and weight
Code difference 0 1 2 3 4 5
Weight 0 0 1 4 4 4
Embodiment 2: the screening of soybean approximation kind
1. soybean application kind totally 6, code name and title are as shown in table 24;
2. application kind is passed through each trait data (table 25) of the acquisition of plantation in 1 year, importing soybean phenotype trait data library;
3. setting 2 for safe distance, " screening " button is clicked, Database Systems list the close of corresponding each application kind Like kind inventory (table 26, Fig. 1).Table 26 only lists the approximate kind that phenotype distance is 0.
Table 24 applies for kind
Table 25 applies for the data (expression status of each character, i.e. code value) of kind First Year acquisition
The part approximation kind that table 36 filters out
This method automatically can be lined up selected approximate kind according to phenotype by Database Systems apart from size, be convenient for By the plantation adjacent with application kind of closest kind when field trial, the specific aim of specific test is improved.

Claims (2)

1. a kind of soybean specific test approximation method for screening varieties based on phenotype distance, characterized in that
(1) weight of each soybean phenotypic character code difference is set
The phenotype trait data of the current still soybean varieties with application potential of acquisition, carries out the phenotype trait data of acquisition whole Reason, establishes soybean varieties phenotype trait data library;According to the expression status observation of each phenotypic character by environmental influence Degree and personnel's observed deviation size, different power is arranged to the code difference of the expression status of each soybean phenotypic character Weight obtains data as shown in Table 1, inputs soybean varieties phenotype trait data library;
Table 1
(2) setting of phenotype distance threshold
To the phenotypic character expression status code difference of pairs of soybean varieties, weight, all phenotypes are assigned by the method for step (1) Weight addition in character obtains two interracial phenotype distances;By the obvious degree of a large amount of phenotype distances and Differences into Row compares, and determines a phenotype distance threshold: and it is inputted soybean varieties phenotype trait data library;
(3) approximate screening varieties
The approximate screening varieties software based on phenotype distance is developed in soybean varieties phenotype trait data library based on foundation;Xiang great The phenotype trait data of application kind to be measured is inputted in beans kind phenotype trait data library, which can be according to step (2) method calculates the phenotype distance of application kind to be measured and each known kind, and is compared with phenotype distance threshold, Phenotype distance is less than approximate kind of the known kind of threshold value as the application kind to be measured.
2. a kind of soybean specific test approximation method for screening varieties based on phenotype distance as described in claim 1, special Sign is, step (2) the phenotype distance threshold is 2, and whens two interracial phenotypes distance < 2 is determined as approximate kind.
CN201811462618.4A 2018-12-03 2018-12-03 A phenotypic distance-based screening method for soybean specificity testing similar varieties Withdrawn CN109616159A (en)

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* Cited by examiner, † Cited by third party
Publication number Priority date Publication date Assignee Title
WO2014003530A4 (en) * 2012-06-28 2014-03-13 Moroccan Foundation For Advanced Science, Innovation & Research (Mascir) Method for increasing the potential for biofuel production from microalgae by using bio-modulators
CN105132551A (en) * 2015-09-01 2015-12-09 山东省农业科学院作物研究所 Method for screening wheat approximate variety by virtue of SSR molecular marker
CN105740655A (en) * 2016-01-29 2016-07-06 山东省农业科学院作物研究所 Approximate variety screening method in soybean specificity test on the basis of phenotypic character
CN108796121A (en) * 2018-07-04 2018-11-13 山东省农业科学院作物研究所 A kind of specific test approximation kind high-efficiency screening method based on genetic similarty

Patent Citations (4)

* Cited by examiner, † Cited by third party
Publication number Priority date Publication date Assignee Title
WO2014003530A4 (en) * 2012-06-28 2014-03-13 Moroccan Foundation For Advanced Science, Innovation & Research (Mascir) Method for increasing the potential for biofuel production from microalgae by using bio-modulators
CN105132551A (en) * 2015-09-01 2015-12-09 山东省农业科学院作物研究所 Method for screening wheat approximate variety by virtue of SSR molecular marker
CN105740655A (en) * 2016-01-29 2016-07-06 山东省农业科学院作物研究所 Approximate variety screening method in soybean specificity test on the basis of phenotypic character
CN108796121A (en) * 2018-07-04 2018-11-13 山东省农业科学院作物研究所 A kind of specific test approximation kind high-efficiency screening method based on genetic similarty

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Title
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Application publication date: 20190412