CN101984446B - Estimating method of genetic similarity index of codominance molecular marker based on relative correlation coefficient - Google Patents

Abstract

The invention discloses a calculation method of genetic similarity index of codominance molecular marker based on relative correlation coefficient. The technical scheme is as follows: obtaining an electrophoresis pattern of each variety or kind of plant by adopting the current codominance molecular marker method; comparing in pairs according to the amplification strip information of the variety or kind of the plant; respectively calculating a genetic similarity index between each two plant varieties and kinds according to a calculation formula of the genetic similarity index; and taking the genetic similarity index as the estimation of the corresponding relative extent of the individuals. The calculation method of genetic similarity index is applied to the codominance molecular marker. The calculation method of the obtained genetic similarity index can effectively respond the relative relationship extent among the colonies based on the relative correlation coefficient.

Description

Codominance molecular labeling genetic resemblance exponential estimation method based on the relationship related coefficient

Technical field

The present invention relates to biology field, relate in particular to a kind of codominance molecular labeling genetic resemblance exponential estimation method based on the relationship related coefficient.

Background technology

Along with development of biology, the detection of genetic diversity develops into chromosome and dna level gradually from morphology, Physiology and biochemistry level, experienced from simple to complicated, from the macroscopic view to the microcosmic, from the evolution of qualitative to quantitative.

Detecting genetic diversity on the dna level mainly is the nucleotide sequence through RFLP (restriction segment length polymorphism), RAPD (randomly amplified polymorphic DNA), SSR some specific genes of technical Analysis such as (microsatellite polymorphisms) or dna segment; Measure its variability; Detect genomic a collection of recognition site; Thereby estimate genomic variability (Zhang Dequan and Yang Yongping, 2008).Research proof, the detection method of dna level can both be selected suitable statistical method according to the individual dna fingerprinting that obtains through electrophoretic separation, can judge genetic purity that kind or strain are interior and the hereditary difference between kind or strain effectively.

Selecting suitable genetic resemblance index calculation method is to carry out the basis (Dalirsefat, 2009) that population genetic diversity is analyzed.The selection of Kosman and Leonard (2005) report genetic similarity computing method depends primarily on the molecular labeling type that test is adopted.RFLP, SSR, SCAR molecular labeling etc. all belong to the codominance molecular labeling, can distinguish the dominance homozygote and the heterozygote of diplont.In the codominance molecular labeling, dominance homozygote, stealthy homozygote all have only a band, and two amplified bands then can appear in the goneoclin individuality.Therefore, generally can not occur all non-existent site of two individual fragments in the codominance molecular labeling similarity coefficient computation process, 0 promptly total type band value is generally 0.

At present; According to different researchists and some applied analysis software (like Phyhp; PAUP and NTSYS etc.) frequency quoting or adopt; The analysis of the genetic resemblance index between codominance molecular labeling sample has following two kinds of computing method usually: Sorensen-Dice similarity index (Barth etc., 2002; Belaj etc., 2003; Cordeiro etc., 2003; Dearborn etc., 2003), Jaccard similarity index (Teulat etc., 2000; Anthony etc., 2002; Cordeiro etc., 2003; etc., 2003).More than two kinds of similarity index values between 0 and 1, can be converted into similar percent (Wang Chengshu and Li Zengzhi, 2002), often be used to weigh genetic resemblance degree between individuality, according to this as judging the far and near foundation of relationship between individuality.

But above-mentioned two kinds of similarity indexes only are used for describing a kind of range index or the similarity index of two binary variable differences or similarity degree, its in essence and between individuality the relationship degree do not have positive connection.Given this, the inventor proposes a kind of new genetic resemblance exponential estimation method according to the definition of relationship related coefficient (relationship coefficient), in order to estimate the genetic resemblance index between codominance molecular labeling kind or strain.

Summary of the invention

The objective of the invention is to overcome relationship degree between existing genetic resemblance index and individuality does not have the defective of positive connection, and a kind of codominance molecular labeling genetic resemblance exponential estimation method based on the relationship related coefficient is provided.

Step based on the codominance molecular labeling genetic resemblance exponential estimation method of relationship related coefficient is following:

1) adopts the codominance molecule labelling method, obtain the electrophoresis pattern of plant variety or plant lines,,, carry out reading and recording with 1 or 0 respectively according to the having or do not have of amplified production band to the electrophoresis pattern of plant variety or plant lines;

2) according to the amplification bands of a spectrum information of plant variety or plant lines, be carried out to relatively, obtain a, b, c value between plant variety or plant lines respectively;

3) according to a between plant variety or plant lines, b, c value calculate respectively plant variety or plant lines in twos between the genetic resemblance index, as the estimation of relationship degree between corresponding plant variety or between plant lines.

Described amplification bands of a spectrum information according to plant variety or plant lines; Be carried out to comparing; The a, b, the c value step that obtain respectively between plant variety or plant lines are: the amplification bands of a spectrum information that compares plant variety or plant lines in pairs; Obtain a, b, c value between plant variety or plant lines, a value is the 1 type spectrum band number that plant variety or plant lines x, y have; The b value is the contained 1 type spectrum band number of plant variety or plant lines x; The c value is the contained 1 type spectrum band number of plant variety or plant lines y; Wherein x, y are expressed as two plant varieties or the plant lines to relatively.

Described calculate respectively plant variety or plant lines in twos between the genetic resemblance index; As the estimating step of relationship degree between corresponding plant variety or between plant lines be: utilize based on the genetic resemblance formula of index of relationship related coefficient calculate respectively plant variety or plant lines in twos between genetic resemblance index Rxy, wherein a value is the 1 type spectrum band number that plant variety or plant lines x, y have; The b value is the contained 1 type spectrum band number of plant variety or plant lines x; The c value is the contained 1 type spectrum band number of plant variety or plant lines y; X, y are expressed as two plant varieties or the plant lines to relatively.

Genetic resemblance index calculation method of the present invention is applicable to the codominance molecular labeling.The genetic resemblance index calculation method of gained can reflect effectively that based on the relationship related coefficient sibship between colony is far and near.

Description of drawings

Fig. 1 is the SSR amplification collection of illustrative plates of P068 primer to 15 rape varieties, among the figure: M:marker DL2000; 1-15: listed 15 rape varieties in the table 1.

Embodiment

Step based on the codominance molecular labeling genetic resemblance exponential estimation method of relationship related coefficient is following:

1) adopts the codominance molecule labelling method, obtain the electrophoresis pattern of plant variety or plant lines,,, carry out reading and recording with 1 or 0 respectively according to the having or do not have of amplified production band to the electrophoresis pattern of plant variety or plant lines;

2) according to the amplification bands of a spectrum information of plant variety or plant lines, be carried out to relatively, obtain a, b, c value between plant variety or plant lines respectively;

3) according to a between plant variety or plant lines, b, c value calculate respectively plant variety or plant lines in twos between the genetic resemblance index, as the estimation of relationship degree between corresponding plant variety or between plant lines.

Described amplification bands of a spectrum information according to plant variety or plant lines; Be carried out to comparing; The a, b, the c value step that obtain respectively between plant variety or plant lines are: the amplification bands of a spectrum information that compares plant variety or plant lines in pairs; Obtain a, b, c value between plant variety or plant lines, a value is the 1 type spectrum band number that plant variety or plant lines x, y have; The b value is the contained 1 type spectrum band number of plant variety or plant lines x; The c value is the contained 1 type spectrum band number of plant variety or plant lines y; Wherein x, y are expressed as two plant varieties or the plant lines to relatively.

Described calculate respectively plant variety or plant lines in twos between the genetic resemblance index; As the estimating step of relationship degree between corresponding plant variety or between plant lines be: utilize based on the genetic resemblance formula of index

of relationship related coefficient calculate respectively plant variety or plant lines in twos between genetic resemblance index Rxy, wherein a value is the 1 type spectrum band number that plant variety or plant lines x, y have; The b value is the contained 1 type spectrum band number of plant variety or plant lines x; The c value is the contained 1 type spectrum band number of plant variety or plant lines y; X, y are expressed as two plant varieties or the plant lines to relatively.

Genetic resemblance formula of index

derivation is following:

1 total type spectrum band number of known plants kind or plant lines x, y is that the collaborating genes group number of plant variety or plant lines x, y is a; The genome number that the contained 1 type spectrum band number of plant variety or plant lines x is plant variety or plant lines x is b; The genome number that the contained 1 type spectrum band number of plant variety or plant lines y is plant variety or plant lines y is c.To contain the frequency of total gene be a/b for x plant variety or plant lines so, and the frequency that y plant variety or plant lines contain total gene is a/c, with this coefficient of inbreeding of estimating x, y plant variety or plant lines offspring is:

$F_{\mathrm{xy}}=\frac{a}{b}\×\frac{a}{c}=\frac{a^2}{\mathrm{bc}}---\left(1\right)$

If the coefficient of inbreeding of x and y plant variety or plant lines is respectively F _xAnd F _y, then the relationship related coefficient between x and y plant variety or plant lines is:

$R_{\mathrm{xy}}=\frac{2F_{\mathrm{xy}}}{\sqrt{(1+F_x)(1+F_y)}}---\left(2\right)$

Because it is individual that x, y plant variety or plant lines are non-inbreeding, so F _x=F _y=0, then (2) formula becomes:

$R_{\mathrm{xy}}=2F_{\mathrm{xy}}=\frac{{2a}^2}{\mathrm{bc}}---\left(3\right)$

But under the bigger situation of a value, utilize (3) formula to estimate that the situation greater than 1 may appear in the relationship degree between individuality, therefore for guaranteeing 0≤R _Xy≤1, and consider and can further (3) formula be reduced to the comparability of genetic resemblance degree between individuality:

$R_{\mathrm{xy}}=\sqrt{\frac{a^2}{\mathrm{bc}}}---\left(4\right)$

Embodiment:

The present invention generally is suitable in analysis of genetic diversity research the codominance molecular labeling, on the rape variety analysis of genetic diversity, is applied as example with the SSR molecular labeling.

1) using 8 pairs of polymorphism SSR primers analyzes 15 rape varieties (table 1); Obtain the electrophoresis pattern (Fig. 1) of 15 rape varieties; According to the having or do not have of amplified production band, carry out reading and recording with 1 or 0 respectively, obtain comprising the SSR finger-print data (table 2) of 22 amplified fragments;

15 rape varieties of table 1 experiment selected

The SSR finger-print data of 15 rape varieties of table 2

2) according to the SSR finger-print data of 15 rape varieties, be carried out to relatively, obtain a, b, c value respectively.Is example with Zhejiang two 758 with assorted No. 4 two rape varieties of magnificent oil: two variety SSR fingerprint collection of illustrative plates compare in pairs, obtain a=8, b=10, c=10;

3) add up any two interracial genetic resemblance indexes (table 3) in 15 rape varieties respectively according to formula

, as the estimation of relationship degree between corresponding kind; With Zhejiang two 758 and assorted No. 4 two rape varieties of China's oil is example: a=8 between two kinds; B=10; C=10 tries to achieve according to formula

Genetic resemblance index between 15 rape varieties of table 3

Claims (1)

1. codominance molecular labeling genetic resemblance exponential estimation method based on the relationship related coefficient is characterized in that its step is following:

1) adopts the codominance molecule labelling method, obtain the electrophoresis pattern of plant variety or plant lines,,, carry out reading and recording with 1 or 0 respectively according to the having or do not have of amplified production band to the electrophoresis pattern of plant variety or plant lines;

2) according to the amplification bands of a spectrum information of plant variety or plant lines, be carried out to relatively, obtain a, b, c value between plant variety or plant lines respectively;

3) according to a between plant variety or plant lines, b, c value calculate respectively plant variety or plant lines in twos between the genetic resemblance index, as the estimation of relationship degree between corresponding plant variety or between plant lines;

Described amplification bands of a spectrum information according to plant variety or plant lines; Be carried out to comparing; The a, b, the c value step that obtain respectively between plant variety or plant lines are: the amplification bands of a spectrum information that compares plant variety or plant lines in pairs; Obtain a, b, c value between plant variety or plant lines, a value is the 1 type spectrum band number that plant variety or plant lines x, y have; The b value is the contained 1 type spectrum band number of plant variety or plant lines x; The c value is the contained 1 type spectrum band number of plant variety or plant lines y; Wherein x, y are expressed as two plant varieties or the plant lines to relatively; Described calculate respectively plant variety or plant lines in twos between the genetic resemblance index, as the estimating step of relationship degree between corresponding plant variety or between plant lines be: utilize genetic resemblance formula of index based on the relationship related coefficient

Calculate respectively plant variety or plant lines in twos between genetic resemblance index R _Xy, wherein a value is plant variety or plant lines x, 1 total type spectrum band number of y; The b value is the contained 1 type spectrum band number of plant variety or plant lines x; The c value is the contained 1 type spectrum band number of plant variety or plant lines y; X, y are expressed as two plant varieties or the plant lines to relatively.

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