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A method for QTL localization framework of quantitative traits of trees based on Richards equation

A technology of quantitative traits and positioning framework, applied in the field of bioinformatics analysis, can solve problems such as incompleteness

Inactive Publication Date: 2021-12-14
BEIJING FORESTRY UNIVERSITY
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  • Summary
  • Abstract
  • Description
  • Claims
  • Application Information

AI Technical Summary

Problems solved by technology

[0004] However, the current research on the establishment of the genetic mechanism of key quantitative traits of trees is not comprehensive, and there is a lack of in-depth analysis of the genetic control of significant QTLs regulating growth and the regulatory network structure between QTLs

Method used

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  • A method for QTL localization framework of quantitative traits of trees based on Richards equation
  • A method for QTL localization framework of quantitative traits of trees based on Richards equation
  • A method for QTL localization framework of quantitative traits of trees based on Richards equation

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Experimental program
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Effect test

Embodiment 1

[0136]Using A computational framework Meng Xu et al., Published formapping the timingof vegetative phase change (New Phytologist; 211: 750-60,2016) stem height growth data disclosed an example of the present invention will be further described in detail. Sample data from the body to Yangke Long deltoides (I-69) as the female parent, Western poplar clones (I-45) male parent to give 450 artificial hybrid progeny, uniform field planted in Jiangsu Zhang Jilin (34.14 ° N, 117.38 ° W). Phenotypic data application includes 64 randomly chosen parent and progeny I-69, I-45 were male forest poplar samples 66 before 14 years (1987-2010) the growth of stem height and diameter growth Growth data, genetic data information distribution SNP 156 362 19 chromosomes. Gene SNP data 94591 is the measured cross mark, hybridization 61,771 SNP markers. Means one marker test cross parents are heterozygous, and the other is homozygous; labeled hybridization from two heterozygous parents.

[0137] 1. poplar...

Embodiment 2

[0193] 1. Fit the growth data of poplar sample diameters using the Aunton Method.

[0194] The Richard equation is fitted with the number of pitched phenotypic data of the above poplar, and the estimation parameters of the equation are obtained. Richard equations are shown in equation (3):

[0195]

[0196] Among them, B 1 Representing growth limit; B 2 Represents shape parameters; b 3 It is the parameter associated with the growth rate, Y represents the fitting value of the diameter growth.

[0197] The fit Richard equation is fitted through the least squares method; the search method of the estimated parameter is BFGS to be Newton Method, find the Richard estimation parameters such that the diameter phenotype value is square and the smallest value residual, specifically via the R language General optimization method OPTIM function implementation.

[0198] Figure 5 The Richard growth curve of the poplar diameter, wherein the light-color curve is a growth curve of 66 samples, a...

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Abstract

The invention provides a method for QTL positioning frame of quantitative traits of trees based on Richards equation, and belongs to the technical field of bioinformatics analysis. The method utilizes the Richards growth equation to fit the growth curve of the quantitative traits of trees, obtains the Richards estimated parameters of the quantitative traits, and obtains the structural parameters of the SAD (1) model according to the correlation of trait phenotypes with time; according to the growth parameters between genotypes Functional mapping of the differences among them, screening of significant QTLs that regulate the growth of quantitative traits of trees; calculation of genetic effect values ​​and heritability of significant QTLs, establishment of regulatory network between QTLs, and identification of key regulatory QTLs that explain the growth process of quantitative traits of trees. The method of the invention has strong biological significance and high positioning precision, and the established genetic effect regulation network provides an effective method for genetic structure analysis and makes the trait growth analysis more comprehensive.

Description

technical field [0001] The invention belongs to the technical field of bioinformatics analysis, and in particular relates to a method for the QTL positioning framework of quantitative traits of trees based on the Richards equation. Background technique [0002] Tree biomass is the basic raw material for forestry production practice and has important ecological and economic value. The growth potential and development characteristics of trees are mainly manifested in the accumulation of quantitative traits such as diameter, stem height, and volume. These traits have no clear boundaries between relative traits, and can only be used quantitatively to distinguish differences in performance between individuals. The change of quantitative traits of trees over time is a genetic process controlled by multiple genes, and the chromosomal loci that control the expression of quantitative traits are called quantitative trait loci (QTL). Establishing the biological correlation between ph...

Claims

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Application Information

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Patent Type & Authority Patents(China)
IPC IPC(8): G16B20/30G16B25/00G16B5/00
CPCG16B20/30G16B25/00G16B5/00
Inventor 张晓宇龚慧莹姜立波邬荣领
Owner BEIJING FORESTRY UNIVERSITY