Method for QTL framework of tree quantitative traits based on Richards equation

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

Inactive Publication Date: 2021-09-03
BEIJING FORESTRY UNIVERSITY
View PDF6 Cites 0 Cited by
  • 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

the structure of the environmentally friendly knitted fabric provided by the present invention; figure 2 Flow chart of the yarn wrapping machine for environmentally friendly knitted fabrics and storage devices; image 3 Is the parameter map of the yarn covering machine
View more

Image

Smart Image Click on the blue labels to locate them in the text.
Viewing Examples
Smart Image
  • Method for QTL framework of tree quantitative traits based on Richards equation
  • Method for QTL framework of tree quantitative traits based on Richards equation
  • Method for QTL framework of tree quantitative traits based on Richards equation

Examples

Experimental program
Comparison scheme
Effect test

Embodiment 1

[0136]The stem height growth data disclosed in A computational framework for mapping the timing of vegetative phase change (New Phytologist; 211:750-60, 2016) published by Meng Xu et al. is used as an example to further describe the present invention in detail. The sample data comes from 450 progenies obtained by artificial crossing with the American black poplar clone (I-69) as the female parent and the European and American poplar clone (I-45) as the male parent, and they were uniformly planted in Zhangji Forest Farm (34.14° N, 117.38°W). The applied phenotypic data include the growth of stem height and diameter growth of 64 randomly selected offspring and female parent I-69, male parent I-45, a total of 66 forest poplar samples in the first 14 years of growth (1987-2010). Data, gene data is 156362 SNP information distributed on 19 chromosomes. In the genetic data, 94591 SNPs are test cross markers, and 61771 SNPs are hybrid markers. Tester markers are those in which one p...

Embodiment 2

[0194] 1. Use the quasi-Newton method to fit the growth data of the poplar sample diameter.

[0195] The above-mentioned phenotypic data of poplar quantitative traits were used to fit the Richard equation, and the estimated parameters of the equation were obtained by searching. The Richard equation is shown in equation (3):

[0196]

[0197] Among them, b 1 Represents growth limit; b 2 represents the shape parameter; b 3 is a parameter related to growth rate, and y represents the fitted value of diameter growth.

[0198] The fitting Richard equation is fitted by the least square method; the search method of the estimated parameter is the BFGS quasi-Newton method, and the Richard estimated parameter that makes the sum of the squares of the diameter phenotype value and the fitted value minimum is found, specifically through the R language General optimization method optim function implementation.

[0199] Figure 5 is the Richard growth curve of poplar diameter, wherein...

the structure of the environmentally friendly knitted fabric provided by the present invention; figure 2 Flow chart of the yarn wrapping machine for environmentally friendly knitted fabrics and storage devices; image 3 Is the parameter map of the yarn covering machine
Login to view more

PUM

No PUM Login to view more

Abstract

The invention provides a method for a QTL framework of tree quantitative traits based on a Richards equation, and belongs to the technical field of bioinformatics analysis. The method comprises the following steps: fitting a growth curve of quantitative characters of trees by utilizing a Richards growth equation to obtain Richards estimation parameters of the quantitative characters, and obtaining structural parameters of an SAD (1) model according to a correlation of character phenotypes along with time; performing functional mapping according to the difference of the growth parameters between the genotypes, and screening significant QTLs for regulating and controlling the quantitative trait growth of the trees; and calculating a significant QTL genetic effect value and heritability, establishing a regulatory structure network between QTLs, and identifying and explaining key regulatory QTLs in a tree quantitative trait growth process. The method provided by 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, so that the character growth analysis is 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 tree quantitative traits 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 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 phenotype and genotyp...

Claims

the structure of the environmentally friendly knitted fabric provided by the present invention; figure 2 Flow chart of the yarn wrapping machine for environmentally friendly knitted fabrics and storage devices; image 3 Is the parameter map of the yarn covering machine
Login to view more

Application Information

Patent Timeline
no application Login to view more
Patent Type & Authority Applications(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
Who we serve
  • R&D Engineer
  • R&D Manager
  • IP Professional
Why Eureka
  • Industry Leading Data Capabilities
  • Powerful AI technology
  • Patent DNA Extraction
Social media
Try Eureka
PatSnap group products

Browse by: Latest US Patents, China's latest patents, Technical Efficacy Thesaurus, Application Domain, Technology Topic.

© 2024 PatSnap. All rights reserved.Legal|Privacy policy|Modern Slavery Act Transparency Statement|Sitemap