Method for detecting additive and dominant genetic effects of DNA methylation sites on quantitative traits and application technology thereof

A technology of dominant inheritance and quantitative traits, applied in biochemical equipment and methods, chemical libraries, combinatorial chemistry, etc., to achieve important theoretical and technical effects

Inactive Publication Date: 2019-04-02
BEIJING FORESTRY UNIVERSITY
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  • Summary
  • Abstract
  • Description
  • Claims
  • Application Information

AI Technical Summary

Benefits of technology

This patented technology allows researchers to study how different parts or organs have been affected with certain genes during their life cycle (morphology). It can help predict future generations' responses towards specific environmental factors that affect these areas more accurately than before they were developed into ornamental wood species.

Problems solved by technology

This patented technical problem addressed in this patents relates to analyzing how various factors affect gene expression levels during certain stages or steps of life cycles such as fertilization, embryogenesis, germination, death caused by cancer chemotherapy, etc., while considering other environmental influences like temperature variations over time.

Method used

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  • Method for detecting additive and dominant genetic effects of DNA methylation sites on quantitative traits and application technology thereof
  • Method for detecting additive and dominant genetic effects of DNA methylation sites on quantitative traits and application technology thereof
  • Method for detecting additive and dominant genetic effects of DNA methylation sites on quantitative traits and application technology thereof

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Experimental program
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Effect test

Embodiment 1

[0042] The specific operation steps are as follows:

[0043] Step 1) Randomly select 300 individuals from the Populus tomentosa germplasm resource bank planted in Guan County, Shandong Province as an associated population, and collect their functional leaves (the 3rd to 5th mature leaves at the top of the branches) at 9:00 to 11:00 in the morning. ), in order to prevent changes in the DNA methylation status, immediately put them into a liquid nitrogen environment (-196°C) for storage after collection.

[0044] Step 2) Genomic DNA of leaf samples was extracted using DNeasy Plant Mini Kit (Qiagen China, Shanghai, China).

[0045] After completing the above steps, the obtained genomic DNA can be further detected, specifically: 2.1, use agarose gel electrophoresis to determine the degree of degradation of the DNA sample and whether there is RNA contamination; 2.2, use RNsae-free water as a blank control, Use Nanodrop to detect the OD260 / OD280 ratio of each DNA sample to determine...

specific Embodiment approach

[0046] Then implement step 3) carry out bisulfite sequencing to the extracted genomic DNA, the method for the DNA library that builds bisulfite treatment according to genomic DNA has become conventional technical method, and the specific embodiment of the present invention is as follows:

[0047] Step 3.1, using Covaris S220 to randomly fragment the genomic DNA to 200-300bp;

[0048] Step 3.2: Carry out end repair and A-tailing on the fragmented DNA fragments, and connect sequencing adapters with all cytosines modified by methylation, the purpose of which is to provide primers required for the next sequencing-by-synthesis process. sequence information;

[0049] In step 3.3, the DNA fragment in step 3.2 is subjected to bisulfite treatment. After treatment, the unmethylated C becomes U (after PCR amplification becomes T), while the methylated C remains unchanged. Specifically, the EZ DNA MethylationGold Kit (Zymo Research, Murphy Ave. Irvine, CA, U.S.A.) can be used;

[0050] ...

Embodiment 2

[0064] The specific operation steps are as follows:

[0065] Step 1) Randomly select 300 individuals from the Populus tomentosa germplasm resource bank planted in Guan County, Shandong Province as the sequencing population, and collect their functional leaves (the 3rd to 5th mature leaves at the top of the branches) at 9:00 to 11:00 in the morning ), in order to prevent changes in the DNA methylation status, immediately put them into a liquid nitrogen environment (-196°C) for storage after collection.

[0066] Step 2) Genomic DNA of leaf samples was extracted using DNeasy Plant Mini Kit (Qiagen China, Shanghai, China).

[0067] After completing the above steps, the obtained genomic DNA can be further detected, specifically: 2.1, use agarose gel electrophoresis to determine the degree of degradation of the DNA sample and whether there is RNA contamination; 2.2, use RNsae-free water as a blank control, Use Nanodrop to detect the OD260 / OD280 ratio of each DNA sample to determine...

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Abstract

The invention provides a method for detecting additive and dominant genetic effects of DNA methylation sites on quantitative traits and an application thereof, and belongs to the field of plant molecular breeding. The method comprises the following steps: 1) collecting population samples of germplasm resources, detecting phenotypic traits, and extracting genomic DNA from the samples; 2) constructing a bisulfite sequencing library by the genomic DNA of the samples, and sequencing; 3) identifying the DNA methylation sites from DNA methylation sequencing data, and genotyping; and 4) carrying outcorrelation analysis of the obtained genotyping data of the DNA methylation sites and the sample phenotypic trait data by a mixed linear model in Tassel 5.0 software package, and screening significantly correlated DNA methylation sites and analyzing the additive and dominant genetic effects. The method can provide new technical guidance for gene marker assisted breeding, and has important theoretical and breeding value.

Description

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Claims

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Application Information

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Owner BEIJING FORESTRY UNIVERSITY
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