Method for identifying plant lncRNA and gene interaction

A plant and gene technology, applied in the field of molecular genetics, can solve the problems of gene false positives, inability to accurately detect functional genes, single prediction method, etc.

Active Publication Date: 2019-03-29
BEIJING FORESTRY UNIVERSITY
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Problems solved by technology

[0003] At present, most of the interactions between plant lncRNAs and genes only consider the sequence similarity between two transcripts, and the identified genes that interact with lncRNAs have false positives; and the prediction method is relatively simple and cannot be accurately detected. Functional genes interacting with lncRNA
Therefore, the prior art lacks a method for accurately identifying plant lncRNA-gene interactions

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  • Method for identifying plant lncRNA and gene interaction
  • Method for identifying plant lncRNA and gene interaction
  • Method for identifying plant lncRNA and gene interaction

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Embodiment 1

[0067] Using a method for identifying plant lncRNA-gene interaction provided by the present invention, the interaction between Populus tomentosa lncRNA LNC-0052611 and the gene Pto-COMT25 is identified.

[0068] Step S1, the SNP genotype data of lncRNA LNC-0052611 and gene Pto-COMT25 in Populus tomentosa natural population, the specific steps are as follows:

[0069] In step S11, the annual Populus tomentosa clone "LM50" planted in Guan County, Shandong Province was used as the experimental material, and its mature xylem was collected as the tissue to be tested for transcriptome sequencing. In order to prevent RNA degradation, it was immediately placed in a liquid nitrogen environment (-196°C) for storage. The collected mature xylem RNA was extracted using the Plant Qiagen RNAeasy kit (Qiagen China, Shanghai, China), and after quality assessment, it was submitted to the biological company for lncRNA and transcriptome sequencing to detect the lncRNA and mRNA expressed in the ti...

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Abstract

The present invention provides a method for identifying plant lncRNA and gene interaction, and relates to the technical field of molecular genetics. The method comprises the following steps: population SNP genotype data of lncRNA and gene are obtained; population expression data of the gene in a studied tissue are obtained; target trait population phenotypic data are obtained; the population SNP genotype data and target trait population phenotypic data are subjected to correlation analysis; the population SNP genotype data and population expression data are subjected to correlation analysis; acorrelation coefficient r of the population SNP genotype data and target trait population phenotypic data is calculated; when three limit conditions are met at the same time, the lncRNA interacts with the gene to commonly affect phenotypic variation of plant target traits. The method is used to accurately detect interaction between populus tomentosa lncRNA LNC-0052611 and gene Pto-COMT25, and theinteraction affects the phenotypic variation of diameter at breast height of populus tomentosa.

Description

technical field [0001] The invention relates to the technical field of molecular genetics, in particular to a method for identifying the interaction between plant lncRNA and genes. Background technique [0002] Long non-coding RNA (Long non-coding RNA, lncRNA) refers to a class of regulatory transcripts that have no protein coding function and are longer than 200nt. Studies have shown that lncRNA can regulate gene expression at multiple levels, thereby affecting the growth and development of plants, such as rice pollen fertility and Arabidopsis photomorphogenesis. The growth and development of plants is a complex, multi-level and multi-gene joint regulation process, and the interaction modes between various genetic factors are even more diverse. At present, the specific mechanism of action of lncRNA is not yet clear. The research on its interaction with genes is mainly based on the principle of base complementary pairing. Gene expression regulation at the level, post-trans...

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Application Information

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Patent Type & Authority Applications(China)
IPC IPC(8): G16B20/00G16B30/00C12Q1/6895
CPCC12Q1/6895C12Q2600/156C12Q2600/158C12Q2600/178G16B20/20G16B20/40G16B30/10G16B40/30C12Q1/6869
Inventor 张德强权明洋杜庆章肖亮卢文杰
Owner BEIJING FORESTRY UNIVERSITY
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