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Method for determining up-regulated genes and down-regulated genes in cotton fiber development process

A development process, cotton fiber technology, applied in the field of plant genes and their encoded proteins, can solve problems such as unclear fiber quality mechanism

Inactive Publication Date: 2016-02-03
XINJIANG AGRI UNIV
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  • Summary
  • Abstract
  • Description
  • Claims
  • Application Information

AI Technical Summary

Problems solved by technology

At present, the mechanism of the excellent fiber quality of sea-island cotton is still unclear.

Method used

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  • Method for determining up-regulated genes and down-regulated genes in cotton fiber development process
  • Method for determining up-regulated genes and down-regulated genes in cotton fiber development process
  • Method for determining up-regulated genes and down-regulated genes in cotton fiber development process

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Experimental program
Comparison scheme
Effect test

Embodiment approach

[0025] According to one embodiment of the present invention, there is provided a method for determining up-regulated or down-regulated genes during cotton fiber development, comprising the following steps:

[0026] Step 1: Obtain the first transcriptome sequencing data and the second transcriptome sequencing data

[0027] Obtain the first transcriptome and the second transcriptome from the samples in the first and second stages of cotton fiber development, respectively, sequence the first and second transcriptomes, and obtain the first transcriptome sequencing data and the second transcriptome The sequencing data, the first transcriptome sequencing data and the second transcriptome sequencing data each comprise a plurality of reads. The samples in the first stage of cotton fiber development and the second stage of cotton fiber development are all derived from cotton ovules.

[0028] In a specific embodiment of the present invention, the first stage of cotton fiber developme...

Embodiment 1

[0053] Example 1: Transcriptome library construction and sequencing

[0054] 1.1 Experimental materials and RNA extraction

[0055] Upland cotton Xinluzhong 36 (Gossypiumhirsutum) Gh36 and Haidao cotton Xinhai 21 (Gossypiumbarbadense) Gb21 were obtained from the Agricultural Science Research Institute of the First Division of Alarnong, Xinjiang. Two varieties of cotton were sown in the field, and the ovules (0DPA) on the day of flowering of Upland cotton and Sea Island cotton were taken respectively. The samples were named xianyang_LZC and xianyang_HZB, and were quickly placed in liquid nitrogen and stored in a -80℃ refrigerator for later use.

[0056] Upland cotton (Gossypiumhirsutum) Gh36 and sea island cotton (Gossypiumbarbadense) Gb21 were the experimental materials (provided by the Agricultural Research Institute of the First Division of Alarnong, Xinjiang). The two strains of cotton were sown in the field, and the fibers of 5, 10, 15, and 25 DPA were picked respectively...

Embodiment 2

[0062] Example 2: Screening of differentially expressed genes

[0063] ——Based on the sequencing data of the same cotton species at different cotton fiber development stages or different cotton species at the same cotton fiber development stage

[0064] 2.1 Transcriptome data statistics and filtering

[0065] Filter the raw data (rawreads or rawdata) according to the requirements. Rawdata or rawreads are obtained from the raw image data obtained by base calling (basecalling) transformation and sequencing. Generally, the contamination of the connector, the repetition of the quality value caused by the PCR in the library construction process, and the quality value The very low reads are removed, and clean reads (Cleanreads) are obtained for subsequent analysis, such as obtaining non-redundant gene sequences Unigenes through multiple assemblies, and using bioinformatics for Unigenes to screen differentially expressed genes and / or analyze differentially expressed genes function, ...

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Abstract

The invention provides a method for determining up-regulated genes and down-regulated genes in a cotton fiber development process. The method includes the steps: acquiring a first transcriptome and a second transcriptome from samples of cotton fibers in a first development stage and a second development stage respectively, and sequencing to obtain sequencing data of the first transcriptome and sequencing data of the second transcriptome; respectively performing primary assembling based on the sequencing data of the first transcriptome and the sequencing data of the second transcriptome to obtain first primary assembling data and second primary assembling data; merging the first primary assembling data and the second primary assembling data, and using overlapped primary genes in the first primary assembling data and the second primary assembling data to perform secondary assembly for acquiring secondary assembling data; performing tertiary assembling on the basis of an overlapping relation between the secondary assembly data and reference genes to obtain tertiary assembling data; calculating expression quantities, in the two samples, of tertiary genes in the tertiary assembling data, acquiring differentially expressed genes according to the condition whether difference of the expression quantities is significant or not, and determining the up-regulated genes and down-regulated genes in the cotton fiber development process.

Description

technical field [0001] The present invention relates to plant genes and their encoded proteins, in particular to differentially expressed genes and encoded proteins during cotton fiber development, and their applications in improving cotton fiber yield and quality. Background technique [0002] Cotton is an important economic crop in my country and plays a main role in the global economy. Sea island cotton (G.barbadense) and upland cotton (G.hirsutum) are currently the most commercially valuable cultivated cotton species in the world. Upland cotton is widely grown due to its high yield and strong environmental adaptability, accounting for 90% of cotton production. On the contrary, sea island cotton accounts for only 5-8% of cotton production, and is expensive due to its excellent fiber quality in terms of length, strength, etc. Both sea island cotton and upland cotton are allotetraploid cotton cultivars, but their fiber quality and developmental processes differ significan...

Claims

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Application Information

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Patent Type & Authority Applications(China)
IPC IPC(8): C12Q1/68C12N15/29C07K14/415C12N15/11C12N15/53C12N9/02C12N15/82
Inventor 陈全家曲延英倪志勇李月刘超康定明
Owner XINJIANG AGRI UNIV
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