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Method for developing SSR (Simple Sequence Repeat) primers of sisal hemp based on transcriptome sequencing

A transcriptome sequencing and transcriptome technology, applied in the field of molecular biology, can solve the problems of lack of SSR markers, unknown sisal genome information, and unreported SSR marker primers, etc., to achieve the effect of filling the scarcity of primers and high development efficiency

Active Publication Date: 2017-09-26
SOUTH SUBTROPICAL CROPS RES INST CHINESE ACAD OF TROPICAL AGRI SCI
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Problems solved by technology

[0005] At present, the genome-wide information of sisal is unknown, the SSR markers are lacking, and the primers for sisal SSR markers have not been reported

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  • Method for developing SSR (Simple Sequence Repeat) primers of sisal hemp based on transcriptome sequencing
  • Method for developing SSR (Simple Sequence Repeat) primers of sisal hemp based on transcriptome sequencing
  • Method for developing SSR (Simple Sequence Repeat) primers of sisal hemp based on transcriptome sequencing

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Embodiment Construction

[0030] The present invention will be further described in detail by examples below, and these examples are only used to illustrate the present invention, and do not limit the scope of the present invention. Unless otherwise specified, the construction and sequencing of the transcriptome library were carried out according to the standard procedure, all kit operations were carried out according to the kit instructions, and all reagents were biological reagents.

[0031] The 18 pairs of SSR marker primer sets provided by the present invention are all from the transcriptome sequence of Rema No. 1, and the nucleic acid sequences of the primers are SEQ ID No.3-SEQ ID No.38. The plant material used was Rema No. 1, and the pathogen was Phytophthora nicotianae.

[0032] one. RNA extraction and transcriptome library construction

[0033] Phytophthora nicotiana preserved in our laboratory was inoculated on potato medium (PDA), cultured at 28°C for 1 week, and then the leaves of Rema 1 ...

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Abstract

The invention discloses a method for developing SSR (Simple Sequence Repeat) primers of sisal hemp based on transcriptome sequencing and belongs to the technical field of molecular biology. A preparation method of the SSR primers comprises the following five steps: extracting Total RNA (Ribonucleic Acid) and constructing a transcriptome library; carrying out transcriptome sequencing and sequence quality analysis; carrying out transcript assembly and SSR labeling analysis; designing the SSR primers; carrying out PCR (Polymerase Chain Reaction) amplification on the primers and electrophoresis analysis on amplified products. According to the method disclosed by the invention, a transcriptome sequence of the sisal hemp at a certain specific period is obtained by using a transcriptome sequencing method; then the SSR labeling analysis is carried out by bioinformatics analysis software, and further the SSR labeled primers of the sisal hemp are developed; the labeling and developing efficiency is high, and the blank of scarce SSR labels of the sisal hemp at present is filled up.

Description

technical field [0001] The invention relates to a method for developing sisal SSR marker primers based on transcriptome sequencing, and belongs to the technical field of molecular biology. Background technique [0002] Sisal is a perennial herb of the Agave genus, which is native to tropical and subtropical regions such as Mexico. There is a serious shortage of germplasm resources preserved in my country, with only more than 100 copies. The existing germplasm resources are mainly obtained through hemp garden selection, hybridization and introduction. The genetic background is vague and the nomenclature is extremely irregular, which brings great inconvenience to the preservation and application of germplasm resources and breeding work. Therefore, a fast and effective method is needed for genetic diversity analysis and resource identification of existing germplasm resources. [0003] Microsatellite DNA (Microsatellite DNA), also known as Simple Sequence Repeat (SSR), is a rep...

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Application Information

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Patent Type & Authority Applications(China)
IPC IPC(8): C12Q1/68C12N15/11C12N15/10G06F19/20
CPCC12Q1/6811C12Q1/6895C12Q2600/156G16B25/00C12Q2531/113C12Q2525/191C12Q2565/125
Inventor 张燕梅周文剑李俊峰鹿志伟杨子平陆军迎
Owner SOUTH SUBTROPICAL CROPS RES INST CHINESE ACAD OF TROPICAL AGRI SCI
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