Method for developing dendranthema SSR (Simple Sequence Repeat) primer based on transcriptome sequencing

A transcriptome sequencing, transcriptome sequencing technology, applied in biochemical equipment and methods, microbial determination/inspection, recombinant DNA technology, etc. Ideas and fields, increasing the effect of raw data

Active Publication Date: 2013-08-07
NANJING AGRICULTURAL UNIVERSITY
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Problems solved by technology

[0005] Current research shows that although a certain number of Chrysanthemum transcriptome sequence information can be retrieved in the NCBI database, most of them are obtained by library construction, the overall number is small, and there is no relevant SSR primer report

Method used

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  • Method for developing dendranthema SSR (Simple Sequence Repeat) primer based on transcriptome sequencing
  • Method for developing dendranthema SSR (Simple Sequence Repeat) primer based on transcriptome sequencing
  • Method for developing dendranthema SSR (Simple Sequence Repeat) primer based on transcriptome sequencing

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Embodiment 1

[0089] The above method was used for high-throughput sequencing using chrysanthemum brain as a material. A total of 70,895 transcriptome sequences were generated, and 1,788 pairs of SSR primers were designed. The specific instructions are as follows:

[0090] Using the chrysanthemum brain of Chrysanthemum genus as material, the stems and leaves were collected for high-throughput sequencing of the transcriptome. A total of 70,895 transcriptome sequences were obtained by sequencing, and a total of 2,813 potential SSR sequences were detected after de-redundancy, accounting for 39.68% of the total. AC / TG content is the highest, followed by CA / GT and CCA / GGT ( figure 1 ). A total of 1788 pairs of SSR primers were designed using the primer3.0 batch design software.

[0091] 100 pairs of SSR primers were randomly selected from 1788 pairs of designed SSR primers, and the success rate of primer design was detected by using chrysanthemum brain DNA. The results showed that 81 pairs of S...

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Abstract

The invention belongs to biotechnology field, and relates to a method for developing a dendranthema SSR (Simple Sequence Repeat) primer based on transcriptome sequencing. A lot of sequence information is processed in batch for searching an SSR sequence and designing an SSR labeled primer based on the transcriptome sequencing by utilizing EST-SSR (Expressed Sequence Tags-Simple Sequence Repeat) interspecific metastasis and using a Perl (Practical Extraction and Reporting Language) programming language method in combination, so that the defects of low efficiency, long time consumption, high cost and the like of the SSR development are conquered. Different dendranthema materials are selected for verifying the designed SSR primer, and the primer is a successful SSR primer if detected out by any strip. By adopting the method, 1788 pairs of SSR primers are successively designed, so that a novel method and thinking are provided for the development of the dendranthema SSR primer to further achieve molecular marker assistant selection breeding and comparative genomics research.

Description

technical field [0001] The invention belongs to the field of biotechnology, and relates to a method for developing SSR primers for Chrysanthemum plants based on transcriptome sequencing. Background technique [0002] Chrysanthemum is a genus of Asteraceae, with about 40 species, mostly available for viewing, native to the subtropical and temperate regions of the Old World. Mainly distributed in East Asia, 19 species, 3 varieties and 9 cultivated varieties are produced in China. The main ones are: wild chrysanthemum, maohua chrysanthemum, chamomile, red chrysanthemum, purple wild chrysanthemum, chrysanthemum brain, cultivated chrysanthemum, etc. Among them, cultivated chrysanthemum is native to my country. It is one of the top ten traditional famous flowers in my country and one of the four major cut flowers in the world. It has a cultivation history of more than 1,600 years. . Chrysanthemum is extremely rich in flower type, flower color, plant type, etc. It is an important...

Claims

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Application Information

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Patent Type & Authority Applications(China)
IPC IPC(8): C12Q1/68C12N15/11
Inventor 陈发棣王海滨宋爱萍王晶晶蒋甲福陈素梅赵爽廖园张飞
Owner NANJING AGRICULTURAL UNIVERSITY
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