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Development method of chrysanthemum SSR (Simple Sequence Repeat) primer

A technology of chrysanthemums and primer pairs, which is applied in biochemical equipment and methods, microbial measurement/testing, DNA/RNA fragments, etc., can solve the problems of SSR time-consuming, laborious, low efficiency, SSR primer reporting, etc., to broaden the thinking and field , overcoming the problem of no SSR primers and the effect of overcoming the difficulty in obtaining chrysanthemum SSR primers

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

[0006] Current studies have shown that although a certain number of EST sequences of chrysanthemums can be retrieved in the NCBI database, it is time-consuming and laborious to develop SSRs using them, and the efficiency is low, and no related SSR primers have been reported yet.

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  • Development method of chrysanthemum SSR (Simple Sequence Repeat) primer
  • Development method of chrysanthemum SSR (Simple Sequence Repeat) primer
  • Development method of chrysanthemum SSR (Simple Sequence Repeat) primer

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Embodiment 1

[0053] A total of 7,180 EST sequences were downloaded from NCBI using the above method, and 363 pairs of SSR primers were developed. The details are as follows:

[0054] Using the Latin name of cultivated chrysanthemum Chrysanthemum morifolium as the key word, the EST data of chrysanthemum was retrieved. A total of 501 potential SSR sequences were detected after removing carriers and redundancy from the obtained data of 7180 sequences, accounting for 6.98% of the total. A total of 363 pairs of SSR primers were designed using primer3.0 batch design software.

[0055] 20 pairs were randomly selected from 363 pairs of designed SSR primers (see Table 1), and 43 cultivated chrysanthemum varieties were used for verification. The results showed that the selected 20 pairs of primers could detect clear amplified bands in 43 varieties, indicating that the success rate of primer design was high. Among these are single, polymorphic-free primer combinations (see figure 1 A); poorly poly...

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Abstract

The invention belongs to biotechnology field, and relates to a development method of a chrysanthemum SSR (Simple Sequence Repeat) primer. A lot of sequence information is processed in batch for searching an SSR sequence and designing an SSR labeled primer by utilizing the existing sequence data in an NCBI (National Center of Biotechnology Information) database 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 cultivated chrysanthemum types are used as materials for verifying the designed SSR primer, and the primer is a successful SSR primer if detected out by any strip. By adopting the method, 363 pairs of SSR primers are successively designed, so that a novel method and thinking are provided for the development of the chrysanthemum 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 a chrysanthemum SSR primer. Background technique [0002] Chrysanthemum (Chrysanthemum morifolium) is native to my country, and its cultivars are mostly hexaploid and aneuploid. 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 ornamental, edible and medicinal value (Li Hongjian , 1993), which has a cultivation history of more than 1600 years. It is formed by natural hybridization of Maohua chrysanthemum, wild chrysanthemum and purple wild chrysanthemum and long-term artificial selection (Chen, 1957; Chen, 1985). Chrysanthemum is extremely rich in flower type, flower color, and plant type. It is an important flower species used in potted plants, cut flowers, and garden covers. It has high ornamental and application value, and occupies a very important position in flower production. [000...

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Application Information

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IPC IPC(8): C12Q1/68C12N15/11
Inventor 陈发棣王海滨齐香玉李丕睿蒋甲福陈素梅廖园房伟民
Owner NANJING AGRICULTURAL UNIVERSITY
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