Method for developing SSR molecular markers on large scale

A molecular marker, large-scale technology, applied in the fields of molecular biology and bioinformatics, can solve the problems of low effectiveness and high repeatability of SSR marker development, and achieve the effect of improving development efficiency

Inactive Publication Date: 2015-08-12
INST OF BAST FIBER CROPS CHINESE ACADEMY OF AGRI SCI
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Problems solved by technology

[0007] Purpose of the invention: The present invention makes improvements to the problems existing in the above-mentioned prior art, that is, the present invention discloses a method for developing SSR molecular markers in large quantities, which can solve the repetitiveness of SSR marker development ca

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  • Method for developing SSR molecular markers on large scale
  • Method for developing SSR molecular markers on large scale
  • Method for developing SSR molecular markers on large scale

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Embodiment Construction

[0043] Specific embodiments of the present invention will be described in detail below.

[0044] Such as figure 1 As shown, taking flax as an example, a method for developing SSR molecular markers in large batches includes the following steps:

[0045] (1) Obtain the genome sequencing sequence or the EST sequence on GenBank, and save the genome sequencing sequence or the EST sequence on GenBank in FAS format;

[0046] (2) Use Tandem Repeats Finder to obtain the genome sequencing sequence obtained in step (1) or the SSR site information of the EST sequence on GenBank, and convert the analysis and summary results into a CSV format file, and establish a database 1. CSV, Tandem Repeats The setting parameters of Finder are (20,2000,2,7,7);

[0047] (3), classify the SSR sites according to the SSR motif type,

[0048] (31) According to the principle of base complementation and shift combination, all SSR types containing 1 to 6 bases are divided into 508 types, see Table 1 at the ...

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Abstract

The invention relates to a method for developing SSR molecular markers on a large scale. The method for developing the SSR molecular markers on the large scale comprises the following steps: firstly, acquiring a genomic sequencing sequence or an EST sequence on GenBank; secondly, acquiring SSR locus information of the genomic sequencing sequence or the EST sequence on the GenBank; thirdly, classifying SSR locus according to SSR sequence motif types; fourthly, carrying out reverse complementary treatment on SSR locus information of a database 3.CSV; fifthly, acquiring SSR molecular markers and upstream and downstream sequences in a database 4.CSV and a database 5.CSV by adopting SSR locus sequence interception software, and creating a sequence database according to the sequence motif types; and sixthly, screening repeated or similar SSR locus in CSV files of SSRs of the same type. The method for developing the SSR molecular markers on the large scale has the advantages that SSR marker locus in a genome can be located, SSR sequence fragments can be intercepted on the large scale, repeatability analysis can be carried out on different SSR sequences, and SSR molecular marker development efficiency is greatly improved.

Description

technical field [0001] The invention belongs to the fields of molecular biology and bioinformatics, and relates to a method for developing SSR molecular markers in large quantities. Background technique [0002] Molecular markers are genetic markers based on the polymorphism of the genetic material nucleic acid of an organism. They have the characteristics of abundant quantity, stable genetics, no restriction on gene expression, and easy operation. Molecular markers can be used to directly detect genome Genetic Variation. It can accurately reveal individual differences among different species, varieties, varieties, and strains of the same species from the level of genetic material DNA, and has unparalleled advantages. Molecular markers have been widely used in the construction of genetic maps and gene mapping, and are considered to be a useful tool for identifying varieties and strains (including hybrids and inbred lines) and analyzing the genetic diversity of germplasm res...

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Application Information

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IPC IPC(8): C12N15/10C12Q1/68
Inventor 邓欣王玉富陈信波龙松华邱财生
Owner INST OF BAST FIBER CROPS CHINESE ACADEMY OF AGRI SCI
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