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Method for developing polymorphic SSR markers based on transcriptome sequences

A transcriptome sequence and polymorphism technology, applied in the field of molecular biology, can solve problems such as high dependence on computer configuration, poor operability, and large amount of calculation, so as to shorten development time and cost, improve effectiveness, and reduce configuration required effect

Inactive Publication Date: 2020-01-10
INST OF FOOD CROPS HUBEI ACAD OF AGRI SCI
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Problems solved by technology

[0005] The invention provides a method for developing polymorphic SSR markers based on transcriptome sequences, which effectively solves the problems of low efficiency, large amount of calculation, poor operability and high dependence on computer configuration of conventional screening methods for polymorphic SSR markers

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  • Method for developing polymorphic SSR markers based on transcriptome sequences
  • Method for developing polymorphic SSR markers based on transcriptome sequences
  • Method for developing polymorphic SSR markers based on transcriptome sequences

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Embodiment Construction

[0026] The technical solutions of the present invention will be clearly and completely described below in conjunction with the accompanying drawings of the present invention. Based on the embodiments of the present invention, all other embodiments obtained by persons of ordinary skill in the art without creative efforts fall within the protection scope of the present invention.

[0027] Such as figure 1 , figure 2 , the application provides a method for developing polymorphic SSR markers based on transcriptome sequences, comprising the following steps:

[0028] S1. First, take several samples of the target species, perform high-throughput sequencing on their transcriptomes to obtain Reads, and remove low-quality sequencing Reads (the number of bases with a quality value Q≤5 accounts for more than 50% of the entire read), so as to ensure Obtain high-quality transcriptome sequences, and then use Trinity software to assemble all the reads obtained by sequencing, and finally ob...

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Abstract

The invention discloses a method for developing polymorphic SSR markers based on transcriptome sequences. The method comprises the following steps: S1, the transcriptome sequences of a plurality of samples of a target species are obtained; S2, potential SSR site information is detected; S3, the types of SSR locus repeats and adjacent nucleotide sequence information of the SSR locus repeats are obtained by screening; S4, polymorphic SSR candidate loci among the samples are screened; and S5, transcriptome sequence sets carrying the polymorphic SSR loci are spliced into a non-repetitive contig Uni-contig, primers are designed according to a side wing conservative sequence of the non-repetitive contig Uni-contig, and marker polymorphic detection is conducted. The polymorphic SSR markers can beeffectively screened through the transcriptome sequences, the configuration requirement for a computer is reduced, the method can be completed by a common computer, the effectiveness of the molecularmarker primers is effectively improved, the development time is shortened, the development cost is reduced, meanwhile, the PCR amplification fragment length of the polymorphic SSR markers and linkagegene function information of the polymorphic SSR markers can further be predicted, the development efficiency of the transcriptome SSR markers is remarkably improved, and molecular assisted breedingand functional gene research are promoted.

Description

technical field [0001] The invention relates to the technical field of molecular biology, in particular to a method for developing polymorphic SSR markers based on transcriptome sequences. Background technique [0002] SSR marker, also known as microsatellite DNA, is a molecular marker based on PCR amplification with specific primers, consisting of 2 to 6 nucleotide sequence repeat motifs. The sequences at both ends of the marker are relatively conservative, and primers are designed according to this conserved region, and the SSR site is amplified by PCR technology, which can directly reflect the genetic polymorphism of the DNA fragment between different samples or species. Given that SSR markers are rich in polymorphisms and randomly distributed in the genome, they have been widely used in the rapid mapping of genes, the construction of fingerprints, and molecular marker-assisted selection breeding. [0003] According to its source, SSR markers are divided into two types: ...

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Application Information

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Patent Type & Authority Applications(China)
IPC IPC(8): C12Q1/6869C12Q1/6895G16B20/30G16B25/20
CPCC12Q1/6869C12Q1/6895C12Q2600/156G16B20/30G16B25/20C12Q2531/113C12Q2525/191
Inventor 郑兴飞胡中立游艾青周黎徐得泽费震江董华林胡建林李珍连
Owner INST OF FOOD CROPS HUBEI ACAD OF AGRI SCI
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