Mining and Development of Novel SSR Markers Using Next Generation Sequencing (NGS) Data in Plants

Microsatellites, or simple sequence repeats (SSRs), are one of the most informative and multi-purpose genetic markers exploited in plant functional genomics. However, the discovery of SSRs and development using traditional methods are laborious, time-consuming, and costly. Recently, the availability...

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Bibliographic Details
Published in:Molecules (Basel, Switzerland) Switzerland), 2018-02, Vol.23 (2), p.399
Main Authors: Taheri, Sima, Lee Abdullah, Thohirah, Yusop, Mohd Rafii, Hanafi, Mohamed Musa, Sahebi, Mahbod, Azizi, Parisa, Shamshiri, Redmond Ramin
Format: Article
Language:English
Subjects:
Arabidopsis - genetics
Binding sites
Cloning
Crops, Agricultural
Data Mining - methods
de novo transcriptome
DNA methylation
Expressed Sequence Tags
Flowers & plants
Gene expression
Genetic diversity
Genetic Markers
Genomes
Genomics
High-Throughput Nucleotide Sequencing - instrumentation
High-Throughput Nucleotide Sequencing - methods
High-Throughput Nucleotide Sequencing - statistics & numerical data
Illumina
Laboratories
Markers
microsatellite
Microsatellite Repeats
Microsatellites
Molecular Sequence Annotation
Mutation
Next-generation sequencing
Oryza - genetics
Polymorphism
Polymorphism, Genetic
Review
Ribosomal DNA
RNA-Seq
short tandem repeat (STR)
Simple sequence repeats
Software
SSR markers
Transcriptome
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Description
Summary:Microsatellites, or simple sequence repeats (SSRs), are one of the most informative and multi-purpose genetic markers exploited in plant functional genomics. However, the discovery of SSRs and development using traditional methods are laborious, time-consuming, and costly. Recently, the availability of high-throughput sequencing technologies has enabled researchers to identify a substantial number of microsatellites at less cost and effort than traditional approaches. Illumina is a noteworthy transcriptome sequencing technology that is currently used in SSR marker development. Although 454 pyrosequencing datasets can be used for SSR development, this type of sequencing is no longer supported. This review aims to present an overview of the next generation sequencing, with a focus on the efficient use of de novo transcriptome sequencing (RNA-Seq) and related tools for mining and development of microsatellites in plants.
ISSN:1420-3049
1420-3049
DOI:10.3390/molecules23020399