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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| Format: | Article |
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MDPI AG
2018-02-01
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| Series: | Molecules |
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| Online Access: | http://www.mdpi.com/1420-3049/23/2/399 |
| _version_ | 1828222250748215296 |
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| author | Sima Taheri Thohirah Lee Abdullah Mohd Rafii Yusop Mohamed Musa Hanafi Mahbod Sahebi Parisa Azizi Redmond Ramin Shamshiri |
| author_facet | Sima Taheri Thohirah Lee Abdullah Mohd Rafii Yusop Mohamed Musa Hanafi Mahbod Sahebi Parisa Azizi Redmond Ramin Shamshiri |
| author_sort | Sima Taheri |
| collection | DOAJ |
| description | 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. |
| first_indexed | 2024-04-12T16:52:26Z |
| format | Article |
| id | doaj.art-1548b50c6a9a479198c17a1f6b99d400 |
| institution | Directory Open Access Journal |
| issn | 1420-3049 |
| language | English |
| last_indexed | 2024-04-12T16:52:26Z |
| publishDate | 2018-02-01 |
| publisher | MDPI AG |
| record_format | Article |
| series | Molecules |
| spelling | doaj.art-1548b50c6a9a479198c17a1f6b99d4002022-12-22T03:24:21ZengMDPI AGMolecules1420-30492018-02-0123239910.3390/molecules23020399molecules23020399Mining and Development of Novel SSR Markers Using Next Generation Sequencing (NGS) Data in PlantsSima Taheri0Thohirah Lee Abdullah1Mohd Rafii Yusop2Mohamed Musa Hanafi3Mahbod Sahebi4Parisa Azizi5Redmond Ramin Shamshiri6Department of Crop Science, Faculty of Agriculture, Universiti Putra Malaysia, 43400 Serdang, Selangor, MalaysiaDepartment of Crop Science, Faculty of Agriculture, Universiti Putra Malaysia, 43400 Serdang, Selangor, MalaysiaDepartment of Crop Science, Faculty of Agriculture, Universiti Putra Malaysia, 43400 Serdang, Selangor, MalaysiaLaboratory of Climate-Smart Food Crop Production, Institute of Tropical Agriculture and Food Security, Universiti Putra Malaysia, 43400 Serdang, Selangor, MalaysiaLaboratory of Climate-Smart Food Crop Production, Institute of Tropical Agriculture and Food Security, Universiti Putra Malaysia, 43400 Serdang, Selangor, MalaysiaLaboratory of Climate-Smart Food Crop Production, Institute of Tropical Agriculture and Food Security, Universiti Putra Malaysia, 43400 Serdang, Selangor, MalaysiaSmart Farming Technology Research Center, Department of Biological and Agricultural Engineering, Faculty of Engineering, Universiti Putra Malaysia, 43400, Serdang, Selangor, MalaysiaMicrosatellites, 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.http://www.mdpi.com/1420-3049/23/2/399SSR markersde novo transcriptomeRNA-SeqmicrosatelliteIlluminashort tandem repeat (STR) |
| spellingShingle | Sima Taheri Thohirah Lee Abdullah Mohd Rafii Yusop Mohamed Musa Hanafi Mahbod Sahebi Parisa Azizi Redmond Ramin Shamshiri Mining and Development of Novel SSR Markers Using Next Generation Sequencing (NGS) Data in Plants Molecules SSR markers de novo transcriptome RNA-Seq microsatellite Illumina short tandem repeat (STR) |
| title | Mining and Development of Novel SSR Markers Using Next Generation Sequencing (NGS) Data in Plants |
| title_full | Mining and Development of Novel SSR Markers Using Next Generation Sequencing (NGS) Data in Plants |
| title_fullStr | Mining and Development of Novel SSR Markers Using Next Generation Sequencing (NGS) Data in Plants |
| title_full_unstemmed | Mining and Development of Novel SSR Markers Using Next Generation Sequencing (NGS) Data in Plants |
| title_short | Mining and Development of Novel SSR Markers Using Next Generation Sequencing (NGS) Data in Plants |
| title_sort | mining and development of novel ssr markers using next generation sequencing ngs data in plants |
| topic | SSR markers de novo transcriptome RNA-Seq microsatellite Illumina short tandem repeat (STR) |
| url | http://www.mdpi.com/1420-3049/23/2/399 |
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