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A Fast Silver Staining Protocol Enabling Simple and Efficient Detection of SSR Markers using a Non-denaturing Polyacrylamide Gel
Published on: April 20, 2018
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Development and Characterization of High-Throughput EST-Based SSR Markers for Pogostemon cablin Using Transcriptome
Puyue Ouyang1,2, Dali Kang3, Xiaolu Mo4
1Agricultural College, Guangxi University, Nanning 530005, China. ouyangpy@gdyzy.edu.cn.
Molecules (Basel, Switzerland)
|August 15, 2018
Summary
Researchers developed 1219 simple sequence repeat (SSR) markers from expressed sequence tags (ESTs) in Patchouli (Pogostemon cablin). These SSR markers are valuable for genetic diversity studies and breeding applications in Patchouli.
Area of Science:
- Plant genetics and genomics
- Molecular breeding and marker development
Background:
- Simple sequence repeats (SSRs), also known as microsatellite markers, are crucial tools for molecular-assisted breeding, comparative genomics, and genetic diversity assessments.
- Expressed sequence tags (ESTs) provide a valuable resource for identifying SSR markers in various plant species.
Purpose of the Study:
- To identify and develop a comprehensive set of SSR markers from ESTs in *Pogostemon cablin* (Patchouli).
- To analyze the characteristics of these SSRs and evaluate their polymorphic potential and cross-species transferability.
Main Methods:
- Investigated 54,546 ESTs from *P. cablin* to identify SSRs.
- Designed 192 primer pairs based on identified SSR-containing ESTs for polymorphism analysis.
- Assessed primer pair transferability across 10 related species.
Main Results:
- Identified 1219 SSRs from 1144 ESTs, with trinucleotides being the most abundant type.
- Developed 192 primer pairs, of which 45 showed polymorphism with 2-4 alleles in 38 *P. cablin* accessions.
- Observed 10-40% cross-species transferability for the developed SSR markers in related species.
Conclusions:
- This study presents the first large-scale development and analysis of SSR markers in *P. cablin*.
- The developed SSR markers are suitable for applications in quantitative trait loci mapping, genetic diversity studies, and cultivar fingerprinting of Patchouli.
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