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Laser-Capture Microdissection RNA-Sequencing for Spatial and Temporal Tissue-Specific Gene Expression Analysis in Plants
Published on: August 5, 2020
Using next-generation sequencing approaches to isolate simple sequence repeat (SSR) loci in the plant sciences
Juan E Zalapa1, Hugo Cuevas, Huayu Zhu
1U. S. Department of Agriculture, Agricultural Research Service, Vegetable Crops Research Unit, 1575 Linden Drive, Madison, Wisconsin 53706, USA. jezalapa@wisc.edu
American Journal of Botany
|December 22, 2011
Summary
Next-generation sequencing (NGS) offers a cost-effective method for developing microsatellite markers in plants. This approach accelerates genetic research by efficiently identifying numerous simple sequence repeat (SSR) loci.
Area of Science:
- Botanical sciences
- Genetics
- Molecular biology
Background:
- Microsatellite markers are crucial for plant genetic research due to their informativeness and versatility.
- Traditional microsatellite development is labor-intensive and expensive, limiting their widespread use.
Purpose of the Study:
- To describe the application of next-generation sequencing (NGS) for developing simple sequence repeat (SSR) markers in plants.
- To highlight the advantages of NGS technologies over traditional methods for SSR discovery.
Main Methods:
- Utilizing next-generation sequencing platforms, specifically 454 and Illumina, for high-throughput identification of microsatellites.
- Reviewing recent studies that demonstrate the efficacy of NGS in discovering plant microsatellites.
- Discussing computational tools and high-throughput genotyping for NGS-based SSR isolation.
Main Results:
- NGS technologies enable the efficient and cost-effective identification of a large number of microsatellite loci.
- Demonstrated successful application of 454 sequencing for SSR discovery in cranberry (Vaccinium macrocarpon Ait.).
- Identified microsatellite loci in the plastome and mitochondriome of cranberry.
Conclusions:
- NGS significantly reduces the cost and effort required for microsatellite marker development.
- Future applications of NGS will expand the availability of genetic markers for understudied crops.
- This technology will enhance genetic research and breeding efforts in important plant species.
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