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Mass Spectrometry-Guided Genome Mining as a Tool to Uncover Novel Natural Products
Published on: March 12, 2020
Eucalyptus microsatellites mined in silico: survey and evaluation
R Yasodha1, R Sumathi, P Chezhian
1Division of Plant Biotechnology, Institute of Forest Genetics and Tree Breeding, P.O.Box 1061, Forest Campus, Coimbatore 641 002, India. yasodha@icfre.org
Journal of Genetics
|June 19, 2008
Summary
This study identified 875 expressed sequence tag-simple sequence repeats (EST-SSRs) in Eucalyptus, finding dinucleotide repeats most common. These SSRs are valuable for developing polymorphic molecular markers in Eucalyptus breeding programs.
Area of Science:
- Plant genomics
- Molecular biology
- Bioinformatics
Background:
- Eucalyptus is a vital tropical timber species with extensive genomic data available.
- Genomic and expressed sequence tag (EST) data offer opportunities for marker development.
- Simple sequence repeats (SSRs) and single nucleotide polymorphisms (SNPs) are key genetic markers.
Purpose of the Study:
- To analyze Eucalyptus ESTs for the development of SSR markers.
- To identify and characterize SSRs within transcribed genes of Eucalyptus.
- To assess the potential of EST-derived SSRs for marker-assisted selection in Eucalyptus.
Main Methods:
- In silico analysis of 15,285 Eucalyptus mRNA sequences.
- Identification and classification of SSR motifs (di-, tri-, tetra-, pentanucleotides).
- Primer design for PCR amplification and evaluation of allelic diversity.
Main Results:
- 875 EST-SSRs were identified from 772 ESTs.
- Dinucleotide repeats were the most abundant SSR type (50.9%).
- 571 SSRs had suitable flanking regions for primer design, and primers showed allelic diversity.
Conclusions:
- EST-derived SSRs are a valuable resource for Eucalyptus genetic research.
- These markers can effectively reveal genetic diversity across different provenances.
- The identified SSRs will aid in Eucalyptus breeding and genetic studies.
