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Genome-wide characterization leading to simple sequence repeat (SSR) markers development in Shorea robusta
Garima Mishra1, Rajendra K Meena1, Rama Kant1
1Division of Genetics & Tree Improvement, Forest Research Institute, Dehradun - 248 195, Uttarakhand, Dehradun, India.
Functional & Integrative Genomics
|January 27, 2023
Summary
This study developed new genomic resources for Shorea robusta, an important timber species. Novel microsatellite markers were identified and validated, providing valuable tools for future population genetic studies.
Area of Science:
- Genomics
- Population Genetics
- Forestry
Background:
- Shorea robusta is a key timber species in Southeast Asian rainforests, yet its genomic diversity is poorly understood.
- Limited genetic resources and molecular markers hinder population genetic studies for this ecologically sensitive species.
Purpose of the Study:
- To perform de novo low-depth genome sequencing of Shorea robusta.
- To identify and validate novel microsatellite (SSR) markers for population genetic analysis.
- To establish genomic databases and species-specific markers for S. robusta.
Main Methods:
- Utilized Illumina paired-end sequencing for low-depth genome sequencing.
- Developed and screened microsatellite repeat sequences to identify SSR primer pairs.
- Validated polymorphic SSR loci across different geographical populations in Uttarakhand, India.
Main Results:
- Assembled approximately 10 gigabases of sequence data, generating 1,97,489 contigs.
- Developed 35,049 simple sequence repeat (SSR) primer pairs, with 24 found to be polymorphic.
- Analyzed genetic diversity using nine polymorphic loci, revealing an average of 2.44 alleles per locus and 0.324 observed heterozygosity.
Conclusions:
- The study successfully generated valuable genomic sequence information and novel SSR markers for Shorea robusta.
- These resources will significantly aid future population genetic studies and conservation efforts for this important timber species.
- The developed markers are applicable to genetic studies within the Shoreae tribe.
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