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Related Experiment Videos

EST databases as a source for molecular markers: lessons from Helianthus.

Catherine H Pashley1, Jennifer R Ellis, David E McCauley

  • 1Department of Biological Sciences, Vanderbilt University, VU Station B 351634, Nashville, TN 37232, USA.

The Journal of Heredity
|July 15, 2006
PubMed
Summary

Expressed sequence tag (EST) databases provide valuable simple sequence repeat (SSR) markers for genetic analysis. EST-derived SSRs show higher transferability across species than anonymous SSRs, aiding evolutionary and population studies.

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Area of Science:

  • Genomics
  • Evolutionary Biology
  • Molecular Genetics

Background:

  • Expressed sequence tag (EST) databases offer a rich source for developing molecular markers.
  • EST-derived markers, originating from transcribed genomic regions, exhibit greater conservation across taxa compared to other marker types.

Purpose of the Study:

  • To assess the utility of EST databases for developing simple sequence repeat (SSR) markers.
  • To evaluate the cross-species transferability of EST-derived SSRs compared to anonymous SSRs.
  • To explore the potential of EST databases for population genetic analyses of rare and invasive plant species.

Main Methods:

  • Utilized the cultivated sunflower (Helianthus annuus) EST database to develop SSR markers.
  • Tested the transferability of EST-derived SSRs across Helianthus verticillatus and Helianthus angustifolius.

Related Experiment Videos

  • Compared transferability rates of EST-derived SSRs with anonymous SSRs.
  • Analyzed primer location (protein-coding vs. untranslated regions) and variability of EST-SSRs.
  • Cross-referenced public EST resources with lists of rare/invasive plant taxa.

    • Main Results:

    • EST-derived SSRs demonstrated over three times higher interspecific transferability (73%) than anonymous SSRs (21%).
    • SSRs with primers in protein-coding regions were more transferable than those from untranslated regions, with comparable variability.
    • Over one-third of sufficiently sized plant EST collections could potentially yield SSRs for rare, endangered, or invasive species analysis.

    Conclusions:

    • EST databases are a powerful resource for developing transferable SSR markers for population genetics and evolutionary studies.
    • EST-derived SSRs facilitate genetic analysis in rare and widespread plant species, including sunflowers.
    • Public EST collections represent a significant, largely untapped resource for studying plant biodiversity and conservation.