Summary
Resource Type
Analysis
Name
Simple Sequence Repeats (SSR) polymorphism confirmation (Q. alba)
Program, Pipeline, Workflow or Method Name
SSR polymorphic test (Q. alba)
Program Version
n/a
Algorithm
Organism
Data Source
Date Performed
Thursday, August 16, 2018 - 15:28

John Carlson at Pennsylvania State University screened a subset of the above predicted SSRs.

Methods

Twelve white oaks were collected, consisting of the two parents of a mapping population and ten unrelated samples from the Pennsylvania State University arboretum (University Park, PA). DNA was extracted using a modified CTAB method, and DNA quality was assessed on 1% agarose gels. Species primer sets were tested against all collected genotypes within a species with a PCR reaction mixture containing between 4-6 ng DNA per reaction volume, and PCR cycles as follows: 95°C-5 min, 35 cycles of 95°C- 30s, 60°C-45s, 72°C-1 min, and a final 72°C-10 min. Both amplification and polymorphism were detected on 2% agarose gels stained with 0.05% (w/v) ethidium bromide. Polymorphism was estimated based on band width.

Results

Of the 100 tested SSRs, 44 successfully amplified and 22 were found to be polymorphic.

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