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To compare the efficiency of the Whole Genome Profiling and SNaPshot technologies for establishing sequence-ready physical maps in the 17 Gb wheat genome, we performed an experiment on a subset of about one third of the 9x BAC library of chromosome 3B that was used to build the chromosome 3B physical map with the SNaPshot technology [ 23].
A subset of 16,128 BAC clones from the 3B BAC library that comprises a total of 56,952 BAC clones (representing 9.6x coverage of wheat chromosome 3B) was used to assemble a physical map with the WGP and SNaPshot technologies.
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A previously described multiplex single base extension genotyping assay (based on Life Technologies/Applied Biosystems SNaPshot technology) was applied to detect common point mutations in various cancer genes [17].
Genotypes were determined by multiplex SNaPshot technology.
Genotyping was performed using multiplex SNaPshot technology with an ABI fluorescence-based assay discrimination method (Applied Biosystems, Foster City, CA, USA).
For the wheat 3B chromosome physical map developed with the SNaPshot technology, the average random overlap of bands was ~10% [ 23].
Thus, we conclude that with less, but more accurate information Whole Genome Profiling builds more robust physical maps in wheat than the SNaPshot technology.
Our results demonstrate that, with a suitable assembly methodology, WGP builds more robust physical maps than the SNaPshot technology in wheat and that WGP can be adapted to any genome.
The following parameters were used to establish the physical map with the fingerprints obtained by the SNaPshot technology: a gel length of 18,000, a FromEnd value of 55 and a tolerance of 4 [ 23].
Tomsic et al (2010) also found that the SNaPshot technology used for ASE determination gave inconsistent results, as evidenced by considerably larger standard deviations compared with pyrosequencing, and that high RNA quality is essential for reproducibility of ASE.
A subset of the wheat 3B chromosome BAC library covering 230 Mb was used to establish a WGP physical map and to compare it to a map obtained with the SNaPshot technology.
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