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Related Experiment Videos

SNP discovery via 454 transcriptome sequencing.

W Brad Barbazuk1, Scott J Emrich, Hsin D Chen

  • 1Donald Danforth Plant Science Center, St Louis, MO 63132, USA.

The Plant Journal : for Cell and Molecular Biology
|July 31, 2007
PubMed
Summary
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High-throughput sequencing of maize transcriptomes identified thousands of single nucleotide polymorphisms (SNPs). This method efficiently discovers gene-associated SNPs for maize genetic studies.

Area of Science:

  • Plant Genomics
  • Molecular Biology
  • Bioinformatics

Background:

  • Shoot apical meristems are crucial for plant development.
  • Identifying genetic variations like single nucleotide polymorphisms (SNPs) is vital for crop improvement.
  • High-throughput sequencing technologies offer powerful tools for genetic analysis.

Purpose of the Study:

  • To sequence the transcriptomes of two maize inbred lines using 454 pyrosequencing.
  • To computationally identify single nucleotide polymorphisms (SNPs) between these maize lines.
  • To validate the identified SNPs for their utility in genetic studies.

Main Methods:

  • Laser capture microdissection (LCM) was used to isolate shoot apical meristems.
  • Massively parallel pyro-sequencing (454 technology) was employed to sequence ESTs.

Related Experiment Videos

  • The POLYBAYES system was adapted to detect SNPs in 454 EST data.

    • Main Results:

    • Over 36,000 putative SNPs were initially detected in maize ESTs from B73 and Mo17 lines.
    • Post-processing reduced the number to over 7000 putative SNPs.
    • Sanger sequencing validated over 85% of the putative SNPs, identifying >4900 valid SNPs in >2400 genes.

    Conclusions:

    • 454-based transcriptome sequencing is effective for high-throughput SNP discovery in maize.
    • This approach efficiently identifies gene-associated SNPs for genetic research.
    • The validated SNPs provide valuable resources for maize genetics and breeding.