Skip to main content

A Technical Platform for PCR-Based SNP Screening in Cereals and Other Crops

  • Protocol
  • First Online:
Cereal Genomics

Part of the book series: Methods in Molecular Biology ((MIMB,volume 1099))

  • 4682 Accesses

Abstract

With the rapid development of sequencing technologies and sequenced genomes, single-nucleotide polymorphisms (SNPs) have become a common genomic tool in the study of biological diversity, genome variation, gene mapping, cloning, and marker-assisted selection. In this chapter, PCR-based SNP screening is discussed in detail. This includes preparation of solutions and buffers, designing of tetra-primers, PCR for DNA amplification, gel electrophoresis, and SNP screening. By grasping the techniques and experience from the wet laboratories, researchers can quickly use this genomic tool to tackle problems in their research.

This is a preview of subscription content, log in via an institution to check access.

Access this chapter

Protocol
USD 49.95
Price excludes VAT (USA)
  • Available as PDF
  • Read on any device
  • Instant download
  • Own it forever
eBook
USD 84.99
Price excludes VAT (USA)
  • Available as EPUB and PDF
  • Read on any device
  • Instant download
  • Own it forever
Softcover Book
USD 119.00
Price excludes VAT (USA)
  • Compact, lightweight edition
  • Dispatched in 3 to 5 business days
  • Free shipping worldwide - see info
Hardcover Book
USD 109.99
Price excludes VAT (USA)
  • Durable hardcover edition
  • Dispatched in 3 to 5 business days
  • Free shipping worldwide - see info

Tax calculation will be finalised at checkout

Purchases are for personal use only

Institutional subscriptions

References

  1. Seeb JE, Carvalho G, Hauser L et al (2011) Single-nucleotide polymorphism (SNP) discovery and applications of SNP genotyping in nonmodel organisms. Mol Ecol Resour 11:1–8

    Article  PubMed  Google Scholar 

  2. Johnson AD (2009) Single-nucleotide polymorphism bioinformatics. A comprehensive review of resources. Circ Cardiovasc Genet 2:530–536

    Article  PubMed  CAS  Google Scholar 

  3. Duran C, Appleby N, Edwards D et al (2009) Molecular genetic markers: discovery, applications, data storage and visualisation. Curr Bioinform 4:16–27

    Article  CAS  Google Scholar 

  4. Moorhead SM, Dykes GA, Cursons RT (2003) An SNP-based PCR assay to differentiate between Listeria monocytogenes lineages derived from phylogenetic analysis of the sigB gene. J Microbiol Methods 55:425–432

    Article  PubMed  CAS  Google Scholar 

  5. http://barleyworld.org/sites/default/files/illuminasnpgenotyping.pdf

  6. Gabriel S, Ziaugra L, Tabbaa D (2009) SNP genotyping using the Sequenom UNIT MassARRAY iPLEX platform. Curr Protoc Hum Genet 60:2.12.1–2.12.18

    Google Scholar 

  7. Elshire RJ, Glaubitz JC, Sun Q et al (2011) A robust, simple genotyping-by-sequencing (GBS) approach for high diversity species. PLoS One 6:e19379

    Article  PubMed  CAS  Google Scholar 

  8. Xie W, Feng Q, Yu H et al (2010) Parent-independent genotyping for constructing an ultrahigh-density linkage map based on population sequencing. Proc Natl Acad Sci U S A 107:10578–10583

    Article  PubMed  CAS  Google Scholar 

  9. Collins A, Ke XY (2012) Primer1: primer design web service for tetra-primer ARMS-PCR. Open Bioinform J 6:55–58

    Article  Google Scholar 

  10. Ye S, Dhillon S, Ke XY et al (2001) An efficient procedure for genotyping single nucleotide polymorphisms. Nucleic Acids Res 29:E88–8

    Article  PubMed  CAS  Google Scholar 

  11. Rozen S, Kaletsky HJ (1998) Primer3. http://primer3.sourceforge.net/

Download references

Author information

Authors and Affiliations

Authors

Editor information

Editors and Affiliations

Rights and permissions

Reprints and permissions

Copyright information

© 2014 Springer Science+Business Media New York

About this protocol

Cite this protocol

Wang, Z. (2014). A Technical Platform for PCR-Based SNP Screening in Cereals and Other Crops. In: Henry, R., Furtado, A. (eds) Cereal Genomics. Methods in Molecular Biology, vol 1099. Humana Press, Totowa, NJ. https://doi.org/10.1007/978-1-62703-715-0_23

Download citation

  • DOI: https://doi.org/10.1007/978-1-62703-715-0_23

  • Published:

  • Publisher Name: Humana Press, Totowa, NJ

  • Print ISBN: 978-1-62703-714-3

  • Online ISBN: 978-1-62703-715-0

  • eBook Packages: Springer Protocols

Publish with us

Policies and ethics