Discovering genetic polymorphisms in next-generation sequencing data
Article first published online: 12 MAR 2009
© 2009 The Authors. Journal compilation © 2009 Blackwell Publishing Ltd
Plant Biotechnology Journal
Volume 7, Issue 4, pages 312–317, May 2009
How to Cite
Imelfort, M., Duran, C., Batley, J. and Edwards, D. (2009), Discovering genetic polymorphisms in next-generation sequencing data. Plant Biotechnology Journal, 7: 312–317. doi: 10.1111/j.1467-7652.2009.00406.x
- Issue published online: 13 APR 2009
- Article first published online: 12 MAR 2009
- Received 29 September 2008; revised 29 November 2008; accepted 5 December 2008.
- molecular markers;
- next generation sequencing;
- single nucleotide polymorphisms (SNPs)
The ongoing revolution in DNA sequencing technology now enables the reading of thousands of millions of nucleotide bases in a single instrument run. However, this data quantity is often compromised by poor confidence in the read quality. The identification of genetic polymorphisms from this data is therefore problematic and, combined with the vast quantity of data, poses a major bioinformatics challenge. However, once these difficulties have been addressed, next-generation sequencing will offer a means to identify and characterize the wealth of genetic polymorphisms underlying the vast phenotypic variation in biological systems. We describe the recent advances in next-generation sequencing technology, together with preliminary approaches that can be applied for single nucleotide polymorphism discovery in plant species.