Complexity reduction of polymorphic sequences (CRoPS): a novel approach for large-scale polymorphism discovery in complex genomes.

• Main Authors: Nathalie J van Orsouw, René C J Hogers, Antoine Janssen, Feyruz Yalcin, Sandor Snoeijers, Esther Verstege, Harrie Schneiders, Hein van der Poel, Jan van Oeveren, Harold Verstegen, Michiel J T van Eijk
• Format: Article
• Language: English
• Published: Public Library of Science (PLoS) 2007-01-01
• Series: PLoS ONE
• Online Access: http://europepmc.org/articles/PMC2048665?pdf=render

Application of single nucleotide polymorphisms (SNPs) is revolutionizing human bio-medical research. However, discovery of polymorphisms in low polymorphic species is still a challenging and costly endeavor, despite widespread availability of Sanger sequencing technology. We present CRoPS as a novel approach for polymorphism discovery by combining the power of reproducible genome complexity reduction of AFLP with Genome Sequencer (GS) 20/GS FLX next-generation sequencing technology. With CRoPS, hundreds-of-thousands of sequence reads derived from complexity-reduced genome sequences of two or more samples are processed and mined for SNPs using a fully-automated bioinformatics pipeline. We show that over 75% of putative maize SNPs discovered using CRoPS are successfully converted to SNPWave assays, confirming them to be true SNPs derived from unique (single-copy) genome sequences. By using CRoPS, polymorphism discovery will become affordable in organisms with high levels of repetitive DNA in the genome and/or low levels of polymorphism in the (breeding) germplasm without the need for prior sequence information.