complexity reduction of polymorphic sequences (crops？) a novel approach for large-scale polymorphism discovery in complex genomes多态序列的复杂性减少(作物)大规模复杂基因组的多态性发现的新途径.pdfVIP

Complexity Reduction of Polymorphic Sequences (CRoPSTM): A Novel Approach for Large-Scale Polymorphism Discovery in Complex Genomes ´ Nathalie J. van Orsouw*, Rene 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 Keygene NV, Wageningen, The Netherlands 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 CRoPSTM as a novel approach for polymorphism discovery by combining the power of reproducible genome complexity reduction of AFLPH 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 SNPWaveH 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. Citation: van Orsouw NJ, Hogers RCJ, Janssen A, Yalcin F, Snoeijers S, et al (2007) Complexity Reduction of Polymorphic Sequences (CRoPSTM): A Novel Approach for Large-Scale Polymorphism Discovery in Complex Genomes. PLoS ONE 2(11): e1172. doi:10.1371/journal.pone.0001172 INTRODUCTION However, despite the fa