title: Complexity reduction of polymorphic sequences (CRoPS): a novel approach for large-scale polymorphism discovery in complex genomes.
abstract: 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.
authors.affiliation: Keygene NV, Wageningen, The Netherlands. nathalie.van-orsouw@keygene.com
authors.forename: Nathalie J
authors.initials: NJ
authors.lastname: van Orsouw
authors.forename: René C J
authors.initials: RC
authors.lastname: Hogers
authors.forename: Antoine
authors.initials: A
authors.lastname: Janssen
authors.forename: Feyruz
authors.initials: F
authors.lastname: Yalcin
authors.forename: Sandor
authors.initials: S
authors.lastname: Snoeijers
authors.forename: Esther
authors.initials: E
authors.lastname: Verstege
authors.forename: Harrie
authors.initials: H
authors.lastname: Schneiders
authors.forename: Hein
authors.initials: H
authors.lastname: van der Poel
authors.forename: Jan
authors.initials: J
authors.lastname: van Oeveren
authors.forename: Harold
authors.initials: H
authors.lastname: Verstegen
authors.forename: Michiel J T
authors.initials: MJ
authors.lastname: van Eijk
mesh_terms: D001483:Base Sequence; D018745:Genome, Plant; D008969:Molecular Sequence Data; D020641:Polymorphism, Single Nucleotide; D012689:Sequence Homology, Nucleic Acid; D003313:Zea mays / Q000235:genetics