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