Skip to main content

Table 1 Comparison of four high-throughput polymorphism detection approaches

From: Restriction Site Tiling Analysis: accurate discovery and quantitative genotyping of genome-wide polymorphisms using nucleotide arrays

Parameter SFP RAD tagging RAD sequencing RSTA
Marker type SNPs and indels Restriction cut site polymorphisms Sequence data: SNPs next to restriction cut sites Restriction cut site polymorphisms: distinguishes SNPs and indels
Number of loci surveyed 92,924 19,200 (elements on an enriched RAD-tag microarray designed from stickleback) 26 nucleotides at 41,622 RAD tags 50,935
Number of polymorphisms identified (informative marker rate) 3,806 (4% at a 5% false discovery rate cutoff) 1,990 (10% at a two-fold signal difference cutoff) Approximately 13,000 (31%) 12,431 (24%)
False discovery rate 3% (117 out of 121 confirmed correct by sequencing) 9% (20 out of 22 confirmed correct by sequencing) Not reported <1% (113 out of 114 confirmed correct by sequencing)
Platform Custom high-density oligonucleotide array (Affymetrix), 25 bp oligo cDNA or genomic tiling array (in house synthesis) Illumina sequencing Custom high-density oligonucleotide array (Agilent), 50 bp oligo
Prior information required EST, 454 or genome sequence EST or RAD-tag library for array synthesis EST or genome sequence to map short sequence reads EST, 454 or genome sequence
Polymorphism identification Hybridization signal difference among study individuals Hybridization signal difference between two study individuals Custom Perl scripts for sequence alignment Genotype clusters across all study individuals
Individual genotype data No No No Yes
Organisms studied Yeast, Arabidopsis, Anopheles, several seed plantsa Drosophila, stickleback, zebrafish, Neurospora Neurospora Purple sea urchin
  1. Numbers are from studies that describe each method: SFP [26]; RAD tagging [25]; RAD sequencing [50]. aSee Gupta et al. [23] for review of high-throughput applications in crop plants.