Table 1 Comparison of four high-throughput polymorphism detection approaches

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 plants^a

Drosophila, stickleback, zebrafish, Neurospora

Neurospora

Purple sea urchin