Reliable allele detection using SNP-based PCR primers containing Locked Nucleic Acid: application in genetic mapping

Table 2 Comparison of the SPD protocol with other SNP genotyping methods.

Method	Accuracy	Cost	Modification	Complexity	Detection equipment/chemicals	Reference
SPD	High	Low	LNA base at 3' end	Low	Standard^a	this paper
FRET	High	Medium	Fluorescence	Medium	Optical system	[16]
BAMPER	Medium	High	Bioluminescence	High	PPi assay, Luminometer, Amplifier and Recorder	[28]
PAMSA	Medium	Low	Internal nucleotide mismatch	Medium	Standard	[31]
SNaPshot	High	Very High	Fluorescence	Medium	Sequencer	[32]
AFLP	High	Medium	³³P or Fluorescence	Medium	Acrylamide gel or sequencer, Restriction enzymes	[33]

^aStandard; consisting of sequencer, thermocycler and agarose gel electrophoresis equipment, FRET; fluorescence resonance energy transfer, PAMSA; PCR amplification of multiple specific alleles, BAMPER; bioluminometric assay using a modified primer extension reaction, PPi; sodium pyrophosphate decahydrate, AFLP; amplified fragment length polymorphism. Assessment of accuracy, cost, complexity of techniques and data interpretation, and robustness follow the criteria proposed by Kofiadi and Rebrikov [34].

ISSN: 1746-4811