Bui TG, Hoa NT, Yen JY, Schafleitner R.

Hereditas. 2017 Jan 26;154:3. doi: 10.1186/s41065-016-0024-y. eCollection 2017.

Abstract

BACKGROUND:

Single nucleotide polymorphism (SNP) markers are the method of choice for genetic analyses including diversity and quantitative trait loci (QTL) studies. Marker validation is essential for QTL studies, but the cost and workload are considerable when large numbers of markers need to be verified. Marker systems with low development costs would be most suitable for this task.

RESULTS:

We have tested allele specific polymerase chain reaction (PCR), tetra markers and a genotyping tool based on the single strand specific nuclease CEL-I to verify randomly selected SNP markers identified previously either with a SNP array or by genotyping by sequencing in rice and mungbean, respectively. The genotyping capacity of allele-specific PCR and tetra markers was affected by the sequence context surrounding the SNP; SNPs located in repeated sequences and in GC-rich stretches could not be correctly identified. In contrast, CEL-I digestion of mixed fragments produced from test and reference DNA reliably pinpointed the correct genotypes, yet scoring of the genotypes became complicated when multiple SNPs were present in the PCR fragments. A cost analysis showed that as long the sample number remains small, CEL-I genotyping is more cost-effective than tetra markers.

CONCLUSIONS:

CEL-I genotyping performed better in terms of genotyping accuracy and costs than tetra markers. The method is highly useful for validating SNPs in small to medium size germplasm panels.

See https://www.ncbi.nlm.nih.gov/pubmed/28149257

Figure 1: Optimization of the incubation temperature for CEL-I treatment. The SNP tested was tetra_12. Incubation at 36 ° was found to be optimal to specifically cut at the mismatch site in position 171 bp of the 269 bp fragment, producing bands with 170 and 99 bp. The additional smaller band below around 90 bp is probably due to the sequence context around the SNP (please refer to the discussion)