A dichotomous key for the discrimination of the already known S-RNase alleles in potato species

•PCR-based approach alone could not detect S-RNase gene polymorphisms in potato species.•In silico PCR assay and restriction enzyme pattern analysis were performed.•A novel dichotomous key was developed to discriminate the S-RNase alleles in potato.•Experimental data validates the utility and efficiency of the dichotomous key.

The potato species exhibit gametophytic self-incompatibility system controlled by a single S-locus with multiple S-haplotypes. Each S-haplotype carries two genetically linked genes, S-RNase and SLF, controlling the female and male specificities, respectively. In the style, the S-RNase gene codes for an allele-specific ribonuclease that is involved in the rejection of pollen that carries the same S-haplotype. This gene has five conserved regions (C1–C5) and two hypervariable domains located between C2 and C3 that play a role in S-RNase allele specificity. Presently, eight nucleotide sequences of S-RNase alleles from Solanum tuberosum and S. chacoense have been reported in potato species. In an effort to discriminate these S-RNase alleles and eventually detect new allelic variants, these sequences were analyzed by in silico PCR, using primers designed on the basis of four conserved regions, and were further examined by restriction enzyme patterns. The development of the in silico approach led to the creation of a novel dichotomous key which was able to unequivocally identify the eight potato S-RNase alleles already known and eventually detect putative alleles when the size and/or the restriction pattern of the amplicons were different from those predicted. Experimental data validates the utility and efficiency of the dichotomous key.