iSNAP: a small RNA-based molecular marker technique

Endogenous non-coding small RNAs usually consist of 20–24 nucleotides, are found ubiquitously throughout the genome and play important regulatory roles in most eucaryotes. In this study, a new kind of PCR-based marker approach using multi-mapped small RNA sequences, called inter small RNA polymorphism (iSNAP), was developed. iSNAP primers were designed based on multi-mapped small RNA and its two end conserved flanking sequences. To demonstrate the marker system, 10 rice and 30 tobacco iSNAP primers were developed and used to construct a rice genetic map and to fingerprint eight tobacco varieties. The results indicate that this technique can be effectively applied in the mapping of rice and fingerprinting of species (such as tobacco) with extremely low genetic diversity and thus provides a new option of molecular marker techniques.