Fast magnetic isolation of simple sequence repeat markers in microfluidic channelsElectronic supplementary information (ESI) available: Further experimental methods and results information. See DOI: 10.1039/c3lc51371h

Simple sequence repeat (SSR) markers are widely used for genome mapping, genetic diversity characterization and medical diagnosis. The fast isolation by AFLP of sequence containing repeats (FIASCO) is a powerful method for SSR marker isolation, but it is laborious, costly, and time consuming and requires multiple rounds of washing. Here, we report a superparamagnetic bead (SPMB)-based FIASCO method in a magnetic field controllable microfluidic chip (MFCM-Chip). This method dramatically reduces the assay time by 4.25-fold and reduces the quantity of magnetic beads and probes by 10-fold through the magnetic capture of (AG) n -containing fragments from Herba Leonuri, followed by washing and eluting on a microchip. The feasibility of this method was further evaluated by PCR and sequencing, and the results showed that the proportion of fragments containing SSRs was 89%, confirming that this platform is a fast and efficient method for SSR marker isolation. This cost-effective platform will make the powerful FIASCO technique more accessible for routine use with a wide variety of materials. We present a novel magnetic system in microfluidic channels for fast and effective isolation of simple sequence repeat markers.