LGC's Trait-Specific SSR Marker Conversion Service

Genotyping simple sequence repeats/short tandem repeats (SSR/STS) in plant breeding programs has led to improvements in all studied plant species for over 30 years. They have proved to be reliable and relevant for fingerprinting, population structure analysis, linkage association studies and trait specific QTL’s. However, discovery, optimisation and validation of SSR/STS markers can be costly and time consuming. SSR/STS markers can no longer compete with the cost efficiency or throughput that can achieved using SNP genotyping platforms such as LGC’s SNPline and Douglas’ Nexar and IntelliQube. In this study we present a process flow whereby trait-specific SSR/STS markers were converted to high-throughput trait-specific SNP KASP markers through a commercial service package.

The process of conversion used long range amplification (3-4 Kb) across target loci and shotgun sequencing to identify novel SNP sequences. These were verified on segregating populations for target traits, to ensure the LD was within the critical level of 0.2. The conversion of SSRs to KASP markers has previously been demonstrated for maize leaf necrosis (MLN) populations in sub-Saharan Africa; the conversion facilitated increased throughput, whereby 5000 samples were screened in 4 weeks (Semagh et al., 2012). This study demonstrates the conversion of 3 STS and 1 SSR trait-specific rice markers in an indica background. KASP markers developed from SNP sequences were subsequently verified to ensure correlation with existing SSR/STS markers in appropriate segregating populations.