Large-scale development of functional markers in Brassica species

Numerous quantitative trait loci (QTL) have been detected in Brassica species, but fine-mapping of major QTL has advanced slowly. The development of functional markers can overcome this barrier. We used publicly available PlantGDB-assembled unique transcripts (PUTs) from Brassica species to design 7836 functional simple sequence repeat (SSR) primer pairs. Functional annotation of the PUTs containing SSRs was done by Blast2GO. The PUTs harbouring SSRs were mainly involved with nucleotide or protein binding and enzyme activity, and preferentially functioned in membranes and cytoplasm. Totally, 210 PUT primer pairs were selected to test their polymorphism, stability, and PCR quality. Approximately 70% (147) of the primer pairs resulted in successful amplification with an average polymorphic information content (PIC) value of 0.49. The highest level of polymorphism was dinucleotide repeat SSRs, followed by tri- and mononucleotide repeats. Approximately 60% of the primer pairs showed good transferability among Brassica species. These results show that the development of markers from PUTs is a feasible and simple approach to develop functional SSR markers on a large scale across Brassica species. In addition, these markers can provide a novel alternative that is a putative approach for rapid determination of candidate genes, genetic mapping, genetic diversity analysis, and comparative mapping in Brassica species.