Analysis of SSR information in transcriptome and their usability in flowering Chinese cabbage

In this study, SSR loci were mined from transcriptome sequencing data of flowering Chinese cabbage using the MIcroSAtellite identification tool(MISA). 11 879 SSR loci, including the types of 1-6 nucleotide repeats with occurring frequency of 1/3.2 kb (312.5/Mb), were discovered from 48 975 transcriptomic unigenes(38.17 Mb). The major types of SSR loci were 1-3 nucleotide repeats, accounted for 99.01% of the SSR loci, of which mono-, di- and tri-nucleotide repeats were 41.11%, 28.23% and 29.67%, respectively Fifty-eight repeat motifs with iteration numbers from 5 to 23 were identified, and the most abundant motifs were A/T, AG/CT, AT/AT, AC/GT, AAG/CTT and AGG/CCT. The lengths of repeat nucleotide sequences for all SSR loci ranged from 10 to 60 bp, with most below 20 bp, and only 7.9% (938 SSR loci) above 20 bp. A total of 676 pairs of SSR primers with the potential to produce polymorphism were designed; 30 primer combinations were randomly selected for amplification tests, of which 22 primer pairs amplified unambiguously with reproducible amplicons and 12 primer combinations produced polymorphisms in four flower Chinese cabbage accessions. These results could provide the foundation for the development and application of SSR markers in flowering Chinese cabbage.