Objective  To search for applicable molecular markers for studying Brassica juncea.

  Method  SSR sites were searched from transcriptional sequencing of B. juncea. Potential primers were designed using Primer 3.0, and polymorphisms of 44 B. juncea germplasms detected from randomly selected 50 pairs of primers for the investigation.

  Result  Totally, 55,636 unigenes were obtained from the transcriptome sequencing. The entire sequence was 48,193,376bp with 9,526 SSR loci identified from 7,834 unigenes at a rate of 14.08%. Of the loci, 1,371 contained more than one SSR locus and 572 compound loci. Of the major repeat types, 51.12% were trinucleotide dominated by AGA/TCT (18.30%), and 41.91% dinucleotide dominated by AG/CT (34.74%). Using Primer 3.0, from 21,282 pairs of SSR primers, 50 were randomly selected for the PCR amplification. Out of 44 amplifications, 41 showed clear and reproducible bands, and 17 with polymorphisms. The 44 germplasms were classified into 4 distinctive groups by UPGMA.

  Conclusion  The SSR markers with high frequency and polymorphism could be acquired from the transcriptome to be used for the genetic diversity analysis and mapping construction on B. juncea.