Objective   The simple sequence repeats (SSRs) in the mitochondrial genome of zicaitai (Brassica rapa var. Purpuraria) were compared with those of other species in the genus.

  Method  MISA software was used to search the mitochondrial genomes of zicaitai as well as 5 other major species and 3 mutants of Brassica rapa. The SSR sequence distributions of the specimens were compared and analyzed.

  Result  In the mitochondrial genomes, 168, 170, 167, 168, 180, 280, 185, 165, and 179 complete SSRs were screened. The sequences showed relative densities of 764, 774, 760, 764, 775, 777, 721, 744, and 771 per Mb with total lengths of 1562, 1577, 1547, 1562, 1664, 2564, 1722, 1524, and 1646 bp that accounted for 0.71%, 0.72%, 0.70%, 0.71%, 0.72%, 0.71%, 0.67%, 0.69%, and 0.71% of the total sequence length of each specimen, respectively. Among the 1-6 different nucleotide repeat units in zicaitai and the other major Brassica species, most SSRs were mononucleotide, which was followed by dinucleotide, tetranucleotide, trinucleotide, and pentanucleotide, but no hexonucleotide. A/T, AG/CT, AT/AT, and C/G were the common repeat unit types in them.

  Conclusion  The mitochondrial genome of zicaitai was 219779 bp with 168 SSRs at the relative density of 764 markers/Mb and 9 bp in length. Mono-, di-, and tetra-nucleotides were the most abundant repeat units, which could potentially be developed as highly polymorphic markers for species differentiation.