Development of polymorphic microsatellite markers in the medicinal plant Gardenia jasminoides (Rubiaceae)

• A total of 12,960 putative SSR motifs from 10,808 SSR-containing unique putative transcripts were identified within the ESTs.
• 25 allelic polymorphism primer pairs were identified and tested in 153 individuals from five populations of G. jasminoides.
• These new EST-SSR markers will facilitate further genetic studies of this economically important plant G. jasminoides.

A total of 12,960 simple sequence repeats (SSR) motifs were identified in the genome of the medicinal plant Gardenia jasminoides using Illumina-based EST sequences. Among the SSRs, mono-nucleotides were the most abundant (56.7%), followed by di- (19%) and tri-nucleotides (16.4%). AG/TC (60.2%), TTC/AAG (25.8%), and TTTC/GAAA (35.9%) repeat motifs were the most abundant of the di-, tri- and tetra-nucleotide motifs, respectively. Subsequently, twenty-five allelic, polymorphic primer pairs were identified and tested in 153 individuals from five natural populations of G. jasminoides. The number of alleles per polymorphic locus (A) ranged from two to eight. Observed and expected heterozygosity varied from 0.095 to 0.857 and 0.182 to 0.832, respectively. The PIC values for each locus ranged from 0.171 to 0.792. These new polymorphic EST-SSR markers will be useful for further genetic studies on this economically important plant.