Objective  EST-SSRs of lemon were searched based on transcriptome data to analyze the genetic diversity of the plant.

Method  SSR loci of lemon transcriptomes were screened using MISA to design primers by Primer 3.0. A clustering of 49 species was secured.

Result  Of the 40193 SSR loci identified, a distribution frequency of 35.67% and an average distribution distance of 1.39 kb were found in the sequences of 80.91% mono-, 9.20% tri-, and 8.67% dinucleotide repeat types with the dominant motifs of A/T, AG/CT, and AAG/CTT, respectively. Twenty-four of the 4561 pairs of primers were selected for validity verification, and 13 by being polymorphic. The amplified 47 alleles had a mean effective value of 3.615 with the mean Ho, He, and PIC of 0.637, 0.516, and 0.528, respectively. At the genetic distance of 0.40, the lemon cultivars were clustered into 5 categories, which were generally consistent with that obtained by the traditional morphological classification.

Conclusion  Thirteen pairs of EST-SSR primers were selected to classify 49 lemon specimens. The resulting clustering agreed with traditional taxonomy. The displayed rich genetic diversity rendered these cultivars an adequate germplasm collection for the development and utilization of lemon plants.