Development and characterization of EST-SSR markers in Rhodomyrtus tomentosa based on transcriptome

Abstract Rhodomyrtus tomentosa (Ait.) Hassk is a flowering evergreen plant with traditional medicine and ornamental usages. This study aimed to develop a set of EST-SSRs markers for genetic diversity analysis of R. tomentosa. Transcriptome sequencing was performed to obtain the expressed sequence tags in different plant tissues. A total of 51,486 unigenes with a mean length of 1,173 bp were achieved. 18,879 SSRs were identified in 14,132 unigenes, in which 3,541 unigenes contained more than one SSR. The top three SSR repeat types were mononucleotide (8,126, 43.04%), dinucleotide (5,846, 31.06%) and trinucleotide (4,610, 24.42%). The most abundance motifs were A/T (7,816, 41.40%), followed by AG/CT (5,002, 26.50%) and AAG/CTT (934, 4.95%). Of these SSRs, 11,726 SSRs were eligible for designing of flanking primers. Among the 100 randomly selected primers, 50 primers generated corresponding PCR products, whereas 23 primers were polymorphic. Thirteen primers with good reproducibility were used to characterize the genetic relationship of sixteen natural R. tomentosa plants. The mean value of observed heterozygosity (Ho), expected heterozygosity (He), fixation index (Fst), and Shannon information index (I) were 0.240, 0.414, 0.413, and 0.641, respectively. UPGMA (unweighted pair-group method with arithmetic averages) dendrogram divided the sixteen R. tomentosa plants into five groups, which were able to distinguish the plants according to geographical origin. This study presented a set of EST-SSRs that could be useful for population genetic relationship analysis in R. tomentosa.