Characterization and novel Est-SSR marker development of an important Chinese medicinal plant, Morinda officinalis How (Rubiaceae)

Morinda officinalis How (Rubiaceae) is well known as one of the four most popular medicinal plants in the southern region of China. In order to assess its genetic diversity and assist the development of its molecular assisted-selection breeding in China, we constructed the transcriptome database of M. officinalis using fresh leaf material and developed novel expressed sequence tag–simple sequence repeat (EST-SSR) markers for this important medicinal plant species. Our study identified 8064 potential EST-SSRs from 6668 unigenes. For perfect repeat motifs, the mononucleotide repeats were most abundant (4221; 52.34%), followed by the trinucleotide repeats (1588; 19.69%), and the dinucleotide ones (1040; 12.90%). The seven most commonly occurring repeat motifs were A/T (4661), AG/CT (588), AAG/CTT (408), AC/GT (353), ATC/ATG (338), AT/AT (296) and AGG/CCT (277). Of a total of 5605 SSR primer sets that were successfully designed de novo, 100 were selected for validation analysis. There, 24 primer sets were polymorphic across the 96 M. officinalis individuals collected from four different populations in Guangdong province. Based on cross-species transferability test, 19 and 22 primer sets produced successful amplification in M. umbellata subsp. obovata and M. parvifolia, respectively. These novel EST-SSR markers with high cross-species transferability between M. officinalis and its closely-related species could serve as aids to future studies in genetic diversity, conservation, assisted-selection breeding and genes associated with the medical uses of the genus.