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

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Abstract

Rhodomyrtus tomentosa 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 1173 bp were achieved. 18,879 SSRs were identified in 14,132 unigenes, in which 3541 unigenes contained more than one SSR. The top three SSR repeat types were mononucleotide (8126, 43.04%), dinucleotide (5846, 31.06%) and trinucleotide (4610, 24.42%). The most abundance motifs were A/T (7816, 41.40%), followed by AG/CT (5002, 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 four groups, which were partially correlated with the geographical origin. This study presented a set of EST-SSRs that could be useful for population genetic relationship analysis in R. tomentosa.

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Data availability

The datasets generated in this study are available in BioProject with the accession number of PRJNA821925 (https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA821925&o=acc_s%3Aa).

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Acknowledgements

We thank Guangxi Pfomic Bioinformation Co., Ltd. for their help in transcriptome analysis.

Funding

This work was supported by Guangxi Key Laboratory of Special Non-wood Forest Cultivation & Utilization (Grant numbers JA-20–01-02 and JA-20–01-05).

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Authors and Affiliations

  1. Guangxi Zhuang Autonomous Region Forestry Research Institute, Nanning, 530002, Guangxi, People’s Republic of China

    Lina Sun, Jinhua Li, Kaidao Sun, Huaxin Wang, Kaitai Yang & Mao Lin

  2. Nanning Goldtech Bioscience Ltd., Nanning, 530007, Guangxi, People’s Republic of China

    Qi Chen

  3. New Technology Entrepreneur Center, Nanning, 530007, Guangxi, People’s Republic of China

    Qi Chen

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  1. Lina Sun
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Contributions

LS, QC, and ML conceived and designed the experiments. LS, JL, KS, HW, and KY collected the samples. LS, JL, and QC performed the transcriptome sequencing and data analysis. LS, KS, HW, KY contributed equally to the EST-SSR validation. LS wrote the paper. QC and ML revised the draft manuscript. ML supervised the whole project.

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Correspondence to Mao Lin.

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Sun, L., Li, J., Sun, K. et al. Development and characterization of EST-SSR markers in Rhodomyrtus tomentosa Hassk. based on transcriptome. Genet Resour Crop Evol 70, 1691–1705 (2023). https://doi.org/10.1007/s10722-022-01528-x

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