Analysis on SSR Loci in Transcriptome and Development of EST-SSR Molecular Markers in Lonicera macranthoides
1 College of Integrated Traditional Chinese and Western Medicine, Hunan University of Chinese Medicine, Changsha, 410208, China
2 Changsha Engineering Technology Research Center of Woody flower, Hunan Academy of Forestry, Changsha, 410004, China
3 Institute of Medicinal Plant Development, Chinese Academy of Medical Science and Peking Union Medical College, Beijing, 100193, China
Molecular Plant Breeding, 2023, Vol. 14, No. 1 doi: 10.5376/mpb.2023.14.0001
Received: 01 Jan., 2023 Accepted: 06 Jan., 2023 Published: 13 Jan., 2023
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This article was first published in Molecular Plant Breeding in Chinese, and here was authorized to translate and publish the paper in English under the terms of Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited.
Preferred citation for this article:
Liu S.S., Qiao Z.Q., Zeng H.J., Li Y.X., Cai N., Liu X.M., and Wang X.M., 2023, Analysis on SSR loci in transcriptome and development of EST-SSR molecular markers in Lonicera macranthoides, Molecular Plant Breeding, 14(1): 1-8 (doi: 10.5376/mpb.2023.14.0001)
Huizhanmao-rendong (Lonicera macranthoides), as a species of original plant of wild honeysuckle flower (Flos Lonicerae), the traditional Chinese medicine, is widely distributed in South China and features high medicinal and economic value. In this study, the SSR loci of 74 057 unigenes in the transcriptome of L. macranthoides were analyzed by MISA. Among them, 15 587 unigenes contained 20 161 SSR loci, and the frequency of SSR was 21.05%. The types of SSR sites in the transcriptome of L. macranthoides were distributed from single nucleotide to six nucleotide repeats. The main repeats were dinucleotide (9 704) and trinucleotide (5 847), accounting for 48.13 % and 29.00 % of the total SSRs, respectively. The main repeat units were AG/CT (6 086), AT/AT (3 071) and A/T (2 826), accounting for 30.79%, 15.23%, and 14.02% of the total SSRs, respectively. There were 4 897 and 3 531 repeats (the numbers of repeats were the most) in 6 and 5 SSR loci, accounting for 24.29 % and 17.51 % of the total SSR number, respectively. By using primer 6.0 software, 17 611 pairs of SSR primers were designed, and 30 pairs of primers were randomly selected for amplification verification. Among them, 14 pairs of amplified bands showed polymorphism, and then the genetic diversity of 6 varieties of L. macranthoides was analyzed by using these 14 pairs of primers. The results will provide a scientific basis for species identification, genetic diversity analysis, and molecular marker-assisted breeding of L. macranthoides.
Lonicera macranthoides; SSR; Mlecular marker; Transcriptome