Molecular Biology Reports

, Volume 46, Issue 6, pp 6547–6556 | Cite as

Development and characterization of genomic microsatellite markers in the tree species, Rhodoleia championii, R. parvipetala, and R. forrestii (Hamamelidaceae)

  • Yanshuang Huang
  • Qianyi Yin
  • Van Truong Do
  • Kaikai Meng
  • Sufang Chen
  • Boyong LiaoEmail author
  • Qiang FanEmail author
Short Communication


Rhodoleia Champion ex Hooker is one of the most primitive relict genera of Hamamelidaceae, a key family exploited to understand the origin and early evolution of flowering plants. Genomic simple sequence repeats (SSRs) were developed for R. championii to perform genetic diversity, phylogeographical structure or even systematic evolution studies of the genus. Among the 278,743 contigs (105,758,242 bps) de novo assembled from the low-coverage whole genome sequencing of R. championii, a total of 9106 SSRs were detected in 8370 contigs, and SSR primer pairs were successfully designed for 6677 SSRs. Among the 110 selected primer pairs, 41 were amplified successfully in the preliminary test of SSR screening. Further amplification of these 41 primer pairs across the 122 individuals collected from six populations of the three Rhodoleia species showed that 32 and 40 SSR markers can be amplified in Vietnam and Jinping populations of R. parvipetala, 41, 33, and 41 SSR markers in Boluo, Hongkong and Xinyi populations of R. championii, 25 SSR markers in Fugong population of R. forrestii, and 20 SSR markers demonstrated to be polymorphic across the three species. Genetic analysis for these 20 polymorphic SSRs showed that Allele number (A) ranged from four to 13 and polymorphic information content (PIC) ranged from 0.479 to 0.876 across the three species. At the population level, observed heterozygosity (HO) ranged from 0.000 to 1.000, and expected heterozygosity (HE) ranged from 0.091 to 0.851. In the present study, we provided the first whole-genome sequencing database for the species R. championii, identified ample SSR loci with designed primers, and revealed that 20 of the 110 selected SSRs were polymorphic across three Rhodoleia species. These provide valuable resources for future studies on genetic study, species delimitation, phylogeography, and conservation of this genus.


Rhodoleia championii Hamamelidaceae Microsatellite Low-coverage whole genome sequencing 



We are grateful to Dr. Zhao Wanyi and Mr. Guo Xibing for their help in plant sampling. This work was supported by the National Natural Science Foundation of China (31670189,31800175, 31570195), Natural Science Foundation of Guangdong Province (2017A030310421, 2018A0303130109, 2018B030320001), the Fourth National Survey on Chinese Material Medical Resources Program for State Administration of Traditional Chinese Medicine of China (2017-152-003), Dongguan Municipal Project for Improvement of Social Science and Technology (2016108101018) and Chang Hungta Science Foundation of Sun Yat-sen University.

Author contributions

BL and QF designed the research. QF, QY, VD and YH collected samples. KM designed the primers. BL and YH generated the data. SC and BL analyzed and interpreted the data. YH wrote the manuscript, and all the authors modified the manuscript.

Compliance with ethical standards

Conflict of interest

The authors declare that they have no conflict of interest.

Supplementary material

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Copyright information

© Springer Nature B.V. 2019

Authors and Affiliations

  1. 1.State Key Laboratory of Bio-control and Guangdong Provincial Key Laboratory of Plant ResourcesSun Yat-sen UniversityGuangzhouChina
  2. 2.Department of BiologyVietnam National Museum of Nature, Vietnam Academy of Science and TechnologyCau GiayVietnam

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