3 Biotech

, 9:292 | Cite as

Development of EST-based SSR and SNP markers in Gastrodia elata (herbal medicine) by sequencing, de novo assembly and annotation of the transcriptome

  • Yunsheng WangEmail author
  • Muhammad Qasim Shahid
  • Fozia Ghouri
  • Sezai Ercişli
  • Faheem Shehzad Baloch
Original Article


Tianma (Gastrodia elata Blume) has unique biological characteristics and high medicinal value. The wild resource of G. elata is being overutilized and should be conserved as it is already included in the list of endangered species in China. The population size of cultivated G. elata is small because of domestication bottleneck. Therefore, it is of utmost importance to evolve high-quality varieties and conserve wild resources of G. elata. In this study, we sequenced tuber transcriptomes of three major cultivated sub-species of Gastrodia elata, namely G. elata BI. f. elata, G. elata Bl. f. glauca S. Chow, and G. elata Bl. f. Viridis, and obtained about 7.8G clean data. The assembled high-quality reads of three sub-species were clustered into 56,884 unigenes. Of these, 31,224 (54.89%), 25,733 (45.24%), 22,629 (39.78%), and 11,856 (20.84%) unigenes were annotated by Nr, Swiss-Port, Eukaryotic Ortholog Groups (KOG), and Kyoto Encyclopedia of Genes and Genomes (KEGG) databases, respectively. Here, a total of 3766 EST-SSRs and 128,921 SNPs were identified from the unigenes. The results not only offer huge number of genes that were responsible for the growth, development, and metabolism of bioactive components, but also a large number of molecular markers were detected for future studies on the conservation genetics and molecular breeding of G. elata.


Traditional Chinese medicine Tianma (Gastrodia elata Blume) Neuron SNP SSR 



This work was supported by Guizhou Provincial Science and Technology Foundation [LH(2015)7754].

Author contributions

YW conceived and designed the experiments; YW performed the experiment. YW, MQS, FG, SE, and FSB wrote and revised the paper. YW, MQS, and FG contributed to data analysis. All authors read and approved the final manuscript.

Compliance with ethical standards

Conflict of interest

The authors declare that they have no conflict of interest.

Supplementary material

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Supplementary material 1 (DOCX 2220 kb)
13205_2019_1823_MOESM2_ESM.docx (9.2 mb)
Supplementary material 2 (DOCX 9391 kb)
13205_2019_1823_MOESM3_ESM.pdf (585 kb)
Supplementary material 3 (PDF 585 kb)


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Copyright information

© King Abdulaziz City for Science and Technology 2019

Authors and Affiliations

  1. 1.College of Environment and Life ScienceKaili UniversityKaili CityChina
  2. 2.State Key Laboratory for Conservation and Utilization of Subtropical Agro-BioresourcesSouth China Agricultural UniversityGuangzhouChina
  3. 3.Guangdong Provincial Key Laboratory of Plant Molecular BreedingSouth China Agricultural UniversityGuangzhouChina
  4. 4.College of AgricultureSouth China Agricultural UniversityGuangzhouChina
  5. 5.Department of Horticulture, Faculty of AgricultureAtaturk UniversityErzurumTurkey
  6. 6.Department of Field Crops, Faculty of Agricultural and Natural SciencesAbant İzzet Baysal UniversityBoluTurkey

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