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Microsatellites characteristics analysis and SSR marker development for Paphiopedilum hirsutissimum based on transcriptome sequencing

Published online by Cambridge University Press:  05 February 2018

Lin Chen Open the ORCID record for Lin Chen [Opens in a new window] ,
Hui Dong ,
Jianwen Wang ,
Longna Li  and
Meng Xu
Lin Chen*
Affiliation:
Co-Innovation Center for Sustainable Forestry in Southern China, Nanjing Forestry University, Nanjing 210037, China
Hui Dong
Affiliation:
Co-Innovation Center for Sustainable Forestry in Southern China, Nanjing Forestry University, Nanjing 210037, China
Jianwen Wang
Affiliation:
Co-Innovation Center for Sustainable Forestry in Southern China, Nanjing Forestry University, Nanjing 210037, China
Longna Li
Affiliation:
Virtual Simulation Experiment Teaching Center of Agricultural Biology, Nanjing Agricultural University, Nanjing 210095, China
Meng Xu
Affiliation:
Co-Innovation Center for Sustainable Forestry in Southern China, Nanjing Forestry University, Nanjing 210037, China
*
*Corresponding authors. E-mail: clinechen@njfu.edu.cn
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Abstract

Paphiopedilum hirsutissimum (Lindl. ex Hook. f.) Stein (Orchidaceae) is a valuable but endangered ornamental plant. In the present study, the microsatellites characteristics were analysed and 14 polymorphic simple sequence repeat (SSR) markers were developed based on the de novo transcriptome sequencing for P. hirsutissimum using Illumina pair-end sequencing technology. A total of 7406 SSRs were detected in 56,688 unigenes, with the occurrence frequency of 13.06% and an average density of one SSR per 5.42 kb; and 150 primer pairs randomly selected from 2090 pairs except mononucleotide repeats were synthesized for verification. These loci were validated in 32 individuals from the concentrated distribution centre, and were successfully amplified using 14 primer sets showing a high level of polymorphism. These SSR markers will be useful in future studies of genetic diversity, the population structure of P. hirsutissimum and make effective conservation strategy.

Keywords

genetic diversityPaphiopedilum hirsutissimumSSRtranscriptome sequencing
Type
Short Communication
Information
Plant Genetic Resources , Volume 16 , Issue 4 , August 2018 , pp. 394 - 396
Copyright
Copyright © NIAB 2018 

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