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Molecules 2018, 23(8), 2014; https://doi.org/10.3390/molecules23082014

Development and Characterization of High-Throughput EST-Based SSR Markers for Pogostemon cablin Using Transcriptome Sequencing

1
Agricultural College, Guangxi University, Nanning 530005, China
2
College of Chinese Materia Medica, Guangdong Food and Drug Vocational College, Guangzhou 510520, China
3
College of Medical Technology, Ningbo College of Health Sciences, Ningbo 315100, China
4
School of Traditional Chinese Medicine, Southern Medical University, Guangzhou 510515, China
These authors contributed equally to this work.
*
Author to whom correspondence should be addressed.
Received: 21 June 2018 / Revised: 16 July 2018 / Accepted: 5 August 2018 / Published: 13 August 2018
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Abstract

Simple sequence repeats (SSRs) or microsatellite markers derived from expressed sequence tags (ESTs) are routinely used for molecular assisted-selection breeding, comparative genomic analysis, and genetic diversity studies. In this study, we investigated 54,546 ESTs for the identification and development of SSR markers in Pogostemon cablin (Patchouli). In total, 1219 SSRs were identified from 1144 SSR-containing ESTs. Trinucleotides (80.8%) were the most abundant SSRs, followed by di- (10.8%), mono- (7.1%), and hexa-nucleotides (1.3%). The top six motifs were CCG/CGG (15.3%), AAG/CTT (15.0%), ACC/GGT (13.5%), AGG/CCT (12.4%), ATC/ATG (9.9%), and AG/CT (9.8%). On the basis of these SSR-containing ESTs, a total of 192 primer pairs were randomly designed and used for polymorphism analysis in 38 accessions collected from different geographical regions of Guangdong, China. Of the SSR markers, 45 were polymorphic and had allele variations from two to four. Furthermore, a transferability analysis of these primer pairs revealed a 10–40% cross-species transferability in 10 related species. This report is the first comprehensive study on the development and analysis of a large set of SSR markers in P. cablin. These markers have the potential to be used in quantitative trait loci mapping, genetic diversity studies, and the fingerprinting of cultivars of P. cablin. View Full-Text
Keywords: Pogostemon cablin; expressed sequence tag (EST); simple sequence repeat (SSR); polymorphism; transferability Pogostemon cablin; expressed sequence tag (EST); simple sequence repeat (SSR); polymorphism; transferability
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Ouyang, P.; Kang, D.; Mo, X.; Tian, E.; Hu, Y.; Huang, R. Development and Characterization of High-Throughput EST-Based SSR Markers for Pogostemon cablin Using Transcriptome Sequencing. Molecules 2018, 23, 2014.

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