Journal
MOLECULES
Volume 23, Issue 8, Pages -Publisher
MDPI
DOI: 10.3390/molecules23082014
Keywords
Pogostemon cablin; expressed sequence tag (EST); simple sequence repeat (SSR); polymorphism; transferability
Funding
- Science and Technology Program of Guangzhou City [201604020041]
- Science and Technology Program of Guangdong Province [2015A040404029]
- Natural Science Foundation of Guangdong Province [2018A030313255]
- Natural Science Project of the Guangdong Food and Drug Vocational College [301009A1807]
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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.
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