Abstract
Background Chimonanthus praecox, belongs to the Calycanthaceae, is a unique traditional famous flower and special economic tree species in China. There are numerous varieties but only a few cultivars were named. At present, EST-SSR markers are widely used to identify different species and varieties, as researchers can identify a large number of microsatellites from transcriptome databases.
Result A total of 162,638 unigenes were assembled by using RNA-seq, and 82,778 unigenes was annotated by Nr, Nt, Swiss-Prot, Pfam, GO, KOG and KEGG databases. A total of 13,556 SSR loci were detected from 11,691 unigenes, with trinucleotide repeat motifs being the most abundant among the six types of repeat motifs. In order to develop markers, 64,440 pairs of SSR primers with polymorphism potential were designed, and 75 pairs of primers were randomly selected for amplification. Among them, seven pairs amplified fragments of the expected size with high polymorphism, and twelve C.praecoxvarieties were clustered into two monophyletic clades by the seven EST-SSR markers.
Conclusion The microsatellites in the transcriptome of C.preacox have the advantages of rich types, strong specificity, and great polymorphism potential. These EST-SSR markers can provide molecular technical methods for identifying different varieties of C.preacox, and can also explore a large number of candidate genes associated to traits.