Characterisation and development of EST-SSR markers in tree peony using transcriptome sequences

Tree peony is a well-known ornamental and medicinal plant in China, as well as a new crop that has been recently demonstrated to exhibit a great potential for edible oil production. However, only limited molecular markers are currently available in this species, which hinders its genetic and breeding studies. The objective of this study was to develop expressed sequence tag (EST)-simple sequence repeat (SSR) markers based on transcriptome sequences in tree peony. A total of 4,373 EST-SSRs were identified from 3,787 unigene sequences with an average of one SSR per 9.24 kb. Di-nucleotide repeats (46.26 %) were the most abundant type followed by tri-, hexa-, tetra-, and penta-nucleotide repeats. Moreover, 788 primer pairs were synthesised, out of which 373 primer pairs (47.3 %) produced successful amplifications, and 149 primer pairs (39.9 %) were polymorphic in both parents of one mapping population. The 30 polymorphic EST-SSR markers were randomly selected to assess polymorphism further in 36 tree peony accessions, in which the polymorphism information content values ranged from 0.36 to 0.85 with a mean of 0.69, thereby indicating a high level of informativeness. Transferability studies indicated that 95.3 % EST-SSR markers were transferable to nine other Paeonia species, thereby expanding their utility. In addition, as a demonstration of utility, a genetic relationship study was performed in 56 accessions. Cluster analysis using the neighbour-joining tree method demonstrated that major clusters corresponded to known pedigree trees. Thus, these newly developed markers will be valuable in facilitating marker-assisted selection breeding in tree peony and its related species.