Development of EST-SSR markers and Generalizability analysis of Cinnamomum officinarum ct. Borneol based on transcriptome sequence

SSR loci were detected in 187,095 unigenes of Cinnamomum officinarum ct. Borneol obtained by transcriptome sequencing using MISA software to explore the distribution pattern and compositional characteristics of SSRs and design primers for primer polymorphism and generalization analysis. The results showed that 90,590 SSR sites were found in 187,095 unigenes, and the frequency of SSR occurrence was 48.42%, with an average of 1 SSR site in 1.99 kb. The total number of unigenes containing SSR sites was 68,573, and the frequency of SSR occurrence (number of sequences containing SSR sites/total number of searched sequences) was 36.65%. Cinnamomum officinarum ct. Borneol EST-SSR repeat types had the highest frequency of occurrence of dinucleotide repeat types, followed by trinucleotide, in addition to mononucleotide. Among the 21,777 dinucleotide repeat SSRs detected, repeat unit AG/CT (16.06%) had the highest number and was the dominant repeat unit, followed by AT/AT (5.37%), AC/GT (2.53%), and CG/CG (0.09%). The trinucleotide AAG/CTT (4.37%) had the highest frequency of occurrence and was the dominant repeating unit. Primer3.0 was used to design and synthesize 118 pairs of SSR primers, 96 pairs were amplified successfully (81.36%), of which 14 pairs showed polymorphism (11.86%), and the average polymorphism information content (PIC) was 0.378 in five different chemotypes. primers belonged to high polymorphic sites. The 14 pairs of EST-SSR primers developed in this study showed 100% generalizability in five species of the same genus, including Cinnamomum longepaniculatum, Cinnamomum kanehirae, Cinnamomum parthenoxylon, Cinnamomum burmanni and Cinnamomum bodinieri. In conclusion, the EST-SSR markers developed based on the transcriptome of Cinnamomum officinarum ct. Borneol have high polymorphism and generalizability, and the method is feasible.