Analysis of SSR information in the pistil transcriptome and the development and characterization of novel tri-nucleotide SSR markers in Corylus

Hazelnuts (Corylus) are one of the most important nut crops and woody oil plants, having high economic and nutritional value. It is important to study the taxonomy, phylogenetics, and genetic diversity in the genus Corylus. In this study, we used the previously constructed pistil transcriptome of the Ping'ou hybrid hazelnut cultivar 'Dawei' to analyze the SSR information and develop novel tri-nucleotide SSR markers in Corylus. The results identified 16,339 sequences containing SSRs, resulting in a percentage of 19.72%. An SSR locus was identified for every 5.67 kb of the examined sequences, and 497 motif sequence types were identified. The di-nucleotide repeat type (63.82%) was the most abundant, followed by the tri-nucleotide repeat type (24.54%). (AAG/CTT)n repeats were dominant among the tri-nucleotide repeats, followed by (AAT/ATT)n, (ATC/ATG)n, (AGG/CCT)n and (ACC/GGT)n repeats. The sequences with a tri-nucleotide repeat were used to design 160 primer pairs, of which 122 primer pairs showed successful PCR amplification in 'Dawei'. Twenty-two primer pairs that showed polymorphism among the 13 tested samples of the three Corylus species were selected, with an average PIC value of 0.50. A dendrogram based on 82 alleles of the 13 samples using the developed SSR primer pairs was generated. The samples were clustered into three main groups in accordance with the species and showed a complete separation in the dendrogram. In conclusion, transcriptome sequencing is an effective tool for SSR marker development, and the newly developed SSR primer pairs will help in genetic and breeding studies in Corylus and related species.