Characteristics of the SSR loci in the Anoplophora chinensis transcriptome
Author of the article:HAN Xiao-Hong；WANG Yi-Fan；LU Ci-Ding；LIN Hao-Yu；SHI Yu-Fei ；HE Huan；ZHANG Fei-Ping；LIANG Guan
Author's Workplace：College of Forestry, Fujian Agriculture and Forestry University, Key Laboratory of Integrated Pest Management in Ecological Forests, Fujian Agriculture and Forestry University, Fuzhou 350002, China；College of Forestry, Fujian Agriculture and Forestry University, Key Laboratory of Integrated Pest Management in Ecological Forests, Fujian Agriculture and Forestry University, Fuzhou 350002, China；College of Forestry, Fujian Agriculture and Forestry University, Key Laboratory of Integrated Pest Management in Ecological Forests, Fujian Agriculture and Forestry University, Fuzhou 350002, China；College of Forestry, Fujian Agriculture and Forestry University, Key Laboratory of Integrated Pest Management in Ecological Forests, Fujian Agriculture and Forestry University, Fuzhou 350002, China；College of Forestry, Fujian Agriculture and Forestry University, Key Laboratory of Integrated Pest Management in Ecological Forests, Fujian Agriculture and Forestry University, Fuzhou 350002, China；College of Forestry, Fujian Agriculture and Forestry University, Key Laboratory of Integrated Pest Management in Ecological Forests, Fujian Agriculture and Forestry University, Fuzhou 350002, China College of Forestry, Fujian Agriculture and Forestry University, Key Laboratory of Integrated Pest Management in Ecological Forests, Fujian Agriculture and Forestry University, Fuzhou 350002, China；College of Forestry, Fujian Agriculture and Forestry University, Key Laboratory of Integrated Pest Management in Ecological Forests, Fujian Agriculture and Forestry University, Fuzhou 350002, China
Key Words：Anoplophora chinensis; transcriptome; SSR; repeat type; motif type; primer
Abstract：[Objectives] SSR (Simple Sequence Repeat) markers are a very useful method for species identification, molecular linkage mapping, and genetic diversity studies. In order to develop molecular markers for Anoplophora chinensis, SSR markers were identified based on transcriptome sequence. This study provides a basis for studies of genetic diversity and the integrated control of A. chinensis. [Methods] The software MISA was used to explore all microsatellite loci in the transcriptome database of A. chinensis. Primers were designed using the software Primer Premier 3.0, and screened using PCR amplification and electrophoresis. [Results] A total of 2 360 SSRs were identified through software analysis; a frequency of 25.31%. These had 1758 sequences, accounting for 18.85% of the total number of sequences. Most repeat types were mononucleotide motifs (79.03%) followed by trinucleotide motifs (12.54%). The dominant repeat type was A/T (99.30%). The proportion of SSR length to 10-11 bp was highest (56.10%), the maximum number of repeats was 10 and the number of SSR loci was 1188 (50.34%). These results indicate the feasibility of using polymorphism analysis to develop SSR markers for A. chinensis．A total of 60 primer pairs were randomly selected and verified by PCR amplification, 53 of which were able to amplify the expected products; a primer availability rate as high as 88% which could be used in future studies. [Conclusion]The information analysis of SSR loci and the design and validation of primers will be helpful for gene mining, and for research on population genetic structure, genetic diversity, evolutionary relationships and the integrated control of A. chinensis.