Analysis of SSR Sequence Characteristics and Primers Design Based on Transcriptome Data of Ophiopogon japonicus
Ophiopogon japonicus,a medicinal plant in the Liliaceae family,is listed as the supreme herb for nourishing Yin and moistening the lung in the Shennong's Classic of Materia Medica.This study employed high-throughput sequencing technology to obtain a total of 53 466 Unigenes from the transcriptome of O.japonicus.A total of 35 832 SSR loci were identified in the Unigenes through se-quence analysis.They were distributed across 24 539 Unigenes,with a high SSR occurrence frequency of 67.02％and an average distribution distance of 4.88 kb.GO and KEGG annotations of 24 539 Uni-genes containing SSR loci revealed their main involvement in biological processes,plant-pathogen in-teraction,and other gene functions and metabolic pathways.Mononucleotide repeats were the most abundant,accounting for 57.06％,with A/T(20 193)being the absolute dominant type among all SSR repeat units.Pentonucleotide repeats had the highest average distribution distance(4 069.34 kb).From the perspective of repeat times,the types with repeat unit 10 or more had the most,with 20 849 ones,accounting for 61.69％.30 different repeats types were randomly selected and primers were designed to amplify the genomic DNA of Chuan-maidong(O.japonicus from Sichuan)and Zhe-maidong(O.japonicus from Zhejiang).The results showed that 28 pairs of primers could amplify bands in two cultivars,of which 16 pairs could amplify the target band.This study explored rich SSR loci information from the transcriptome data of O.japonicus,providing data and research foundation for genetic evaluation of resources and molecular marker assisted breeding research.
万方数据
维普
