Development and polymorphism analysis of SSR molecular markers in Tussilago farfara transcriptome / 中草药

ABSTRACT

Objective: The SSR loci information in the transcriptome of Tussilago farfara was analyzed and specific primers were designed, so as to provide powerful tools for molecular marker-assisted breeding in this plant. Methods: SSR loci in 18 938 unigenes with length of 1 kb or more obtained by transcriptome sequencing were searched by using MISA. SSR primers were designed by Primer3 and 55 pairs were randomly selected for the polymorphic analysis on 18 samples collected from different habitats. Results: A total of 4 688 SSRs were detected in the transcriptome of T. farfara, distributed in 3 844 unigenes with the distribution frequency of 24.75%. SSR loci occurred every 7 979 bp. Trinucleotide repeats appeared to be the most abundant SSRs with a frequency of 37.12%, followed by mononucleotide (32.36%) and dinucleotide (28.20%). Among all 60 repeat motifs, A/T (31.42%), AG/CT (12.80%), and ATC/ATG (9.62%) were the predominant repeat types. For validating the availability of the SSR primers, 55 pairs of primers were randomly selected for polymorphism analysis. Among them, 42 pairs (76.36%) produced clear and reproductive bands and 14 pairs showed polymorphism. Eighteen plants were divided into three groups by UPGMA. Conclusion: The SSR markers in the transcriptome of T. farfara show high frequency, rich type, and high polymorphism, which will provide the abundant candidate markers for genetic diversity, genetic mapping construction and marker-assisted breeding study for this plant.