Abstract: Objective To develop specific molecular markers of Scutellaria baicalensis and perform genetic diversity analysis and molecular marker-assisted breeding. Methods Single nucleotide polymorphisms(SNP)and insertion and deletion polymorphisms(InDel)sites in the transcriptome of flowers and roots of Scutellaria baicalensis were analyzed. Results The results showed that an average of 216 067 SNPs were found in the transcriptome of 18 skullcap flowers and roots, and the ratio of conversion to transversion was 1.42~1.61, and the number of loci distributed in the exome region was the largest, and the number of loci with missense mutations was the largest. The average number of InDel loci in each sample was 22 864, and the number of insertion loci was greater than that of the deletion type, which was the most distributed in the gene and had the most frameshift insertions. Conclusion The results show that the transcriptome of the flowers and roots of Scutellaria baicalensis is rich in SNPs and InDel loci, and has high polymorphisms, which provides data support for the development of specific molecular markers in Scutellaria baicalensis.

Key words: Scutellaria baicalensis Georgi, transcriptome, SNP, InDel