Objective: To study the genetic basis of the formation of indigenous Chinese medicine materials.

Methods: The 5S-rRNA gene spacer regions in F. thunbergii from different habitats were amplified with AS and AS-1 as primers, and then sequenced. Total alkaloid contents were assayed by acid dye colorimetry, and 2 main alkaloid contents were assayed by pre-column derivatization and gas chromatographic method.

Result: The sequenues of 5S-rRNA gene spacer regions in F. thunbergii from different habitats were same, and the length of them was 588 bp. They had same content total alkaloid. The results of gas chromatography showed that they had same kinds of monomer alkaloids, but the contents of different monomer alkaloids were different.

Conclusion: The difference of alkaloid content in F. thunbergii from various habitats isn't resulted from base sequence variation, but from microenvironment.

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