貓腥草(Praxelis clematidea (Griseb.) R. M. King & H. Rob)為菊科貓腥草屬一年生草本植物，原生於南美，現已成為臺灣農地的入侵雜草。由於貓腥草與紫花藿香薊(Ageratum houstonianum Mill.)及藿香薊 (A. conyzoides L.) 的植株形態極為相似，未開花之前不易區別，造成鑑定上的困擾。分子標誌己普遍運用於植物種類之鑑別，本研究針對貓腥草與紫花藿香薊及藿香薊5.8S rRNA-ITS 核酸序列進行選殖及解序，並建立PCR-RFLP、allelic-specific PCR 及ISSR 的分子標誌。貓腥草與紫花藿香薊及藿香薊的5.8S rRNA-ITS 序列長度不同，分別為644 bp、646 bp及646 bp，其中紫花藿香薊及藿香薊5.8S rRNA-ITS 序列完全相同，而貓腥草與紫花藿香薊者一致性(identity)為80%。經由ITS 序列比對，貓腥草與紫花藿香薊及藿香薊之間有Fok I、Not I、Sml I 及Stu I 4 種限制酵素切位的差異，5.8S rRNA-ITS核酸片段經4 種限制酵素反應，故發展 PCR-RFLP 鑑定方法；另於ITS 序列差異處設計專一性引子，建立allelic-specific PCR 鑑定方法，可分別於貓腥草與紫花藿香薊及藿香薊增幅353 bp 及485 bp 片段；此外利用ISSR UBC #822、844、857及868 等4 組引子可增幅200-2,000 bp 之間的2 至8 條多型性核酸條帶，可明顯區別貓腥草、紫花藿香薊及藿香薊。Allelic-specific PCR 及ISSR 兩種分子標誌具有簡易、快速及明確等特點，可應用於入侵植物的監測及管理，進而維護臺灣原生物種之生態多樣性與平衡。

Praxelis (Praxelis clematidea (Griseb.) R. M. King & H. Rob) is an annualCompositae plant and native to South America, became an invasive plant in Taiwan inrecent decades. As the morphological characteristics is similar, Praxelis has been easilymisidentified with Ageratum (Ageratum houstonianum Mill.) and Goat weed (A.conyzoides L.) before blossom. DNA-based molecular markers have been used to detectthe genetic diversity of invaded alien species. Novel methods for the identification ofthe invasive plant Praxelis, Ageratum and Goat weed at the early stage of plantdevelopment have established in this study, based on direct sequencing of the internaltranscribes spacer (ITS) region of 18S-26S ribosomal DNA (rDNA), PCR-restrictionfragment length polymorphism (RFLP), allelic-specific PCR and inter-simple sequencerepeat (ISSR) markers. The 5.8S rRNA-ITS regions of Praxelis, Ageratum and Goatweed were 644, 646 and 646 bp, respectively. The PCR product on the 5.8S rRNA-ITSof Praxelis, Ageratum and Goat weed were digested with the restriction endonucleaseFok I、Not I、Sml I and Stu I. Each fragment gave unique electrophoretic profiles.Among one hundred ISSR UBC primers, only #822, 844, 857 and 868 primers cansignificantly distinguish Praxelis, Ageratum and Goat weed by 2-8 differentpolymorphic markers. The specific primers of AS-PCR were designed from the 5.8SrRNA-ITS nucleotide polymorphism to differentiate Praxelis, Ageratum and Goat weed,via multiplex PCR to produce unique 353 bp, 485 bp and 485 bp single bands,respectively. AS-PCR and ISSR markers may assist the effective management in invasionplant Praxelis and maintain the balance of biodiversity in agricultural ecosystems.