基于低拷贝核基因AOX1和MCM5的扩增结果，对采自南京的水芹〔Oenanthe javanica （Bl.） DC.〕野生种和太湖流域6个地方品种进行了遗传多样性分析，并基于ISSR标记开发了两步法鉴定‘玉祁红芹’（‘Yuqihongqin’）的SCAR标记。结果显示：水芹6个地方品种的AOX1基因中检测到22个SNP位点和7个InDel位点；MCM5基因中检测到33个SNP位点，其中3个位于编码区且均为同义突变，还有1个位于非编码区的InDel位点。与MCM5基因相比，AOX1基因提供的信息位点更多，基于AOX1基因构建的水芹野生种和6个地方品种的ML遗传关系树的支持率相对较高；其中‘玉祁红芹’、‘苏州圆叶芹’（‘Suzhouyuanyeqin’）和‘梅南水芹’（‘Meinanshuiqin’）的遗传关系较近，而‘常熟白芹’（‘Changshubaiqin’）、‘溧阳白芹’（‘Liyangbaiqin’）和‘江阴青芹’（‘Jiangyinqingqin’）的遗传关系较近。基于ISSR-880引物扩增得到‘溧阳白芹’的特异性片段，设计的第1对SCAR引物鉴定出‘玉祁红芹’和‘溧阳白芹’2个地方品种，再利用ISSR-836引物扩增得到‘玉祁红芹’特异性片段，设计的第2对SCAR引物在‘玉祁红芹’所有单株中扩增出特异性条带，而在‘溧阳白芹’所有单株中均未出现此条带。本研究开发的两步法鉴别‘玉祁红芹’的ISSR-SCAR标记可为水芹其他地方品种的鉴定、保存和利用提供参考。

 The genetic diversity of wild species of Oenanthe javanica （Bl.） DC. collected from Nanjing and 6 local cultivars in Taihu Lake basin was analyzed based on the amplification results of low copy nuclear gene AOX1 and MCM5， and SCAR markers of a two-step identification method for ‘Yuqihongqin’ were developed based on ISSR markers. The results show that 22 SNP loci and 7 InDel loci are detected in AOX1 gene in 6 local cultivars of O. javanica； 33 SNP loci are detected in MCM5 gene， in which， 3 SNP loci are synonymic mutations and located in coding region， and 1 InDel locus is located in non-coding region. Compared with MCM5 gene， AOX1 gene provides more information sites, and the support rate of ML genetic relationship tree of wild species and 6 local cultivars of O. javanica based on AOX1 gene is relatively high； in which， the genetic relationship of ‘Yuqihongqin’， ‘Suzhouyuanyeqin’， and ‘Meinanshuiqin’ is relatively close， and that of ‘Changshubaiqin’， ‘Liyangbaiqin’， and ‘Jiangyinqingqin’ is relatively close. The specific fragment of ‘Liyangbaiqin’ is amplified with ISSR-880 primer， and 2 local cultivars of ‘Yuqihongqin’ and ‘Liyangbaiqin’ are identified with the first designed pair of SCAR primers. Afterwards， the specific fragment of ‘Yuqihongqin’ is amplified by using ISSR-836 primer， and specific bands can only be amplified in all individuals of ‘Yuqihongqin’ with the second designed pair of SCAR primers， while these bands are not appearing in all individuals of ‘Liyangbaiqin’. The ISSR-SCAR markers of the two-step identification method for ‘Yuqihongqin’ developed in this study can provide references for the identification， preservation， and utilization of other local cultivars of O. javanica.